Publications

• Blencowe M, Furterer A, Wang Q, Gao F, Rosenberger M, Pei L, Nomoto H, Mawla AM, Huising MO, Coppola G, Yang X, Butler PC, Gurlo T. IAPP-induced beta cell stress recapitulates the islet transcriptome in type 2 diabetes.. Diabetologia, 2021.
• Brown KM, Xu M, Sargen M, Jang H, Zhang M, Zhang T, Zhu B, Jones K, Kim J, Mendoza L, Hayward NK, Tucker MA, Goldstein AM, Yang XR, Stewart DR, Hicks B, Consonni D, Pesatori AC, Fargnoli MC, Peris K, Stratigos A, Menin C, Ghiorzo P, Puig S, Nagore E, MelaNostrum Consortium, Andresson T, Nussinov R, Calista D, Landi MT. Novel MAPK/AKT-impairing germline NRAS variant identified in a melanoma-prone family.. Familial cancer, 2021.
• Ding J, Blencowe M, Nghiem T, Ha SM, Chen YW, Li G, Yang X. Mergeomics 2.0: a web server for multi-omics data integration to elucidate disease networks and predict therapeutics.. Nucleic acids research, 2021.
• Li J, Pan L, Pembroke WG, Rexach JE, Godoy MI, Condro MC, Alvarado AG, Harteni M, Chen YW, Stiles L, Chen AY, Wanner IB, Yang X, Goldman SA, Geschwind DH, Kornblum HI, Zhang Y. Conservation and divergence of vulnerability and responses to stressors between human and mouse astrocytes.. Nature communications, 2021.
• Littman R, Hemminger Z, Foreman R, Arneson D, Zhang G, Gómez-Pinilla F, Yang X, Wollman R. Joint cell segmentation and cell type annotation for spatial transcriptomics.. Molecular systems biology, 2021.
• Abubakar M, Zhang J, Ahearn TU, Koka H, Guo C, Lawrence SM, Mutreja K, Figueroa JD, Ying J, Lissowska J, Lyu N, Garcia-Closas M, Yang XR. Tumor-Associated Stromal Cellular Density as a Predictor of Recurrence and Mortality in Breast Cancer: Results from Ethnically Diverse Study Populations.. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2021.
• Hong J, Arneson D, Umar S, Ruffenach G, Cunningham CM, Ahn IS, Diamante G, Bhetraratana M, Park JF, Said E, Huynh C, Le T, Medzikovic L, Humbert M, Soubrier F, Montani D, Girerd B, Trégouët DA, Channick R, Saggar R, Eghbali M, Yang X. Single-Cell Study of Two Rat Models of Pulmonary Arterial Hypertension Reveals Connections to Human Pathobiology and Drug Repositioning.. American journal of respiratory and critical care medicine, 2021.
• Noble EE, Olson CA, Davis E, Tsan L, Chen YW, Schade R, Liu C, Suarez A, Jones RB, de La Serre C, Yang X, Hsiao EY, Kanoski SE. Gut microbial taxa elevated by dietary sugar disrupt memory function.. Translational psychiatry, 2021.
• Zhang Z, Park JW, Ahn IS, Diamante G, Sivakumar N, Arneson D, Yang X, van Veen JE, Correa SM. Estrogen receptor alpha in the brain mediates tamoxifen-induced changes in physiology in mice.. eLife, 2021.
• van Weperen VYH, Littman RJ, Arneson DV, Contreras J, Yang X, Ajijola OA. Single-cell transcriptomic profiling of satellite glial cells in stellate ganglia reveals developmental and functional axial dynamics.. Glia, 2021.
• Blencowe M, Ahn IS, Saleem Z, Luk H, Cely I, Mäkinen VP, Zhao Y, Yang X. Gene networks and pathways for plasma lipid traits via multitissue multiomics systems analysis.. Journal of lipid research, 2021.
• Diamante G, Cely I, Zamora Z, Ding J, Blencowe M, Lang J, Bline A, Singh M, Lusis AJ, Yang X. Systems toxicogenomics of prenatal low-dose BPA exposure on liver metabolic pathways, gut microbiota, and metabolic health in mice.. Environment international, 2020.
• Arneson D, Yang X, Wang K. MethylResolver-a method for deconvoluting bulk DNA methylation profiles into known and unknown cell contents.. Communications biology, 2020.
