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Introduction

Dr. Tom is a web-based solution for the convenient analysis, visualization and interpretation of all types of RNA data, including mRNA, miRNA, and lncRNA. Designed by a team of expert scientists and bioinformaticians at BGI with collective experience across thousands of research projects, Dr. Tom provides a wide range of intuitive and interactive data visualization tools specifically designed to save you time in your differential expression or pathway analysis research.

In addition, powerful analysis tools and advanced algorithms allow you to mine your data to gain new insight and more value beyond standard available RNA analysis services. Data from many of the world’s leading databases have been integrated into the Dr. Tom system allowing users to reference and cross check all results and findings. Dr. Tom is already relied upon by thousands of scientists and researchers, and has shown itself to be a valuable and important tool in addition to any institution’s own internal data curation and analysis efforts.

To learn more, email us for a no obligation discussion about access.

Click HERE to check the Dr. Tom supported species.

Publications

Below listed paper published using Dr.Tom for data mining and visualizaiton.

	Title	Description	Pulication Date	Citation	Journal	IF
1	STYK1 promotes tumor growth and metastasis by reducing SPINT2/HAI-2 expression in non-small cell lung cancer	The data were analyzed on the Dr. Tom network platform of BGI (http://report.bgi.com).	2019/6/4	Ma Z, Liu D, Li W, et al. STYK1 promotes tumor growth and metastasis by reducing SPINT2/HAI-2 expression in non-small cell lung cancer. Cell Death Dis. 2019;10(6):435. Published 2019 Jun 4. doi:10.1038/s41419-019-1659-1	Cell Death & Disease	8.462
2	Co-inhibition of HDAC and MLL-menin interaction targets MLL-rearranged acute myeloid leukemia cells via disruption of DNA damage checkpoint and DNA repair	The KEGG pathway and GO bioinformatics analyses were performed by the BGI, using the Dr. TOM approach, an in-house customized data mining system of the BGI.	2019/10/7	Ye J, Zha J, Shi Y, et al. Co-inhibition of HDAC and MLL-menin interaction targets MLL-rearranged acute myeloid leukemia cells via disruption of DNA damage checkpoint and DNA repair. Clin Epigenetics. 2019;11(1):137. Published 2019 Oct 7. doi:10.1186/s13148-019-0723-0	Clinical Epigenetics	6.55
3	Analysis of the Differential Exosomal miRNAs of DC2.4 Dendritic Cells Induced by Toxoplasma gondii Infection	The interaction network of these miRNAs and mRNAs, and the key driver genes among the predicted target genes, were analyzed with Dr. Tom online software developed by Beijing Genomic Institute (BGI)	2019/11/5	Li DL, Zou WH, Deng SQ, Peng HJ. Analysis of the Differential Exosomal miRNAs of DC2.4 Dendritic Cells Induced by Toxoplasma gondii Infection. Int J Mol Sci. 2019;20(21):5506. Published 2019 Nov 5. doi:10.3390/ijms20215506	International Journal Of Molecular Sciences	5.923
4	EHD1 impairs decidualization by regulating the Wnt4/β-catenin signaling pathway in recurrent implantation failure	The DEGs related to endocytosis or the Wnt pathway were further analyzed using the Dr-TOM online analysis tool with the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases.	2019/11/6	Zhou Q, Yan G, Ding L, et al. EHD1 impairs decidualization by regulating the Wnt4/β-catenin signaling pathway in recurrent implantation failure. EBioMedicine. 2019;50:343-354. doi:10.1016/j.ebiom.2019.10.018	EBio Medicine	8.140
5	Comparative Transcriptome Analysis between a Novel Allohexaploid Cotton Progeny CMS Line LD6A and Its Maintainer Line LD6B	All clean data were analyzed by Dr. Tom, an online software developed by BGI (http://report.bgi.com)	2019/12/5	Zheng J, Kong X, Li B, et al. Comparative Transcriptome Analysis between a Novel Allohexaploid Cotton Progeny CMS Line LD6A and Its Maintainer Line LD6B. Int J Mol Sci. 2019;20(24):6127. Published 2019 Dec 5. doi:10.3390/ijms20246127	International Journal Of Molecular Sciences	5.923
6	MYB20, MYB42, MYB43, and MYB85 Regulate Phenylalanine and Lignin Biosynthesis during Secondary Cell Wall Formation	Data were analyzed on the Dr. Tom system from BGI	2019/12/23	Geng P, Zhang S, Liu J, et al. MYB20, MYB42, MYB43, and MYB85 Regulate Phenylalanine and Lignin Biosynthesis during Secondary Cell Wall Formation. Plant Physiol. 2020;182(3):1272-1283. doi:10.1104/pp.19.01070	Plant Physiology	8.341
7	Differential Gene Expression Patterns Between Apical and Basal Inner Hair Cells Revealed by RNA-Seq	http://biosys.bgi.com	2020/1/21	Tang F, Chen X, Jia L, Li H, Li J, Yuan W. Differential Gene Expression Patterns Between Apical and Basal Inner Hair Cells Revealed by RNA-Seq. Front Mol Neurosci. 2020 Jan 21;12:332. doi: 10.3389/fnmol.2019.00332. PMID: 32038162; PMCID: PMC6985465.	Frontiers in Molecular Neuroscience	5.630
8	Autophagy and Hsp70 activation alleviate oral epithelial cell death induced by food-derived hypertonicity	The RNA-seq data were analysed on an online system (Dr. Tom) provided by BGI	2020/1/23	Yang J, Zhang H, Sun S, et al. Autophagy and Hsp70 activation alleviate oral epithelial cell death induced by food-derived hypertonicity. Cell Stress Chaperones. 2020;25(2):253-264. doi:10.1007/s12192-020-01068-2	Cell Stress & Chaperones	3.66
9	Chemical-defined medium supporting the expansion of human mesenchymal stem cells	All the analyses were conducted with the online bioinformatic platform Dr. Tom (biosys.bgi.com/) provided by BGI	2020/3/19	Xu et al. Stem Cell Research & Therapy (2020) 11:125 https://doi.org/10.1186/s13287-020-01641-7	Stem Cell Research & Therapy	6.834
10	RIPK3 Promotes JEV Replication in Neurons via Downregulation of IFI44L	The results were analyzed using the Dr. Tom network platform of BGI and GraphPad Prism	2020/3/24	Bian P, Ye C, Zheng X, et al. RIPK3 Promotes JEV Replication in Neurons via Downregulation of IFI44L. Front Microbiol. 2020;11:368. Published 2020 Mar 24. doi:10.3389/fmicb.2020.00368	Frontiers In Microbiology	5.644
11	Elicitation of integrated immunity in mice by a novel pneumococcal polysaccharide vaccine conjugated with HBV surface antigen	GO terms were determined for the differentially expressed genes using the BGI Gene Analysis System (Dr. TOM)	2020/4/14	Qian W, Huang Z, Chen Y, et al. Elicitation of integrated immunity in mice by a novel pneumococcal polysaccharide vaccine conjugated with HBV surface antigen. Sci Rep. 2020;10(1):6470. Published 2020 Apr 14. doi:10.1038/s41598-020-62185-7	Scientific Reports	4.373
12	Transcriptome Analysis of Gene Expression Profiles of Tomato Yellow Leaf Curl Virus-Infected Whiteflies over Different Viral Acquisition Access Periods	. Data mining and figure presentation process were analyzed by BGI in-house customized data mining system called Dr.Tom (http://biosys.bgi.com).	2020/5/11	Li M, Zhao J, Su YL. Transcriptome Analysis of Gene Expression Profiles of Tomato Yellow Leaf Curl Virus-Infected Whiteflies over Different Viral Acquisition Access Periods. Insects. 2020 May 11;11(5):297. doi: 10.3390/insects11050297. PMID: 32403443; PMCID: PMC7290374.	Insects	2.764
13	Gasdermin D in macrophages restrains colitis by controlling cGAS-mediated inflammation	The data mining and figure presentation process, including KEGG, GSEA, Gene Network Analysis, the heatmap, and clustering, are all done by the BGI in-house customized data mining system called Dr.Tom (http://report.bgi.com)	2020/5/20	Ma C, Yang D, Wang B, et al. Gasdermin D in macrophages restrains colitis by controlling cGAS-mediated inflammation. Sci Adv. 2020;6(21):eaaz6717. Published 2020 May 20. doi:10.1126/sciadv.aaz6717	Science Advances	14.134
14	Suppressor of cytokine signaling 1 inhibits the maturation of dendritic cells involving the nuclear factor kappa B signaling pathway in the glioma microenvironment	Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, signaling pathway enrichment for differentially expressed genes (DEGs) was conducted. Using the Dr Tom network platform of BGI (http://report.bgi.com), the obtained data were processed further.	2020/6/30	He M, Chen X, Luo M, et al. Suppressor of cytokine signaling 1 inhibits the maturation of dendritic cells involving the nuclear factor kappa B signaling pathway in the glioma microenvironment. Clin Exp Immunol. 2020;202(1):47-59. doi:10.1111/cei.13476	Clinical And Experimental Immunology	4.334
15	Histone-fold centromere protein W (CENP-W) is associated with the biological behavior of hepatocellular carcinoma cells	After that, a database was built and analyzed by Dr. Tom online system	2020/7/7	Zhou Z, Zhou Z, Huang Z, He S, Chen S. Histone-fold centromere protein W (CENP-W) is associated with the biological behavior of hepatocellular carcinoma cells. Bioengineered. 2020;11(1):729-742. doi:10.1080/21655979.2020.1787776	Bioengineered	3.261
16	FTH1 Inhibits Ferroptosis Through Ferritinophagy in the 6-OHDA Model of Parkinson’s Disease	The data were visualized by using the Dr.Tom system provided by BGI.	2020/9/21	Tian Y, Lu J, Hao X, et al. FTH1 Inhibits Ferroptosis Through Ferritinophagy in the 6-OHDA Model of Parkinson's Disease. Neurotherapeutics. 2020;17(4):1796-1812. doi:10.1007/s13311-020-00929-z	Neurotherapeutics	7.622
17	The innate immune effector ISG12a promotes cancer immunity by suppressing the canonical Wnt/β-catenin signaling pathway	Images were obtained using the Dr. Tom system.	2020/9/22	Deng R, Zuo C, Li Y, et al. The innate immune effector ISG12a promotes cancer immunity by suppressing the canonical Wnt/β-catenin signaling pathway. Cell Mol Immunol. 2020;17(11):1163-1179. doi:10.1038/s41423-020-00549-9	Cellular & Molecular Immunology	11.53
18	Cell-Type Transcriptome Atlas of Human Aortic Valves Reveal Cell Heterogeneity and Endothelial to Mesenchymal Transition Involved in Calcific Aortic Valve Disease	All differentially expressed genes (DEGs) were submitted to the online tool Dr. TOM software (BGI-Shenzhen, China) for gene ontology and pathway enrichment analysis. For the DEGs, P<0.001 was accepted as significant.	2020/10/15	Xu K, Xie S, Huang Y, Zhou T, Liu M, Zhu P, Wang C, Shi J, Li F, Sellke FW, Dong N. Cell-Type Transcriptome Atlas of Human Aortic Valves Reveal Cell Heterogeneity and Endothelial to Mesenchymal Transition Involved in Calcific Aortic Valve Disease. Arterioscler Thromb Vasc Biol. 2020 Dec;40(12):2910-2921. doi: 10.1161/ATVBAHA.120.314789. Epub 2020 Oct 22. PMID: 33086873.	Arteriosclerosis, Thrombosis, and Vascular Biology	8.312
19	Hexokinase 2 Promotes Cell Growth and Tumor Formation Through the Raf/MEK/ERK Signaling Pathway in Cervical Cancer	Subsequent data analysis was performed by Dr. Tom on-line system from the Beijing Genomics Institute.	2020/11/26	Cui N, Li L, Feng Q, Ma HM, Lei D, Zheng PS. Hexokinase 2 Promotes Cell Growth and Tumor Formation Through the Raf/MEK/ERK Signaling Pathway in Cervical Cancer. Front Oncol. 2020;10:581208. Published 2020 Nov 26. doi:10.3389/fonc.2020.581208	Frontiers In Oncology	6.243
20	Identification of critical pathways and potential therapeutic targets in poorly differentiated duodenal papilla adenocarcinoma	Based on the DR.TOM system of BGI, the Gene Ontology (GO) enrichment analysis was performed concentrated on the terms biological process (BP), cellular component (CC) and molecular function (MF) and the KEGG pathway analysis was carried out to determine the significant pathways of the DEGs.	2021/1/6	Lu Y, Li W, Liu G, et al. Identification of critical pathways and potential therapeutic targets in poorly differentiated duodenal papilla adenocarcinoma. Cancer Cell Int. 2021;21(1):9. Published 2021 Jan 6. doi:10.1186/s12935-020-01709-7	Cancer Cell International	5.72
21	Bioinformatics analysis of Transcriptome genes in osteoarthritis rats treated with pilose antler	The comparison of differentially expressed genes (DEGs), enrichment analysis, genes classification, and miRNA-mRNA linked network were studied within Dr.Tom system.	2021/1/6	Yao B, Zhou Z, Zhang M, Leng X, Zhao D. Investigating the molecular control of deer antler extract on articular cartilage. J Orthop Surg Res. 2021;16(1):8. Published 2021 Jan 6. doi:10.1186/s13018-020-02148-w	Journal Of Orthopaedic Surgery And Research	2.351
22	Blockade of Macrophage CD147 Protects Against Foam Cell Formation in Atherosclerosis	We performed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Set Enrichment Analysis (GSEA) with a Dr. Tom II system provided by BGI.	2021/1/8	Lv JJ, Wang H, Cui HY, et al. Blockade of Macrophage CD147 Protects Against Foam Cell Formation in Atherosclerosis. Front Cell Dev Biol. 2021;8:609090. Published 2021 Jan 8. doi:10.3389/fcell.2020.609090	Frontiers In Cell And Developmental Biology	6.68
23	tPA Mobilizes Immune Cells That Exacerbate Hemorrhagic Transformation in Stroke	Repository Persistent ID / URL http://biosys.bgi.com	2021/1/8	Shi K, Zou M, Jia DM, Shi S, Yang X, Liu Q, Dong JF, Sheth KN, Wang X, Shi FD. tPA Mobilizes Immune Cells That Exacerbate Hemorrhagic Transformation in Stroke. Circ Res. 2021 Jan 8;128(1):62-75. doi: 10.1161/CIRCRESAHA.120.317596. Epub 2020 Oct 19. PMID: 33070717.	Circulation Research	17.364
24	Overexpression of HOXA9 upregulates NF-κB signaling to promote human hematopoiesis and alter the hematopoietic differentiation potentials	Analysis of gene functions was performed using the Dr. Tom Multi-Group Data Mining System (http://report.bgi.com).	2021/1/11	Zeng J, Yi D, Sun W, et al. Overexpression of HOXA9 upregulates NF-κB signaling to promote human hematopoiesis and alter the hematopoietic differentiation potentials. Cell Regen. 2021;10(1):9. Published 2021 Jan 11. doi:10.1186/s13619-020-00066-0	Cell Regeneration	/
25	lncRNA expression profiles and associated ceRNA network analyses in epicardial adipose tissue of patients with coronary artery disease	Dr. Tom's network platform of BGI (https://biosys.bgi.com) was applied to construct and visualize the network.	2021/1/15	Wang QC, Wang ZY, Xu Q, Chen XL, Shi RZ. lncRNA expression profiles and associated ceRNA network analyses in epicardial adipose tissue of patients with coronary artery disease. Sci Rep. 2021;11(1):1567. Published 2021 Jan 15. doi:10.1038/s41598-021-81038-5	Scientific Reports	4.373
26	Identification of Critical Pathways and Potential Key Genes in Poorly Differentiated Pancreatic Adenocarcinoma	Based on the DR.TOM system of BGI, we analyzed the functional enrichment of DEGs, concentrating on the pathways interrelated with these genes that were enriched in the terms biological process, molecular function and cellular component.	2021/1/27	Lu Y, Li D, Liu G, et al. Identification of Critical Pathways and Potential Key Genes in Poorly Differentiated Pancreatic Adenocarcinoma. Onco Targets Ther. 2021;14:711-723. Published 2021 Jan 27. doi:10.2147/OTT.S279287	Oncotargets And Therapy	4.144
27	LncRNA SNHG1 and RNA binding protein hnRNPL form a complex and coregulate CDH1 to boost the growth and metastasis of prostate cancer	The further analysis including heatmap, gene set enrichment analysis, and gene annotation of sequencing data was completed by BGI Dr. Tom system.	2021/2/1	Tan X, Chen WB, Lv DJ, et al. LncRNA SNHG1 and RNA binding protein hnRNPL form a complex and coregulate CDH1 to boost the growth and metastasis of prostate cancer. Cell Death Dis. 2021;12(2):138. Published 2021 Feb 1. doi:10.1038/s41419-021-03413-4	Cell Death & Disease	8.463
28	Transcriptome profiling of long noncoding RNAs and mRNAs in spinal cord of a rat model of paclitaxel-induced peripheral neuropathy identifies potential mechanisms mediating neuroinflammation and pain	The possible target binding of lncRNA/mRNA and miRNA was predicted by Dr. Tom system from BGI with database TargetScan, miRanda and RNAhybrid. Based on the interplayed relationships, a network was established and then visualized using the Cytoscape software	2021/2/18	Li Y, Yin C, Liu B, et al. Transcriptome profiling of long noncoding RNAs and mRNAs in spinal cord of a rat model of paclitaxel-induced peripheral neuropathy identifies potential mechanisms mediating neuroinflammation and pain. J Neuroinflammation. 2021;18(1):48. Published 2021 Feb 18. doi:10.1186/s12974-021-02098-y	Journal of Neuroinflammation	6.605
29	Schisandrin B for the treatment of male infertility	Volcano plot of SB‐mediated changes of testicular genes by software of Dr Tom (v2.0, Beijing Genomics Institute, BGI Shenzhen, China)	2021/2/23	Zou DX, Meng XD, Xie Y, et al. Schisandrin B for the treatment of male infertility. Clin Transl Med. 2021;11(2):e333. doi:10.1002/ctm2.333	Clinical and Translational Medicine	9.706
30	High Glucose Causes Distinct Expression Patterns of Primary Human Skin Cells by RNA Sequencing	GO and KEGG enrichment analysis of DEGs was performed using the Dr. TOM approach, which is an online database of BGI	2021/3/8	Zhang S, Ke Z, Yang C, et al. High Glucose Causes Distinct Expression Patterns of Primary Human Skin Cells by RNA Sequencing. Front Endocrinol (Lausanne). 2021;12:603645. Published 2021 Mar 8. doi:10.3389/fendo.2021.603645	Frontiers In Endocrinology	5.55
31	Absence of EpCAM in cervical cancer cells is involved in sluginduced epithelial‐mesenchymal transition	Subsequent data analysis was performed online by Dr. Tom from the Beijing Genomics Institute.	2021/3/10	Liu X, Feng Q, Zhang Y, Zheng P, Cui N. Absence of EpCAM in cervical cancer cells is involved in sluginduced epithelial-mesenchymal transition. Cancer Cell Int. 2021;21(1):163. Published 2021 Mar 10. doi:10.1186/s12935-021-01858-3	Cancer Cell International	5.722
32	Spatiotemporal Immunomodulation Using Biomimetic Scaffold Promotes Endochondral Ossification‐Mediated Bone Healing	Single end 50‐base reads were generated on a BGISEQ200 platform (BGI, Shenzhen, China) and data were analyzed with Dr. Tom	2021/3/16	Liu Y, Yang Z, Wang L, et al. Spatiotemporal Immunomodulation Using Biomimetic Scaffold Promotes Endochondral Ossification-Mediated Bone Healing. Adv Sci (Weinh). 2021;8(11):e2100143. doi:10.1002/advs.202100143	Advanced Science	16.802
33	GRP75‐mediated upregulation of HMGA1 stimulates stage I lung adenocarcinoma progression by activating JNK/c‐JUN signaling	mRNA‐sequencing analysis was performed by Huada Genomics Institute (BGI) and KEGG pathway analysis was conducted with the Dr. Tom program (https://biosys.bgi.com).	2021/3/23	Qiao GB, Wang RT, Wang SN, Tao SL, Tan QY, Jin H. GRP75-mediated upregulation of HMGA1 stimulates stage I lung adenocarcinoma progression by activating JNK/c-JUN signaling. Thorac Cancer. 2021;12(10):1558-1569. doi:10.1111/1759-7714.13944	Thoracic Cancer	3.502
34	Serum from Acute-on-chronic Liver Failure Patients May Affect Mesenchymal Stem Cells Transplantation by Impairing the Immunosuppressive Function of Cells	All the analyses were conducted with the online bioinformatic platform Dr. Tom (biosys.bgi.com/) provided by BGI.	2021/3/30	Zheng Y, Zhu S, Zheng X, et al. Serum from Acute-on-chronic Liver Failure Patients May Affect Mesenchymal Stem Cells Transplantation by Impairing the Immunosuppressive Function of Cells. J Clin Transl Hepatol. 2021;9(4):503-513. doi:10.14218/JCTH.2021.00014	Journal Of Clinical And Translational Hepatology	4.102
