Dr. Tao Zeng

Associate Professor
   Guangzhou Laboratory, Guangzhou, China

  Present address (office): Guangzhou Bio-island International Service Apartment B2, Guangzhou, China
  Phone (office): +86-18721274525
  E-mail: zeng_tao(at)gzlab.ac.cn; zengtao(at)sibs.ac.cn
  Sites online: Researchgate, Researcher ID, ScholarMate , Loop , LinkedIn, ORCID , Google scholar , GitHub

Education:
• 2006~2010 Wuhan University , School of computer, Received the doctor's degree.
• 2003~2006 Wuhan University, School of mathematics and statistics , Received the master's degree.
• 1999~2003 Wuhan University, School of mathematics and statistics , Received the bachelor's degree.

Research Interests:
  Bioinformatics, Computational systems biology, Machine learning, Graph theory, Precision medicine

Research and professional experence:
• 2021/10-now, associate Professor, Guangzhou Laboratory
• 2020/10-2021/10, associate Professor, Shanghai Institute of Nutrition and Health, CAS
• 2019/07-2020/09, associate Professor, Shanghai Research Center for Brain Science and Brain-Inspired Intelligence
• 2014/12-2019/07, associate Professor, Key Laboratory of Systems Biology , Institute of Biochemistry and Cell Biology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences
• 2013/01-2014/11, assistant Professor, Key Laboratory of Systems Biology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences
• 2011/01-2012/12, post-doctor, Key Laboratory of Systems Biology , Shanghai Institutes for Biological Sciences , Chinese Academy of Sciences
• 2008/07-2009/12, research-associate, BioInformatics Research Centre , School of Computer Engineering , Nanyang Technological University , Singapore

Academic activities:
• The academic secretary of The 557th Session of XIANGSHAN-SCIENCE Conferences: Big Data, Precision Medicine and Bioinformatics
• The organizing chair of Bio-synergy 2015
• The invited report at School of Mathematical Sciences, Peking University (2020)
• The invited report at The 9th National Conference on Bioinformatics and Systems Biology of China, Shanghai (2020)
• The invited report at 1st CAS Life Science Forum, Urumqi (2019)
• The invited report at School of Mathematics, South China University of Technology (2019)
• The invited report at The Fourth CCF Bioinformatics Conference, GuangZhou (CBC 2019)
• The invited report at School of Mathematics, South China University of Technology (2018)
• The invited report at National Tianyuan Northwest Center for Mathematics, Xi`an Jiaotong University (2018)
• The Editor of Research Topics (2018) - Machine learning advanced dynamic omics data analysis for precision medicine
• The Editor of Research Topics (2020) - Cross-Domain Analysis for “All of Us” Precision Medicine
• The Editor of Research Topics (2020) - RNA Modification and Non-Coding RNAs in Human Disease
• The report on Highlights sessions of ISB 2015 and ISB 2018
• The invited report at Shanghai Bioinformatics Seminar (2016)
• The invited report at School of Mathematics, South China University of Technology (2016)
• The invited talk on YOCSEF (WuHan 2020)
• The invited talk on Bone related diseases Summit Forum hold by Shanghai Sixth People’s Hospital (ShangHai 2021)
• The invited talk on Precision medicine big data Forum hold by Kunming Yan'an Hospital (KunMing 2022)
• The reviewers for peer-review journals, such as: Bioinformatics, GPB, TCBB, JTB, AIIM, SREP, BMC Bioinformatics, BMC Genomics, BMC Cancer, BMC Systems Biology, CBM, MBS, Methods, IET SYB, IJBRA, IJMI, IJDMB, Heliyon, IEEE Access, Plos CB, Computational and Structural Biotechnology Journal, Journal of Cellular and Molecular Medicine, Computational Biology and Chemistry, OMICS: A Journal of Integrative Biology, etc
• The program committee member of ISB 2013 , ISB 2014 , ISB 2015 , ISB 2016 , ISB 2017 , TBC 2017 , InCob 2017 ,ISB 2018 , ICIC 2018 , BIBM 2018 , ICIC 2019 , BIBM 2019 , BIBM 2020, BIBM 2021, BIBM 2022 , ICIC 2022

Projcts and awards:
• NSFC (31200987, 11871456, 12371485). (PI)
• The Knowledge Innovation Program of SIBS CAS (2013KIP218). (PI)
• The Natural Science Foundation of Shanghai (17ZR1446100). (PI)
• The Opening Foundation of Shanghai Municipal Science and Technology Major Project (2017SHZDZX01). (PI)
• The Strategic Priority Research Program of CAS (XDB13040700).
• The National Key R&D Program - Special Project on Precision Medicine (2016YFC0903400)).
• The National key research and development program of China (2017YFA0505500).
• Project from Shanghai cooperative center for transformation & innovation. (Co-PI)
• Travel grant from BIBM2010
• Travel grants from IDDF2018, IDDF2019, IDDF2023
• Best paper awards from ISB2013
• Best paper awards from ISB2014
• Best paper awards from BIBM2016
• Best paper awards from InCob2017
• Best poster awards from 1st national systems biology conference (china,shanghai,2019)
• Poster of Distinction awards from IDDF2021

Teaching area and courses:
Bioinformatics, 2013~2021 in SIBS.

Publication:

Journal paper:

-------------------------------------------------------2024-----------------------------------------------------
[1] Yuan C, Yu XT, Wang J, Shu B, Wang XY, Huang C, Lv X, Peng QQ, Qi WH, Zhang J, Zheng Y, Wang SJ, Liang QQ, Shi Q, Li T, Huang H, Mei ZD, Zhang HT, Xu HB, Cui J, Wang H, Zhang H, Shi BH, Sun P, Zhang H, Ma ZL, Feng Y, Chen L, Zeng T , Tang DZ, Wang YJ. Multi-modal molecular determinants of clinically relevant osteoporosis subtypes. Cell Discov. 2024 Mar 12;10(1):28. doi: 10.1038/s41421-024-00652-5. PMID: 38472169; PMCID: PMC10933295. (Co-corresponding author)