• Ruffenach G, O'Connor E, Vaillancourt M, Hong J, Cao N, Sarji S, Moazeni S, Papesh J, Grijalva V, Cunningham CM, Shu L, Chattopadhyay A, Tiwari S, Mercier O, Perros F, Umar S, Yang X, Gomes AV, Fogelman AM, Reddy ST, Eghbali M. Oral 15-Hydroxyeicosatetraenoic Acid Induces Pulmonary Hypertension in Mice by Triggering T Cell-Dependent Endothelial Cell Apoptosis.. Hypertension (Dallas, Tex. : 1979), 2020.
• Lau YCC, Ding JA, Simental A, Mirzoyan H, Lee W, Diamante G, Cely I, Tran M, Morselli M, Dang J, Kaczor-Urbanowicz KE, Sayre J, Stiles L, Yang X, Pellegrini M, Fiala M. Omega-3 fatty acids increase OXPHOS energy for immune therapy of Alzheimer disease patients.. FASEB journal : official publication of the Federation of American Societies for Experimental Biology, 2020.
• Yang X. Multitissue Multiomics Systems Biology to Dissect Complex Diseases.. Trends in molecular medicine, 2020.
• Liu W, Venugopal S, Majid S, Ahn IS, Diamante G, Hong J, Yang X, Chandler SH. Single-cell RNA-seq analysis of the brainstem of mutant SOD1 mice reveals perturbed cell types and pathways of amyotrophic lateral sclerosis.. Neurobiology of disease, 2020.
• Gao J, Littman R, Diamante G, Xiao X, Ahn IS, Yang X, Cole TA, Tontonoz P. Therapeutic IDOL Reduction Ameliorates Amyloidosis and Improves Cognitive Function in APP/PS1 Mice.. Molecular and cellular biology, 2020.
• Lee SD, Priest C, Bjursell M, Gao J, Arneson DV, Ahn IS, Diamante G, van Veen JE, Massa MG, Calkin AC, Kim J, Andersén H, Rajbhandari P, Porritt M, Carreras A, Ahnmark A, Seeliger F, Maxvall I, Eliasson P, Althage M, Åkerblad P, Lindén D, Cole TA, Lee R, Boyd H, Bohlooly-Y M, Correa SM, Yang X, Tontonoz P, Hong C. IDOL regulates systemic energy balance through control of neuronal VLDLR expression.. Nature metabolism, 2019.
• Zhang G, Byun HR, Ying Z, Blencowe M, Zhao Y, Hong J, Shu L, Chella Krishnan K, Gomez-Pinilla F, Yang X. Differential metabolic and multi-tissue transcriptomic responses to fructose consumption among genetically diverse mice.. Biochimica et biophysica acta. Molecular basis of disease, 2019.
• Seldin M, Yang X, Lusis AJ. Systems genetics applications in metabolism research.. Nature metabolism, 2019.
• Bhetraratana M, Orozco LD, Hong J, Diamante G, Majid S, Bennett BJ, Ahn IS, Yang X, Lusis AJ, Araujo JA. Diesel exhaust particles dysregulate multiple immunological pathways in murine macrophages: Lessons from microarray and scRNA-seq technologies.. Archives of biochemistry and biophysics, 2019.
• Rege SD, Royes L, Tsai B, Zhang G, Yang X, Gomez-Pinilla F. Brain Trauma Disrupts Hepatic Lipid Metabolism: Blame It on Fructose?. Molecular nutrition & food research, 2019.
• Zhao Y, Jhamb D, Shu L, Arneson D, Rajpal DK, Yang X. Multi-omics integration reveals molecular networks and regulators of psoriasis.. BMC systems biology, 2019.
• Kurt Z, Barrere-Cain R, LaGuardia J, Mehrabian M, Pan C, Hui ST, Norheim F, Zhou Z, Hasin Y, Lusis AJ, Yang X. Tissue-specific pathways and networks underlying sexual dimorphism in non-alcoholic fatty liver disease.. Biology of sex differences, 2018.
• Ying Z, Byun HR, Meng Q, Noble E, Zhang G, Yang X, Gomez-Pinilla F. Biglycan gene connects metabolic dysfunction with brain disorder.. Biochimica et biophysica acta. Molecular basis of disease, 2018.
• Arneson D, Zhang G, Ying Z, Zhuang Y, Byun HR, Ahn IS, Gomez-Pinilla F, Yang X. Single cell molecular alterations reveal target cells and pathways of concussive brain injury.. Nature communications, 2018.
