Xia Yang*

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. 2022 01; 65(1):173-187. view on PubMed

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. Fam Cancer. 2022 07; 21(3):347-355. view on PubMed

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 Res. 2021 07 02; 49(W1):W375-W387. view on PubMed

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. Nat Commun. 2021 06 25; 12(1):3958. view on PubMed

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. Mol Syst Biol. 2021 06; 17(6):e10108. view on PubMed

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 Epidemiol Biomarkers Prev. 2021 07; 30(7):1397-1407. view on PubMed

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. Am J Respir Crit Care Med. 2021 04 15; 203(8):1006-1022. view on PubMed

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. Transl Psychiatry. 2021 03 31; 11(1):194. view on PubMed

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 03 01; 10. view on PubMed

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 05; 69(5):1281-1291. view on PubMed

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. J Lipid Res. 2021; 62:100019. view on PubMed

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. Environ Int. 2021 01; 146:106260. view on PubMed

Arneson D, Yang X, Wang K. MethylResolver-a method for deconvoluting bulk DNA methylation profiles into known and unknown cell contents. Commun Biol. 2020 08 03; 3(1):422. view on PubMed

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. 2020 09; 76(3):985-996. view on PubMed

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 J. 2020 08; 34(8):9982-9994. view on PubMed

Yang X. Multitissue Multiomics Systems Biology to Dissect Complex Diseases. Trends Mol Med. 2020 08; 26(8):718-728. view on PubMed

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. Neurobiol Dis. 2020 07; 141:104877. view on PubMed

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. Mol Cell Biol. 2020 03 30; 40(8). view on PubMed

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. Nat Metab. 2019 11; 1(11):1089-1100. view on PubMed

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. Biochim Biophys Acta Mol Basis Dis. 2020 01 01; 1866(1):165569. view on PubMed

Seldin M, Yang X, Lusis AJ. Systems genetics applications in metabolism research. Nat Metab. 2019 11; 1(11):1038-1050. view on PubMed

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. Arch Biochem Biophys. 2019 12 15; 678:108116. view on PubMed

Rege SD, Royes L, Tsai B, Zhang G, Yang X, Gomez-Pinilla F. Brain Trauma Disrupts Hepatic Lipid Metabolism: Blame It on Fructose? Mol Nutr Food Res. 2019 08; 63(15):e1801054. view on PubMed

Zhao Y, Jhamb D, Shu L, Arneson D, Rajpal DK, Yang X. Multi-omics integration reveals molecular networks and regulators of psoriasis. BMC Syst Biol. 2019 01 14; 13(1):8. view on PubMed

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. Biol Sex Differ. 2018 10 22; 9(1):46. view on PubMed

Ying Z, Byun HR, Meng Q, Noble E, Zhang G, Yang X, Gomez-Pinilla F. Biglycan gene connects metabolic dysfunction with brain disorder. Biochim Biophys Acta Mol Basis Dis. 2018 12; 1864(12):3679-3687. view on PubMed

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. Nat Commun. 2018 09 25; 9(1):3894. view on PubMed

Gomez-Pinilla F, Yang X. System biology approach intersecting diet and cell metabolism with pathogenesis of brain disorders. Prog Neurobiol. 2018 10; 169:76-90. view on PubMed

Arneson D, Zhang Y, Yang X, Narayanan M. Shared mechanisms among neurodegenerative diseases: from genetic factors to gene networks. J Genet. 2018 Jul; 97(3):795-806. view on PubMed

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 Rep. 2018 05 22; 23(8):2392-2404. view on PubMed

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 Syst. 2018 Jan 24; 6(1):103-115.e7. view on PubMed

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 Res. 2017 03 17; 19(1):31. view on PubMed

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 Feb; 16:184-194. view on PubMed

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 Metab. 2017 02 07; 25(2):248-261. view on PubMed

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 11 04; 17(1):874. view on PubMed

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 09 09; 17(1):722. view on PubMed

Zhao Y, Forst CV, Sayegh CE, Wang IM, Yang X, Zhang B. Molecular and genetic inflammation networks in major human diseases. Mol Biosyst. 2016 07 19; 12(8):2318-41. view on PubMed

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 May; 7:157-66. view on PubMed

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. Arterioscler Thromb Vasc Biol. 2016 05; 36(5):928-41. view on PubMed

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. Arterioscler Thromb Vasc Biol. 2015 Oct; 35(10):2207-17. view on PubMed

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. Mol Syst Biol. 2015 Apr 16; 11(1):799. view on PubMed

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 Feb 14; 16:88. view on PubMed

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. Arterioscler Thromb Vasc Biol. 2015 Apr; 35(4):1011-21. view on PubMed

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. Circ Cardiovasc Genet. 2014 Dec; 7(6):911-9. view on PubMed

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 Epidemiol Biomarkers Prev. 2014 Jun; 23(6):1121-4. view on PubMed

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 May; 9(5):685-92. view on PubMed

Meng Q, Mäkinen VP, Luk H, Yang X. Systems Biology Approaches and Applications in Obesity, Diabetes, and Cardiovascular Diseases. Curr Cardiovasc Risk Rep. 2013 Feb; 7(1):73-83. view on PubMed

Yang X, Zhang B, Zhu J. Functional genomics- and network-driven systems biology approaches for pharmacogenomics and toxicogenomics. Curr Drug Metab. 2012 Sep 01; 13(7):952-67. view on PubMed

Yang X. Use of functional genomics to identify candidate genes underlying human genetic association studies of vascular diseases. Arterioscler Thromb Vasc Biol. 2012 Feb; 32(2):216-22. view on PubMed

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. Fam Cancer. 2010 Dec; 9(4):625-33. view on PubMed

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. Int J Cancer. 2009 Dec 15; 125(12):2912-7. view on PubMed

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. Hum Immunol. 2009 Nov; 70(11):910-4. view on PubMed

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. 2007 May; 18(4):439-47. view on PubMed

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. Diagn Mol Pathol. 2006 Sep; 15(3):157-61. view on PubMed

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. Pharmacogenet Genomics. 2006 Aug; 16(8):547-53. view on PubMed

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 Genet. 2005 Dec 30; 6 Suppl 1:S102. view on PubMed

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 Genet. 2005 Dec 30; 6 Suppl 1:S14. view on PubMed

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 Epidemiol Biomarkers Prev. 2005 Apr; 14(4):900-5. view on PubMed

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 Genet. 2003 Dec 31; 4 Suppl 1:S101. view on PubMed