-------------------------------------------------------2023-----------------------------------------------------
[1]  Liang J, Li ZW, Sun ZN, Bi Y, Cheng H, Zeng T , Guo WF. Latent space search based multimodal optimization with personalized edge-network biomarker for multi-purpose early disease prediction. Brief Bioinform. 2023 Sep 22;24(6):bbad364. doi: 10.1093/bib/bbad364. PMID: 37833844. (Co-corresponding author)

[2]  Zeng T , Zhang C. Editorial: Expert opinions in integrative bioinformatics: 2022. Front Bioinform. 2023 May 19;3:1218466. doi: 10.3389/fbinf.2023.1218466. PMID: 37274753; PMCID: PMC10235704. (Corresponding author)

[3]  Liu Y, Li Y, Zeng T . Multi-omics of extracellular vesicles: An integrative representation of functional mediators and perspectives on lung disease study. Front Bioinform. 2023 Feb 9;3:1117271. doi: 10.3389/fbinf.2023.1117271. PMID: 36844931; PMCID: PMC9947558. (Co-corresponding author)

[4]  Li M, Wang L, Cong L, Wong CC, Zhang X, Chen H, Zeng T , Li B, Jia X, Huo J, Huang Y, Ren X, Peng S, Fu G, Xu L, Sung JJY, Kuang M, Li X, Yu J. Spatial proteomics of immune microenvironment in nonalcoholic steatohepatitis-associated hepatocellular carcinoma. Hepatology. 2024 Mar 1;79(3):560-574. doi: 10.1097/HEP.0000000000000591. Epub 2023 Sep 21. PMID: 37733002; PMCID: PMC10871559.

-------------------------------------------------------2022-----------------------------------------------------
[1]  Yu XT, Chen M, Guo J, Zhang J, Zeng T . Noninvasive detection and interpretation of gastrointestinal diseases by collaborative serum metabolite and magnetically controlled capsule endoscopy. Comput Struct Biotechnol J. 2022 Oct 6;20:5524-5534. doi: 10.1016/j.csbj.2022.10.001. PMID: 36249561; PMCID: PMC9550535. (Co-corresponding author)

[2]  Tang H, Yu X, Liu R, Zeng T . Vec2image: an explainable artificial intelligence model for the feature representation and classification of high-dimensional biological data by vector-to-image conversion. Brief Bioinform. 2022 Mar 10;23(2):bbab584. doi: 10.1093/bib/bbab584. PMID: 35106553; PMCID: PMC8921615. (Co-corresponding author)

[3]  Zhang C, Chen Y, Zeng T , Zhang C, Chen L. Deep latent space fusion for adaptive representation of heterogeneous multi-omics data. Brief Bioinform. 2022 Mar 10;23(2):bbab600. doi: 10.1093/bib/bbab600. PMID: 35079777.(Co-corresponding author)

[4]  Yuan K, Zeng T , Chen L. Interpreting Functional Impact of Genetic Variations by Network QTL for Genotype-Phenotype Association Study. Front Cell Dev Biol. 2022 Jan 26;9:720321. doi: 10.3389/fcell.2021.720321. PMID: 35155440; PMCID: PMC8826544.(Co-corresponding author)

[5]  Zhang C, Zhang H, Ge J, Mi T, Cui X, Tu F, Gu X, Zeng T , Chen L. Landscape dynamic network biomarker analysis reveals the tipping point of transcriptome reprogramming to prevent skin photodamage. J Mol Cell Biol. 2022 Jan 21;13(11):822-833. doi: 10.1093/jmcb/mjab060. Erratum in: J Mol Cell Biol. 2022 Apr 05;: PMID: 34609489; PMCID: PMC8782598.(Co-corresponding author)

[6]  Zhang L, Shi J, Du D, Niu N, Liu S, Yang X, Lu P, Shen X, Shi N, Yao L, Zhang R, Hu G, Lu G, Zhu Q, Zeng T , Liu T, Xia Q, Huang W, Xue J. Ketogenesis acts as an endogenous protective programme to restrain inflammatory macrophage activation during acute pancreatitis. EBioMedicine. 2022 Apr;78:103959. doi: 10.1016/j.ebiom.2022.103959. Epub 2022 Mar 25. PMID: 35339899; PMCID: PMC8960978.

[7]  Yu H, Li L, Huffman A, Beverley J, Hur J, Merrell E, Huang HH, Wang Y, Liu Y, Ong E, Cheng L, Zeng T , Zhang J, Li P, Liu Z, Wang Z, Zhang X, Ye X, Handelman SK, Sexton J, Eaton K, Higgins G, Omenn GS, Athey B, Smith B, Chen L, He Y. A new framework for host-pathogen interaction research. Front Immunol. 2022 Dec 15;13:1066733. doi: 10.3389/fimmu.2022.1066733. PMID: 36591248; PMCID: PMC9797517.

[8]  Li ZD, Yu X, Mei Z, Zeng T, Chen L, Xu XL, Li H, Huang T, Cai YD. Identifying luminal and basal mammary cell specific genes and their expression patterns during pregnancy. PLoS One. 2022 Apr 29;17(4):e0267211. doi: 10.1371/journal.pone.0267211. PMID: 35486595; PMCID: PMC9053804.

[9]  Zhang YH, Li ZD, Zeng T , Chen L, Huang T, Cai YD. Screening gene signatures for clinical response subtypes of lung transplantation. Mol Genet Genomics. 2022 Sep;297(5):1301-1313. (Co-first authors)

[10]  Li ZD, Guo W, Zeng T , Yin J, Feng KY, Huang T, Cai YD. Detecting Brain Structure-Specific Methylation Signatures and Rules for Alzheimer's Disease. Front Neurosci. 2022 May 2;16:895181.

[11]  Li Z, Guo W, Zeng T , Yin J, Feng K, Huang T, Cai YD. Detecting Brain Structure-Specific Methylation Signatures and Rules for Alzheimer's Disease. Front Neurosci. 2022 May 2;16:895181. doi: 10.3389/fnins.2022.895181. PMID: 35585924; PMCID: PMC9108872.