• Gomez-Pinilla F, Yang X. System biology approach intersecting diet and cell metabolism with pathogenesis of brain disorders.. Progress in neurobiology, 2018.
• Arneson D, Zhang Y, Yang X, Narayanan M. Shared mechanisms among neurodegenerative diseases: from genetic factors to gene networks.. Journal of genetics, 2018.
• Camacho J, Truong L, Kurt Z, Chen YW, Morselli M, Gutierrez G, Pellegrini M, Yang X, Allard P. The Memory of Environmental Chemical Exposure in C. elegans Is Dependent on the Jumonji Demethylases jmjd-2 and jmjd-3/utx-1.. Cell reports, 2018.
• Chella Krishnan K, Kurt Z, Barrere-Cain R, Sabir S, Das A, Floyd R, Vergnes L, Zhao Y, Che N, Charugundla S, Qi H, Zhou Z, Meng Y, Pan C, Seldin MM, Norheim F, Hui S, Reue K, Lusis AJ, Yang X. Integration of Multi-omics Data from Mouse Diversity Panel Highlights Mitochondrial Dysfunction in Non-alcoholic Fatty Liver Disease.. Cell systems, 2018.
• Li M, Tse LA, Chan WC, Kwok CH, Leung SL, Wu C, Yu WC, Lee PM, Tsang KH, Law SH, Vermeulen R, Gu F, Caporaso NE, Yu IT, Wang F, Yang XR. Nighttime eating and breast cancer among Chinese women in Hong Kong.. Breast cancer research : BCR, 2017.
• Meng Q, Zhuang Y, Ying Z, Agrawal R, Yang X, Gomez-Pinilla F. Traumatic Brain Injury Induces Genome-Wide Transcriptomic, Methylomic, and Network Perturbations in Brain and Blood Predicting Neurological Disorders.. EBioMedicine, 2017.
• von Scheidt M, Zhao Y, Kurt Z, Pan C, Zeng L, Yang X, Schunkert H, Lusis AJ. Applications and Limitations of Mouse Models for Understanding Human Atherosclerosis.. Cell metabolism, 2016.
• Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Mäkinen VP, Yang X. Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems.. BMC genomics, 2016.
• Arneson D, Bhattacharya A, Shu L, Mäkinen VP, Yang X. Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration.. BMC genomics, 2016.
• Zhao Y, Forst CV, Sayegh CE, Wang IM, Yang X, Zhang B. Molecular and genetic inflammation networks in major human diseases.. Molecular bioSystems, 2016.
• 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 W, 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, 2016.
• Zhao Y, Chen J, Freudenberg JM, Meng Q, Rajpal DK, Yang X. Network-Based Identification and Prioritization of Key Regulators of Coronary Artery Disease Loci.. Arteriosclerosis, thrombosis, and vascular biology, 2016.
• Brænne I, Civelek M, Vilne B, Di Narzo A, Johnson AD, Zhao Y, Reiz B, Codoni V, Webb TR, Foroughi Asl H, Hamby SE, Zeng L, Trégouët DA, Hao K, Topol EJ, Schadt EE, Yang X, Samani NJ, Björkegren JL, Erdmann J, Schunkert H, Lusis AJ, Leducq Consortium CAD Genomics‡. Prediction of Causal Candidate Genes in Coronary Artery Disease Loci.. Arteriosclerosis, thrombosis, and vascular biology, 2015.
• 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, 2015.
• Zhu J, Chen C, Yang B, Guo Y, Ai H, Ren J, Peng Z, Tu Z, Yang X, Meng Q, Friend S, Huang L. A systems genetics study of swine illustrates mechanisms underlying human phenotypic traits.. BMC genomics, 2015.
• Huan T, Rong J, Tanriverdi K, Meng Q, Bhattacharya A, McManus DD, Joehanes R, Assimes TL, McPherson R, Samani NJ, Erdmann J, Schunkert H, 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 genomic analyses.. Arteriosclerosis, thrombosis, and vascular biology, 2015.
• Chan KH, Huang YT, Meng Q, Wu C, Reiner A, Sobel EM, Tinker L, Lusis AJ, Yang X, Liu S. Shared molecular pathways and gene networks for cardiovascular disease and type 2 diabetes mellitus in women across diverse ethnicities.. Circulation. Cardiovascular genetics, 2014.