35	Characterization of Chicken Skin Yellowness and Exploration of Genes Involved in Skin Yellowness Deposition in Chicken	GO term enrichment and KEGG pathway analysis of the DEGs were performed using the online-accessible Dr. TOM program	2021/3/31	Wu J, Lin Z, Chen G, et al. Characterization of Chicken Skin Yellowness and Exploration of Genes Involved in Skin Yellowness Deposition in Chicken. Front Physiol. 2021;12:585089. Published 2021 Mar 31. doi:10.3389/fphys.2021.585089	Frontiers In Physiology	4.563
36	Mesenchymal stem cells induce tumor stroma formation and epithelial-mesenchymal transition through SPARC expression in colorectal cancer	Gene Ontology (GO; geneontology.org) and Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/) pathway analyses were performed using the RNA Data Visualization System Dr. TOM (Beijing Genomics Institute; http://www.bgi.com/global/dr-tom/), a BGI in-house customized data mining system which combines different published software	2021/4/16	Naito T, Yuge R, Kitadai Y, et al. Mesenchymal stem cells induce tumor stroma formation and epithelial‑mesenchymal transition through SPARC expression in colorectal cancer. Oncol Rep. 2021;45(6):104. doi:10.3892/or.2021.8055	Oncology Reports	3.901
37	Anti-oxidative effect of zinc in human umbilical cord mesenchymal stem cells	The BGI Dr. Tom operating system was used for KEGG pathway enrichment and gene ontology analysis.	2021/4/30	Lu X, Lin Y, Lin X, Zhang Q, Wang Z, Mi X, Wang R, Zhang X, Luan X, Liu Y, Li B, Tan Y, Fang Y. Anti-oxidative effect of zinc in human umbilical cord mesenchymal stem cells. Biophys Rep. 2021 Apr 30;7(2):142-151. doi: 10.52601/bpr.2021.200046. PMID: 37288149; PMCID: PMC10235909.	Biophysics Reports	\
38	Vesicle transporter GOLT1B mediates the cell membrane localization of DVL2 and PD-L2 and promotes colorectal cancer metastasis	KEGG, GO and GSEA analyses were performed on Dr. Tom platform (BGI-tech, China) to determine the genes and signal pathways related to GOLT1B knockdown in CRC cells	2021/5/31	Liu T, Liu B, Liu Y, et al. Vesicle transporter GOLT1B mediates the cell membrane localization of DVL2 and PD-L2 and promotes colorectal cancer metastasis. Cancer Cell Int. 2021;21(1):287. Published 2021 May 31. doi:10.1186/s12935-021-01991-z	Cancer Cell International	5.722
39	SHED aggregate exosomes shuttled miR-26a promote angiogenesis in pulp regeneration via TGF-β/SMAD2/3 signalling	The mentioned miRNA information of SA-Exo and S-Exo was available online (https://biosys.bgi.com/#/report/login).	2021/6/7	Wu M, Liu X, Li Z, Huang X, Guo H, Guo X, Yang X, Li B, Xuan K, Jin Y. SHED aggregate exosomes shuttled miR-26a promote angiogenesis in pulp regeneration via TGF-β/SMAD2/3 signalling. Cell Prolif. 2021 Jul;54(7):e13074. doi: 10.1111/cpr.13074. Epub 2021 Jun 7. PMID: 34101281; PMCID: PMC8249784.	Cell proliferation	6.833
40	OsFes1C, a potential nucleotide exchange factor for OsBiP1, is involved in the ER and salt stress responses	The Venn analysis and Cluster analysis for DEGs was performed on the Dr Tom network platform of BGI (http://report.bgi.com).	2021/6/8	Qian, D., Xiong, S., Li, M., Tian, L., & Qing Qu, L. (2021). OsFes1C, a potential nucleotide exchange factor for OsBiP1, is involved in the ER and salt stress responses. Plant physiology, 187(1), 396–408. https://doi.org/10.1093/plphys/kiab263	Plant Physiology	8.341
41	LDHA-Mediated Glycolytic Metabolism in Nucleus Pulposus Cells Is a Potential Therapeutic Target for Intervertebral Disc Degeneration	We use Dr.Tom Mass Spectrometry Cloud System (BGI, China) to perform protein difference analysis, differential protein GO analysis, and differential protein pathway enrichment on experimental reports.	2021/6/10	Wu, Longxi et al. “LDHA-Mediated Glycolytic Metabolism in Nucleus Pulposus Cells Is a Potential Therapeutic Target for Intervertebral Disc Degeneration.” BioMed research international vol. 2021 9914417. 10 Jun. 2021, doi:10.1155/2021/9914417	Biomed Research International	3.413
42	Traditional Chinese Medicine Xihuang Wan Inhibited Lewis Lung Carcinoma in a Syngeneic Model, Equivalent to Cytotoxic Chemotherapy, by Altering Multiple Signaling Pathways	The data were analyzed on the Dr. Tom II network platform of the BGI (https://biosys.bgi.com/)	2021/7/3	Zhang Z, Wang J, Duan H, et al. Traditional Chinese Medicine Xihuang Wan Inhibited Lewis Lung Carcinoma in a Syngeneic Model, Equivalent to Cytotoxic Chemotherapy, by Altering Multiple Signaling Pathways. In Vivo. 2021;35(4):2005-2014. doi:10.21873/invivo.12469	In Vivo	2.153
43	Effects of long-term culture on the biological characteristics and RNA profiles of human bone-marrow-derived mesenchymal stem cells	The following all analyses including heatmap, GO, KEGG, and GSEA et al. of annotated DE gene were conducted with the online bioinformatic platform Dr. Tom (https://biosys.bgi.com/) provided by BGI	2021/8/19	Wang S, Wang Z, Su H, et al. Effects of long-term culture on the biological characteristics and RNA profiles of human bone-marrow-derived mesenchymal stem cells. Mol Ther Nucleic Acids. 2021;26:557-574. Published 2021 Aug 19. doi:10.1016/j.omtn.2021.08.013	Molecular Therapy-nucleic Acids	8.884
44	Short-Term High Fructose Intake Impairs Diurnal Oscillations in the Murine Cornea	To examine the relationships between specific rhythmic genes and KEGG pathways, KEGG network diagrams were visualized using a BGI in-house customized data mining system termed Dr. Tom (http://biosys.bgi.com)	2021/8/20	He J, Jiao X, Sun X, et al. Short-Term High Fructose Intake Impairs Diurnal Oscillations in the Murine Cornea. Invest Ophthalmol Vis Sci. 2021;62(10):22. doi:10.1167/iovs.62.10.22	Investigative Ophthalmology & Visual Science	4.79
45	Imipramine impedes glioma progression by inhibiting YAP as a Hippo pathway independent manner and synergizes with temozolomide	Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were applied for the analysis of DEGs using the Dr. Tom online software (BGI).	2021/9/1	Wang Y, Wang X, Wang X, et al. Imipramine impedes glioma progression by inhibiting YAP as a Hippo pathway independent manner and synergizes with temozolomide. J Cell Mol Med. 2021;25(19):9350-9363. doi:10.1111/jcmm.16874	Journal Of Cellular And Molecular Medicine	5.311
46	Ascorbic acid supports ex vivo generation of plasmacytoid dendritic cells from circulating hematopoietic stem cells	Gene expression was calculated based on the reads, and differentially expressed genes and gene ontology analyses were analyzed on BGI’s software analysis platform Dr. Tom.	2021/9/2	Laustsen A, van der Sluis RM, Gris-Oliver A, et al. Ascorbic acid supports ex vivo generation of plasmacytoid dendritic cells from circulating hematopoietic stem cells. Elife. 2021;10:e65528. Published 2021 Sep 2. doi:10.7554/eLife.65528	Elife	8.14
47	Improving the Rice Photosynthetic Efficiency and Yield by Editing OsHXK1 via CRISPR/Cas9 System	Differential gene expression between WT (HHZ) RNA-seq data and both CH1/HZ and CH5/HZ RNA-seq data collected at 12 a.m. was analyzed using the Dr. Tom platform (http://report.bgi.com accessed on 25 July 2021, BGI)	2021/9/2	Zheng S, Ye C, Lu J, et al. Improving the Rice Photosynthetic Efficiency and Yield by Editing OsHXK1 via CRISPR/Cas9 System. Int J Mol Sci. 2021;22(17):9554. Published 2021 Sep 2. doi:10.3390/ijms22179554	International Journal Of Molecular Sciences	5.923
48	PDGF-D activation by macrophage-derived uPA promotes AngII-induced cardiac remodeling in obese mice	The data mining and figure presentation process, including the gene ontology term analysis, KEGG, and GSEA, were all done by the BGI in-house customized data mining system called Dr.Tom, which combined different published software.	2021/9/6	Cheng YW, Zhang ZB, Lan BD, et al. PDGF-D activation by macrophage-derived uPA promotes AngII-induced cardiac remodeling in obese mice. J Exp Med. 2021;218(9):e20210252. doi:10.1084/jem.20210252	Journal of Experimental Medicine	12.314
49	TNF-α-mediated m6A modification of ELMO1 triggers directional migration of mesenchymal stem cell in ankylosing spondylitis	The sequencing data analysis, including heatmap clustering, principal component analysis (PCA), Venn diagram creation, gene ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, were performed using BGI Dr. Tom 2.0.	2021/9/10	Xie Z, Yu W, Zheng G, et al. TNF-α-mediated m6A modification of ELMO1 triggers directional migration of mesenchymal stem cell in ankylosing spondylitis. Nat Commun. 2021;12(1):5373. Published 2021 Sep 10. doi:10.1038/s41467-021-25710-4	Nature Communications	14.91
50	Once-monthly hemin suppresses inflammatory and autoreactive CD4+ T cell responses to robustly ameliorate experimental rheumatoid arthritis	Venn diagram was generated using the Dr. Tom BGI online supporting system	2021/9/10	Sun B, Li G, Guo L, et al. Once-monthly hemin suppresses inflammatory and autoreactive CD4+ T cell responses to robustly ameliorate experimental rheumatoid arthritis. iScience. 2021;24(10):103101. Published 2021 Sep 10. doi:10.1016/j.isci.2021.103101	iScience	5.451
51	Overexpressed GNA13 induces temozolomide sensitization via down-regulating MGMT and p-RELA in glioma	The analysis of the RNA-seq was visualized using the network platform of Dr. Tom Data Visualisation Solution on BGI	2021/10/15	Liu Y, Du Z, Xu Z, et al. Overexpressed GNA13 induces temozolomide sensitization via down-regulating MGMT and p-RELA in glioma. Am J Transl Res. 2021;13(10):11413-11426. Published 2021 Oct 15.	American Journal Of Translational Research	4.06
52	Hexokinases 2 promoted cell motility and distant metastasis by elevating fibronectin through Akt1/p-Akt1 in cervical cancer cells	Subsequent data analysis was performed online by Dr. Tom from the Beijing Genomics Institute.	2021/11/10	Chen Q, Li L, Liu X, et al. Hexokinases 2 promoted cell motility and distant metastasis by elevating fibronectin through Akt1/p-Akt1 in cervical cancer cells. Cancer Cell Int. 2021;21(1):600. Published 2021 Nov 10.	Cancer Cell International	5.72
53	Colloidal Self-Assembled Patterns Maintain the Pluripotency and Promote the Hemopoietic Potential of Human Embryonic Stem Cells	The analysis of gene function was performed with the multi-group data mining system of Dr. Tom (http://report.bgi.com).	2021/11/16	Lin, J., Zeng, J., Sun, W., Liu, K., Enkhbat, M., Yi, D., Harati, J., Liu, J., Kingshott, P., Chen, B., Ma, F., & Wang, P. Y. (2021). Colloidal Self-Assembled Patterns Maintain the Pluripotency and Promote the Hemopoietic Potential of Human Embryonic Stem Cells. Frontiers in cell and developmental biology, 9, 771773. https://doi.org/10.3389/fcell.2021.771773	Frontiers In Cell And Developmental Biology	6.68
54	MyD88 in Macrophages Enhances Liver Fibrosis by Activation of NLRP3 Inflammasome in HSCs	All data mining, and figure presentation were conducted on the Dr Tom network platform of BGI	2021/11/17	Ge S, Yang W, Chen H, et al. MyD88 in Macrophages Enhances Liver Fibrosis by Activation of NLRP3 Inflammasome in HSCs. Int J Mol Sci. 2021;22(22):12413. Published 2021 Nov 17.	International Journal Of Molecular Sciences	5.923
55	Halofuginone Sensitizes Lung Cancer Organoids to Cisplatin via Suppressing PI3K/AKT and MAPK Signaling Pathways	The heatmap of DEGs ( log2FC ≥ 1, p ≤ 0.001) and KEGG analysis ( log2FC ≥ 1, p ≤ 0.05) in NSCLC cell lines were performed by the BGI using the Dr. TOM approach, a customized data mining system from BGI.	2021/11/24	Li, H., Zhang, Y., Lan, X., Yu, J., Yang, C., Sun, Z., Kang, P., Han, Y., & Yu, D. (2021). Halofuginone Sensitizes Lung Cancer Organoids to Cisplatin via Suppressing PI3K/AKT and MAPK Signaling Pathways. Frontiers in cell and developmental biology, 9, 773048. https://doi.org/10.3389/fcell.2021.773048	Frontiers In Cell And Developmental Biology	6.68
56	A New Nanomaterial Based on Extracellular Vesicles Containing Chrysin-Induced Cell Apoptosis Through Let-7a in Tongue Squamous Cell Carcinoma	Using Dr.Tom software (BGI, China), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and the GO enrichment analysis of differentially expressed miRNAs were determined.	2021/11/26	Yang Z, Liu D, Zhou H, et al. A New Nanomaterial Based on Extracellular Vesicles Containing Chrysin-Induced Cell Apoptosis Through Let-7a in Tongue Squamous Cell Carcinoma. Front Bioeng Biotechnol. 2021;9:766380. Published 2021 Nov 26. doi:10.3389/fbioe.2021.766380	Frontiers in Bioenginerring and Biotechnology	4.885
57	Combined Developmental Toxicity of the Pesticides Difenoconazole and Dimethomorph on Embryonic Zebrafish	Transcriptomic results were analyzed using the BGI Dr.Tom online work platform (https://biosys.bgi.com, accessed on 1 October 2021).	2021/12/1	Fan R, Zhang W, Jia L, et al. Combined Developmental Toxicity of the Pesticides Difenoconazole and Dimethomorph on Embryonic Zebrafish. Toxins (Basel). 2021;13(12):854. Published 2021 Dec 1. doi:10.3390/toxins13120854	Toxins	3.991
58	FGL1 as a Novel Mediator and Biomarker of Malignant Progression in Clear Cell Renal Cell Carcinoma	The Dr. Tom network platform developed by Beijing Genomic Institute (BGI; http://report.bgi.com) was used to perform the protein–protein interaction (PPI) analysis after defining the differentially expressed genes (DEGs), gene ontology (GO) enrichment analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis.	2021/12/9	Lv Z, Cui B, Huang X, et al. FGL1 as a Novel Mediator and Biomarker of Malignant Progression in Clear Cell Renal Cell Carcinoma. Front Oncol. 2021;11:756843. Published 2021 Dec 9. doi:10.3389/fonc.2021.756843	Frontiers In Oncology	5.076
59	Antagonistic Effects of Enrofloxacin on Carbendazim-Induced Developmental Toxicity in Zebrafish Embryos	Transcriptomic results were analyzed using the BGI Dr.Tom online work platform (https://biosys.bgi.com, accessed on 1 October 2021)	2021/12/10	Fan R, Zhang W, Jia L, et al. Antagonistic Effects of Enrofloxacin on Carbendazim-Induced Developmental Toxicity in Zebrafish Embryos. Toxics. 2021;9(12):349. Published 2021 Dec 10. doi:10.3390/toxics9120349	Toxics	3.709
60	Hypoxic pancreatic cancer derived exosomal miR-30b-5p promotes tumor angiogenesis by inhibiting GJA1 expression	Differential expression mRNAs were identified by utilizing Dr.Tom online analysis platform	2022/1/1	Chen K, Wang Q, Liu X, Wang F, Yang Y, Tian X. Hypoxic pancreatic cancer derived exosomal miR-30b-5p promotes tumor angiogenesis by inhibiting GJA1 expression. Int J Biol Sci. 2022;18(3):1220-1237. Published 2022 Jan 1. doi:10.7150/ijbs.67675	International Journal Of Biological Sciences	5.169
61	Long-Term Enhancement of NMDA Receptor Function in Inhibitory Neurons Preferentially Modulates Potassium Channels and Cell Adhesion Molecules	GO enrichment was conducted using Dr. Tom online system provided by BGI	2022/1/4	Xia D, Zhang X, Deng D, et al. Long-Term Enhancement of NMDA Receptor Function in Inhibitory Neurons Preferentially Modulates Potassium Channels and Cell Adhesion Molecules. Front Pharmacol. 2022;12:796179. Published 2022 Jan 4. doi:10.3389/fphar.2021.796179	Frontiers in Pharmacology	4.627
62	Hsa_circ_0003258 promotes prostate cancer metastasis by complexing with IGF2BP3 and sponging miR-653-5p	The other analyses including heatmap, gene set enrichment analysis was completed by BGI Dr. Tom system.	2022/1/5	Yu YZ, Lv DJ, Wang C, et al. Hsa_circ_0003258 promotes prostate cancer metastasis by complexing with IGF2BP3 and sponging miR-653-5p. Mol Cancer. 2022;21(1):12. Published 2022 Jan 5. doi:10.1186/s12943-021-01480-x	Molecular Cancer	17.794
63	Screening and Identification of Novel Potential Biomarkers for Breast Cancer Brain Metastases	GO (including biological processes (BP), molecular functions (MF), and cellular components (CC)) and KEGG enrichment analysis of DEGs were performed using DR.TOM system of BGI Tech as previously described	2022/1/13	Wang L, Zeng D, Wang Q, Liu L, Lu T, Gao Y. Screening and Identification of Novel Potential Biomarkers for Breast Cancer Brain Metastases. Front Oncol. 2022;11:784096. Published 2022 Jan 13. doi:10.3389/fonc.2021.784096	Frontiers in Oncology	5.076
64	Piezo1-mediated mechanosensation in bone marrow macrophages promotes vascular niche regeneration after irradiation injury	Gene ontology (GO) and functional enrichment analysis were conducted on all differentially expressed genes (DEGs) identified using the Dr. Tom analysis system (https://biosys.bgi.com, Shenzhen Huada Gene Science and Technology Service Co., Ltd., Shenzhen, China).	2022/1/16	Zhang X, Hou L, Li F, et al. Piezo1-mediated mechanosensation in bone marrow macrophages promotes vascular niche regeneration after irradiation injury. Theranostics. 2022;12(4):1621-1638. Published 2022 Jan 16. doi:10.7150/thno.64963	Theranostics	9.399
65	Shoc2 recognizes bacterial flagellin and mediates antibacterial Erk/Stat signaling in an invertebrate	The Venn diagram analysis was performed using the Dr. Tom analysis platform at BGI, and visualized using an online Venn tool	2022/1/24	Zhao BR, Wang XX, Wang XW. Shoc2 recognizes bacterial flagellin and mediates antibacterial Erk/Stat signaling in an invertebrate. PLoS Pathog. 2022;18(1):e1010253. Published 2022 Jan 24. doi:10.1371/journal.ppat.1010253	PLoS Pathogens	6.501
66	Characterization of transcriptional landscape in bone marrow-derived mesenchymal stromal cells treated with aspirin by RNA-seq	Biological function Gene Ontology (GO), Kyoto Gene and Genome Encyclopedia (KEGG) signal pathway, and gene set enrichment analysis (GSEA) enrichment analysis were performed in the Dr. Tom online software	2022/1/24	Liu X, Zhan Y, Xu W, et al. Characterization of transcriptional landscape in bone marrow-derived mesenchymal stromal cells treated with aspirin by RNA-seq. PeerJ. 2022;10:e12819. Published 2022 Jan 24. doi:10.7717/peerj.12819	PeerJ	2.572
67	Effects of the NF-κB Signaling Pathway Inhibitor BAY11-7082 in the Replication of ASFV	Using BGI’s Dr. Tom multi-omics data mining system, clustering heat map, Venn, GO, and KEGG analysis and results display of differential genes and proteins were performed.	2022/1/31	Gao Q, Yang Y, Feng Y, et al. Effects of the NF-κB Signaling Pathway Inhibitor BAY11-7082 in the Replication of ASFV. Viruses. 2022;14(2):297. Published 2022 Jan 31. doi:10.3390/v14020297	Viruses	4.225
68	Salt-Induced Hepatic Inflammatory Memory Contributes to Cardiovascular Damage Through Epigenetic Modulation of SIRT3	All analysis were performed on the Dr.Tom analysis system constructed by BGI-Shenzhen, China.	2022/1/31	Gao P, You M, Li L, Zhang Q, Fang X, Wei X, Zhou Q, Zhang H, Wang M, Lu Z, Wang L, Sun F, Liu D, Zheng H, Yan Z, Yang G, Zhu Z. Salt-Induced Hepatic Inflammatory Memory Contributes to Cardiovascular Damage Through Epigenetic Modulation of SIRT3. Circulation. 2022 Feb;145(5):375-391. doi: 10.1161/CIRCULATIONAHA.121.055600. Epub 2022 Jan 31. PMID: 35100024.	Circulation	25.449
69	Photoprotection contributes to freezing tolerance as revealed by RNA-seq profiling of Rhododendron leaves during cold acclimation and deacclimation over time	Analyses of KEGG pathway enrichment in this study were performed via the BGI Dr. Tom system, which uses the pHYPER function in R.	2022/1/31	Liu B, Zhao FM, Cao Y, et al. Photoprotection contributes to freezing tolerance as revealed by RNA-seq profiling of rhododendron leaves during cold acclimation and deacclimation over time [published online ahead of print, 2022 Jan 18]. Hortic Res. 2022;9:uhab025. doi:10.1093/hr/uhab025	Horticulture Research	5.279