-------------------------------------------------------2021-----------------------------------------------------
[1]  Zeng T , Yu XT, Chen Z. Applying artificial intelligence in the microbiome for gastrointestinal diseases: A review. J Gastroenterol Hepatol. 2021 Apr;36(4):832-840. doi: 10.1111/jgh.15503. (Corresponding author)

[2]  Zeng T , Huang T, Lu C. Editorial: Cross-Domain Analysis for "All of Us" Precision Medicine. Front Genet. 2021 Jul 1;12:713771. doi: 10.3389/fgene.2021.713771. PMID: 34276803; PMCID: PMC8280781.(Corresponding author)

[3]  Guo WF, Yu XT, Shi QQ, Liang J, Zhang SW, Zeng T . Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis. PLoS Comput Biol. 2021 May 6;17(5):e1008962. doi: 10.1371/journal.pcbi.1008962. Online ahead of print.(Co-corresponding author)

[4]  Wang L, Xu YN, Chu CC, Jing Z, Chen Y, Zhang J, Pu M, Mi T, Du Y, Liang Z, Doraiswamy C, Zeng T , Wu J, Chen L. Facial Skin Microbiota-Mediated Host Response to Pollution Stress Revealed by Microbiome Networks of Individual. mSystems. 2021 Aug 31;6(4):e0031921. doi: 10.1128/mSystems.00319-21. Epub 2021 Jul 27. PMID: 34313461; PMCID: PMC8407115.(Co-corresponding author)

[5]  Guo WF, Zhang SW, Feng YH, Liang J, Zeng T , Chen L. Network controllability-based algorithm to target personalized driver genes for discovering combinatorial drugs of individual patients. Nucleic Acids Res. 2021 Apr 19;49(7):e37. doi: 10.1093/nar/gkaa1272. (Co-corresponding author)

[6]  Zhang C, Zhang H, Ge J, Mi T, Cui X, Tu F, Gu X, Zeng T , Chen L. Landscape dynamic network biomarker analysis reveals the tipping point of transcriptome reprogramming to prevent skin photodamage. J Mol Cell Biol. 2021 Oct 5:mjab060. doi: 10.1093/jmcb/mjab060. Epub ahead of print. PMID: 34609489. (Co-corresponding author)

[7]  Chen L, Zhou X, Zeng T , Pan X, Zhang YH, Huang T, Fang Z, Cai YD. Recognizing Pattern and Rule of Mutation Signatures Corresponding to Cancer Types. Front Cell Dev Biol. 2021 Aug 26;9:712931. doi: 10.3389/fcell.2021.712931. PMID: 34513841; PMCID: PMC8427289.

[8]  Zhang YH, Guo W, Zeng T , Zhang S, Chen L, Gamarra M, Mansour RF, Escorcia-Gutierrez J, Huang T, Cai YD. Identification of Microbiota Biomarkers With Orthologous Gene Annotation for Type 2 Diabetes. Front Microbiol. 2021 Jul 9;12:711244. doi: 10.3389/fmicb.2021.711244. PMID: 34305880; PMCID: PMC8299781.

[9]  Zhang YH, Zeng T , Chen L, Huang T, Cai YD. Determining protein-protein functional associations by functional rules based on gene ontology and KEGG pathway. Biochim Biophys Acta Proteins Proteom. 2021 Jun;1869(6):140621. doi: 10.1016/j.bbapap.2021.140621. Epub 2021 Feb 6.

[10]  Yuan F, Li Z, Chen L, Zeng T , Zhang YH, Ding S, Huang T, Cai YD. Identifying the Signatures and Rules of Circulating Extracellular MicroRNA for Distinguishing Cancer Subtypes. Front Genet. 2021 Mar 9;12:651610. doi: 10.3389/fgene.2021.651610. eCollection 2021.

[11]  Zhang YH, Li H, Zeng T , Chen L, Li Z, Huang T, Cai YD. Identifying Transcriptomic Signatures and Rules for SARS-CoV-2 Infection. Front Cell Dev Biol. 2021 Jan 11;8:627302. doi: 10.3389/fcell.2020.627302. eCollection 2020.

[12]  Zhang YH, Li Z, Zeng T , Chen L, Li H, Gamarra M, Mansour RF, Escorcia-Gutierrez J, Huang T, Cai YD. Investigating gene methylation signatures for fetal intolerance prediction. PLoS One. 2021 Apr 22;16(4):e0250032. doi: 10.1371/journal.pone.0250032. eCollection 2021.

[13]  Pan XY, Li H, Zeng T , Li Z, Chen L, Huang T, Cai YD. Identification of Protein Subcellular Localization With Network and Functional Embeddings. Front Genet. 2021 Jan 20;11:626500. doi: 10.3389/fgene.2020.626500. eCollection 2020.

[14]  Chen L, Li Z, Zeng T , Zhang YH, Li H, Huang T, Cai YD. Predicting gene phenotype by multi-label multi-class model based on essential functional features. Mol Genet Genomics. 2021 Apr 29. doi: 10.1007/s00438-021-01789-8. Online ahead of print.

[15]  Zhang YH, Li Z, Zeng T , Chen L, Li H, Huang T, Cai YD. Detecting the Multiomics Signatures of Factor-Specific Inflammatory Effects on Airway Smooth Muscles. Front Genet. 2021 Jan 13;11:599970. doi: 10.3389/fgene.2020.599970. eCollection 2020.

[16]  Chen L, Li Z, Zeng T , Zhang YH, Feng K, Huang T, Cai YD. Identifying COVID-19-Specific Transcriptomic Biomarkers with Machine Learning Methods. Biomed Res Int. 2021 Jul 6;2021:9939134. doi: 10.1155/2021/9939134. PMID: 34307679; PMCID: PMC8272456.

[17]  Zhang YH, Li Z, Lu L, Zeng T, Chen L, Li H, Huang T, Cai YD. Analysis of the Sequence Characteristics of Antifreeze Protein. Life (Basel). 2021 Jun 3;11(6):520. doi: 10.3390/life11060520. PMID: 34204983; PMCID: PMC8226703.