• Wu L, Goldstein AM, Yu K, Yang XR, Rabe KG, Arslan AA, Canzian F, Wolpin BM, Stolzenberg-Solomon R, Amundadottir LT, Petersen GM. Variants associated with susceptibility to pancreatic cancer and melanoma do not reciprocally affect risk.. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2014.
• Hyland PL, Burke LS, Pfeiffer RM, Rotunno M, Sun D, Patil P, Wu X, Tucker MA, Goldstein AM, Yang XR. Constitutional promoter methylation and risk of familial melanoma.. Epigenetics, 2014.
• Meng Q, Mäkinen VP, Luk H, Yang X. Systems Biology Approaches and Applications in Obesity, Diabetes, and Cardiovascular Diseases.. Current cardiovascular risk reports, 2012.
• Yang X, Zhang B, Zhu J. Functional genomics- and network-driven systems biology approaches for pharmacogenomics and toxicogenomics.. Current drug metabolism, 2012.
• Yang X. Use of functional genomics to identify candidate genes underlying human genetic association studies of vascular diseases.. Arteriosclerosis, thrombosis, and vascular biology, 2012.
• Yang XR, Liang X, Pfeiffer RM, Wheeler W, Maeder D, Burdette L, Yeager M, Chanock S, Tucker MA, Goldstein AM. Associations of 9p21 variants with cutaneous malignant melanoma, nevi, and pigmentation phenotypes in melanoma-prone families with and without CDKN2A mutations.. Familial cancer, 2010.
• Yang XR, Pfeiffer RM, Wheeler W, Yeager M, Chanock S, Tucker MA, Goldstein AM. Identification of modifier genes for cutaneous malignant melanoma in melanoma-prone families with and without CDKN2A mutations.. International journal of cancer, 2009.
• Yu KJ, Gao X, Chen CJ, Yang XR, Diehl SR, Goldstein A, Hsu WL, Liang XS, Marti D, Liu MY, Chen JY, Carrington M, Hildesheim A. Association of human leukocyte antigens with nasopharyngeal carcinoma in high-risk multiplex families in Taiwan.. Human immunology, 2009.
• Anderson WF, Matsuno RK, Sherman ME, Lissowska J, Gail MH, Brinton LA, Yang XR, Peplonska B, Chen BE, Rosenberg PS, Chatterjee N, Szeszenia-Dabrowska N, Bardin-Mikolajczak A, Zatonski W, Devesa SS, García-Closas M. Estimating age-specific breast cancer risks: a descriptive tool to identify age interactions.. Cancer causes & control : CCC, 2007.
• Yang XR, Charette LA, Garcia-Closas M, Lissowska J, Paal E, Sidawy M, Hewitt SM, Rimm DL, Sherman ME. Construction and validation of tissue microarrays of ductal carcinoma in situ and terminal duct lobular units associated with invasive breast carcinoma.. Diagnostic molecular pathology : the American journal of surgical pathology, part B, 2006.
• Gaudet MM, Chanock S, Lissowska J, Berndt SI, Yang XR, Peplonska B, Brinton LA, Welch R, Yeager M, Bardin-Mikolajczak A, Sherman ME, Sutter TR, Garcia-Closas M. Genetic variation of Cytochrome P450 1B1 (CYP1B1) and risk of breast cancer among Polish women.. Pharmacogenetics and genomics, 2006.
• Kerstann KF, Jacobs K, Yang XR, Bergen AW, Goldin LR, Goldstein AM. Identification of susceptibility loci for complex diseases in a case-control association study using the Genetic Analysis Workshop 14 dataset.. BMC genetics, 2005.
• Yang XR, Jacobs K, Kerstann KF, Bergen AW, Goldstein AM, Goldin LR. Linkage analysis of the GAW14 simulated dataset with microsatellite and single-nucleotide polymorphism markers in large pedigrees.. BMC genetics, 2005.
• Yang XR, Diehl S, Pfeiffer R, Chen CJ, Hsu WL, Dosemeci M, Cheng YJ, Sun B, Goldstein AM, Hildesheim A, Chinese and American Genetic Epidemiology of NPC Study Team. Evaluation of risk factors for nasopharyngeal carcinoma in high-risk nasopharyngeal carcinoma families in Taiwan.. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology, 2005.
• Bergen AW, Yang XR, Bai Y, Beerman MB, Goldstein AM, Goldin LR, Framingham Heart Study. Genomic regions linked to alcohol consumption in the Framingham Heart Study.. BMC genetics, 2003.