Introduction
We are a group in the CAS Key Laboratory of Genomic and Precision Medicine at Beijing Institute of Genomics, Chinese Academy of Sciences. Our research focuses on developing computational approaches for genetics and genomics studies and fine mapping genetic variants and genes associated with human complex diseases. We are particularly interested in Artificial intelligence (AI) approaches in analyzing biological data. Our research focuses on the following areas.
1. Developing machine learning and deep learning approaches to decode and interpret the functions of genetic variants associated with diseases.
2. Developing approaches of network medicine to integrate multi-omics data and to understand the genetic architectures underlying human complex diseases.
3. Cancer bioinformatics. Using pan-cancer omics data as well as single-cell RNA-sequencing data, we develop and apply approaches to understand the driving forces in tumorigenesis and to identify driver mutations, genes, and pathways in cancer.
Group leader
Dr. JIA Peilin, Principal Investigator at Beijing Institute of Genomics, obtained her Ph.D. degree of bioinformatics from Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, in 2008. She received her postdoctoral training in Virginia CommonWealth University and Vanderbilt University. Her research focuses on two major directions: (1) genetic and genomic studies of psychiatric diseases and (2) integrative studies of cancer omics data. She has developed various computational methods and tools to help interpret and prioritize causal variants and genes underlying human complex diseases such as dmGWAS, gamGWAS, EW_dmGWAS, VarWalker, MSEA, CNet, SZGR, deTS, TSEA-DB, CSEA-DB, and DeepFun.
Selected Publications
1. Pei G, Hu R, Dai Y, Manuel AM, Zhao Z*, Jia P* (accepted) Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations. Nucleic Acids Research
2. Dai Y, Hu R, Manuel AM, Liu A, Jia P*, Zhao Z* (accepted) CSEA-DB: An omnibus for human complex trait and cell type associations. Nucleic Acids Research
3. Pei G, Hu R, Dai Y, Zhao Z*, Jia P* (2020) Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network. Oncogene 39:5031-5041. PMCID: PMC7334101
4. Jia P, Dai Y, Hu R, Pei G, Manuel A, Zhao Z (2020) TSEA-DB: A trait-tissue association map for human complex traits and diseases. Nucleic Acids Research 48(D1):D1022-D1030
5. Jia P, Pei G, Zhao Z (2019) CNet: A multi-omics approach to detecting clinically associated, combinatory genomic signatures. Bioinformatics 35(24):5207-5215
6. Pei G, Dai, Y, Zhao Z*, Jia P* (2019) deTS: tissue-specific enrichment analysis to decode tissue specificity. Bioinformatics 35(19):3842-3845
7. Huang Y, Wang J, Jia P, Li X, Pei G, Wang C, Fang X, Zhao Z, Cai Z, Yi X, Wu S, Zhang B (2019) Clonal architectures predict clinical outcome in clear cell renal cell carcinoma. Nature Communications 10(1):1245
8. Jia P, Zhao Z (2019) Characterization of tumor-suppressor gene inactivation events in 33 cancer types. Cell Reports 26:496-506
9. Jia P, Chen X, Xie W, Kendler KS, Zhao Z (2019) Mega-analysis of Odds Ratio (MegaOR): A convergent method for deep understanding the genetic evidence in schizophrenia. Schizophrenia Bulletin 45(3), 698-708
10. Jia P, Chen X, Fanous AH, Zhao Z (2018) Convergent roles of de novo mutations and common variants in schizophrenia in tissue-specific and spatiotemporal co-expression network. Translational Psychiatry 8(1):105
11. Jia P, Zhao Z (2016) Impacts of somatic mutations on gene expression: an association perspective. Briefings in Bioinformatics 18(3):413-425
12. Jia P, Han G, Zhao J, Lu P, Zhao Z (2017) SZGR2.0: a one-stop shop of schizophrenia-associated genes. Nucleic Acids Research 45(D1):D915-D924
13. Jia P, Zhao Z, Hulgan T, Bush W, Samuels DC, Bloss C, Heaton R, Ellis R, Schork N, Marra C, Collier AC, Clifford D, Gelman B, Sacktor N, Morgello S, Simpson D, McCutchan JA, Letendre S, Barnholtz-Sloan J, Franklin DR, and Grant I for the CHARTER Study Group, Kallianpur, AR (2017) Genome-wide association study of HIV-Associated Neurocognitive Disorder (HAND): a CHARTER Group Study. American Journal of Medical Genetics, 174(4):413-426
14. McGirt LY#, Jia P#, Baerenwald DA, Dahlman K, Zic JA, Zwerner JP, Hucks D, Dave U, Zhao Z, Eischen CM (2015) Whole genome analysis reveals oncogenic alterations in mycosis fungoides. Blood 126(4): 508-519
15. Wang Q, Yu H, Zhao Z*, Jia P* (2015) EW_dmGWAS: Edge-Weighted dense module search for genome-wide association studies and gene expression profiles. Bioinformatics, 31, 2591-2594
16. Jia P, Wang Q, Chen Q, Hutchinson K, Pao W, Zhao Z (2014) MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis. Genome Biology 15:489 (editors’ pick)
17. Jia P, Jin H, Meador CB, Xia J, Ohashi K, Liu L, Pirazzoli V, Dahlman KB, Politi K, Michor F, Zhao Z, Pao W (2013) Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance. Genome Research 23:1434-1445
18. Jia P, Wang L, Fanous, AH, Pato CN, Edwards TL, The International Schizophrenia Consortium, Zhao Z (2012) Network-assisted investigation of combined causal signals from genome-wide association studies in schizophrenia. PLoS Computational Biology 8(7): e1002587
19. Jia P#, Zheng S#, Long J, Zheng W, Zhao Z (2011) dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics. 27(1) 95-102
20. Jia P, Sun J, Guo AY, Zhao Z (2010) SZGR: A comprehensive schizophrenia gene resource. Molecular Psychiatry 15:453-462
Awards and Honors
2011 2010 NARSAD Young Investigator Award (2011-2013), National Alliance for Research on Schizophrenia and Depression
2011 Finalist, the 2010/2011 Vanderbilt Postdoc of the Year Award