-------------------------------------------------------2020-----------------------------------------------------
[1]  Hu J, Zeng T , Xia Q, Huang L, Zhang Y, Zhang C, Zeng Y, Liu H, Zhang S, Huang G, Wan W, Ding Y, Hu F, Yang C, Chen L, Wang W. Identification of Key Genes for the Ultrahigh Yield of Rice Using Dynamic Cross-tissue Network Analysis. Genomics Proteomics Bioinformatics. 2020 Jul 28:S1672-0229(20)30091-7. doi: 10.1016/j.gpb.2019.11.007. (Co-first author)

[2]  Yu X, Wang Z, Zeng T . Essential gene expression pattern of head and neck squamous cell carcinoma revealed by tumor-specific expression rule based on single-cell RNA sequencing. Biochim Biophys Acta Mol Basis Dis. 2020 Mar 28;1866(7):165791. doi: 10.1016/j.bbadis.2020.165791. (Co-corresponding author)

[3]  Tang H, Tang Y, Zeng T , Chen L. Gene expression analysis reveals the tipping points during infant brain development for human and chimpanzee. BMC Genomics. 2020 Mar 5;21(Suppl 1):74. doi: 10.1186/s12864-020-6465-8.

[4]  Zeng T, Huang T, Lu C. Editorial: Machine Learning Advanced Dynamic Omics Data Analysis for Precision Medicine. Front Genet. 2020 Feb 4;10:1343. doi: 10.3389/fgene.2019.01343. eCollection 2019. (Corresponding author)

[5]  Zhang S, Zeng T, Hu B, Zhang YH, Feng K, Chen L, Niu Z, Li J, Huang T, Cai YD. Discriminating Origin Tissues of Tumor Cell Lines by Methylation Signatures and Dys-Methylated Rules. Front Bioeng Biotechnol. 2020 May 26;8:507. doi: 10.3389/fbioe.2020.00507.

[6]  Zhang S, Zhao J, Lv X, Fan J, Lu Y, Zeng T , Wu H, Chen L, Zhao Y. Analysis on gene modular network reveals morphogen-directed development robustness in Drosophila.Cell Discov. 2020 Jun 30;6:43. doi: 10.1038/s41421-020-0173-z. eCollection 2020.

[7]  Li Y, Omori A, Flores RL, Satterfield S, Nguyen C, Ota T, Tsurugaya T, Ikuta T, Ikeo K, Kikuchi M, Leong JCK, Reich A, Hao M, Wan W, Dong Y, Ren Y, Zhang S, Zeng T , Uesaka M, Uchida Y, Li X, Shibata TF, Bino T, Ogawa K, Shigenobu S, Kondo M, Wang F, Chen L, Wessel G, Saiga H, Cameron RA, Livingston B, Bradham C, Wang W, Irie N.Genomic insights of body plan transitions from bilateral to pentameral symmetry in Echinoderms. Commun Biol. 2020 Jul 10;3(1):371. doi: 10.1038/s42003-020-1091-1.

[8]  Li ML, Tang H, Shao Y, Wang MS, Xu HB, Wang S, Irwin DM, Adeola AC, Zeng T, Chen L, Li Y, Wu DD. Evolution and transition of expression trajectory during human brain development. BMC Evol Biol. 2020 Jun 23;20(1):72. doi: 10.1186/s12862-020-01633-4.

[9]  Yuan F, Pan X, Zeng T, Zhang YH, Chen L, Gan Z, Huang T, Cai YD. Identifying Cell-Type Specific Genes and Expression Rules Based on Single-Cell Transcriptomic Atlas Data. Front Bioeng Biotechnol. 2020 Apr 29;8:350.

[10]  Li M, Pan X, Zeng T , Zhang YH, Feng K, Chen L, Huang T, Cai YD. Alternative Polyadenylation Modification Patterns Reveal Essential Posttranscription Regulatory Mechanisms of Tumorigenesis in Multiple Tumor Types. Biomed Res Int. 2020 Jun 15;2020:6384120. doi: 10.1155/2020/6384120. eCollection 2020.

[11]  Zhang Y, Zeng T, Chen L, Ding S, Huang T, Cai YD. Identification of COVID-19 Infection-Related Human Genes Based on a Random Walk Model in a Virus-Human Protein Interaction Network. Biomed Res Int. 2020 Jul 8;2020:4256301.

[12]  Pan X, Zeng T , Zhang YH, Chen L, Feng K, Huang T, Cai YD. Investigation and Prediction of Human Interactome Based on Quantitative Features. Front Bioeng Biotechnol. 2020 Jul 17;8:730. doi: 10.3389/fbioe.2020.00730.

[13]  Zhang YH, Pan XY, Zeng T , Chen L, Huang T, Cai YD. Identifying the RNA signatures of coronary artery disease from combined lncRNA and mRNA expression profiles. Genomics. 2020 Sep 9;S0888-7543(20)30508-5. doi: 10.1016/j.ygeno.2020.09.016.

[14]  Pan XY, Zeng T , Zhang YH, Chen L, Feng KY, Huang T, Cai YD. Investigation and Prediction of Human Interactome Based on Quantitative Features. Front Bioeng Biotechnol. 2020 Jul 17;8:730. doi: 10.3389/fbioe.2020.00730.

[15]  Chen L, Li Z, Zeng T , Zhang YH, Liu D, Li H, Huang T, Cai YD. Identifying Robust Microbiota Signatures and Interpretable Rules to Distinguish Cancer Subtypes. Front Mol Biosci. 2020 Nov 4;7:604794. doi: 10.3389/fmolb.2020.604794.

[16]  Zhang YH, Li Z, Zeng T , Pan X, Chen L, Liu D, Li H, Huang T, Cai YD. Distinguishing Glioblastoma Subtypes by Methylation Signatures. Front Genet. 2020 Nov 24;11:604336.

-------------------------------------------------------2019-----------------------------------------------------
[1]  Guo WF, Zhang SW, Zeng T , Akutsu T, Chen L. Network control principles for identifying personalized driver genes in cancer. Brief Bioinform. 2019 Nov 10. pii: bbz089. doi: 10.1093/bib/bbz089. (Co-corresponding author)

[2]  Guo W, Zhang SW, Zeng T , Li Y, Gao J, Chen L. A novel network control model for identifying personalized driver genes in cancer. PLoS Comput Biol. 2019 Nov 25;15(11):e1007520. doi: 10.1371/journal.pcbi.1007520. [Epub ahead of print] (Co-corresponding author)

[3]  Zeng T , Dai H. Single-Cell RNA Sequencing-Based Computational Analysis to Describe Disease Heterogeneity. Front Genet. 2019 Jul 12;10:629. doi: 10.3389/fgene.2019.00629. (Corresponding author)

[4]  Lu Y, Fang Z, Zeng T , Li M, Chen Q, Zhang H, Zhou Q, Hu Y, Chen L, Su S. Chronic hepatitis B: dynamic change in Traditional Chinese Medicine syndrome by dynamic network biomarkers. Chin Med. 2019 Nov 21;14:52. doi: 10.1186/s13020-019-0275-4. eCollection 2019.