70	Down regulated oncogene KIF2C inhibits growth, invasion, and metastasis of hepatocellular carcinoma through the Ras/MAPK signaling pathway and epithelial-to-mesenchymal transition	To further elucidate a change in the underlying mechanism, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was analyzed by phyper, based on hypergeometric testing with the Dr. Tom network platform of BGI (http://report.bgi.com).	2022/2/1	Mo S, Fang D, Zhao S, et al. Down regulated oncogene KIF2C inhibits growth, invasion, and metastasis of hepatocellular carcinoma through the Ras/MAPK signaling pathway and epithelial-to-mesenchymal transition. Ann Transl Med. 2022;10(3):151. doi:10.21037/atm-21-6240	Annals of Translational Medicine	3.64
71	Phenotypical screening on metastatic PRCC-TFE3 fusion translocation renal cell carcinoma organoids reveals potential therapeutic agents	The volcano plot and heatmap of differentially expressed genes (log2 of fold change > 1, q < 0.05) were generated by BGI using the Dr. TOM approach, a customized data mining system from BGI.	2022/2/3	Cao C, Lan X, Shang B, et al. Phenotypical screening on metastatic PRCC-TFE3 fusion translocation renal cell carcinoma organoids reveals potential therapeutic agents. Clin Transl Oncol. 2022;24(7):1333-1346. doi:10.1007/s12094-021-02774-8	Clinical & Translational Oncology	2.861
72	TSG-6 promotes Cancer Cell aggressiveness in a CD44-Dependent Manner and Reprograms Normal Fibroblasts to create a Pro-metastatic Microenvironment in Colorectal Cancer	Altered genes with heat maps were analyzed by employing the Dr. Tom platform (BGI-tech, China), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG).	2022/2/7	Liu B, Liu T, Liu Y, et al. TSG-6 promotes Cancer Cell aggressiveness in a CD44-Dependent Manner and Reprograms Normal Fibroblasts to create a Pro-metastatic Microenvironment in Colorectal Cancer. Int J Biol Sci. 2022;18(4):1677-1694. Published 2022 Feb 7. doi:10.7150/ijbs.69178	International Journal Of Biological Sciences	5.169
73	Integrated Au-Nanoroded Biosensing and Regulating Platform for Photothermal Therapy of Bradyarrhythmia	Data analysis is based on interactive software Dr. Tom by BGI Group.	2022/2/7	Fang J, Liu D, Xu D, et al. Integrated Au-Nanoroded Biosensing and Regulating Platform for Photothermal Therapy of Bradyarrhythmia. Research (Wash D C). 2022;2022:9854342. Published 2022 Feb 7. doi:10.34133/2022/9854342	Research	8.806
74	Comprehensive Transcriptome Analysis of mRNA Expression Patterns Associated With Enhanced Biological Functions in Periodontal Ligament Stem Cells Subjected to Short-Term Hypoxia Pretreatment	We conducted a Gene Ontology (GO) functional enrichment analysis and KEGG pathway enrichment analysis using the Dr. Tom program (https://biosys.bgi.com) provided by BGI Tech (BGI-Shenzhen, China), and Q values <0.05 were considered to indicate significant DEG enrichment.	2022/2/8	Li ZB, Yang HQ, Li K, et al. Comprehensive Transcriptome Analysis of mRNA Expression Patterns Associated With Enhanced Biological Functions in Periodontal Ligament Stem Cells Subjected to Short-Term Hypoxia Pretreatment. Front Genet. 2022;13:797055. Published 2022 Feb 8. doi:10.3389/fgene.2022.797055	Frontiers in Genetics	3.792
75	Upregulation of NOD1 and NOD2 contribute to cancer progression through the positive regulation of tumorigenicity and metastasis in human squamous cervical cancer	The transcriptome sequencing (differential expression genes, DEG) of CSCC and normal cervical tissue (from Cancer Hospital) were identified by BGISEQ platform and analyzed on the DR. TOM network platform of BGI	2022/2/8	Zhang Y, Li N, Yuan G, et al. Upregulation of NOD1 and NOD2 contribute to cancer progression through the positive regulation of tumorigenicity and metastasis in human squamous cervical cancer. BMC Med. 2022;20(1):55. Published 2022 Feb 8. doi:10.1186/s12916-022-02248-w	BMC Medicine	7.947
76	Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease	ll analysis were performed on the Dr. Tom analysis system constructed by BGI-Shenzhen, China.	2022/2/15	You M, Liu Y, Wang B, Li L, Zhang H, He H, Zhou Q, Cao T, Wang L, Zhao Z, Zhu Z, Gao P, Yan Z. Asprosin induces vascular endothelial-to-mesenchymal transition in diabetic lower extremity peripheral artery disease. Cardiovasc Diabetol. 2022 Feb 15;21(1):25. doi: 10.1186/s12933-022-01457-0. PMID: 35168605.	Cardiovascular Diabetology	7.744
77	Sulfonamide functional head on short-chain perfluorinated substance drives developmental toxicity	Data analysis and visualization was also conducted by BGI and their Dr. Tom platform	2022/2/18	Rericha Y, Cao D, Truong L, Simonich MT, Field JA, Tanguay RL. Sulfonamide functional head on short-chain perfluorinated substance drives developmental toxicity. iScience. 2022;25(2):103789. Published 2022 Jan 18. doi:10.1016/j.isci.2022.103789	iScience	4.953
78	Exploring neuronal mechanisms involved in the scratching behavior of a mouse model of allergic contact dermatitis by transcriptomics	Dr. Tom system (BGI, Shenzhen, China) was used to perform functional enrichment analysis of DEGs.	2022/2/19	Liu B, Chen R, Wang J, et al. Exploring neuronal mechanisms involved in the scratching behavior of a mouse model of allergic contact dermatitis by transcriptomics. Cell Mol Biol Lett. 2022;27(1):16. Published 2022 Feb 19. doi:10.1186/s11658-022-00316-w	Cellular & Molecular Biology Letters	4.202
79	Effects of the Surface Charge of Graphene Oxide Derivatives on Ocular Compatibility	To obtain the biological pathways of DEGs, an analysis was performed based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database using Dr. Tom software (http://biosys.bgi.com in 16 December 2021).	2022/2/22	Rong L, Fu Y, Li Q, et al. Effects of the Surface Charge of Graphene Oxide Derivatives on Ocular Compatibility. Nanomaterials (Basel). 2022;12(5):735. Published 2022 Feb 22. doi:10.3390/nano12050735	Nanomaterials	4.478
80	HNF1A POU Domain Mutations Found in Japanese Liver Cancer Patients Cause Downregulation of HNF4A Promoter Activity with Possible Disruption in Transcription Networks	The KEGG enrichment pathway and GO bioinformatic analyses were conducted using BGI’s Dr. TOM approach, an in-house customized data-mining system of the BGI.	2022/2/24	Haque E, Teeli AS, Winiarczyk D, et al. HNF1A POU Domain Mutations Found in Japanese Liver Cancer Patients Cause Downregulation of HNF4A Promoter Activity with Possible Disruption in Transcription Networks. Genes (Basel). 2022;13(3):413. Published 2022 Feb 24. doi:10.3390/genes13030413	Genes	3.729
81	ALKBH5-Mediated m6A Modification of A20 Regulates Microglia Polarization in Diabetic Retinopathy	The bioinformatics analysis was performed using BGI Dr. Tom 2.0, including heatmap clustering, gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and protein-protein interaction (PPI) network.	2022/3/1	Chen T, Zhu W, Wang C, et al. ALKBH5-Mediated m6A Modification of A20 Regulates Microglia Polarization in Diabetic Retinopathy. Front Immunol. 2022;13:813979. Published 2022 Mar 1. doi:10.3389/fimmu.2022.813979	Frontiers in Immunology	5.787
82	HDAC7 promotes NSCLC proliferation and metastasis via stabilization by deubiquitinase USP10 and activation of β-catenin-FGF18 pathway	The Dr. Tom online platform of BGI was used for data analysis (http://report.bgi.com).	2022/3/11	Guo K, Ma Z, Zhang Y, et al. HDAC7 promotes NSCLC proliferation and metastasis via stabilization by deubiquitinase USP10 and activation of β-catenin-FGF18 pathway. J Exp Clin Cancer Res. 2022;41(1):91. Published 2022 Mar 11. doi:10.1186/s13046-022-02266-9	Journal of Experimental & Clinical Cancer Research	7.958
83	The photomorphogenic repressors BBX28 and BBX29 integrate light and brassinosteroid signaling to inhibit seedling development in Arabidopsis	GO analysis was performed using Dr. Tom software (https://biosys.bgi.com/#/main), and the results were plotted using REVIGO with R (Supek et al., 2011).	2022/3/16	The photomorphogenic repressors BBX28 and BBX29 integrate light and brassinosteroid signaling to inhibit seedling development in Arabidopsis	Plant Cell	11.29
84	KDM5B promotes tumorigenesis of Ewing sarcoma via FBXW7/CCNE1 axis	The KEGG enrichment analysis and the Venn diagram for DEGs were performed by the BGI, using the Dr. TOM approach, an in-house customized data mining system of the BGI.	2022/4/15	Chen B, Chen H, Lu S, et al. KDM5B promotes tumorigenesis of Ewing sarcoma via FBXW7/CCNE1 axis. Cell Death Dis. 2022;13(4):354. Published 2022 Apr 15. doi:10.1038/s41419-022-04800-1	Cell Death & Disease	8.462
85	Deciphering Risperidone-Induced Lipogenesis by Network Pharmacology and Molecular Validation	After mapping the data, normalization was performed, and fragments per kilobase million (FPKM) mapped reads were calculated using the DC.TOM platform.	2022/4/18	Fu Y, Yang K, Huang Y, Zhang Y, Li S, Li WD. Deciphering Risperidone-Induced Lipogenesis by Network Pharmacology and Molecular Validation. Front Psychiatry. 2022 Apr 18;13:870742. doi: 10.3389/fpsyt.2022.870742. PMID: 35509887; PMCID: PMC9058120.	Frontiers in psychiatry	4.7
86	PCV2 and PRV Coinfection Induces Endoplasmic Reticulum Stress via PERK-eIF2α-ATF4-CHOP and IRE1-XBP1-EDEM Pathways	Biological networks analysis of DEGs was performed via the Dr. TOM system, using key driver analysis (KDA), and protein–protein interaction network (PPI network).	2022/4/19	Chen S, Li X, Zhang X, et al. PCV2 and PRV Coinfection Induces Endoplasmic Reticulum Stress via PERK-eIF2α-ATF4-CHOP and IRE1-XBP1-EDEM Pathways. Int J Mol Sci. 2022;23(9):4479. Published 2022 Apr 19. doi:10.3390/ijms23094479	International Journal Of Molecular Sciences	5.923
87	JEV Infection Induces M-MDSC Differentiation Into CD3+ Macrophages in the Brain	Subsequent data analysis was performed using the online system provided by Dr. Tom	2022/4/21	Zhang N, Gao X, Zhang W, et al. JEV Infection Induces M-MDSC Differentiation Into CD3+ Macrophages in the Brain. Front Immunol. 2022;13:838990. Published 2022 Apr 21. doi:10.3389/fimmu.2022.838990	Frontiers in Immunology	5.787
88	Atractylenolide-1 Targets FLT3 to Regulate PI3K/AKT/HIF1-α Pathway to Inhibit Osteogenic Differentiation of Human Valve Interstitial Cells	Differentially expressed gene (DEG), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) pathway enrichment analyses were performed using the online platform “Dr. Tom 2.0” designed by BGI Tech Co., LTD.	2022/4/25	Wang J, Zhang P, Zhang J, Ma Z, Tian X, Liu Y, Lv G, Qu L. Atractylenolide-1 Targets FLT3 to Regulate PI3K/AKT/HIF1-α Pathway to Inhibit Osteogenic Differentiation of Human Valve Interstitial Cells. Front Pharmacol. 2022 Apr 25;13:899775. doi: 10.3389/fphar.2022.899775. PMID: 35571096; PMCID: PMC9097085.	Frontiers in Pharmacology	4.627
89	Alcohol‐associated fibrosis in females is mediated by female‐specific activation of lysine demethylases KDM5B and KDM5C	Gene ontology analysis (Dr. Tom tool from BGI Genomics) showed that Ahr knockdown in Kdm5b/Kdm5c knockdown mice affected genes involved in xenobiotic metabolism both in males and in females	2022/4/25	Schonfeld M, Averilla J, Gunewardena S, Weinman SA, Tikhanovich I. Alcohol-associated fibrosis in females is mediated by female-specific activation of lysine demethylases KDM5B and KDM5C. Hepatol Commun. 2022 Aug;6(8):2042-2057. doi: 10.1002/hep4.1967. Epub 2022 Apr 25. PMID: 35468265; PMCID: PMC9315128.	Hepatology Communications	5.073
90	Activation of α7 nicotinic acetylcholine receptor promotes HIV-1 transcription	Data were analyzed in online analysis software Dr. Tom	2022/4/27	Wen J, Zhao C, Chen J, Song S, Lin Z, Xie S, Qi H, Wang J, Su X. Activation of α7 nicotinic acetylcholine receptor promotes HIV-1 transcription. Cell Insight. 2022 Apr 27;1(3):100028. doi: 10.1016/j.cellin.2022.100028. PMID: 37193048; PMCID: PMC10120325.	Cell Insight	\
91	The Host CYP1A1-Microbiota Metabolic Axis Promotes Gut Barrier Disruption in Methicillin-Resistant Staphylococcus aureus-Induced Abdominal Sepsis	All the data were analyzed using the online Dr. Tom network platform of BGI	2022/4/27	Ma X, Jin H, Chu X, et al. The Host CYP1A1-Microbiota Metabolic Axis Promotes Gut Barrier Disruption in Methicillin-Resistant Staphylococcus aureus-Induced Abdominal Sepsis. Front Microbiol. 2022;13:802409. Published 2022 Apr 27. doi:10.3389/fmicb.2022.802409	Frontiers In Microbiology	5.644
92	MyD88 in hepatic stellate cells enhances liver fibrosis via promoting macrophage M1 polarization	All data mining, and figure presentation were conducted on the Dr Tom network platform of BGI (http://report.bgi.com).	2022/4/28	Zhang J, Liu Y, Chen H, et al. MyD88 in hepatic stellate cells enhances liver fibrosis via promoting macrophage M1 polarization. Cell Death Dis. 2022;13(4):411. Published 2022 Apr 28. doi:10.1038/s41419-022-04802-z	Cell Death & Disease	8.462
93	A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model	Functional annotation, classification and enrichment (GO, KEGG) analysis were performed by the BGI in-house customized data mining system called Dr.Tom (http://report.bgi.com).	2022/5/5	Zhang X, Xuan J, Yao C, et al. A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model. BMC Bioinformatics. 2022;23(1):162. Published 2022 May 5. doi:10.1186/s12859-022-04702-1	BMC Bioinformatics	2.974
94	A 3D-printed scaffold-based osteosarcoma model allows to investigate tumor phenotypes and pathogenesis in an in vitro bone-mimicking niche	ioinformatic analysis of RNA sequencing data was performed by DR. TOM provided by BGI (https://biosys.bgi.com).	2022/5/25	Wang ML, Xu NY, Tang RZ, Liu XQ. A 3D-printed scaffold-based osteosarcoma model allows to investigate tumor phenotypes and pathogenesis in an in vitro bone-mimicking niche. Mater Today Bio. 2022;15:100295. Published 2022 May 25. doi:10.1016/j.mtbio.2022.100295	Materials Today Bio	7.348
95	Calreticulin Identified as One of the Androgen Response Genes That Trigger Full Regeneration of the Only Capable Mammalian Organ, the Deer Antler	Venn diagram and the volcano plot were drawn using Dr. Tom software	2022/6/13	Guo Q, Zheng J, Ba H, Sun H, Zhai J, Wang W, Li C. Calreticulin Identified as One of the Androgen Response Genes That Trigger Full Regeneration of the Only Capable Mammalian Organ, the Deer Antler. Front Cell Dev Biol. 2022 Jun 13;10:862841. doi: 10.3389/fcell.2022.862841. PMCID: PMC9235033.	Frontiers In Cell And Developmental Biology	6.68
96	Harmane Potentiates Nicotine Reinforcement Through MAO-A Inhibition at the Dose Related to Cigarette Smoking	The RNA-seq data were analyzed using the online analysis system Dr. Tom provided by BGI,1 and the visualization tool provided by Dr. Tom includes the drawing of bubble diagrams and Venn diagrams.	2022/6/27	Ding Z, Li X, Chen H, Hou H, Hu Q. Harmane Potentiates Nicotine Reinforcement Through MAO-A Inhibition at the Dose Related to Cigarette Smoking. Front Mol Neurosci. 2022 Jun 27; 15: 925272. doi: 10.3389/fnmol.2022.925272	Frontiers in Molecular Neuroscience	5.630
97	Dehydrocorydaline Accelerates Cell Proliferation and Extracellular Matrix Synthesis of TNFα-Treated Human Chondrocytes by Targeting Cox2 through JAK1-STAT3 Signaling Pathway	Furthermore, GO function enrichment analysis and KEGG signal pathway enrichment analysis were performed utilizing Dr. Tom and Omicshare online software.	2022/6/30	Sha Y, Zhang B, Chen L, Wang C, Sun T. Dehydrocorydaline Accelerates Cell Proliferation and Extracellular Matrix Synthesis of TNFα-Treated Human Chondrocytes by Targeting Cox2 through JAK1-STAT3 Signaling Pathway. Int J Mol Sci. 2022 Jun 30;23(13):7268. doi: 10.3390/ijms23137268.	International Journal Of Molecular Sciences	5.923
98	Fluidic Flow Enhances the Differentiation of Placental Trophoblast-Like 3D Tissue from hiPSCs in a Perfused Macrofluidic Device	Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs were both performed using the Dr. Tom system from BGI.	2022/6/30	Deng P, Cui K, Shi Y, Zhu Y, Wang Y, Shao X, Qin J. Fluidic Flow Enhances the Differentiation of Placental Trophoblast-Like 3D Tissue from hiPSCs in a Perfused Macrofluidic Device. Front Bioeng Biotechnol. 2022 Jun 30;10:907104. doi: 10.3389/fbioe.2022.907104. PMID: 35845423; PMCID: PMC9280037.	Frontiers in Bioenginerring and Biotechnology	4.885
99	Recapitulation of growth factor-enriched microenvironment via BMP receptor activating hydrogel	The Dr. Tom software was used to screen out the different genes.	2022/7/5	Zhang Q, Liu Y, Li J, Wang J, Liu C. Recapitulation of growth factor-enriched microenvironment via BMP receptor activating hydrogel. Bioact Mater. 2022 Jul 5;20:638-650. doi: 10.1016/j.bioactmat.2022.06.012. PMID: 35846838; PMCID: PMC9270210.	Bioactive Materials	11.658
100	SNTA1-deficient human cardiomyocytes demonstrate hypertrophic phenotype and calcium handling disorder	The RNA-seq data associated with this manuscript can be inquired from biosys.bgi.com (Username: F20FTSNCWLJ4149_PEOxzmR).	2022/7/7	Dong T, Zhao Y, Jin HF, Shen L, Lin Y, Si LL, Chen L, Liu JC. SNTA1-deficient human cardiomyocytes demonstrate hypertrophic phenotype and calcium handling disorder. Stem Cell Res Ther. 2022 Jun 30;13(1):288. doi: 10.1186/s13287-022-02955-4. PMID: 35773684; PMCID: PMC9248201	Stem Cell Research & Therapy	6.834
101	Inflammation accelerates BCR-ABL1+ B-ALL development through upregulation of AID	All the data were analyzed with the online bioinformatics platform Dr. Tom (http://report.bgi.com) provided by BGI.	2022/7/11	Zhang P, Qin M, Wang Y, Chen X, Miao Y, Yuan M, Zhou W, Li D, Wang D, Wang M, Ai L, Ma Y, Dong Y, Ji Y. Inflammation accelerates BCR-ABL1+ B-ALL development through upregulation of AID. Blood Adv. 2022 Jul 12;6(13):4060-4072. doi: 10.1182/bloodadvances.2021005017. PMID: 35816360; PMCID: PMC9278295.	Blood Advances	5.855
102	Interrogation on the Cellular Nano-Interface and Biosafety of Repeated Nano-Electroporation by Nanostraw System	The RNA sequencing results were presented in the interactive data mining system named Dr.Tom at the BGI Institute.	2022/7/13	Zhang A, Fang J, Wang J, Xie X, Chen HJ, He G. Interrogation on the Cellular Nano-Interface and Biosafety of Repeated Nano-Electroporation by Nanostraw System. Biosensors (Basel). 2022 Jul 13;12(7):522. doi: 10.3390/bios12070522. PMID: 35884325; PMCID: PMC9313307.	Biosensors (Basel)	4.379
103	LncRNA and mRNA expression profiles in brown adipose tissue of obesity-prone and obesity-resistant mice	GSEA was performed on BGI’s Dr.Tom system (http://biosys.bgi.com) with the software package provided by the Broad Institute, based on the MSigDB (Molecular Signatures Database).	2022/7/20	Wang C, Duan M, Lin J, Wang G, Gao H, Yan M, Chen L, He J, Liu W, Yang F, Zhu S. LncRNA and mRNA expression profiles in brown adipose tissue of obesity-prone and obesity-resistant mice. iScience. 2022 Jul 20;25(8):104809. doi: 10.1016/j.isci.2022.104809. PMID: 35992072; PMCID: PMC9382264.	iScience	4.953
104	A temperature-regulated circuit for feeding behavior	The correlational analysis, enrichment analysis and clustering analysis of DEGs were carried out on the Dr. Tom system (an interactive report system developed by BGI).	2022/7/22	Qian S, Yan S, Pang R, Zhang J, Liu K, Shi Z, Wang Z, Chen P, Zhang Y, Luo T, Hu X, Xiong Y, Zhou Y. A temperature-regulated circuit for feeding behavior. Nat Commun. 2022 Jul 22;13:4229. doi: 10.1038/s41467-022-31917-w. PMCID: PMC9307622.	Nature Communications	14.91
