office: 2000D Terasaki building
research interests: Integrative genomics and systems biology of common metabolic diseases
Common metabolic disorders such as coronary artery disease, diabetes, and obesity represent top health concerns worldwide. These diseases are not only highly interconnected but also linked to various other diseases such as cancers and neurodegenerative diseases. We hypothesize that the complex interactions between genetic and environmental risk factors perturb specific gene networks which in turn induce variations in disease susceptibility and therapeutic response. Research in our lab employs integrative genomics and systems biology approaches that leverage various large-scale molecular datasets, such as genome-wide genetic, transcriptional, epigenomic, and relevant phenotypic data from human and rodent populations to identify causal molecular alterations and the subsequently perturbed molecular networks that contribute to the development of obesity, diabetes, and cardiovascular diseases. The candidate causal components and networks identified will serve as the basis for therapeutic target and biomarker discovery as well as for patient stratification with respect to clinical outcome or pharmacological response.
Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco, LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Makinen VP, Yang X, "Mergeomics: Integration of Diverse Genomics Resources to Identify Pathogenic Perturbations to Biological Systems", BMC Genomics, 17 : 874- (2016) [link].
Arneson D, Bhattacharya A, Shu L, Makinen VP, Yang X, "Mergeomics: A Web Server for Identifying Pathological Pathways, Networks, and Key Regulators via Multidimensional Data Integration", BMC Genomics, 17 : 722- (2016) [link].
Chen Y, Shu L, Qiu Z, Lee DY, Settle S, Hee SQ, Telesca D, Yang X, Allard P, "Exposure to the BPA-Substitute Bisphenol S Causes Unique Alterations of Germline Function", PLOS Genetics, 12 (7): e1006223- (2016) [link].
Meng Q, Ying Z, Noble E, Zhao Y, Agrawal R, Mikhail A, Zhuang Y, Tyagi E, Zhang Q, Lee JH, Morselli M, Orozco L, Guo Q, Kilts TM, Zhu J, Zhang B, Pellegrini M, Xiao X, Young MF, Gomez-Pinilla F, Yang X., "Systems Nutrigenomics Reveals Brain Gene Networks Linking Metabolic and Brain Disorders", EBioMedicine, 7 : 157-166 (2016) [link].
Zhao Y, Chen J, Freudenberg JM, Meng Q, CARDIoGRAM Consortium, Rajpal DK, Yang X., "Network-based Identification and Prioritization of Key Regulators of Coronary Artery Disease Loci", Arteriosclerosis, Thrombosis, and Vascular Biology, 36 : 928-941 (2016) [link].
Zhao, Y., Barrere-Cain, R., and Yang, X., "Nutritional Systems Biology of Type 2 Diabetes", Genes & Nutrition, 10 : 31- (2015) [link].
Huan T, Meng Q, Saleh MA, Norlander AE, Joehanes R, Zhu J, Chen BH, Zhang B, Johnson AD, Ying S, Courchesne P, Raghavachari N, Wang R, Liu P, International Consortium for Blood Pressure GWAS (ICBP), O'Donnell CJ, Vasan R, Munson PJ, Madhur MS, Harrison DG, Yang X*, Levy D*., "Integrative network analysis reveals molecular mechanisms of blood pressure regulation", Molecular Systems Biology, 11 : 799- (2015) [link].
Huan T, Rong J, Tanriverdi K, Meng Q, Bhattacharya A, McManus D, Joehanes R, Assimes TL, McPherson R, Samani NJ, Erdmann J, Schunkert H, Coronary ARteryDIsease Genome wide Replication and Meta-analysis (CARDIoGRAM) Consortium, Courchesne P, Munson PJ, Johnson AD, O'Donnell CJ, Zhang B, Larson MG, Freedman JE*, Levy D*, Yang X*., "Dissecting the Roles of microRNAs in Coronary Heart Disease via Integrative Genomics Analyses", Arteriosclerosis, Thrombosis, and Vascular Biology, 35 (4): 1011-1021 (2015) [link].
Huan T, Esko T, Peters MJ, Pilling LC, Schramm K, Schurmann C, et al., Yang X*, Prokisch H*, Volker U*, van Meurs JBJ*, Ferrucci L*, Levy D*, "A Meta-analysis of Gene Expression Signatures of Blood Pressure and Hypertension", PLOS Genetics, 11 (3): e1005035- (2015) [link].
Makinen VP, Civelek M, Meng Q, Zhang B, Zhu J, Levian C, Huan T, Segre AV, Ghosh S, Vivar J, Nikpay M, Stewart AFR, Nelson CP, Willenborg C, Erdmann J, Blakenberg S, O'Donnell CJ, Marz W, Laaksonen R, Epstein SE, Kathiresan S, Shah SH, Hazen SL, Reilly MP,Muredach P,Cardio-gram Consortium, Lusis AJ, Samani NJ, Schunkert H, Quertermous T, McPherson R, Yang X*, Assimes T*, "Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease", PLOS Genetics, 10 (7): e1004502- (2014) [link].