[5]  Dai H, Li L, Zeng T, Chen L. Cell-specific network constructed by single-cell RNA sequencing data. Nucleic Acids Res. 2019 Mar 13. pii: gkz172. doi: 10.1093/nar/gkz172.

[6]  Tang H, Zeng T , Chen L. High-Order Correlation Integration for Single-Cell or Bulk RNA-seq Data Analysis. Front Genet. 2019 Apr 26;10:371. doi: 10.3389/fgene.2019.00371. (Co-corresponding author)

[7]  Gao W, Sun YB, Zhou WW, Xiong ZJ, Chen L, Li H, Fu TT, Xu K, Xu W, Ma L, Chen YJ, Xiang XY, Zhou L, Zeng T, Zhang S, Jin JQ, Chen HM, Zhang G, Hillis DM, Ji X, Zhang YP, Che J. Genomic and transcriptomic investigations of the evolutionary transition from oviparity to viviparity. Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3646-3655.

[8]  Lu Y, Fang Z, Li M, Qian C, Zeng T, Lu L, Chen Q, Zhang H, Zhou Q, Sun Y, Xue X, Hu Y, Chen L, Su S. Dynamic edge-based biomarker noninvasively predicts hepatocellular carcinoma with hepatitis B virus infection for individual patients based on blood testing.J Mol Cell Biol. 2019 Mar 29. pii: mjz025. doi: 10.1093/jmcb/mjz025. [Epub ahead of print]

[9]  Gao D, Zhang L, Song D, Lv J, Wang L, Zhou S, Li Y, Zeng T , Zeng Y, Zhang J, Wang X. Values of integration between lipidomics and clinical phenomes in patients with acute lung infection, pulmonary embolism, or acute exacerbation of chronic pulmonary diseases: a preliminary study. J Transl Med. 2019 May 20;17(1):162. doi: 10.1186/s12967-019-1898-z.

[10]  Shi QQ, Hu B, Zeng Tand Zhang CC. Multi-view Subspace Clustering Analysis for Aggregating Multiple Heterogeneous Omics Data. Front. Genet., 20 August 2019 | https://doi.org/10.3389/fgene.2019.00744

[11]  Zeng T , Xiangtian Yu, Chengming Zhang. Pan-cancer study of progressive protein signatures for digestive cancers.Gut, 2019, 68 (Suppl 1) A15-A16; DOI: 10.1136/gutjnl-2019-IDDFAbstracts.29. (ePoster) (Corresponding author)

[12]  Chen L, Zeng T , Pan X, Zhang YH, Huang T and Cai YD. Identifying Methylation Pattern and Genes Associated with Breast Cancer Subtypes. Int. J. Mol. Sci. 2019, 20(17), 4269; https://doi.org/10.3390/ijms20174269. (Co-first author)

[13]  Song D, Tang L, Wang L, Huang J, Zeng T , Fang H, Wang X. Roles of TGFβ1 in the expression of phosphoinositide 3-kinase isoform genes and sensitivity and response of lung telocytes to PI3K inhibitors. Cell Biol Toxicol. 2019 Sep 15. doi: 10.1007/s10565-019-09487-3.

[14]  Chen L, Pan XY, Zeng T , Zhang YH, Huang T, Cai YD. Identifying essential signature genes and expression rules associated with distinctive development stages of early embryonic cells. IEEE Access, 2019, 7:128570 - 128578. DOI:10.1109/ACCESS.2019.2939556. (Co-first author)

[15]  Pan XY, Zeng T, Yuan F, Zhang YH, Chen L, Zhu LC, Wan SB, Huang T, Cai YD. Screening of Methylation Signature and Gene Functions Associated With the Subtypes of Isocitrate Dehydrogenase-Mutation Gliomas. Frontiers in Bioengineering and Biotechnology, 2019, 7:339. DOI=10.3389/fbioe.2019.00339. (Co-first author)

[16]  Chen L, Pan X, Zeng T , Zhang Y-H, Zhang Y, Huang T and Cai Y-D. Immunosignature Screening for Multiple Cancer Subtypes Based on Expression Rule. Front. Bioeng. Biotechnol. 2019, 7:370. doi: 10.3389/fbioe.2019.00370 (Co-first author)

[17]  Choobdar S, Ahsen ME, Crawford J, ..., Zeng T , ..., Sven Bergmann & Daniel Marbach. Assessment of network module identification across complex diseases. Nature Methods, 16:843–852 (2019). (Consortium author)

[18]  Zhang S, Pan X, Zeng T , Guo W, Gan Z, Zhang YH, Chen L, Zhang Y, Huang T, Cai YD. Copy Number Variation Pattern for Discriminating MACROD2 States of Colorectal Cancer Subtypes. Front Bioeng Biotechnol. 2019 Dec 19;7:407. doi: 10.3389/fbioe.2019.00407. eCollection 2019. (Co-first author)

[19]  Sun S, Yu X, Sun F, Tang Y, Zhao J, Zeng T . Dynamically characterizing individual clinical change by the steady state of disease-associated pathway. BMC Bioinformatics. 2019 Dec 24;20(Suppl 25):697. doi: 10.1186/s12859-019-3271-x. (Co-corresponding author)

[20]  Song D, Tang L, Huang J, Wang L, Zeng T , Wang X. Roles of transforming growth factor-β and phosphatidylinositol 3-kinase isoforms in integrin β1-mediated bio-behaviors of mouse lung telocytes. J Transl Med. 2019 Dec 30;17(1):431. doi: 10.1186/s12967-019-02181-2.