105	Regulation of metabolic and transcriptional responses by the thyroid hormone in cellular models of murine macrophages	The gene ontology of biological processes (GO-p) and Kyoto Encyclopedia of Genes and Genomes (KEEG) bioinformatics analysis were performed using BGI propietary Dr. TOM software, an in-house customized data mining system of the BGI (https://biosys.bgi.com).	2022/7/22	López-Mateo I, Rodríguez-Muñoz D, de La Rosa JV, Castrillo A, Alemany S, Aranda A. Regulation of metabolic and transcriptional responses by the thyroid hormone in cellular models of murine macrophages. Front Immunol. 2022 Jul 22;13:923727. doi: 10.3389/fimmu.2022.923727. PMID: 35935955; PMCID: PMC9353060.	Frontiers in Immunology	5.787
106	ZAKβ is activated by cellular compression and mediates contraction‐induced MAP kinase signaling in skeletal muscle	The sequencing data analysis, including principal component analysis (PCA) and Venn diagram creation, was performed using BGI Dr. Tom 2.0.	2022/7/28	Nordgaard C, Vind AC, Stonadge A, Kjøbsted R, Snieckute G, Antas P, Blasius M, Reinert MS, Del Val AM, Bekker-Jensen DB, Haahr P, Miroshnikova YA, Mazouzi A, Falk S, Perrier-Groult E, Tiedje C, Li X, Jakobsen JR, Jørgensen NO, Wojtaszewski JF, Mallein-Gerin F, Andersen JL, Pennisi CP, Clemmensen C, Kassem M, Jafari A, Brummelkamp T, Li VS, Wickström SA, Olsen JV, Blanco G, Bekker-Jensen S. ZAKβ is activated by cellular compression and mediates contraction-induced MAP kinase signaling in skeletal muscle. EMBO J. 2022 Sep 1;41(17):e111650. doi: 10.15252/embj.2022111650. Epub 2022 Jul 28. PMID: 35899396; PMCID: PMC9434084.	EMBO Journal	10.905
107	Circulating exo-miR-154-5p regulates vascular dementia through endothelial progenitor cell-mediated angiogenesis	Gene expression data were evaluated on Dr. Tom system (BGI, Wuhan, China).	2022/7/29	Han X, Zhou L, Tu Y, Wei J, Zhang J, Jiang G, Shi Q, Ying H. Circulating exo-miR-154-5p regulates vascular dementia through endothelial progenitor cell-mediated angiogenesis. Front Cell Neurosci. 2022 Jul 29;16:881175. doi: 10.3389/fncel.2022.881175. PMID: 35966195; PMCID: PMC9372489.	Frontiers in Cell Neuroscience	4.442
108	Biocompatible exosome-modified fibrin gel accelerates the recovery of spinal cord injury by VGF-mediated oligodendrogenesis	The data obtained were analysed using BGI Dr. Tom online system.	2022/8/2	He X, Yang L, Dong K, Zhang F, Liu Y, Ma B, Chen Y, Hai J, Zhu R, Cheng L. Biocompatible exosome-modified fibrin gel accelerates the recovery of spinal cord injury by VGF-mediated oligodendrogenesis. J Nanobiotechnology. 2022 Aug 2;20(1):360. doi: 10.1186/s12951-022-01541-3. PMID: 35918769; PMCID: PMC9344707.	Journal of Nanobiotechnology	7.433
109	BTApep-TAT peptide inhibits ADP-ribosylation of BORIS to induce DNA damage in cancer	The differential gene expression analysis was performed by the Dr. Tom online system (BGI-Shenzhen, China, http://biosys.bgi.com).	2022/8/2	Zhang Y, Fang M, Li S, Xu H, Ren J, Tu L, Zuo B, Yao W, Liang G. BTApep-TAT peptide inhibits ADP-ribosylation of BORIS to induce DNA damage in cancer. Mol Cancer. 2022 Aug 2;21(1):158. doi: 10.1186/s12943-022-01621-w. PMID: 35918747; PMCID: PMC9344678.	Molecular Cancer	17.794
110	Dodder-transmitted mobile systemic signals activate a salt-stress response characterized by a transcriptome change in Citrus sinensis	Clean data and count numbers of the RNA sequencing libraries were assessed and summarized using the transcriptional analysis website Dr. Tom.	2022/8/9	Duan S, Xu Z, Li XY, Liao P, Qin HK, Mao YP, Dai WS, Ma HJ, Bao ML. Dodder-transmitted mobile systemic signals activate a salt-stress response characterized by a transcriptome change in Citrus sinensis. Front Plant Sci. 2022 Aug 9;13:986365. doi: 10.3389/fpls.2022.986365. PMID: 36046588; PMCID: PMC9422749.	Frontiers in Plant Science	4.754
111	Structural insight into ASH1L PHD finger recognizing methylated histone H3K4 and promoting cell growth in prostate cancer	The data were analyzed using the BGI Dr. Tom multi-omics integration analysis website (https://biosys.bgi.com/#/report/login).	2022/8/10	Yu M, Jia Y, Ma Z, Ji D, Wang C, Liang Y, Zhang Q, Yi H, Zeng L. Structural insight into ASH1L PHD finger recognizing methylated histone H3K4 and promoting cell growth in prostate cancer. Front Oncol. 2022 Aug 10;12:906807. doi: 10.3389/fonc.2022.906807. PMCID: PMC9399681.	Frontiers In Oncology	6.243
112	Identification of solamargine as a cisplatin sensitizer through phenotypical screening in cisplatin-resistant NSCLC organoids	The heatmap of differentially expressed genes (DEGs) (log2FC ≥ 1, p ≤ 0.001) and KEGG analysis (log2FC ≥ 1, p ≤ 0.05) in NSCLC cell lines were performed by the BGI, using the Dr. TOM approach, a customized data mining system from BGI.	2022/8/10	Han Y, Shi J, Xu Z, Zhang Y, Cao X, Yu J, Li J, Xu S. Identification of solamargine as a cisplatin sensitizer through phenotypical screening in cisplatin-resistant NSCLC organoids. Front Pharmacol. 2022 Aug 10;13:802168. doi: 10.3389/fphar.2022.802168. PMCID: PMC9399411.	Frontiers in Pharmacology	4.627
113	Effects of Extracellular Vesicles from Osteogenic Differentiated Human BMSCs on Osteogenic and Adipogenic Differentiation Capacity of Naïve Human BMSCs	The following bioinformatics analyses including Venn diagram, GO, and KEGG et al. of annotated protein were conducted with the bioinformatics platform STRING database (http://string-db.org, accessed on 10 April 2021) and the platform Dr. Tom (https://biosys.bgi.com, accessed on 10 April 2021) provided by the Beijing Genomics Institute (BGI).	2022/8/11	Wang C, Stöckl S, Li S, Herrmann M, Lukas C, Reinders Y, Sickmann A, Grässel S. Effects of Extracellular Vesicles from Osteogenic Differentiated Human BMSCs on Osteogenic and Adipogenic Differentiation Capacity of Naïve Human BMSCs. Cells. 2022 Aug 11;11(16):2491. doi: 10.3390/cells11162491. PMID: 36010568; PMCID: PMC9406723.	Cells	5.54
114	Interaction network of African swine fever virus structural protein p30 with host proteins	In addition, GO and KEGG enrichment analysis and visualization were performed using the Dr. Tom data analysis platform developed by the BGI.	2022/8/15	Chen X, Chen X, Liang Y, Xu S, Weng Z, Gao Q, Huang Z, Zhang G, Gong L. Interaction network of African swine fever virus structural protein p30 with host proteins. Front Microbiol. 2022 Aug 15;13:971888. doi: 10.3389/fmicb.2022.971888. PMID: 36090090; PMCID: PMC9451658.	Frontiers In Microbiology	5.644
115	SU4312 Represses Glioma Progression by Inhibiting YAP and Inducing Sensitization to the Effect of Temozolomide	DEGs were analyzed using Dr. Tom online software (BGI) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, with Q-values < 0.05 for the pathways shown in the graph.	2022/8/16	Wang X, Zhou Y, Wang Y, Wang X, Zhang Y, Mao Y, Zhang L, Qi J, Zhang Y, Lyu F, Gu L, Yu R, Zhou X. SU4312 Represses Glioma Progression by Inhibiting YAP and Inducing Sensitization to the Effect of Temozolomide. J Clin Med. 2022 Aug 16;11(16):4765. doi: 10.3390/jcm11164765. PMID: 36013004; PMCID: PMC9410026.	Journal of Clinical Medicine	4.411
116	Inorganic nanosheets facilitate humoral immunity against medical implant infections by modulating immune co-stimulatory pathways	The collected data were analyzed with the software of Dr.Tom	2022/8/18	Yang C, Luo Y, Shen H, Ge M, Tang J, Wang Q, Lin H, Shi J, Zhang X. Inorganic nanosheets facilitate humoral immunity against medical implant infections by modulating immune co-stimulatory pathways. Nat Commun. 2022 Aug 18;13(1):4866. doi: 10.1038/s41467-022-32405-x. PMID: 35982036; PMCID: PMC9388665.	Nature Communications	14.91
117	Up-regulated IL-17 and Tnf signaling in bone marrow cells of young male osteogenesis imperfecta mice	Gene Set Enrichment Analysis (GSEA) based on the KEGG database was also performed using BGI Dr. Tom and results with P ≤ 0.05 and Q ≤ 0.25 were considered statistically significant.	2022/8/23	Shao C, Liu Y, Li J, Liu Z, Zhao Y, Jing Y, Lv Z, Fu T, Wang Z, Li G. Up-regulated IL-17 and Tnf signaling in bone marrow cells of young male osteogenesis imperfecta mice. PeerJ. 2022 Aug 23;10:e13963. doi: 10.7717/peerj.13963. PMCID: PMC9415356.	PeerJ	2.572
118	Dysregulation of EZH2/miR-138-5p Axis Contributes to Radiosensitivity in Hepatocellular Carcinoma Cell by Downregulating Hypoxia-Inducible Factor 1 Alpha (HIF-1α)	The sequencing data analysis, including heat map clustering, Venn diagram creation, gene ontology (GO) analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, was performed using BGI Dr. Tom 2.0.	2022/8/29	Bai B, Liu Y, Fu XM, Qin HY, Li GK, Wang HC, Sun SL. Dysregulation of EZH2/miR-138-5p Axis Contributes to Radiosensitivity in Hepatocellular Carcinoma Cell by Downregulating Hypoxia-Inducible Factor 1 Alpha (HIF-1α). Oxid Med Cell Longev. 2022 Aug 29;2022:7608712. doi: 10.1155/2022/7608712. PMID: 36071871; PMCID: PMC9444475.	Oxidative Medicine and Cellular Longevity	5.496
119	Transcriptome analysis of microRNAs, circRNAs, and mRNAs in the dorsal root ganglia of paclitaxel-induced mice with neuropathic pain	All these data can be extracted manually by utilizing Dr. Tom on-line analysis system provided by BGI Genomics Inc	2022/8/31	Mao Q, Tian L, Wei J, Zhou X, Cheng H, Zhu X, Li X, Gao Z, Zhang X, Liang L. Transcriptome analysis of microRNAs, circRNAs, and mRNAs in the dorsal root ganglia of paclitaxel-induced mice with neuropathic pain. Front Mol Neurosci. 2022 Aug 31;15:990260. doi: 10.3389/fnmol.2022.990260. PMID: 36117915; PMCID: PMC9470859.	Frontiers in Molecular Neuroscience	5.63
120	CircSMARCC1 facilitates tumor progression by disrupting the crosstalk between prostate cancer cells and tumor-associated macrophages via miR-1322/CCL20/CCR6 signaling	Additional analysis, including a heatmap, gene set enrichment analysis (GSEA) was completed using the BGI Dr. Tom system.	2022/9/1	Xie T, Fu DJ, Li ZM, Lv DJ, Song XL, Yu YZ, Wang C, Li KJ, Zhai B, Wu J, Feng NH, Zhao SC. CircSMARCC1 facilitates tumor progression by disrupting the crosstalk between prostate cancer cells and tumor-associated macrophages via miR-1322/CCL20/CCR6 signaling. Mol Cancer. 2022 Sep 1;21(1):173. doi: 10.1186/s12943-022-01630-9. PMID: 36045408; PMCID: PMC9434883.	Molecular Cancer	17.794
121	N-acetylcysteine regulates dental follicle stem cell osteogenesis and alveolar bone repair via ROS scavenging	The significant levels were corrected by Q value with a threshold (Q value < 0.05) by Bonferroni. Differential expression analysis was performed using the DESeq2 (v1.4.5), Dr. Tom (BGI, Shenzhen, China) and R language (v4.0.3) ComplexHeatmap package (v2.4.3) with Q value < 0.05 and fold change > 1.5. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed by Dr. Tom (BGI, Shenzhen, China) and R language TopGO package (v2.42.0) and ClusterProfiler package (v3.18.1).	2022/9/8	Meng Z, Liu J, Feng Z, Guo S, Wang M, Wang Z, Li Z, Li H, Sui L. N-acetylcysteine regulates dental follicle stem cell osteogenesis and alveolar bone repair via ROS scavenging. Stem Cell Res Ther. 2022 Sep 8;13(1):466. doi: 10.1186/s13287-022-03161-y. PMID: 36076278; PMCID: PMC9461171.	Stem Cell Research & Therapy	6.834
122	Identification of the co-differentially expressed hub genes involved in the endogenous protective mechanism against ventilator-induced diaphragm dysfunction	After library preparation and sequencing on an MGISEQ-2000 sequencing platform, data analysis was performed on the Dr. Tom platform (http://report.bgi.com; Huada Gene Science and Technology Service Co., Ltd., Shenzhen, China).	2022/9/9	Zhang D, Hao W, Niu Q, Xu D, Duan X. Identification of the co-differentially expressed hub genes involved in the endogenous protective mechanism against ventilator-induced diaphragm dysfunction. Skelet Muscle. 2022 Sep 9;12(1):21. doi: 10.1186/s13395-022-00304-w. PMID: 36085166; PMCID: PMC9461262.	Skeletal Muscle	4.222
123	PEX5R/Trip8b-HCN2 channel regulating neuroinflammation involved in perioperative neurocognitive disorders	Expression heatmaps were produced by Dor. Tom from BGI (a web-based multi-omics visualization tool: https://biosys.bgi.com/#/report/mrna/en/help).	2022/9/14	Xu F, Wang Y, Han L, Deng D, Ding Y, Ma L, Zhang Q, Chen X. PEX5R/Trip8b-HCN2 channel regulating neuroinflammation involved in perioperative neurocognitive disorders. Cell Biosci. 2022 Sep 14;12(1):156. doi: 10.1186/s13578-022-00892-6. PMID: 36104739; PMCID: PMC9476339.	Cell & Bioscience	7.5
124	Cytokine nanosponges suppressing overactive macrophages and dampening systematic cytokine storm for the treatment of hemophagocytic lymphohistiocytosis	Volcano map, Cluster analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and Key driver analysis (KDA) of the DEGS were conducted by Dr. Tom system (https://biosys.bgi.com).	2022/9/20	Wang H, Liu H, Li J, Liu C, Chen H, Li J, Sun C, Guo T, Pang Z, Zhang B, Hu Y. Cytokine nanosponges suppressing overactive macrophages and dampening systematic cytokine storm for the treatment of hemophagocytic lymphohistiocytosis. Bioact Mater. 2022 Sep 20;21:531-546. doi: 10.1016/j.bioactmat.2022.09.012. PMID: 36185750; PMCID: PMC9508173.	Bioactive Materials	16.874
125	PFKFB4 facilitates palbociclib resistance in oestrogen receptor‐positive breast cancer by enhancing stemness	The related analyses, including Venn, heatmap and GO enrichment analysis, were accomplished by BGI Dr. Tom system and BioJupies online tool.	2022/9/20	Wang S, Bei Y, Tian Q, He J, Wang R, Wang Q, Sun L, Ke J, Xie C, Shen P. PFKFB4 facilitates palbociclib resistance in oestrogen receptor-positive breast cancer by enhancing stemness. Cell Prolif. 2023 Jan;56(1):e13337. doi: 10.1111/cpr.13337. Epub 2022 Sep 20. PMID: 36127291; PMCID: PMC9816941.	Cell proliferation	7.17
126	Rice cellulose synthase-like protein OsCSLD4 coordinates the trade-off between plant growth and defense	The RNA-seq data was analyzed on the online Dr. Tom system from BGI (https://biosys.bgi.com/) and has been deposited in National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database with accession number PRJNA853163.	2022/9/26	Liu X, Yin Z, Wang Y, Cao S, Yao W, Liu J, Lu X, Wang F, Zhang G, Xiao Y, Tang W, Deng H. Rice cellulose synthase-like protein OsCSLD4 coordinates the trade-off between plant growth and defense. Front Plant Sci. 2022 Sep 26;13:980424. doi: 10.3389/fpls.2022.980424. PMID: 36226281; PMCID: PMC9548992.	Frontiers in Plant Science	6.627
127	Hepatocyte-Specific Smad4 Deficiency Alleviates Liver Fibrosis via the p38/p65 Pathway	The Kyoto encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed by using Phyper in R. All analyses were conducted on the Dr Tom network platform of BGI (http://report.bgi.com)	2022/10/2	Wei M, Yan X, Xin X, Chen H, Hou L, Zhang J. Hepatocyte-Specific Smad4 Deficiency Alleviates Liver Fibrosis via the p38/p65 Pathway. Int J Mol Sci. 2022 Oct 2;23(19):11696. doi: 10.3390/ijms231911696. PMID: 36232998; PMCID: PMC9570188.	International Journal Of Molecular Sciences	6.208
128	A Comparative Analysis of the Wound Healing-Related Heterogeneity of Adipose-Derived Stem Cells Donors	The GO bioinformatics and heat map gene expression analyses were carried out using the visualization tool Dr. TOM	2022/10/14	Ren G, Peng Q, Emmersen J, Zachar V, Fink T, Porsborg SR. A Comparative Analysis of the Wound Healing-Related Heterogeneity of Adipose-Derived Stem Cells Donors. Pharmaceutics. 2022 Oct 6;14(10):2126. doi: 10.3390/pharmaceutics14102126. PMID: 36297561; PMCID: PMC9608503.	Pharmaceutics	6.525
129	Transcriptomic profile analysis of the left atrium in spontaneously hypertensive rats in the early stage	Principal component analysis, volcano plot and protein–protein interaction network analysis were performed in BGI online system (Dr.Tom). Key driver gene analysis (KDA) was carried out using BGI online system (Dr.Tom).	2022/10/17	Fang Q, Wang J, Wei J, Long X, Wang Y, He J, Yuan X, Du J. Transcriptomic profile analysis of the left atrium in spontaneously hypertensive rats in the early stage. Front Pharmacol. 2022 Oct 17;13:989636. doi: 10.3389/fphar.2022.989636. PMID: 36324689; PMCID: PMC9620422.	Frontiers in Pharmacology	5.988
130	Stearoyl-CoA Desaturase-1 dependent lipid droplets accumulation in cancer-associated fibroblasts facilitates the progression of lung cancer	The raw transcriptomic reads were mapped to a reference genome and the gene expression levels by using BGI Dr.Tom 3.0.	2022/10/18	Zhang Y, Gu Z, Wan J, Lou X, Liu S, Wang Y, Bian Y, Wang F, Li Z, Qin Z. Stearoyl-CoA Desaturase-1 dependent lipid droplets accumulation in cancer-associated fibroblasts facilitates the progression of lung cancer. Int J Biol Sci. 2022 Oct 18;18(16):6114-6128. doi: 10.7150/ijbs.74924. PMID: 36439884; PMCID: PMC9682541.	International Journal Of Biological Sciences	7.69
131	The Antimicrobial Peptide AMP-17 Derived from Musca domestica Inhibits Biofilm Formation and Eradicates Mature Biofilm in Candida albicans	Data mining and figure presentation processes were analyzed by BGI’s in-house customized data mining system called Dr. Tom (http://biosys.bgi.com accessed on 22 April 2021).	2022/10/25	Sun C, Zhao X, Jiao Z, Peng J, Zhou L, Yang L, Huang M, Tian C, Guo G. The Antimicrobial Peptide AMP-17 Derived from Musca domestica Inhibits Biofilm Formation and Eradicates Mature Biofilm in Candida albicans. Antibiotics (Basel). 2022 Oct 25;11(11):1474. doi: 10.3390/antibiotics11111474. PMID: 36358129; PMCID: PMC9686669.	Antibiotics (Basel)	3.9
132	Synthesis and Antitumor Activities of Novel Mitochondria-Targeted Dihydroartemisinin Ether Derivatives	RNA-seq analysis was outsourced to BGI Genomics (Wuhan, China), and the results were analyzed on the Dr. Tom system from BGI (https://biosys.bgi.com/).	2022/11/1	Xu C, Xiao L, Lin P, Yang X, Zou X, Mu L, Yang X. Synthesis and Antitumor Activities of Novel Mitochondria-Targeted Dihydroartemisinin Ether Derivatives. ACS Omega. 2022 Oct 18;7(43):38832-38846. doi: 10.1021/acsomega.2c04562. PMID: 36340114; PMCID: PMC9631890.	ACS Omega	4.132
133	Resistance to ATR inhibitors is mediated by loss of the nonsense-mediated decay factor UPF2	DEG Venn diagram figures and bubble plots were generated using the Dr. Tom Data Visualization software (BGI).	2022/11/2	O'Leary PC, Chen H, Doruk YU, Williamson T, Polacco B, McNeal AS, Shenoy T, Kale N, Carnevale J, Stevenson E, Quigley DA, Chou J, Feng FY, Swaney DL, Krogan NJ, Kim M, Diolaiti ME, Ashworth A. Resistance to ATR Inhibitors Is Mediated by Loss of the Nonsense-Mediated Decay Factor UPF2. Cancer Res. 2022 Nov 2;82(21):3950-3961. doi: 10.1158/0008-5472.CAN-21-4335. PMID: 36273492; PMCID: PMC9633439.	Cancer Research	6.44
134	Molecular, cellular and neurological consequences of infection by the neglected human pathogen Nocardia	The Kyoto Encyclopedia of Genes and Genomes (KEGG) and clustering analysis of DEGs were completed on Dr. Tom system (https://biosys.bgi.com).	2022/11/19	Ji X, Han L, Zhang W, Sun L, Xu S, Qiu X, Fan S, Li Z. Molecular, cellular and neurological consequences of infection by the neglected human pathogen Nocardia. BMC Biol. 2022 Nov 9;20(1):251. doi: 10.1186/s12915-022-01452-7. PMID: 36352407; PMCID: PMC9647956.	BMC Biology	7.364