-------------------------------------------------------2018-----------------------------------------------------
[1]  Wang L, Yu X, Zhang C, Zeng T . Detecting Personalized Determinants During Drug Treatment from Omics Big Data. Curr Pharm Des. 2018;24(32):3727-3738. doi: 10.2174/1381612824666181106102111. (Corresponding author)

[2]  Zeng T, Lu Wang, Xiangtian Yu . A revisit on personalized critical variance of gut microbiota during the occurrence of Type I Diabetes. Gut, 2018, 67(Suppl 2):A7. (ePoster) (Corresponding author)

[3]  Shaoyan Sun, Xiangtian Yu, Fengnan Sun, Ying Tang, Juan Zhao, and Zeng T . Characterizing and Discriminating Individual Steady State of Disease-Associated Pathway. Intelligent Computing Theories and Application, LNCS 10954, 2018, pp.533-538. (Co-corresponding author)

[4]  Hu J, Zeng T , Xia Q, Qian Q, Yang C, Ding Y, Chen L, Wang W. Unravelling miRNA regulation in yield of rice (Oryza sativa) based on differential network model. Scientific Reportsvolume 8, Article number: 8498, 2018. (Co-first author)

[5]  Guo Weifeng, Zhang SW, Liu LL, Liu F, Shi QQ, Zhang L, Tang Y, Zeng T, Chen L. Discovering personalized driver mutation profiles of single samples in cancer by network control strategy. Bioinformatics. 2018 Jan 10. doi: 10.1093/bioinformatics/bty006. [Epub ahead of print] (Co-corresponding author)

[6] Guo Weifeng, Zhang SW, Shi QQ, Zhang CM, Zeng T, Chen L. A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification.    BMC Genomics. 2018 Jan 19;19(Suppl 1):924. doi: 10.1186/s12864-017-4332-z. (Co-corresponding author)

[7]  Zhang JS, Guo JM, Zhang M, Yu XT, Yu XQ, Guo WF, Zeng T, Chen LN. Efficient Mining Multi-mers in a Variety of Biological Sequences. doi:10.1109/TCBB.2018.2828313. (Co-corresponding author)

[8]  Yu XT, Zeng T. Integrative Analysis of Omics Big Data. Methods Mol Biol. 2018;1754:109-135. doi: 10.1007/978-1-4939-7717-8_7. (Chapter)

[9]  Yu XT, Wang L, Zeng T. Revisit of Machine Learning Supported Biological and Biomedical Studies. Methods Mol Biol. 2018;1754:183-204. doi: 10.1007/978-1-4939-7717-8_11. (Chapter)

-------------------------------------------------------2017-----------------------------------------------------
[1] Yu X, Zhang J, Sun S, Zhou X, Zeng T, Chen L. Individual-specific edge-network analysis for disease prediction. Nucleic Acids Res. 2017 Nov 16;45(20):e170. doi: 10.1093/nar/gkx787. PubMed PMID: 28981699. (Co-corresponding author)

[2] Shi Q, Zhang C, Peng M, Yu X, Zeng T, Liu J, Chen L. Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data. Bioinformatics. 2017 Sep 1;33(17):2706-2714. doi: 10.1093/bioinformatics/btx176. PubMed PMID: 28520848. (Co-corresponding author)

[3] Zhang C, Liu J, Shi Q, Zeng T , Chen L. Comparative network stratification analysis for identifying functional interpretable network biomarkers. BMC Bioinformatics. 2017 Mar 14;18(Suppl 3):48. doi: 10.1186/s12859-017-1462-x. PubMed PMID: 28361683. (Co-corresponding author)

[4] Li M, Li C, Liu WX, Liu C, Cui J, Li Q, Ni H, Yang Y, Wu C, Chen C, Zhen X, Zeng T , Zhao M, Chen L, Wu J, Zeng R, Chen L. Dysfunction of PLA2G6 and CYP2C44-associated network signals imminent carcinogenesis from chronic inflammation to hepatocellular carcinoma. J Mol Cell Biol. 2017 Jun 26. doi: 10.1093/jmcb/mjx021. [Epub ahead of print] PubMed PMID: 28655161.

[5] Shi Q, Zhang C, Guo W, Zeng T , Lu L, Jiang Z, Wang Z, Liu J, Chen L. Local network component analysis for quantifying transcription factor activities. Methods. 2017 Jul 15;124:25-35. doi: 10.1016/j.ymeth.2017.06.018. Epub 2017 Jul 12. PubMed PMID: 28710010. )

[7] Zhang C, Liu J, Shi QQ, Zeng T , Chen L. Differential function analysis: identifying structure and activation variations in dysregulated pathways. SCIENCE CHINA Information Sciences, Vol. 60 012108:1–012108:16, 2017. (Co-corresponding author)

-------------------------------------------------------2016-----------------------------------------------------
[1] Yang Y, Lin X, Lu X, Luo G, Zeng T, Tang J, Jiang F, Li L, Cui X, Huang W, Hou G, Chen X, Ouyang Q, Tang S, Sun H, Chen L, Gonzalez FJ, Wu M, Cong W, Chen L, Wang H. Interferon-microRNA signalling drives liver precancerous lesion formation and hepatocarcinogenesis. Gut. 2016 Feb 9. pii: gutjnl-2015-310318. doi: 10.1136/gutjnl-2015-310318. [Epub ahead of print] PubMed PMID: 26860770.

-------------------------------------------------------2015-----------------------------------------------------
[1] Zeng T, Zhang W, Yu X, Liu X, Li M, Chen L. Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals. Brief Bioinform. 2015 Sep 26. pii: bbv078. [Epub ahead of print] PubMed PMID: 26411472.

[2] Yu X, Zeng T, Li G. Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples. BMC Genomics. 2015 Nov 10;16:918. doi: 10.1186/s12864-015-2188-7. PubMed PMID: 26556243; PubMed Central PMCID: PMC4641376. (Co-corresponding author)

[3] Kang H, Cho KH, Zhang XD, Zeng T, Chen L. Inferring Sequential Order of Somatic Mutations during Tumorgenesis based on Markov Chain Model. IEEE/ACM Trans Comput Biol Bioinform. 2015 Sep-Oct;12(5):1094-103. doi: 10.1109/TCBB.2015.2424408. PubMed PMID: 26451822. (Co-corresponding author)

[4] Yu X, Zeng T, Wang X, Li G, Chen L. Unravelling personalized dysfunctional gene network of complex diseases based on differential network model. J Transl Med. 2015 Jun 13;13:189. doi: 10.1186/s12967-015-0546-5. PubMed PMID: 26070628; PubMed Central PMCID: PMC4467679.

[5] Shi Q, Liu X, Zeng T, Wang W, Chen L. Detecting disease genes of non-small lung cancer based on consistently differential interactions. Cancer Metastasis Rev. 2015 Jun;34(2):195-208. doi: 10.1007/s10555-015-9561-5. PubMed PMID: 26004969.

[6] Yang D, Zhou J, Zeng T, Yang Z, Wang X, Hu J, Song Y, Chen L, Peer D, Wang X, Bai C. Serum chemokine network correlates with chemotherapy in non-small cell lung cancer. Cancer Lett. 2015 Aug 28;365(1):57-67. doi: 10.1016/j.canlet.2015.05.001. Epub 2015 May 11. PubMed PMID: 25976768.

[7] Chen S, Liu J, Zeng T. Measuring the quality of linear patterns in biclusters. Methods. 2015 Jul 15;83:18-27. doi: 10.1016/j.ymeth.2015.04.005. Epub 2015 Apr 15. PubMed PMID: 25890245.

[8] Zhang W, Zeng T, Liu X, Chen L. Diagnosing phenotypes of single-sample individuals by edge biomarkers. J Mol Cell Biol. 2015 Jun;7(3):231-41. doi: 10.1093/jmcb/mjv025. Epub 2015 Apr 26. PubMed PMID: 25917597. (Co-first author)

-------------------------------------------------------2014-----------------------------------------------------
[1] Zeng T, Zhang W, Yu X, Liu X, Li M, Liu R, Chen L. Edge biomarkers for classification and prediction of phenotypes. Sci China Life Sci. 2014 Nov;57(11):1103-14. doi: 10.1007/s11427-014-4757-4. Epub 2014 Oct 17. Review. PubMed PMID: 25326072.

[2] Wen Z, Zhang W, Zeng T, Chen L. MCentridFS: a tool for identifying module biomarkers for multi-phenotypes from high-throughput data. Mol Biosyst. 2014 Nov;10(11):2870-5. doi: 10.1039/c4mb00325j. PubMed PMID: 25099602.

[3] Zeng T, Wang DC, Wang X, Xu F, Chen L. Prediction of dynamical drug sensitivity and resistance by module network rewiring-analysis based on transcriptional profiling. Drug Resist Updat. 2014 Jul;17(3):64-76. doi: 10.1016/j.drup.2014.08.002. Epub 2014 Aug 13. Review. PubMed PMID: 25156319.

[4] Zhang W, Zeng T, Chen L. EdgeMarker: Identifying differentially correlated molecule pairs as edge-biomarkers. J Theor Biol. 2014 Dec 7;362:35-43. doi: 10.1016/j.jtbi.2014.05.041. Epub 2014 Jun 12. PubMed PMID: 24931676. (Co-corresponding author)

[5] Zeng T, Zhang CC, Zhang W, Liu R, Liu J, Chen L. Deciphering early development of complex diseases by progressive module network. Methods. 2014 Jun 1;67(3):334-43. doi: 10.1016/j.ymeth.2014.01.021. Epub 2014 Feb 21. PubMed PMID: 24561825.

[6] Zhao M, Chang HT, Zhou Q, Zeng T, Shih CS, Liu ZP, Chen L, Wei DQ. Predicting protein-ligand interactions based on chemical preference features with its application to new D-amino acid oxidase inhibitor discovery. Curr Pharm Des. 2014;20(32):5202-11. PubMed PMID: 24410568.

[7] Li M, Zeng T, Liu R, Chen L. Detecting tissue-specific early warning signals for complex diseases based on dynamical network biomarkers: study of type 2 diabetes by cross-tissue analysis. Brief Bioinform. 2014 Mar;15(2):229-43. doi: 10.1093/bib/bbt027. Epub 2013 Apr 25. PubMed PMID: 23620135. (Co-first author)

------------------------------------------------2013 and before-------------------------------------------------
[1] Zeng T, Sun SY, Wang Y, Zhu H, Chen L. Network biomarkers reveal dysfunctional gene regulations during disease progression. FEBS J. 2013 Nov;280(22):5682-95. doi: 10.1111/febs.12536. Epub 2013 Oct 22. Review. PubMed PMID: 24107168.

[2] Tarca AL, Lauria M, Unger M, Bilal E, Boue S, Kumar Dey K, Hoeng J, Koeppl H, Martin F, Meyer P, Nandy P, Norel R, Peitsch M, Rice JJ, Romero R, Stolovitzky G, Talikka M, Xiang Y, Zechner C; IMPROVER DSC Collaborators. Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge. Bioinformatics. 2013 Nov 15;29(22):2892-9. doi: 10.1093/bioinformatics/btt492. Epub 2013 Aug 20. (Collaborators)

[3] Sun SY, Liu ZP, Zeng T, Wang Y, Chen L. Spatio-temporal analysis of type 2 diabetes mellitus based on differential expression networks. Sci Rep. 2013;3:2268. doi: 10.1038/srep02268. PubMed PMID: 23881262; PubMed Central PMCID: PMC3721080.

[4] Zeng T, Chen L. Tracing dynamic biological processes during phase transition. BMC Syst Biol. 2012;6 Suppl 1:S12. doi: 10.1186/1752-0509-6-S1-S12. Epub 2012 Jul 16. Erratum in: BMC Syst Biol. 2012 Jul 16;6 Suppl 1:S23. PubMed PMID: 23046764; PubMed Central PMCID: PMC3403121.

[5] Xiong Y, Liu J, Zhang W, Zeng T. Prediction of heme binding residues from protein sequences with integrative sequence profiles. Proteome Sci. 2012 Jun 21;10 Suppl 1:S20. doi: 10.1186/1477-5956-10-S1-S20. PubMed PMID: 22759579; PubMed Central PMCID: PMC3380730.

[6] Zeng T, Li J, Liu J. Distinct interfacial biclique patterns between ssDNA-binding proteins and those with dsDNAs. Proteins. 2011 Feb;79(2):598-610. doi: 10.1002/prot.22908. PubMed PMID: 21120860.