135	A PD-L1-targeting chimeric switch receptor enhances efficacy of CAR-T cell for pleural and peritoneal metastasis	The genes with FC ≥ 2 and Q value ≤ 0.001 were selected to perform enrichment analysis using the Dr. Tom network platform of BGI (http://report.bgi.com).	2022/11/19	Ma, Q., He, X., Zhang, B. et al. A PD-L1-targeting chimeric switch receptor enhances efficacy of CAR-T cell for pleural and peritoneal metastasis. Sig Transduct Target Ther 7, 380 (2022). https://doi.org/10.1038/s41392-022-01198-2	Signal Transduction and Targeted Therapy	38.104
136	The tapetal tissue is essential for the maintenance of redox homeostasis during microgametogenesis in tomato	A total of three biological replicates were used for each sample set. GO enrichment, KEGG enrichment and statistical analysis were performed through the Dr Tom platform (BGI).	2022/11/19	Salazar-Sarasua B, López-Martín MJ, Roque E, Hamza R, Cañas LA, Beltrán JP, Gómez-Mena C. The tapetal tissue is essential for the maintenance of redox homeostasis during microgametogenesis in tomato. Plant J. 2022 Dec;112(5):1281-1297. doi: 10.1111/tpj.16014. Epub 2022 Nov 19. PMID: 36307971; PMCID: PMC10100220.	Plant Journal	6.68
137	LINC00924-induced fatty acid metabolic reprogramming facilitates gastric cancer peritoneal metastasis via hnRNPC-regulated alternative splicing of Mnk2	Gene set enrichment analysis (GSEA) of differentially expressed genes was performed on the Dr. Tom network platform at BGI	2022/11/23	He Q, Yang C, Xiang Z, Huang G, Wu H, Chen T, Dou R, Song J, Han L, Song T, Wang S, Xiong B. LINC00924-induced fatty acid metabolic reprogramming facilitates gastric cancer peritoneal metastasis via hnRNPC-regulated alternative splicing of Mnk2. Cell Death Dis. 2022 Nov 23;13(11):987. doi: 10.1038/s41419-022-05436-x. PMID: 36418856; PMCID: PMC9684446.	Cell Death & Disease	7.47
138	Targeted xCT‐mediated Ferroptosis and Protumoral Polarization of Macrophages Is Effective against HCC and Enhances the Efficacy of the Anti‐PD‐1/L1 Response	KEGG analysis was performed on the Dr.Tom website (https://biosys.bgi.com/) to examine the enriched regulatory signaling pathways of the DEGs. Results with an adjusted p < 0.05 were considered statistically significant.	2022/11/28	Tang B, Zhu J, Wang Y, Chen W, Fang S, Mao W, Xu Z, Yang Y, Weng Q, Zhao Z, Chen M, Ji J. Targeted xCT-mediated Ferroptosis and Protumoral Polarization of Macrophages Is Effective against HCC and Enhances the Efficacy of the Anti-PD-1/L1 Response. Adv Sci (Weinh). 2023 Jan;10(2):e2203973. doi: 10.1002/advs.202203973. Epub 2022 Nov 28. PMID: 36442849; PMCID: PMC9839855.	Advanced Science	12.89
139	SERPINB2, an Early Responsive Gene to Epigallocatechin Gallate, Inhibits Migration and Promotes Apoptosis in Esophageal Cancer Cells	The analysis for RNA-seq data was conducted using Dr. Tom System developed by BGI (https://biosys.bgi.com (accessed on 5 January 2021)).	2022/11/30	Chen Z, Wei Y, Zheng Y, Zhu H, Teng Q, Lin X, Wu F, Zhou F. SERPINB2, an Early Responsive Gene to Epigallocatechin Gallate, Inhibits Migration and Promotes Apoptosis in Esophageal Cancer Cells. Cells. 2022 Nov 30;11(23):3852. doi: 10.3390/cells11233852. PMID: 36497110; PMCID: PMC9738437.	Cells	4.99
140	PGCLCs of human 45,XO reveal pathogenetic pathways of neurocognitive and psychosocial disorders	Heat maps were constructed using pheatmap (R-package) in Dr.Tom (biosys.bgi.com).	2022/12/1	Shang D, Lan T, Wang Y, Li X, Liu Q, Dong H, Xu B, Cheng H, Zhou R. PGCLCs of human 45,XO reveal pathogenetic pathways of neurocognitive and psychosocial disorders. Cell Biosci. 2022 Dec 1;12(1):194. doi: 10.1186/s13578-022-00925-0. PMID: 36457060; PMCID: PMC9716775.	Cell & Bioscience	6.33
141	Sustained high glucose intake accelerates type 1 diabetes in NOD mice	The Dr. Tom platform independently developed by BGI was used to carry out more in-depth analysis of DEGs, such as cluster analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis.	2022/12/5	Li X, Wang L, Meng G, Chen X, Yang S, Zhang M, Zheng Z, Zhou J, Lan Z, Wu Y, Wang L. Sustained high glucose intake accelerates type 1 diabetes in NOD mice. Front Endocrinol (Lausanne). 2022 Dec 5;13:1037822. doi: 10.3389/fendo.2022.1037822. PMID: 36545340; PMCID: PMC9760976.	Frontiers in Endocrinology	4.32
142	Innate and Adaptive Immune Responses Induced by Aspergillus fumigatus Conidia and Hyphae	The Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com) was adopted for subsequent analysis and data mining.	2022/12/6	Luo Y, Liu F, Deng L, Xu J, Kong Q, Shi Y, Sang H. Innate and Adaptive Immune Responses Induced by Aspergillus fumigatus Conidia and Hyphae. Curr Microbiol. 2022 Dec 6;80(1):28. doi: 10.1007/s00284-022-03102-1. PMID: 36474044; PMCID: PMC9734344.	Current Microbiology	2.17
143	Ox40-Cre–mediated deletion of BRD4 reveals an unexpected phenotype of hair follicle stem cells in alopecia	Heatmaps, KEGG pathways, and GSEA were generated using Dr. Tom platform (https://biosys.bgi.com/).	2022/12/8	Wen M, Ying Y, Xiao X, Arnold PR, Wang G, Chu X, Ghobrial RM, Li XC. Ox40-Cre-mediated deletion of BRD4 reveals an unexpected phenotype of hair follicle stem cells in alopecia. JCI Insight. 2022 Dec 8;7(23):e164534. doi: 10.1172/jci.insight.164534. PMID: 36256455; PMCID: PMC9746908.	JCI Insight	6.88
144	Ginsenoside Rd protects transgenic Caenorhabditis elegans from β-amyloid toxicity by activating oxidative resistant	The data were analyzed on the Dr Tom network platform of BGI (http://report.bgi.com).	2022/12/15	Mi L, Fan M, Liu T, Wu D, Wang Y, Li F, Cai Y, Qiu Z, Liu D, Cao L. Ginsenoside Rd protects transgenic Caenorhabditis elegans from β-amyloid toxicity by activating oxidative resistant. Front Pharmacol. 2022 Dec 15;13:1074397. doi: 10.3389/fphar.2022.1074397. PMID: 36588689; PMCID: PMC9797510.	Frontiers in Pharmacology	4.75
145	Increased expression of miR-194-5p through the circPVRL3/miR-194-5p/SOCS2 axis promotes proliferation and metastasis in pancreatic ductal adenocarcinoma by activating the PI3K/AKT signaling pathway	The mRNA-seq was implemented by the DNBSEQ platform (BGI company, Shenzhen, China), and subsequent data were analyzed by Dr.Tom system (BGI, Shenzhen, China).	2022/12/20	Chi B, Zheng Y, Xie F, Fu W, Wang X, Gu J, Yang J, Yin J, Cai L, Tang P, Li J, Guo S, Wang H. Increased expression of miR-194-5p through the circPVRL3/miR-194-5p/SOCS2 axis promotes proliferation and metastasis in pancreatic ductal adenocarcinoma by activating the PI3K/AKT signaling pathway. Cancer Cell Int. 2022 Dec 20;22(1):415. doi: 10.1186/s12935-022-02835-0. PMID: 36539807; PMCID: PMC9764499.	Cancer Cell International	5.99
146	Neurogenesis potential of oligodendrocyte precursor cells from oligospheres and injured spinal cord	Bioinformatics analysis was carried out with the online platform Dr. Tom (BGI Company).	2022/12/22	Zhao Q, Zhu Y, Ren Y, Yin S, Yu L, Huang R, Song S, Hu X, Zhu R, Cheng L, Xie N. Neurogenesis potential of oligodendrocyte precursor cells from oligospheres and injured spinal cord. Front Cell Neurosci. 2022 Dec 22;16:1049562. doi: 10.3389/fncel.2022.1049562. PMID: 36619671; PMCID: PMC9813964.	Frontiers in Cellular Neuroscience	4.58
147	A Zinc‐ and Calcium‐Rich Lysosomal Nanoreactor Rescues Monocyte/Macrophage Dysfunction under Sepsis	The visualization of the results was made using Dr. Tom system (BGI‐Shenzhen, China)	2023/1/3	Zhao Q, Gong Z, Wang J, Fu L, Zhang J, Wang C, Miron RJ, Yuan Q, Zhang Y. A Zinc- and Calcium-Rich Lysosomal Nanoreactor Rescues Monocyte/Macrophage Dysfunction under Sepsis. Adv Sci (Weinh). 2023 Feb;10(6):e2205097. doi: 10.1002/advs.202205097. Epub 2023 Jan 3. PMID: 36596693; PMCID: PMC9951326.	Advanced Science	13.89
148	Prolonged anesthesia induces neuroinflammation and complement-mediated microglial synaptic elimination involved in neurocognitive dysfunction and anxiety-like behaviors	In terms of functional enrichment analysis, all DEGs (differentially expressed genes) were mapped to terms in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) databases. Dor. Tom from BGI (a web-based multiomics visualization tool: https://biosys.bgi.com/#/report/mrna/en/help) was used to analyze and visualize the results of RNA-seq.	2023/1/5	Xu F, Han L, Wang Y, Deng D, Ding Y, Zhao S, Zhang Q, Ma L, Chen X. Prolonged anesthesia induces neuroinflammation and complement-mediated microglial synaptic elimination involved in neurocognitive dysfunction and anxiety-like behaviors. BMC Med. 2023 Jan 5;21(1):7. doi: 10.1186/s12916-022-02705-6. PMID: 36600274; PMCID: PMC9814183.	BMC Medicine	9.3
149	Discovery of rafoxanide as a novel agent for the treatment of non-small cell lung cancer	GO functional enrichment and KEGG pathway analyses were carried out by the Dr. Tom platform (BGI-tech, China)	2023/1/13	Hu A, Liu J, Wang Y, Zhang M, Guo Y, Qin Y, Liu T, Men Y, Chen Q, Liu T. Discovery of rafoxanide as a novel agent for the treatment of non-small cell lung cancer. Sci Rep. 2023 Jan 13;13(1):693. doi: 10.1038/s41598-023-27403-y. PMID: 36639421; PMCID: PMC9839764.	Scientific Reports	4.996
150	CTSB promotes sepsis-induced acute kidney injury through activating mitochondrial apoptosis pathway	The proteomics experiments were carried out by the HuaDa company (HuaDa, China) and bioinformatics analysis was performed by Dr.TOM on-line system software developed by the Beijing Genomics Institute (http://report.bgi.com).	2023/1/13	Wang Y, Xi W, Zhang X, Bi X, Liu B, Zheng X, Chi X. CTSB promotes sepsis-induced acute kidney injury through activating mitochondrial apoptosis pathway. Front Immunol. 2023 Jan 13;13:1053754. doi: 10.3389/fimmu.2022.1053754. PMID: 36713420; PMCID: PMC9880165.	Frontiers in Immunology	6.23
151	Characterization of mesenchymal stem cells in pre-B acute lymphoblastic leukemia	Gene set enrichment analysis (GSEA) using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and gene ontology (GO) enrichment analysis was performed using Dr. Tom	2023/1/20	Hughes AM, Kuek V, Oommen J, Chua GA, van Loenhout M, Malinge S, Kotecha RS, Cheung LC. Characterization of mesenchymal stem cells in pre-B acute lymphoblastic leukemia. Front Cell Dev Biol. 2023 Jan 20;11:1005494. doi: 10.3389/fcell.2023.1005494. PMID: 36743421; PMCID: PMC9897315.	Frontiers In Cell And Developmental Biology	5.12
152	Protective Effects of Lactobacillus gasseri against High-Cholesterol Diet-Induced Fatty Liver and Regulation of Host Gene Expression Profiles	The DEGs were analyzed with GO (http://www.geneontology.org/, accessed on 7 December 2020), the Database for Annotation, Visualization and Integrated Discovery (DAVID), KEGG (http://www.kegg.jp/kegg/pathway.html, accessed on 7 December 2020) enrichment annotation and BGI online system, Dr. Tom (BGI-Shenzhen, Shenzhen, China) to take insight to the changes in gene expression and signaling.	2023/1/20	He T, Lykov N, Luo X, Wang H, Du Z, Chen Z, Chen S, Zhu L, Zhao Y, Tzeng C. Protective Effects of Lactobacillus gasseri against High-Cholesterol Diet-Induced Fatty Liver and Regulation of Host Gene Expression Profiles. Int J Mol Sci. 2023 Jan 20;24(3):2053. doi: 10.3390/ijms24032053. PMCID: PMC9917166.	International Journal Of Molecular Sciences	6.208
153	Long-term statins administration exacerbates diabetic nephropathy via ectopic fat deposition in diabetic mice	The analysis of DEGs and KEGG pathways was performed at Dr.tom online (https://biosys.bgi.com).	2023/1/24	Huang TS, Wu T, Wu YD, Li XH, Tan J, Shen CH, Xiong SJ, Feng ZQ, Gao SF, Li H, Cai WB. Long-term statins administration exacerbates diabetic nephropathy via ectopic fat deposition in diabetic mice. Nat Commun. 2023 Jan 24;14(1):390. doi: 10.1038/s41467-023-35944-z. PMID: 36693830; PMCID: PMC9873739.	Nature Communications	17.694
154	BPDE, the Migration and Invasion of Human Trophoblast Cells, and Occurrence of Miscarriage in Humans: Roles of a Novel lncRNA-HZ09	The differentially expressed mRNAs with differences >2-fold and p<0.05 were generated from read counts using the online bioinformatic platform Dr. Tom provided by BGI (biosys.bgi.com).	2023/1/31	Dai M, Huang W, Huang X, Ma C, Wang R, Tian P, Chen W, Zhang Y, Mi C, Zhang H. BPDE, the Migration and Invasion of Human Trophoblast Cells, and Occurrence of Miscarriage in Humans: Roles of a Novel lncRNA-HZ09. Environ Health Perspect. 2023 Jan;131(1):17009. doi: 10.1289/EHP10477. Epub 2023 Jan 31. PMID: 36719213; PMCID: PMC9888265.	Environmental Health Perspectives	9.05
155	Vascular and pulmonary effects of ibuprofen on neonatal lung development	The analysis was performed on the Dr. Tom platform generated by BGI (https://biosys.bgi.com/).	2023/2/2	Chen X, Han D, Wang X, Huang X, Huang Z, Liu Y, Zhong J, Walther FJ, Yang C, Wagenaar GTM. Vascular and pulmonary effects of ibuprofen on neonatal lung development. Respir Res. 2023 Feb 2;24(1):39. doi: 10.1186/s12931-023-02342-4. PMID: 36732726; PMCID: PMC9893598.	Respiratory Research	5.42
156	Satellite glial cells drive the transition from acute to chronic pain in a rat model of hyperalgesic priming	The DeRNAs were further subjected to pathway (KEGG) and gene ontology (GO) enrichment analyses using Dr. Tom (BGI).	2023/2/2	Du J, Yi M, Xi D, Wang S, Liu B, Shao X, Liang Y, He X, Fang J, Fang J. Satellite glial cells drive the transition from acute to chronic pain in a rat model of hyperalgesic priming. Front Mol Neurosci. 2023 Feb 2;16:1089162. doi: 10.3389/fnmol.2023.1089162. PMID: 36818653; PMCID: PMC9931746.	Frontiers in Molecular Neuroscience	4.49
157	Targeting polymerase θ impairs tumorigenesis and enhances radiosensitivity in lung adenocarcinoma	The subsequent analysis and data mining were performed on Dr. Tom multiomics data‐mining system (https://biosys.bgi.com).	2023/2/2	Rao X, Xing B, Wu Z, Bin Y, Chen Y, Xu Y, Zhou D, Zhou X, Wu C, Ye W, Chen W, Wang G, Zhang S, Dong X, Meng R, Wu G, Zhou R. Targeting polymerase θ impairs tumorigenesis and enhances radiosensitivity in lung adenocarcinoma. Cancer Sci. 2023 May;114(5):1943-1957. doi: 10.1111/cas.15727. Epub 2023 Feb 2. PMID: 36642785; PMCID: PMC10154803.	Cancer Science	5.43
158	Boris knockout eliminates AOM/DSS‐induced in situ colorectal cancer by suppressing DNA damage repair and inflammation	Differentially expressed mRNAs, Pearson's correlation heatmap, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enriched were analyzed using the Dr Tom system (https://biosys.bgi.com/#/main).	2023/2/5	Zuo BW, Yao WX, Fang MD, Ren J, Tu LL, Fan RJ, Zhang YM. Boris knockout eliminates AOM/DSS-induced in situ colorectal cancer by suppressing DNA damage repair and inflammation. Cancer Sci. 2023 May;114(5):1972-1985. doi: 10.1111/cas.15732. Epub 2023 Feb 5. PMID: 36692143; PMCID: PMC10154901.	Cancer Science	5.43
159	Young and undamaged recombinant albumin alleviates T2DM by improving hepatic glycolysis through EGFR and protecting islet β cells in mice	The Dr. Tom web tool (https://biosys.bgi.com/) was used to visualize the DEGs and enriched pathways. Gene set enrichment analysis (GSEA) was performed to identify significantly enriched pathways in the KEGG databases using the Dr. Tom web tool.	2023/2/6	Liu, H., Ju, A., Dong, X. et al. Young and undamaged recombinant albumin alleviates T2DM by improving hepatic glycolysis through EGFR and protecting islet β cells in mice. J Transl Med 21, 89 (2023). https://doi.org/10.1186/s12967-023-03957-3	Journal of Translational Medicine	6.91
160	Sirt1 Negatively Regulates Cellular Antiviral Responses by Preventing the Cytoplasmic Translocation of Interferon-Inducible Protein 16 in Human Cells	To gain insight into the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analyses of annotated differently expressed genes were performed by Dr. Tom (https://biosys.bgi.com/).	2023/2/7	Wang J, Qin X, Huang Y, Zhang G, Liu Y, Cui Y, Wang Y, Pei J, Ma S, Song Z, Zhu X, Wang H, Yang B. Sirt1 Negatively Regulates Cellular Antiviral Responses by Preventing the Cytoplasmic Translocation of Interferon-Inducible Protein 16 in Human Cells. J Virol. 2023 Feb 28;97(2):e0197522. doi: 10.1128/jvi.01975-22. Epub 2023 Feb 7. PMID: 36749073; PMCID: PMC9973000.	Journal of Virology	5.4
161	“Slow walk” mimetic tensile loading maintains human meniscus tissue resident progenitor cells homeostasis in photocrosslinked gelatin hydrogel	Gene expression profiles were analyzed by RNA sequencing (BGI, Shenzhen, Guangdong, China), and further analysis was performed by means of the related software Dr. Tom (BGI, Shenzhen, Guangdong, China).	2023/2/8	Sun J, Chan YT, Ho KWK, Zhang L, Bian L, Tuan RS, Jiang Y. "Slow walk" mimetic tensile loading maintains human meniscus tissue resident progenitor cells homeostasis in photocrosslinked gelatin hydrogel. Bioact Mater. 2023 Feb 8;25:256-272. doi: 10.1016/j.bioactmat.2023.01.025. PMID: 36825224; PMCID: PMC9941420.	Bioactive Materials	17.36
162	Brain‐Derived Neurotrophic Factor Precursor Contributes to a Proinflammatory Program in Monocytes/Macrophages After Acute Myocardial Infarction	Gene expression levels were quantified using the software developed by Dr Tom. Differentially expressed genes were identified using the same software by Dr Tom, with a fold change >1 and a Q value <0.05.	2023/2/8	Li JN, Luo RY, Luo C, Hu ZL, Zha AH, Shen WY, Li Q, Li H, Fu D, Dai RP. Brain-Derived Neurotrophic Factor Precursor Contributes to a Proinflammatory Program in Monocytes/Macrophages After Acute Myocardial Infarction. J Am Heart Assoc. 2023 Mar 21;12(6):e028198. doi: 10.1161/JAHA.122.028198. Epub 2023 Feb 8. PMID: 36752235; PMCID: PMC10111532.	Journal of the American Heart Association	5.27
163	Molecular Mechanisms of Oxidative Stress Relief by CAPE in ARPE−19 Cells	All analyses were performed on the Dr. Tom analysis system constructed by MGI.	2023/2/10	Ren C, Zhou P, Zhang M, Yu Z, Zhang X, Tombran-Tink J, Barnstable CJ, Li X. Molecular Mechanisms of Oxidative Stress Relief by CAPE in ARPE-19 Cells. Int J Mol Sci. 2023 Feb 10;24(4):3565. doi: 10.3390/ijms24043565. PMID: 36834980; PMCID: PMC9959600.	International Journal Of Molecular Sciences	6.208
164	Comprehensive Analysis of Gene Expression Profiling to Explore Predictive Markers for Eradication Therapy Efficacy against Helicobacter pylori-Negative Gastric MALT Lymphoma	Gene Ontology (GO; geneontology.org) and Kyoto Encyclopedia of Genes and Genomes (KEGG; http://www.genome.jp/kegg/, accessed on 1 January 2022) pathway analyses were performed using the RNA Data Visualization System Dr. TOM (Beijing Genomics Institute; http://www.bgi.com/global/dr-tom/, accessed on 1 January 2022), a BGI in-house customized data mining system that combines different published software.	2023/2/14	Takigawa H, Yuge R, Miyamoto R, Otani R, Kadota H, Hiyama Y, Hayashi R, Urabe Y, Sentani K, Oue N, Kitadai Y, Oka S, Tanaka S. Comprehensive Analysis of Gene Expression Profiling to Explore Predictive Markers for Eradication Therapy Efficacy against Helicobacter pylori-Negative Gastric MALT Lymphoma. Cancers (Basel). 2023 Feb 14;15(4):1206. doi: 10.3390/cancers15041206. PMID: 36831547; PMCID: PMC9954119.	Cancers (Basel)	3.77
165	Lactiplantibacillus pentosus P2020 protects the hyperuricemia and renal inflammation in mice	KEGG pathway enrichment of differential genes was performed on the Dr. Tom analysis platform of Beijing Genomics Institute Co., Ltd.	2023/2/20	Wang Z, Song L, Li X, Xiao Y, Huang Y, Zhang Y, Li J, Li M, Ren Z. Lactiplantibacillus pentosus P2020 protects the hyperuricemia and renal inflammation in mice. Front Nutr. 2023 Feb 20;10:1094483. doi: 10.3389/fnut.2023.1094483. PMID: 36891165; PMCID: PMC9987516.	Frontiers in Nutrition	4.76
166	Regulatory mechanism of MeGI on sexuality in Diospyros oleifera	Gene Ontology (GO) classification and enrichment analyses, Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses and key driver analyses (KDAs) of differentially expressed genes (DEGs) were performed using the Dr. Tom system (BGI).	2023/2/22	Mai Y, Sun P, Suo Y, Li H, Han W, Diao S, Wang L, Yuan J, Wang Y, Ye L, Zhang Y, Li F, Fu J. Regulatory mechanism of MeGI on sexuality in Diospyros oleifera. Front Plant Sci. 2023 Feb 22;14:1046235. doi: 10.3389/fpls.2023.1046235. PMID: 36909399; PMCID: PMC9994623.	Frontiers in Plant Science	5.32
167	Effect of Dietetic Obesity on Testicular Transcriptome in Cynomolgus Monkeys	Analysis of RNA-sequencing data was conducted using the ‘Dr. Tom’ system	2023/2/23	Zhang Y, Qi J, Zhao J, Li M, Zhang Y, Hu H, Wei L, Zhou K, Qin H, Qu P, Cao W, Liu E. Effect of Dietetic Obesity on Testicular Transcriptome in Cynomolgus Monkeys. Genes (Basel). 2023 Feb 23;14(3):557. doi: 10.3390/genes14030557. PMID: 36980830; PMCID: PMC10048326.	Genes	3.37
168	Knockdown of MEF2D inhibits the development and progression of B-cell acute lymphoblastic leukemia	The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed according to the Dr. Tom approach, an in-house customized data mining system of the Shenzhen Genomics Institute (BGI-Huada Gene).	2023/2/28	Chang N, Feng J, Liao P, Hu Y, Li M, He Y, Li Y. Knockdown of MEF2D inhibits the development and progression of B-cell acute lymphoblastic leukemia. Transl Cancer Res. 2023 Feb 28;12(2):287-300. doi: 10.21037/tcr-22-1778. Epub 2023 Feb 1. PMID: 36915581; PMCID: PMC10007885.	Translational Cancer Research	0.85
169	Increased retinoic acid signaling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway	BGI used Illumina sequencing technology and developed the Dr.Tom system for further sequencing analysis.	2023/3/6	Zhou MJ, Yang JJ, Ma TY, Feng GX, Wang XL, Wang LY, Ge YZ, Gao R, Liu HL, Shan L, Kong L, Chen XH. Increased retinoic acid signaling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway. Exp Mol Med. 2023 Mar;55(3):597-611. doi: 10.1038/s12276-023-00957-7. Epub 2023 Mar 6. PMID: 36879115; PMCID: PMC10073150.	Experimental & Molecular Medicine	12.49
170	Collectin-11 promotes cancer cell proliferation and tumor growth	Further analysis of annotated genes was conducted in BGI Dr. Tom platform (https://biosys.bgi.com).	2023/3/8	Wang JX, Cao B, Ma N, Wu KY, Chen WB, Wu W, Dong X, Liu CF, Gao YF, Diao TY, Min XY, Yong Q, Li ZF, Zhou W, Li K. Collectin-11 promotes cancer cell proliferation and tumor growth. JCI Insight. 2023 Mar 8;8(5):e159452. doi: 10.1172/jci.insight.159452. PMID: 36883567; PMCID: PMC10077485.	JCI Insight	7.76
171	Combination therapy with ultrasound and 2D nanomaterials promotes recovery after spinal cord injury via Piezo1 downregulation	The results were then analysed using a BGI Dr. Tom online system according to a standard protocol.	2023/3/15	Zhang F, He X, Dong K, Yang L, Ma B, Liu Y, Liu Z, Chen B, Zhu R, Cheng L. Combination therapy with ultrasound and 2D nanomaterials promotes recovery after spinal cord injury via Piezo1 downregulation. J Nanobiotechnology. 2023 Mar 15;21(1):91. doi: 10.1186/s12951-023-01853-y. PMID: 36922816; PMCID: PMC10018903.	Journal of Nanobiotechnology	9.73
172	Cryptosporidium uses CSpV1 to activate host type I interferon and attenuate antiparasitic defenses	Differential expression analysis was performed by the BGI, using the Dr. TOM data system.	2023/3/16	Deng S, He W, Gong AY, Li M, Wang Y, Xia Z, Zhang XT, Huang Pacheco AS, Naqib A, Jenkins M, Swanson PC, Drescher KM, Strauss-Soukup JK, Belshan M, Chen XM. Cryptosporidium uses CSpV1 to activate host type I interferon and attenuate antiparasitic defenses. Nat Commun. 2023 Mar 16;14(1):1456. doi: 10.1038/s41467-023-37129-0. PMID: 36928642; PMCID: PMC10020566.	Nature Communications	17.694
173	High-fat intake reshapes the circadian transcriptome profile and metabolism in murine meibomian glands	KEGG and GO enrichment analysis were performed by online bioinformatic platform Dr. Tom,2 an online software developed by Beijing Genomic Institute (BGI)	2023/3/16	Zou S, Liu J, Si H, Huang D, Qi D, Pei X, Lu D, Huang S, Li Z. High-fat intake reshapes the circadian transcriptome profile and metabolism in murine meibomian glands. Front Nutr. 2023 Mar 16;10:1146916. doi: 10.3389/fnut.2023.1146916. PMID: 37006922; PMCID: PMC10062204.	Frontiers in Nutrition	4.82
174	Ribonuclease inhibitor 1 (RNH1) deficiency cause congenital cataracts and global developmental delay with infection-induced psychomotor regression and anemia	Volcano plot and sequence coverage randomness were analyzed using the Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).	2023/3/20	Hedberg-Oldfors C, Mitra S, Molinaro A, Visuttijai K, Fogelstrand L, Oldfors A, Sterky FH, Darin N. Ribonuclease inhibitor 1 (RNH1) deficiency cause congenital cataracts and global developmental delay with infection-induced psychomotor regression and anemia. Eur J Hum Genet. 2023 Aug;31(8):887-894. doi: 10.1038/s41431-023-01327-7. Epub 2023 Mar 20. PMID: 36935417; PMCID: PMC10400601.	European Journal of Human Genetics	5.2
175	Transgelin promotes lung cancer progression via activation of cancer-associated fibroblasts with enhanced IL-6 release	The data mining and graph presentation process, including Venn diagram, KEGG, heat map, and clustering, were all performed by Dr. Tom, a customized data mining system within the BGI.	2023/3/29	Sun C, Zhang K, Ni C, Wan J, Duan X, Lou X, Yao X, Li X, Wang M, Gu Z, Yang P, Li Z, Qin Z. Transgelin promotes lung cancer progression via activation of cancer-associated fibroblasts with enhanced IL-6 release. Oncogenesis. 2023 Mar 29;12(1):18. doi: 10.1038/s41389-023-00463-5. PMID: 36990991; PMCID: PMC10060230.	Oncogenesis	6.13
176	OTUB1 promotes osteoblastic bone formation through stabilizing FGFR2	RNA-seq analysis was performed using the Dr. Tom Multi-Omics Data Mining System (https://biosys.bgi.com).	2023/4/7	Zhu Q, Fu Y, Cui CP, Ding Y, Deng Z, Ning C, Hu F, Qiu C, Yu B, Zhou X, Yang G, Peng J, Zou W, Liu CH, Zhang L. OTUB1 promotes osteoblastic bone formation through stabilizing FGFR2. Signal Transduct Target Ther. 2023 Apr 7;8(1):142. doi: 10.1038/s41392-023-01354-2. PMID: 37024477; PMCID: PMC10079838.	Signal Transduction and Targeted Therapy	38.31
177	Focal Cryo-Immunotherapy with Intratumoral IL-12 Prevents Recurrence of Large Murine Tumors	Samples were sent to BGI Genomics (Hong Kong, China) to perform transcriptome sequencing using their DNBSEQTM platform with a read length of 100 paired-end base pairs. Data analysis was performed using the BGI software platform, Dr. Tom.	2023/4/8	Vrabel MR, Schulman JA, Gillam FB, Mantooth SM, Nguyen KG, Zaharoff DA. Focal Cryo-Immunotherapy with Intratumoral IL-12 Prevents Recurrence of Large Murine Tumors. Cancers (Basel). 2023 Apr 8;15(8):2210. doi: 10.3390/cancers15082210. PMCID: PMC10137033.	Cancers (Basel)	3.77
178	Identification of hub genes associated with head and neck squamous cell carcinoma by integrated bioinformatics approach and RNA-seq validation analysis	The Dr. Tom network platform (http://report.bgi.com) developed by the BGI was used to obtain fragments per kilo base million reads FPKM expression values.	2023/4/15	Shabeer A, Mustafa S, Bukhari RS, Abdel-Maksoud MA, Almutairi SM, Al-Qahtani WH, Chandio K, Khan NY, Gul J, Aufy M. Identification of hub genes associated with head and neck squamous cell carcinoma by integrated bioinformatics approach and RNA-seq validation analysis. Am J Cancer Res. 2023 Apr 15;13(4):1259–77. PMCID: PMC10164813.	American Journal Of Cancer Research	5.12
179	Altered zinc homeostasis in a primary cell culture model of the retinal pigment epithelium	All the statistical analyses were conducted using the online bioinformatic platform Dr. Tom provided by BGI.	2023/4/17	Álvarez-Barrios A, Álvarez L, Artime E, García M, Lengyel I, Pereiro R, González-Iglesias H. Altered zinc homeostasis in a primary cell culture model of the retinal pigment epithelium. Front Nutr. 2023 Apr 17;10:1124987. doi: 10.3389/fnut.2023.1124987. PMID: 37139441; PMCID: PMC10149808.	Frontiers in Nutrition	4.82
180	Decidual derived exosomal miR-99a-5p targets Ppp2r5a to inhibit trophoblast invasion in response to CeO2NPs exposure	The target gene prediction analysis of the 10 significantly different miRNAs was performed using the Dr. Tom system to obtain 169 target genes	2023/4/20	Zhong H, Geng Y, Gao R, Chen J, Chen Z, Mu X, Zhang Y, Chen X, He J. Decidual derived exosomal miR-99a-5p targets Ppp2r5a to inhibit trophoblast invasion in response to CeO2NPs exposure. Part Fibre Toxicol. 2023 Apr 20;20(1):14. doi: 10.1186/s12989-023-00524-y. PMID: 37081566; PMCID: PMC10116836.	Particle and Fibre Toxicology	9.5
181	A strategy of local hydrogen capture and catalytic hydrogenation for enhanced therapy of chronic liver diseases	The functional enrichment analysis of differentially expressed genes (DEGs), including Kyoto Encyclopedia of Gene and Genomes (KEGG), pathway enrichment analysis were performed using Dr. Tom, an online analysis system of BGI.	2023/4/23	Tao G, Liu F, Jin Z, Liu B, Wang H, Li D, Tang W, Chen Y, He Q, Qin S. A strategy of local hydrogen capture and catalytic hydrogenation for enhanced therapy of chronic liver diseases. Theranostics. 2023 Apr 23;13(8):2455–70. doi: 10.7150/thno.80494. PMCID: PMC10196827.	Theranostics	12.17
182	Macrophages maintain mammary stem cell activity and mammary homeostasis via TNF-α-PI3K-Cdk1/Cyclin B1 axis	For single cell RNA-seq analysis, Dr.Tom network platform of BGI was used	2023/5/2	Zhou Y, Ye Z, Wei W, Zhang M, Huang F, Li J, Cai C. Macrophages maintain mammary stem cell activity and mammary homeostasis via TNF-α-PI3K-Cdk1/Cyclin B1 axis. NPJ Regen Med. 2023 May 2;8(1):23. doi: 10.1038/s41536-023-00296-1. PMID: 37130846; PMCID: PMC10154328.	NPJ Regenerative Medicine	6.95
183	Global Down-regulation of Gene Expression Induced by Mouse Mammary Tumor Virus (MMTV) in Normal Mammary Epithelial Cells	The results were submitted to the BGI in-house software Dr. Tom accessed through an online server for further analysis.	2023/5/2	Ahmad W, Panicker NG, Akhlaq S, Gull B, Baby J, Khader TA, Rizvi TA, Mustafa F. Global Down-regulation of Gene Expression Induced by Mouse Mammary Tumor Virus (MMTV) in Normal Mammary Epithelial Cells. Viruses. 2023 May 2;15(5):1110. doi: 10.3390/v15051110. PMID: 37243196; PMCID: PMC10223558.	Viruses	4.59
184	Plasma-derived exosomal let-7c-5p, miR-335–3p, and miR-652–3p as potential diagnostic biomarkers for stable coronary artery disease	The DEmiRNAs were analyzed using the DESeq2 (Love et al., 2014) on Dr. Tom Multi-omics Data Mining System (https://biosys.bgi.com) developed by BGI	2023/5/9	Han J, Cui X, Yuan T, Yang Z, Liu Y, Ren Y, Wu C, Bian Y. Plasma-derived exosomal let-7c-5p, miR-335–3p, and miR-652–3p as potential diagnostic biomarkers for stable coronary artery disease. Front Physiol. 2023 May 9;14:1161612. doi: 10.3389/fphys.2023.1161612. PMCID: PMC10203605.	Frontiers In Physiology	3.92
185	Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation	The data were analyzed on the Dr. Tom network platform of BGI.	2023/5/9	Wang L, Lv WQ, Yang JT, Lin X, Liu HM, Tan HJ, Quan RP, Long PP, Shen H, Shen J, Deng HW, Xiao HM. Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation. Front Microbiol. 2023 May 9;14:1117905. doi: 10.3389/fmicb.2023.1117905. PMCID: PMC10203953.	Frontiers In Microbiology	4.97
186	Reduced APPL1 impairs osteogenic differentiation of mesenchymal stem cells by facilitating MGP expression to disrupt the BMP2 pathway in osteoporosis	Finally, Venn diagram creation, gene ontology (GO, http://www.geneontology.org/) and Kyoto Encyclopedia of Genes and Genomes (KEGG, https://www.kegg.jp/) enrichment analyses were performed using BGI’s Dr Tom Multi-Omics Data Visualization System.	2023/5/13	Yuan W, Liu W, Zhang Y, Wang X, Xu C, Li Q, Ji P, Wang J, Feng P, Wu Y, Shen H, Wang P. Reduced APPL1 impairs osteogenic differentiation of mesenchymal stem cells by facilitating MGP expression to disrupt the BMP2 pathway in osteoporosis. J Biol Chem. 2023 Jun;299(6):104823. doi: 10.1016/j.jbc.2023.104823. Epub 2023 May 13. PMID: 37187293; PMCID: PMC10318529.	Journal of Biological Chemistry	4.8
187	CD301b+ macrophage: the new booster for activating bone regeneration in periodontitis treatment	For all upregulated and downregulated DEGs, GO and GSEA analyses were performed using the free online Dr. TOM II Platform. The top seventy-eight upregulated DEGs associated with the process of osteogenic induction regulation were used for heat map analysis.	2023/5/17	Wang C, Zhao Q, Chen C, Li J, Zhang J, Qu S, Tang H, Zeng H, Zhang Y. CD301b+ macrophage: the new booster for activating bone regeneration in periodontitis treatment. Int J Oral Sci. 2023 May 17;15(1):19. doi: 10.1038/s41368-023-00225-4. PMID: 37198150; PMCID: PMC10192316.	International Journal of Oral Science	14.6
188	Extracellular vesicles from iPSC-MSCs alleviate chemotherapy-induced mouse ovarian damage via the ILK-PI3K/AKT pathway	Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed using the Dr. Tom Data Analysis System (https://biosys.bgi.com).	2023/5/18	Cao RC, Lv Y, Lu G, Liu HB, Wang W, Tan C, Su XW, Xiong Z, Ma JL, Chan WY. Extracellular vesicles from iPSC-MSCs alleviate chemotherapy-induced mouse ovarian damage via the ILK-PI3K/AKT pathway. Zool Res. 2023 May 18;44(3):620-635. doi: 10.24272/j.issn.2095-8137.2022.340. PMID: 36866625; PMCID: PMC10236296.	Zoological Research	4.74
189	High glucose-induced IL-7/IL-7R upregulation of dermal fibroblasts inhibits angiogenesis in a paracrine way in delayed diabetic wound healing	Functional enrichment analysis Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs was performed using the Dr. TOM approach, an online database of BGI.	2023/5/22	Gao R, Zhou P, Li Y, Li Q. High glucose-induced IL-7/IL-7R upregulation of dermal fibroblasts inhibits angiogenesis in a paracrine way in delayed diabetic wound healing. J Cell Commun Signal. 2023 Sep;17(3):1023-1038. doi: 10.1007/s12079-023-00754-x. Epub 2023 May 22. PMID: 37217704; PMCID: PMC10409704.	Journal of Cell Communication and Signaling	4.1
190	Cuproptosis-related lncRNAs forecast the prognosis of acute myeloid leukemia	The subsequent analyses were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).	2023/5/31	Zhang T, Liao D, Hu Y. Cuproptosis-related lncRNAs forecast the prognosis of acute myeloid leukemia. Transl Cancer Res. 2023 May 31;12(5):1175–95. doi: 10.21037/tcr-22-2526. Epub 2023 Apr 18. PMCID: PMC10248575.	Translational Cancer Research	0.85
191	Influence of Estrus on Dairy Cow Milk Exosomal miRNAs and Their Role in Hormone Secretion by Granulosa Cells	Differential expression analysis was performed using the DESeq on the Dr. Tom Multi-omics Data Mining System (https://biosys.bgi.com (accessed on 22 November 2021). Q value ≤ 0.05 and |log2FC| > 1 was used to consider the significance of expression differences.	2023/6/1	Liu W, Du C, Nan L, Li C, Wang H, Fan Y, Zhou A, Zhang S. Influence of Estrus on Dairy Cow Milk Exosomal miRNAs and Their Role in Hormone Secretion by Granulosa Cells. Int J Mol Sci. 2023 Jun 1;24(11):9608. doi: 10.3390/ijms24119608. PMID: 37298559; PMCID: PMC10253592.	International Journal Of Molecular Sciences	6.208
192	Analysis of lncRNA-miRNA-mRNA Expression in the Troxerutin-Mediated Prevention of Radiation-Induced Lung Injury in Mice	Subsequent analysis and data mining were performed on Dr Tom Multi-omics Data mining system (https://biosys.bgi.com)	2023/6/3	Zhang N, Song GY, Hu YJ, Wang X, Chao TZ, Wu YY, Xu P. Analysis of lncRNA-miRNA-mRNA Expression in the Troxerutin-Mediated Prevention of Radiation-Induced Lung Injury in Mice. J Inflamm Res. 2023 Jun 3;16:2387–99. doi: 10.2147/JIR.S397327. PMCID: PMC10246569.	Journal of Inflammation Research	4.38
193	A single-cell transcriptome atlas of pig skin characterizes anatomical positional heterogeneity	In the global clusters, GO analysis was implemented with the Dr. Tom platform of BGI. KEGG analysis, which was also performed with the Dr. Tom platform of BGI, further identified gene biological function, including signal transduction pathways, metabolic pathways, and so on in dermal cell populations.	2023/6/5	Zou Q, Yuan R, Zhang Y, Wang Y, Zheng T, Shi R, Zhang M, Li Y, Fei K, Feng R, Pan B, Zhang X, Gong Z, Zhu L, Tang G, Li M, Li X, Jiang Y. A single-cell transcriptome atlas of pig skin characterizes anatomical positional heterogeneity. Elife. 2023 Jun 5;12:e86504. doi: 10.7554/eLife.86504. PMID: 37276016; PMCID: PMC10241519.	eLife	7.4
194	Hyperplastic Human Macromass Cartilage for Joint Regeneration	The sequencing data analysis, including heatmap clustering, principal component analysis (PCA), sample correlation, Venn diagram creation, GO analysis, GSEA analysis, and KEGG pathway analysis, were performed using BGI Dr. Tom 2.0.	2023/7/3	Wen Y, Chen Y, Wu W, Zhang H, Peng Z, Yao X, Zhang X, Jiang W, Liao Y, Xie Y, Shen X, Sun H, Hu J, Liu H, Chen X, Chen J, Ouyang H. Hyperplastic Human Macromass Cartilage for Joint Regeneration. Adv Sci (Weinh). 2023 Sep;10(26):e2301833. doi: 10.1002/advs.202301833. Epub 2023 Jul 3. PMID: 37395375; PMCID: PMC10502860.	Advanced Science	15.1
195	Chronic stress accelerates glioblastoma progression via DRD2/ERK/β-catenin axis and Dopamine/ERK/TH positive feedback loop	For data analysis, genes with |log2FC|> 1.0 and adjusted P values (Q values) < 0.05 were selected as differentially expressed genes (DEGs) using the Dr. Tom online software (BGI Genomics).	2023/7/7	Wang Y, Wang X, Wang K, Qi J, Zhang Y, Wang X, Zhang L, Zhou Y, Gu L, Yu R, Zhou X. Chronic stress accelerates glioblastoma progression via DRD2/ERK/β-catenin axis and Dopamine/ERK/TH positive feedback loop. J Exp Clin Cancer Res. 2023 Jul 7;42(1):161. doi: 10.1186/s13046-023-02728-8. PMID: 37415171; PMCID: PMC10327168.	Journal of Experimental & Clinical Cancer Research	11.3
196	Downregulation of VPS13C promotes cisplatin resistance in cervical cancer by upregulating GSTP1	KEGG pathway analysis and gene set enrichment analysis (GSEA) were conducted with the Dr. Tom program (https://biosys.bgi.com).	2023/7/10	Tan X, Wang X, Liao X, Wang X, Jiang Z, Liang W, Cao C, Gong D, Hu Z, Tian X. Downregulation of VPS13C promotes cisplatin resistance in cervical cancer by upregulating GSTP1. iScience. 2023 Jul 10;26(8):107315. doi: 10.1016/j.isci.2023.107315. PMCID: PMC10372835.	iScience	5.8
197	Type-I interferons promote innate immune tolerance in macrophages exposed to Mycobacterium ulcerans vesicles	The sequencing analysis was performed, and graph (heatmap/pathway enrichment) were generated with Dr. Tom software (BGI).	2023/7/10	Bernard Q, Goumeidane M, Chaumond E, Robbe-Saule M, Boucaud Y, Esnault L, Croué A, Jullien J, Marsollier L, Marion E. Type-I interferons promote innate immune tolerance in macrophages exposed to Mycobacterium ulcerans vesicles. PLoS Pathog. 2023 Jul 10;19(7):e1011479. doi: 10.1371/journal.ppat.1011479. PMID: 37428812; PMCID: PMC10358927.	PLoS Pathogens	6.7
198	Co-targeting RANK pathway treats and prevents acquired resistance to CDK4/6 inhibitors in luminal breast cancer	The web-based solution Dr. Tom (BGI, https://biosys.bgi.com/) and GSEA software (Broad Institute, Massachusetts, USA)52 using MSigDB v6.2 Hallmarks gene sets collection, were used for calculating enrichment scores (assuming all expressed genes) in tumor tissue and TCGA datasets, respectively.	2023/7/13	Gomes, I., Gallego-Paez, L. M., Jiménez, M., Santamaria, P. G., Mansinho, A., Sousa, R., Abreu, C., Suárez, E. G., Costa, L., & Casimiro, S. (2023). Co-targeting RANK pathway treats and prevents acquired resistance to CDK4/6 inhibitors in luminal breast cancer. Cell reports. Medicine, 4(8), 101120. https://doi.org/10.1016/j.xcrm.2023.101120	Cell Reports Medicine	14.3
199	PFDN2 promotes cell cycle progression via the hnRNPD-MYBL2 axis in gastric cancer	The GSEA for differentially expressed genes was performed on the Dr. Tom network platform of BGI (http://report.bgi.com).	2023/7/18	He Q, Ding Z, Chen T, Wu H, Song J, Xiang Z, Yang C, Wang S, Xiong B. PFDN2 promotes cell cycle progression via the hnRNPD-MYBL2 axis in gastric cancer. Front Oncol. 2023 Jul 18;13:1164070. doi: 10.3389/fonc.2023.1164070. PMID: 37538116; PMCID: PMC10395514.	Frontiers In Oncology	4.7
200	Aloe-emodin inhibits African swine fever virus replication by promoting apoptosis via regulating NF-κB signaling pathway	The Dr.Tom multi-omics data mining system of BGI was used to perform KEGG analysis of the differentially expressed genes and the results were displayed.	2023/7/19	Luo Y, Yang Y, Wang W, Gao Q, Gong T, Feng Y, Wu D, Zheng X, Zhang G, Wang H. Aloe-emodin inhibits African swine fever virus replication by promoting apoptosis via regulating NF-κB signaling pathway. Virol J. 2023 Jul 19;20(1):158. doi: 10.1186/s12985-023-02126-8. PMID: 37468960; PMCID: PMC10357809.	Virology Journal	4.8
201	Myo1d promotes alpha-synuclein transfer from brain microvascular endothelial cells to pericytes through tunneling nanotubes	Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and Gene Ontology (GO) enrichment analysis were performed using the Dr.Tom system developed by BGI Genomics.	2023/7/22	Duan Q, Zhang Q, Nie K, Huang R, Yang J, He P, Tie Z, Huang H, Ma G, Zhang Y, Gao Y, Wang L. Myo1d promotes alpha-synuclein transfer from brain microvascular endothelial cells to pericytes through tunneling nanotubes. iScience. 2023 Jul 22;26(8):107458. doi: 10.1016/j.isci.2023.107458. PMCID: PMC10416064.	iScience	5.8
202	ESRRB Inhibits the TGFβ Signaling Pathway to Drive Cell Proliferation in Cervical Cancer	The data were analyzed on the free online Dr. Tom Platform (https://biosys.bgi.com/#/report/login).	2023/7/23	Li QS, Zheng PS. ESRRB Inhibits the TGFβ Signaling Pathway to Drive Cell Proliferation in Cervical Cancer. Cancer Res. 2023 Sep 15;83(18):3095-3114. doi: 10.1158/0008-5472.CAN-23-0067. PMID: 37350664; PMCID: PMC10502452.	Cancer Research	11.2
203	Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars	All the downstream analyses were based on high-quality clean data. Dr. Tom system from BGI company was used for the following bioinformatics analyses.	2023/7/27	Tang K, Li L, Zhang B, Zhang W, Zeng N, Zhang H, Liu D, Luo Z. Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars. BMC Genomics. 2023 Jul 27;24(1):421. doi: 10.1186/s12864-023-09436-9. PMID: 37501179; PMCID: PMC10373417.	BMC Genomics	4.4
204	Persistent ER stress causes GPI anchor deficit to convert a GPI-anchored prion protein into pro-PrP via the ATF6–miR449c-5p–PIGV axis	The Dr Tom Multi-Omics Data Mining system (https://biosys.bgi.com) was used for subsequent data analysis.	2023/7/28	Li J, Li S, Yu S, Yang J, Ke J, Li H, Chen H, Lu M, Sy MS, Gao Z, Li C. Persistent ER stress causes GPI anchor deficit to convert a GPI-anchored prion protein into pro-PrP via the ATF6-miR449c-5p-PIGV axis. J Biol Chem. 2023 Jun 28;299(8):104982. doi: 10.1016/j.jbc.2023.104982. Epub ahead of print. PMID: 37390992; PMCID: PMC10388210.	Journal of Biological Chemistry	4.8
205	Modelling host- Trypanosoma brucei gambiense interactions in vitro using human induced pluripotent stem cell-derived cortical brain organoids	Subsequent downstream analysis, including differential gene expression and pathway analysis using Gene Ontology (RRID: SCR_002811), were conducted on the Dr. Tom analysis suite built by BGI.	2023/7/28	Chandrasegaran P, Nabilla Lestari A, Sinton MC et al. Modelling host-Trypanosoma brucei gambiense interactions in vitro using human induced pluripotent stem cell-derived cortical brain organoids [version 2; peer review: 2 approved]. F1000Research 2023, 12:437 (https://doi.org/10.12688/f1000research.131507.2)	F1000Research	\
206	Exosomal-miR-129-2-3p derived from Fusobacterium nucleatum-infected intestinal epithelial cells promotes experimental colitis through regulating TIMELESS-mediated cellular senescence pathway	Subsequently, data analysis and graphing were performed using the Dr. Tom Multi-Omics Data Mining System (https://biosys.bgi.com).	2023/8/7	Wei S, Wu X, Chen M, Xiang Z, Li X, Zhang J, Dong W. Exosomal-miR-129-2-3p derived from Fusobacterium nucleatum-infected intestinal epithelial cells promotes experimental colitis through regulating TIMELESS-mediated cellular senescence pathway. Gut Microbes. 2023 Jan-Dec;15(1):2240035. doi: 10.1080/19490976.2023.2240035. PMID: 37550944; PMCID: PMC10411316.	Gut Microbes	12.2
207	Interleukin-34-NF-κB signaling aggravates myocardial ischemic/reperfusion injury by facilitating macrophage recruitment and polarization	Gene set enrichment analysis (GSEA) based on the KEGG and GO pathway dataset downloaded from the official website was performed using the Dr. Tom BGI Genomics platform.	2023/8/7	Zhuang, L., Zong, X., Yang, Q., Fan, Q., & Tao, R. (2023). Interleukin-34-NF-κB signaling aggravates myocardial ischemic/reperfusion injury by facilitating macrophage recruitment and polarization. EBioMedicine, 95, 104744. Advance online publication. https://doi.org/10.1016/j.ebiom.2023.104744	EBioMedicine	10
208	Low‐Dose Staphylococcal Enterotoxin C2 Mutant Maintains Bone Homeostasis via Regulating Crosstalk between Bone Formation and Host T‐Cell Effector Immunity	KEGG pathway analyses were carried out based on the DR.TOM system of BGI.	2023/8/8	Wang H, Lin S, Feng L, Huang B, Lu X, Yang Z, Jiang Z, Li YC, Zhang X, Wang M, Wang B, Kong L, Pan Q, Bai S, Li Y, Yang Y, Lee WYW, Currie PD, Lin C, Jiang Y, Chen J, Tortorella MD, Li H, Li G. Low-Dose Staphylococcal Enterotoxin C2 Mutant Maintains Bone Homeostasis via Regulating Crosstalk between Bone Formation and Host T-Cell Effector Immunity. Adv Sci (Weinh). 2023 Oct;10(28):e2300989. doi: 10.1002/advs.202300989. Epub 2023 Aug 8. PMID: 37552005; PMCID: PMC10558680.	Advanced Science	15.1
209	Elabela inhibits TRAF1/NF-κB induced oxidative DNA damage to promote diabetic foot ulcer wound healing	The Dr. Tom network platform of the BGI (http://report.bgi.com) was applied for analysis.	2023/8/9	Hong Y, Li J, Zhong Y, Yang S, Pei L, Huang Z, Chen X, Wu H, Zheng G, Zeng C, Wu H, Wang T. Elabela inhibits TRAF1/NF-κB induced oxidative DNA damage to promote diabetic foot ulcer wound healing. iScience. 2023 Aug 9;26(9):107601. doi: 10.1016/j.isci.2023.107601. PMID: 37664606; PMCID: PMC10469767.	iScience	5.8
210	Amelioration of non-alcoholic fatty liver disease by targeting adhesion G protein-coupled receptor F1 (Adgrf1)	RNA-seq was performed by BGI and analyzed by Dr. Tom system (BGI, Shenzhen, China).	2023/8/15	Wu M, Lo TH, Li L, Sun J, Deng C, Chan KY, Li X, Yeh ST, Lee JTH, Lui PPY, Xu A, Wong CM. Amelioration of non-alcoholic fatty liver disease by targeting adhesion G protein-coupled receptor F1 (Adgrf1). Elife. 2023 Aug 15;12:e85131. doi: 10.7554/eLife.85131. PMID: 37580962; PMCID: PMC10427146.	eLife	7.7
211	Targeting sphingosine 1-phosphate receptor 3 inhibits T-cell exhaustion and regulates recruitment of proinflammatory macrophages to improve antitumor efficacy of CAR-T cells against solid tumor	Genes with fold change(FC)≥2 and Q value≤0.001 were selected to perform enrichment analysis using the Dr Tom network platform of BGI (http://biosys.bgi.com).	2023/8/17	Gao, G., Liao, W., Shu, P., Ma, Q., He, X., Zhang, B., Qin, D., & Wang, Y. (2023). Targeting sphingosine 1-phosphate receptor 3 inhibits T-cell exhaustion and regulates recruitment of proinflammatory macrophages to improve antitumor efficacy of CAR-T cells against solid tumor. Journal for immunotherapy of cancer, 11(8), e006343. https://doi.org/10.1136/jitc-2022-006343	Journal for ImmunoTherapy of Cancer	10.9
212	Targeting macrophage M1 polarization suppression through PCAF inhibition alleviates autoimmune arthritis via synergistic NF-κB and H3K9Ac blockade	Sequencing data analysis, including heatmap clustering, Venn diagram creation, gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and gene set enrichment analysis (GSEA), was performed using BGI Dr. Tom 2.0.	2023/8/19	Li, J., Ye, F., Xu, X. et al. Targeting macrophage M1 polarization suppression through PCAF inhibition alleviates autoimmune arthritis via synergistic NF-κB and H3K9Ac blockade. J Nanobiotechnol 21, 280 (2023). https://doi.org/10.1186/s12951-023-02012-z	Journal of Nanobiotechnology	10.2
213	SET Domain Group 703 Regulates Planthopper Resistance by Suppressing the Expression of Defense-Related Genes	Data analysis was conducted using the Dr. Tom system from BGI http://report.bgi.com (accessed on 10 July 2020).	2023/8/21	Wen P, He J, Zhang Q, Qi H, Zhang A, Liu D, Sun Q, Wang Y, Li Q, Wang W, et al. SET Domain Group 703 Regulates Planthopper Resistance by Suppressing the Expression of Defense-Related Genes. International Journal of Molecular Sciences. 2023; 24(16):13003. https://doi.org/10.3390/ijms241613003	International Journal Of Molecular Sciences	5.6
214	Akkermansia muciniphila inhibits tryptophan metabolism via the AhR/β-catenin signaling pathway to counter the progression of colorectal cancer	The data mining and figure presentation process, including KEGG, the heatmap, and clustering, are all done by the BGI in-house customized data mining system called Dr.Tom (http://report.bgi.com).	2023/8/21	Zhang L, Ji Q, Chen Q, Wei Z, Liu S, Zhang L, Zhang Y, Li Z, Liu H, Sui H. Akkermansia muciniphila inhibits tryptophan metabolism via the AhR/β-catenin signaling pathway to counter the progression of colorectal cancer. Int J Biol Sci. 2023 Aug 21;19(14):4393-4410. doi: 10.7150/ijbs.85712. PMID: 37781044; PMCID: PMC10535706.	International Journal Of Biological Sciences	9.2
215	Comprehensive transcriptomics and metabolomics analyses reveal that hyperhomocysteinemia is a high risk factor for coronary artery disease in a chinese obese population aged 40–65: a prospective cross-sectional study	The subsequent analysis and data mining were performed using Dr. Tom multi-omics data mining system (https://biosys.bgi.com).	2023/8/24	Zhang CY, Xu RQ, Wang XQ, Sun LF, Mo P, Cai RJ, Lin XZ, Luo CF, Ou WC, Lu LJ, Zhong Y, Chen JY. Comprehensive transcriptomics and metabolomics analyses reveal that hyperhomocysteinemia is a high risk factor for coronary artery disease in a chinese obese population aged 40-65: a prospective cross-sectional study. Cardiovasc Diabetol. 2023 Aug 24;22(1):219. doi: 10.1186/s12933-023-01942-0. PMID: 37620823; PMCID: PMC10463368.	Cardiovascular Diabetology	9.3
216	MicroRNA expression profiles of stress susceptibility and resilience in the prelimbic and infralimbic cortex of rats after single prolonged stress	All analysis of RNA sequencing data was performed by DR. TOM online system provided by BGI.	2023/8/24	Huang G, Iqbal J, Shen D, Xue YX, Yang M, Jia X. MicroRNA expression profiles of stress susceptibility and resilience in the prelimbic and infralimbic cortex of rats after single prolonged stress. Front Psychiatry. 2023 Aug 24;14:1247714. doi: 10.3389/fpsyt.2023.1247714. PMCID: PMC10488707.	Frontiers in psychiatry	4.7
217	E3 ubiquitin ligase TRIM21 targets TIF1γ to regulate β-catenin signaling in glioblastoma	GO pathway enrichment analysis were performed using Dr. Tom, an online analysis system of BGI.	2023/9/4	Li Y, Bao L, Zheng H, Geng M, Chen T, Dai X, Xiao H, Yang L, Mao C, Qiu Y, Xu Y, Wang D, Li MX, Chen Q. E3 ubiquitin ligase TRIM21 targets TIF1γ to regulate β-catenin signaling in glioblastoma. Theranostics. 2023 Sep 4;13(14):4919-4935. doi: 10.7150/thno.85662. PMID: 37771771; PMCID: PMC10526654.	Theranostics	12.17
218	Mesenchymal stem cells in synovial fluid increase in number in response to synovitis and display more tissue-reparative phenotypes in osteoarthritis	All data were analyzed using Dr. Tom, a BGI data mining system.	2023/9/8	Furuoka H, Endo K, Sekiya I. Mesenchymal stem cells in synovial fluid increase in number in response to synovitis and display more tissue-reparative phenotypes in osteoarthritis. Stem Cell Res Ther. 2023 Sep 8;14(1):244. doi: 10.1186/s13287-023-03487-1. PMID: 37679780; PMCID: PMC10485949.	Stem Cell Research & Therapy	7.5
219	High-throughput sequencing reveals Jatrorrhizine inhibits colorectal cancer growth by ferroptosis-related genes	In the Dr.TOM system, we identified 244 differentially expressed genes .	2023/9/14	Huang L, Sha Y, Liang W, Mo C, Li C, Deng Y, Gong W, Hou X, Ou M. High-throughput sequencing reveals Jatrorrhizine inhibits colorectal cancer growth by ferroptosis-related genes. BMC Med Genomics. 2023 Sep 14;16(1):217. doi: 10.1186/s12920-023-01619-3. PMID: 37710311; PMCID: PMC10500743.	BMC Medical Genomics	2.7
220	Long-term potentiation-based screening identifies neuronal PYGM as a synaptic plasticity regulator participating in Alzheimer’s disease	Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed using the Dr. Tom platform (https://report.bgi.com) of BGI (China).	2023/9/18	Wang T, Zhou YQ, Wang Y, Zhang L, Zhu X, Wang XY, Wang JH, Han LK, Meng J, Zhang X, Luo H, Ma QL, Wang ZX, Zhang YW. Long-term potentiation-based screening identifies neuronal PYGM as a synaptic plasticity regulator participating in Alzheimer's disease. Zool Res. 2023 Sep 18;44(5):867-881. doi: 10.24272/j.issn.2095-8137.2023.123. PMID: 37537141; PMCID: PMC10559100.	Zoological Research	4.74
221	Analysis of shared ceRNA networks and related-hub genes in rats with primary and secondary photoreceptor degeneration	The data were analyzed on the Dr. Tom II network platform of the BGI.	2023/9/21	Liang J, Fang D, Yao F, Chen L, Zou Z, Tang X, Feng L, Zhuang Y, Xie T, Wei P, Li P, Zheng H, Zhang S. Analysis of shared ceRNA networks and related-hub genes in rats with primary and secondary photoreceptor degeneration. Front Neurosci. 2023 Sep 21;17:1259622. doi: 10.3389/fnins.2023.1259622. PMCID: PMC10552924.	Frontiers in neuroscience	4.3
222	Evaluating Prophylactic Effect of Bovine Colostrum on Intestinal Barrier Function in Zonulin Transgenic Mice: A Transcriptomic Study	Based on the Dr. Tom Data Visualization Solution System of BGI Genomics, the functional enrichment of DEGs was analyzed, concentrating on the terms “biological process”, “molecular function”, and “cellular component”.	2023/9/29	Asbjornsdottir, B., Sigurdsson, S., Miranda-Ribera, A., Fiorentino, M., Konno, T., Lan, J., Gudmundsson, L. S., Gottfredsson, M., Lauth, B., Birgisdottir, B. E., & Fasano, A. (2023). Evaluating Prophylactic Effect of Bovine Colostrum on Intestinal Barrier Function in Zonulin Transgenic Mice: A Transcriptomic Study. International journal of molecular sciences, 24(19), 14730. https://doi.org/10.3390/ijms241914730	International Journal Of Molecular Sciences	6.208
223	Beta-1,4-galactosyltransferase-3 deficiency suppresses the growth of immunogenic tumors in mice	Data analysis and visualization were performed using BGI’s in-house customized data-mining system, Dr. Tom.	2023/10/9	Wei, H., Naruse, C., Takakura, D., Sugihara, K., Pan, X., Ikeda, A., Kawasaki, N., & Asano, M. (2023). Beta-1,4-galactosyltransferase-3 deficiency suppresses the growth of immunogenic tumors in mice. Frontiers in Immunology, 14, 1272537. https://doi.org/10.3389/fimmu.2023.1272537	Frontiers in Immunology	7.3
224	Oral exposure to Staphylococcus aureus enterotoxin B could promote the Ovalbumin-induced food allergy by enhancing the activation of DCs and T cells	The gene quantification analysis and other investigations based on gene expression (principal component, correlation, differential gene screening), significant enrichment analysis on differentially expressed genes among the screened samples, significance enrichment analysis of pathway, clustering, protein interaction networks, and transcription factors were performed using Dr.Tom online system of BGI Genomics (https://biosys.bgi.com, could be turned into English) after the filtered clean reads were aligned to the reference sequence.	2023/10/16	Yuan, J., Tong, P., Meng, X., Wu, Y., Li, X., Gao, J., & Chen, H. (2023). Oral exposure to Staphylococcus aureus enterotoxin B could promote the Ovalbumin-induced food allergy by enhancing the activation of DCs and T cells. Frontiers in immunology, 14, 1250458. https://doi.org/10.3389/fimmu.2023.1250458	Frontiers in Immunology	7.3
225	KRT17 from skin cells with high glucose stimulation promotes keratinocytes proliferation and migration	Normalization and differential expression analyses were estimated from count data using DEGseq package in analysis system of Dr. Tom from BGI	2023/10/19	Zhou, P., Feng, H., Qin, W., & Li, Q. (2023). KRT17 from skin cells with high glucose stimulation promotes keratinocytes proliferation and migration. Frontiers in Endocrinology, 14, 1237048. https://doi.org/10.3389/fendo.2023.1237048	Frontiers In Endocrinology	5.2
226	Efficacy of exon-skipping therapy for DMD cardiomyopathy with mutations in actin binding domain 1	All data were submitted to the online tool Dr. TOM software (BGI) for PCA and GO and pathway enrichment analyses.	2023/10/19	Shiba, N., Yang, X., Sato, M., Kadota, S., Suzuki, Y., Agata, M., Nagamine, K., Izumi, M., Honda, Y., Koganehira, T., Kobayashi, H., Ichimura, H., Chuma, S., Nakai, J., Tohyama, S., Fukuda, K., Miyazaki, D., Nakamura, A., & Shiba, Y. (2023). Efficacy of exon-skipping therapy for DMD cardiomyopathy with mutations in actin binding domain 1. Molecular Therapy. Nucleic Acids, 34, 102060. https://doi.org/10.1016/j.omtn.2023.102060	Molecular Therapy-nucleic Acids	8.8
227	C-type natriuretic peptide improves maternally aged oocytes quality by inhibiting excessive PINK1/Parkin-mediated mitophagy	Dr. Tom (Dr. Tom is a web-based solution that offers convenient analysis, visualization, and interpretation of various types of RNA data, https://www.bgi.com/global/service/dr-tom) was used for difference analysis, GO analysis, KEGG analysis, and other analyses.	2023/10/20	Zhang, H., Li, C., Liu, Q., Li, J., Wu, H., Xu, R., Sun, Y., Cheng, M., Zhao, X., Pan, M., Wei, Q., & Ma, B. (2023). C-type natriuretic peptide improves maternally aged oocytes quality by inhibiting excessive PINK1/Parkin-mediated mitophagy. eLife, 12, RP88523. https://doi.org/10.7554/eLife.88523	eLife	7.4
228	The response of Arabidopsis to the apocarotenoid β-cyclocitric acid reveals a role for SIAMESE-RELATED 5 in root development and drought tolerance	Standard bioinformatics analyses were performed by the Doctor Tom platform of BGI Genomics.	2023/10/26	Braat, J., Jaonina, M., David, P., Leschevin, M., Légeret, B., D'Alessandro, S., Beisson, F., & Havaux, M. (2023). The response of Arabidopsis to the apocarotenoid β-cyclocitric acid reveals a role for SIAMESE-RELATED 5 in root development and drought tolerance. PNAS nexus, 2(11), pgad353. https://doi.org/10.1093/pnasnexus/pgad353	PNAS Nexus	8.6
229	PACAP–Sirtuin3 alleviates cognitive impairment through autophagy in Alzheimer’s disease	Mouse hippocampal mRNA profiles were filtered with SOAPnuke (v1.5.2) [55], and differentially expressed genes were analyzed using the Dr. Tom online platform (BGI Genomics Co., Ltd.).	2023/10/27	Wang, Q., Wang, Y., Li, S., & Shi, J. (2023). PACAP-Sirtuin3 alleviates cognitive impairment through autophagy in Alzheimer's disease. Alzheimer's research & therapy, 15(1), 184. https://doi.org/10.1186/s13195-023-01334-2	Alzheimers Research & Therapy	9
230	OsCIPK9 Interacts with OsSOS3 and Affects Salt-Related Transport to Improve Salt Tolerance	RNA-seq was performed using the BGI T7 platform, and analyses of DEGs (Differentially Expressed Genes), KEGG (Kyoto Encyclopedia of Genes and Genomes), and GO (Gene Ontology) were performed using Dr. Tom website produced by BGI, China (https://biosys.bgi.com, accessed on 20 January 2023).	2023/10/30	Zhou, Z., Tang, W., Sun, Z., Li, J., Yang, B., Liu, Y., Wang, B., Xu, D., Yang, J., & Zhang, Y. (2023). OsCIPK9 Interacts with OsSOS3 and Affects Salt-Related Transport to Improve Salt Tolerance. Plants (Basel, Switzerland), 12(21), 3723. https://doi.org/10.3390/plants12213723	Plants (Basel)	4.5
231	Vacuolar Sugar Transporter TMT2 Plays Crucial Roles in Germination and Seedling Development in Arabidopsis	The heatmap, Venn diagram, KEGG pathway, and GO analysis of DEGs were performed using the Dr. Tom Multi-omics Data Mining System (https://biosys.bgi.com), accessed on 25 October 2021.	2023/11/1	Cao, Y., Hu, J., Hou, J., Fu, C., Zou, X., Han, X., Jia, P., Sun, C., Xu, Y., Xue, Y., Zou, Y., Liu, X., Chen, X., Li, G., Guo, J., Xu, M., & Fu, A. (2023). Vacuolar Sugar Transporter TMT2 Plays Crucial Roles in Germination and Seedling Development in Arabidopsis. International journal of molecular sciences, 24(21), 15852. https://doi.org/10.3390/ijms242115852	International Journal Of Molecular Sciences	5.6
232	Pulsatillae radix extract alleviates DSS-induced colitis via modulating gut microbiota and inflammatory signaling pathway in mice	The KEGG pathway analysis and GSEA for the differential genes were carried out on the Dr. Tom platform from Beijing Genomics Institute Co., Ltd.	2023/11/2	Li X, Wang Z, Gao H, Xiao Y, Li M, Huang Y, Liu G, Guo Y, Song L, Ren Z. Pulsatillae radix extract alleviates DSS-induced colitis via modulating gut microbiota and inflammatory signaling pathway in mice. Heliyon. 2023 Nov 2;9(11):e21869. doi: 10.1016/j.heliyon.2023.e21869. PMID: 38034600; PMCID: PMC10685249.	Heliyon	4
233	MAP kinase ERK5 modulates cancer cell sensitivity to extrinsic apoptosis induced by death-receptor agonists	Finally, functional enrichment analyses were performed using Dr. Tom software (BGI), the gene set enrichment analysis (GSEA) software and the gene ontology (GO) collection (MSigDB v7.1).	2023/11/2	Espinosa-Gil, S., Ivanova, S., Alari-Pahissa, E., Denizli, M., Villafranca-Magdalena, B., Viñas-Casas, M., Bolinaga-Ayala, I., Gámez-García, A., Faundez-Vidiella, C., Colas, E., Lopez-Botet, M., Zorzano, A., & Lizcano, J. M. (2023). MAP kinase ERK5 modulates cancer cell sensitivity to extrinsic apoptosis induced by death-receptor agonists. Cell death & disease, 14(11), 715. https://doi.org/10.1038/s41419-023-06229-6	Cell Death & Disease	9
234	Tau reduction attenuates autism-like features in Fmr1 knockout mice	Analysis of Gene Ontology (GO) enrichment was performed on BGI’s Dr. Tom platform (https://report.bgi.com).	2023/11/7	Zhao, S., Jiang, X., Han, L., Jiang, Y., Wang, Y., Meng, J., Zhu, X., Zhang, X., Luo, H., & Zhang, Y. W. (2023). Tau reduction attenuates autism-like features in Fmr1 knockout mice. Molecular Autism, 14, 42. https://doi.org/10.1186/s13229-023-00574-1	Molecular Autism	6.2
235	MicroRNA-200 Loaded Lipid Nanoparticles Promote Intestinal Epithelium Regeneration in Canonical MicroRNA-Deficient Mice	And, mall RNA sequencing data of Lgr5-GFPhigh cells was analyzed on the Dr. Tom Multiomics Data Mining System (BGI).	2023/11/8	Wei X, Yu S, Zhang T, Liu L, Wang X, Wang X, Chan YS, Wang Y, Meng S, Chen YG. MicroRNA-200 Loaded Lipid Nanoparticles Promote Intestinal Epithelium Regeneration in Canonical MicroRNA-Deficient Mice. ACS Nano. 2023 Nov 28;17(22):22901-22915. doi: 10.1021/acsnano.3c08030. Epub 2023 Nov 8. PMID: 37939210; PMCID: PMC10690841.	ACS Nano	17.1
236	A novel transgenic mouse line with hippocampus-dominant and inducible expression of truncated human tau	Kyoto encyclopedia of genes and genomes (KEGG) enrichment and the relationship network of KEGG pathways of DEGs were analyzed by Dr. Tom software (BGI, Shenzhen, China).	2023/11/10	Gao, Y., Wang, Y., Lei, H., Xu, Z., Li, S., Yu, H., Xie, J., Zhang, Z., Liu, G., Zhang, Y., Zheng, J., & Wang, J. Z. (2023). A novel transgenic mouse line with hippocampus-dominant and inducible expression of truncated human tau. Translational Neurodegeneration, 12, 51. https://doi.org/10.1186/s40035-023-00379-5	Translational Neurodegeneration	12.6
237	CD39+CD55− Fb Subset Exhibits Myofibroblast-Like Phenotype and Is Associated with Pain in Osteoarthritis of the Knee	Key driver gene analysis (KDA) was conducted using the BGI online system (Dr.Tom)	2023/11/14	Tsuchiya, M., Ohashi, Y., Kodera, Y., Satoh, M., Matsui, T., Fukushima, K., Iwase, D., Aikawa, J., Mukai, M., Inoue, G., Takaso, M., & Uchida, K. (2023). CD39+CD55- Fb Subset Exhibits Myofibroblast-Like Phenotype and Is Associated with Pain in Osteoarthritis of the Knee. Biomedicines, 11(11), 3047. https://doi.org/10.3390/biomedicines11113047	Biomedicines	4.7
238	The influence of inflammation on the characteristics of adipose-derived mesenchymal stem cells (ADMSCs) and tissue repair capability in a hepatic injury mouse model	Sangerbox (http://sangerbox.com/index.html) and Dr.Tom (BGI.Tech) software was utilized to analyze and describe the gene expression characteristics of the MSCs.	2023/11/19	Xiao, J., Gong, X., Fu, Z., Song, X., Ma, Q., Miao, J., Cai, R., Yan, Z., Wang, S., Li, Q., Chen, Y., Yang, L., Bian, X., & Chen, Y. (2023). The influence of inflammation on the characteristics of adipose-derived mesenchymal stem cells (ADMSCs) and tissue repair capability in a hepatic injury mouse model. Stem cell research & therapy, 14(1), 334. https://doi.org/10.1186/s13287-023-03532-z	Stem Cell Research & Therapy	7.5
239	TSTA3 overexpression promotes malignant characteristics in LUSC by regulating LAMP2-mediated autophagy and tumor microenvironment	The subsequent analysis and data mining were performed on Dr. Tom II network platform (https://biosys.bgi.com).	2023/11/20	Guo, Y., Hao, Y., Shen, L., Du, Y., Wang, X., Gao, L., Feng, X., Zhai, Y., Liu, Z., Xu, E., Yang, Y., Xi, Y., Yang, B., & Zhang, L. (2023). TSTA3 overexpression promotes malignant characteristics in LUSC by regulating LAMP2-mediated autophagy and tumor microenvironment. Cancer cell international, 23(1), 285. https://doi.org/10.1186/s12935-023-03109-z	Cancer Cell International	5.8
240	Transcriptomic and metabolomic analyses reveal that ABA increases the salt tolerance of rice significantly correlated with jasmonic acid biosynthesis and flavonoid biosynthesis	The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).	2023/11/21	Han, C., Chen, G., Zheng, D., & Feng, N. (2023). Transcriptomic and metabolomic analyses reveal that ABA increases the salt tolerance of rice significantly correlated with jasmonic acid biosynthesis and flavonoid biosynthesis. Scientific reports, 13(1), 20365. https://doi.org/10.1038/s41598-023-47657-w	Scientific Reports	4.6
241	Low-dose radiotherapy combined with dual PD-L1 and VEGFA blockade elicits antitumor response in hepatocellular carcinoma mediated by activated intratumoral CD8+ exhausted-like T cells	The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).	2023/11/24	Li, S., Li, K., Wang, K., Yu, H., Wang, X., Shi, M., Liang, Z., Yang, Z., Hu, Y., Li, Y., Liu, W., Li, H., Cheng, S., Ye, L., & Yang, Y. (2023). Low-dose radiotherapy combined with dual PD-L1 and VEGFA blockade elicits antitumor response in hepatocellular carcinoma mediated by activated intratumoral CD8+ exhausted-like T cells. Nature communications, 14(1), 7709. https://doi.org/10.1038/s41467-023-43462-1	Nature Communications	16.6
242	LINC01133 can induce acquired ferroptosis resistance by enhancing the FSP1 mRNA stability through forming the LINC01133-FUS-FSP1 complex	The samples were sent to the BGI Corporation (Shenzhen, China) for next-generation sequencing via the BGISEQ-500 sequencer. The differentially expressed genes (DEGs), Gene Set Enrichment Analysis (GSEA), and transcription factors extraction were performed by Dr Tom from BGI (https://biosys.bgi.com/#/report/login).	2023/11/25	Wang, S., Chen, J., Li, P., & Chen, Y. (2023). LINC01133 can induce acquired ferroptosis resistance by enhancing the FSP1 mRNA stability through forming the LINC01133-FUS-FSP1 complex. Cell death & disease, 14(11), 767. https://doi.org/10.1038/s41419-023-06311-z	Cell Death & Disease	9
243	Intracellular delivery of nitric oxide enhances the therapeutic efficacy of mesenchymal stem cells for myocardial infarction	The analyses of hierarchical clustering and heatmap were performed using the online Dr. Tom system (biosys.bgi.com) to compare differential gene expression of ADMSCs in healthy people and patients with diabetes.	2023/11/29	Hao T, Ji G, Qian M, Li QX, Huang H, Deng S, Liu P, Deng W, Wei Y, He J, Wang S, Gao W, Li T, Cheng J, Tian J, Pan L, Gao F, Li Z, Zhao Q. Intracellular delivery of nitric oxide enhances the therapeutic efficacy of mesenchymal stem cells for myocardial infarction. Sci Adv. 2023 Nov 29;9(48):eadi9967. doi: 10.1126/sciadv.adi9967. PMCID: PMC10686553.	Science Advances	13.6
244	Inhibitory receptor CD47 binding to plasma TSP1 suppresses NK-cell IFN-γ production via activating the JAK/STAT3 pathway during HIV infection	Transcriptome results were analysed using the Dr. Tom platform (biosys.bgi.com, Huada gene).	2023/11/30	Lang B, Wang M, Zhang Z, Fu Y, Han X, Hu Q, Ding H, Shang H, Jiang Y. Inhibitory receptor CD47 binding to plasma TSP1 suppresses NK-cell IFN-γ production via activating the JAK/STAT3 pathway during HIV infection. J Transl Med. 2023 Nov 30;21(1):869. doi: 10.1186/s12967-023-04667-6. PMID: 38037074; PMCID: PMC10688093.	Journal of Translational Medicine	7.4
245	Functional and analytical recapitulation of osteoclast biology on demineralized bone paper	Further sequencing data analysis was processed in Dr.Tom system (BGI). Transcripts per million (TPM) value was used for the expression heatmap	2023/12/7	Park Y, Sato T, Lee J. Functional and analytical recapitulation of osteoclast biology on demineralized bone paper. Nat Commun. 2023 Dec 7;14(1):8092. doi: 10.1038/s41467-023-44000-9. PMID: 38062034; PMCID: PMC10703810.	Nature Communications	16.6
246	Integration of ATAC-seq and RNA-seq identifies MX1-mediated AP-1 transcriptional regulation as a therapeutic target for Down syndrome	Functional enrichment analysis of Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) were performed using the online Dr. Tom software (https://biosys.bgi.com), in which Qvalue < 0.05 was used as significance threshold in GO and KEGG analysis, while |NES| > 1, p < 0.05 and FDR < 0.25 were applied to filter enriched pathways in GSEA.	2023/12/9	Guo Z, Zhu Y, Xiao H, Dai R, Yang W, Xue W, Zhang X, Hao B, Liao S. Integration of ATAC-seq and RNA-seq identifies MX1-mediated AP-1 transcriptional regulation as a therapeutic target for Down syndrome. Biol Res. 2023 Dec 9;56(1):67. doi: 10.1186/s40659-023-00474-x. PMID: 38066591; PMCID: PMC10709892.	Biological Research	6.7
247	Transcriptome research of human amniocytes identifies hub genes associated with developmental dysplasia in down syndrome	The correlation heatmap, mRNA expression distribution, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Set Enrichment Analysis (GSEA) were performed on the online Dr. Tom software (https://biosys.bgi.com) with p adj (Q value) < 0.05 as the threshold.	2023/12/12	Guo Z, Xiao H, Yang W, Li T, Hao B, Liao S. Transcriptome research of human amniocytes identifies hub genes associated with developmental dysplasia in down syndrome. Aging (Albany NY). 2023 Dec 12;15(23):14086-14108. doi: 10.18632/aging.205291. Epub 2023 Dec 12. PMID: 38095646; PMCID: PMC10756088.	Aging-US	5.2
248	Severity of Peripheral Infection Differentially Affects Brain Functions in Mice via Microglia-Dependent and -Independent Mechanisms	The subsequent analyses and data mining were performed on the Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com/, accessed on 12 July 2023)	2023/12/18	Le YP, Saito K, Parajuli B, Sakai K, Kubota Y, Miyakawa M, Shinozaki Y, Shigetomi E, Koizumi S. Severity of Peripheral Infection Differentially Affects Brain Functions in Mice via Microglia-Dependent and -Independent Mechanisms. Int J Mol Sci. 2023 Dec 18;24(24):17597. doi: 10.3390/ijms242417597. PMCID: PMC10743593.	International Journal Of Molecular Sciences	5.6
249	Didymin alleviates metabolic dysfunction-associated fatty liver disease (MAFLD) via the stimulation of Sirt1-mediated lipophagy and mitochondrial biogenesis	Data mining analysis was conducted utilizing Dr. Tom multiple omics data mining system (https://biosys.bgi.com).	2023/12/19	Yang JW, Zou Y, Chen J, Cui C, Song J, Yang MM, Gao J, Hu HQ, Xia LQ, Wang LM, Lv XY, Chen L, Hou XG. Didymin alleviates metabolic dysfunction-associated fatty liver disease (MAFLD) via the stimulation of Sirt1-mediated lipophagy and mitochondrial biogenesis. J Transl Med. 2023 Dec 19;21(1):921. doi: 10.1186/s12967-023-04790-4. PMID: 38115075; PMCID: PMC10731721.	Journal of Translational Medicine	7.4
250	Drug monomers from Salvia miltiorrhiza Bge. promoting tight junction protein expression for therapeutic effects on lung cancer	Biological function Gene Ontology (GO) and Kyoto Gene and Genome Encyclopedia (KEGG) signal pathway enrichment analysis were performed using the online platform “Dr. Tom 2.0” designed by BGI Tech Co., LTD.	2023/12/21	Zhu G, Li D, Wang X, Guo Q, Zhao Y, Hou W, Li J, Zheng Q. Drug monomers from Salvia miltiorrhiza Bge. promoting tight junction protein expression for therapeutic effects on lung cancer. Sci Rep. 2023 Dec 21;13(1):22928. doi: 10.1038/s41598-023-50163-8. PMID: 38129556; PMCID: PMC10739844.	Scientific Reports	4.6
251	Preliminary Study on the Formation Mechanism of Malformed Sweet Cherry (Prunus avium L.) Fruits in Southern China Using Transcriptome and Metabolome Data	The subsequent analysis and data mining were performed on the Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com, (accessed on 4 December 2021)).	2023/12/21	Zhang W, Xu Y, Jing L, Jiang B, Wang Q, Wang Y. Preliminary Study on the Formation Mechanism of Malformed Sweet Cherry (Prunus avium L.) Fruits in Southern China Using Transcriptome and Metabolome Data. Int J Mol Sci. 2023 Dec 21;25(1):153. doi: 10.3390/ijms25010153. PMCID: PMC10779264.	International Journal Of Molecular Sciences	5.6
252	The origins and dynamic changes of C3- and S100A10-positive reactive astrocytes after spinal cord injury	Bioinformatics analysis, including heatmap, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was carried out with the online platform Dr. Tom (BGI Company).	2023/12/22	Zhao Q, Ren YL, Zhu YJ, Huang RQ, Zhu RR, Cheng LM, Xie N. The origins and dynamic changes of C3- and S100A10-positive reactive astrocytes after spinal cord injury. Front Cell Neurosci. 2023 Dec 22;17:1276506. doi: 10.3389/fncel.2023.1276506. PMCID: PMC10766709.	Frontiers in Cellular Neuroscience	5.3
253	Comparative Transcriptomic Analyses for the Optimization of Thawing Regimes during Conventional Cryopreservation of Mature and Immature Human Testicular Tissue	RNA-seq analysis was performed using the Dr. Tom System (https://biosys.bgi.com, accessed on 25 August 2023).	2023/12/22	Pei C, Todorov P, Cao M, Kong Q, Isachenko E, Rahimi G, Mallmann-Gottschalk N, Uribe P, Sanchez R, Isachenko V. Comparative Transcriptomic Analyses for the Optimization of Thawing Regimes during Conventional Cryopreservation of Mature and Immature Human Testicular Tissue. Int J Mol Sci. 2023 Dec 22;25(1):214. doi: 10.3390/ijms25010214. PMCID: PMC10778995.	International Journal Of Molecular Sciences	5.6
254	Comprehensive Transcriptomic and Metabolomic Analysis Revealed the Functional Differences in Pigeon Lactation between Male and Female during the Reproductive Cycle	A bioinformatics analysis was conducted using the Dr. Tom web platform provided by BGI (http://report.bgi.com, accessed on 8 May 2022).	2023/12/24	Fu Y, Song Y, Jiang D, Pan J, Li W, Zhang X, Chen W, Tian Y, Shen X, Huang Y. Comprehensive Transcriptomic and Metabolomic Analysis Revealed the Functional Differences in Pigeon Lactation between Male and Female during the Reproductive Cycle. Animals (Basel). 2023 Dec 24;14(1):75. doi: 10.3390/ani14010075. PMID: 38200806; PMCID: PMC10778231.	Animals	3
255	KRT17 From Keratinocytes With High Glucose Stimulation Inhibit Dermal Fibroblasts Migration Through Integrin α11	Normalization and differential expression analyses were estimated from count data using the DEGseq package in the analysis system of Dr. Tom from BGI. Differentially expressed genes (DEGs) were screened using FDR-adjusted q values (q values ≤ 0.05), and fold changes ≥1.2. DEGs were extracted for GO functional enrichment analysis and KEGG pathway enrichment analysis using the analysis system of Dr. Tom from the BGI. Data visualization was performed using a bubble diagram.	2024/1/2	Zhou P, Li Y, Zhang S, Chen DX, Gao R, Qin P, Yang C, Li Q. KRT17 From Keratinocytes With High Glucose Stimulation Inhibit Dermal Fibroblasts Migration Through Integrin α11. J Endocr Soc. 2024 Jan 2;8(2):bvad176. doi: 10.1210/jendso/bvad176. PMID: 38205163; PMCID: PMC10776312.	Journal of the Endocrine Society	4.1
256	Didymin protects pancreatic beta cells by enhancing mitochondrial function in high-fat diet-induced impaired glucose tolerance	he library construction and sequencing procedures were executed at Shenzhen BGI Genomics Co. The Dr. Tom multiple omics data mining system (https://biosys.bgi.com) was utilized for conducting data mining analysis.	2024/1/3	Yang J, Zou Y, Lv X, Chen J, Cui C, Song J, Yang M, Hu H, Gao J, Xia L, Wang L, Chen L, Hou X. Didymin protects pancreatic beta cells by enhancing mitochondrial function in high-fat diet-induced impaired glucose tolerance. Diabetol Metab Syndr. 2024 Jan 3;16:7. doi: 10.1186/s13098-023-01244-1. PMCID: PMC10762818.	Diabetology & Metabolic Syndrome	4.8
257	Whole transcriptome sequencing for revealing the pathogenesis of sporotrichosis caused by Sporothrix globosa	Gene Set Enrichment Analysis (GSEA) was performed using Dr. Tom (a data analysis platform from BGI) with the official software package of GSEA.	2024/1/3	Liu Z, Li SS, Zhang GY, Lv S, Wang S, Li FQ. Whole transcriptome sequencing for revealing the pathogenesis of sporotrichosis caused by Sporothrix globosa. Sci Rep. 2024 Jan 3;14(1):359. doi: 10.1038/s41598-023-50728-7. PMID: 38172590; PMCID: PMC10764346.	Scientific Reports	4.6