[7] Zeng T, Li J. Maximization of negative correlations in time-course gene expression data for enhancing understanding of molecular pathways. Nucleic Acids Res. 2010 Jan;38(1):e1. doi: 10.1093/nar/gkp822. Epub 2009 Oct 23. PubMed PMID: 19854949; PubMed Central PMCID: PMC2800212.

[8] Zeng T, Liu J. Mixture classification model based on clinical markers for breast cancer prognosis. Artif Intell Med. 2010 Feb-Mar;48(2-3):129-37. doi: 10.1016/j.artmed.2009.07.008. Epub 2009 Dec 14. PubMed PMID: 20005686.

[9] Gu C, Zeng T, Li Y, Xu Z, Mo Z, Zheng C. Structure-function analysis of mutant RNA-dependent RNA polymerase complexes with VPg. Biochemistry (Mosc). 2009 Oct;74(10):1132-41. PubMed PMID: 19916926. (Co-first author)

[10] Zeng T, Zhongxi Mo. Bioinformatics analysis of mutant structure and functional sites of foot-and-mouth disease virus RNA-dependent RNA polymerase. Journal of Computational and Theoretical Nanoscience, v 4, n 7-8, p 1330-1336, November/December 2007.

[11] Zhongxi Mo, Zeng T . Improved genetic algorithm for problem of genome rearrangement. Wuhan University Journal of Natural Sciences, v 11, n 3, p 498-502, May 2006.

Conference paper:
[1] Lu wang, Xiangtian Yu, Tao Zeng. A revisit on personalized critical variance of gut microbiota during the occurrence of Type I Diabetes. IDDF 2018. (ePoster)

[2] Tao Zeng. Improving the discrimination and interpretability for complex diseases by network biomarker. 16th SCBA International Symposium, 2017, pp.298. (Abstract)

[3] Weifeng Guo, Shaowu Zhang, Qianqian Shi, Chengming Zhang, Tao Zeng and Luonan Chen . A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification. International Conference on Bioinformatics (InCoB) 2017.

[4] Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng and Luonan Chen. Comparative network stratification analysis for identifying functional interpretable network biomarkers. The Asia Pacific Bioinformatics Conference (APBC) 2017.

[5] Chuanchao Zhang, Juan Liu, Tao Zeng, and Luonan Chen. Integration of multiple heterogeneous omics data .The IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2016.

[6] Chuanchao Zhang, Juan Liu, Qianqian Shi, Tao Zeng, Luonan Chen. Identification of phenotypic networks based on whole transcriptome by comparative network decomposition. 2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp: 189-194.

[7] Tao Zeng, Ziming Wang, Luonan Chen: Detecting Phosphorylation Determined Active Protein Interaction Network during Cancer Development by Robust Network Component Analysis. DTMBIO '14 Proceedings of the ACM 8th International Workshop on Data and Text Mining in Bioinformatics ,DTMBIO@CIKM 2014, pp.49. (Abstract)

[8] Tao Zeng, Ruozhao Wang, Luonan Chen. Module network rewiring in response to therapy. IEEE 6th International Conference on Systems Biology, ISB 2012, p 197-202.

[9] Tao Zeng, Luonan Chen. Identifying temporal trace of biological process during phase transition. Systems Biology (ISB), 2011 IEEE International Conference on, pp:368-373.

[10] Guanying Piao, Bangguo Qian, Shigeru Saito, ZP Liu, Tao Zeng, Y. Wang, Jiarui Wu, Huarong Zhou, L. Chen, K. Horimoto. Phenotype-difference oriented identification of molecular functions for diabetes progression in Goto-Kakizaki rat. Systems Biology (ISB), 2011 IEEE International Conference on, pp:111-116.

[11] Yi Xiong, Wen Zhang, Tao Zeng, Juan Liu. Prediction of heme binding sites in heme proteins using an integrative sequence profile coupling evolutionary information with physicochemical properties. Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, p 143-146, 2011.

[12] Jinyan Li, Qian Liu, Tao Zeng. Negative correlations in collaboration: concepts and algorithms. Knowledge Discovery and Data Mining, KDD2010, p 463-472, 2010.

[13] Tao Zeng, Xuan Guo, Juan Liu. Discovering negative correlated gene sets from integrative gene expression data for cancer prognosis. Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010, p 489-492, 2010,

[14] Tao Zeng, Fei Luo, Juan Liu. Biological pathway conducting microarray-based cancer classification. Proceedings of the 2009 2nd International Conference on Biomedical Engineering and Informatics, BMEI 2009, 2009.

[15] Tao Zeng, Juan Liu. A novel mixture classifier and its application in breast cancer prognosis. 2nd International Conference on Bioinformatics and Biomedical Engineering, iCBBE 2008, p 564-568, 2008.

[16] Tao Zeng, Juan Liu. Analysis on time-lagged gene clusters in time series gene expression data. Proceedings - 2007 International Conference on Computational Intelligence and Security, CIS 2007, p 182-185, 2007.

Chinese book & chapter:
[1] 陈洛南, 曾涛. 2.13 大数据时代的生物信息学与系统生物学新进展. 中国科学院《2016科学发展报告》, ISBN：978-7-03-048895-4.

Softwares:

♥ MCentridFS (Multi-class Centroid Feature Selection): supply a tool for the optimal module analysis on the biological active network

♥ PMNminer (Progressive module network analysis): supply a computational framework for the cross-tissue analysis on the phenotype-dynamics of biological process (e.g. disease occurance and progression)

♥ IEApackage (Integrative enrichment analysis): supply a software package for the functional enrichment analysis on the heterogeneous samples

♥ PFA (Pattern fusion analysis): supply an integrative tool to identify sample-patterns from different omics profiles by optimally adjusting the effects of each data type to the hidden patterns.

♥ CNS (Comparative Network Stratification): supply a computational methods to directly identify functional network biomarkers with both discriminative power on disease states and readable interpretation on biological functions.

♥ DFApackage (Differential function analysis): supply a general framework to identify the changes of element-structure and expression-activation of biological functions, based on comparative non-negative matrix factorization (cNMF).

♥ SCS (Single-sample Controller Strategy): supply a new single-sample controller strategy (SCS) to identify personalized driver mutation profiles from network controllability perspective.

♥ eTMpy (Endogenous target mimic (eTMs) screen package): supply a python script for screening the endogenous target mimic in plant.

Photos: