*Co-corresponding author
+Equal contribution
Lab member
Preprints
Blencowe M*, Saleem Z, Liu R, Tseng I, Wier J, Yang X*. Multitissue Multiomics Integration Reveals Tissue-Specific Pathways, Gene Networks, and Drug Candidates for Type 1 Diabetes. [BioRxiv link]
Fuqua BK, Moses L, McLachlan S, Pan C, Davis RC, Hui ST, Che N, Zhou Z, Ng C, Charugundla S, Blencowe M, Saleem Z,…, Yang X, Eskin E, Vulpe CD, Lusis AJ. The Genetic Architecture of Dietary Iron Overload and Associated Pathology in Mice. [bioRxiv link]
Ha S, Ahn IS, , ,,, , , Cross-tissue multiomics studies reveal gut-brain interactions mediating the effect of Akkermansia muciniphila in counteracting fructose-induced obesity. [bioRxiv link]
, , , , , , , , , , , ,, , , , , , , ,, BCAA catabolism drives adipogenesis via an intermediate metabolite and promotes subcutaneous adipose tissue expansion during obesity. [bioRxiv link]
Published/Accepted
2024
Wang G+, Li G+, Song A, Zhao Y, Yu J, Dai W, Salas M, Qin H, Medrano L, Dow J, Li A, Brown L, Armstrong B, Fueger PT, Yu H, Zhu Y, Shao M, Wu X, Jiang L, Dang W, Campisi J, Yang X, Wang Q. Distinct Adipose Progenitor Cells Emerging with Age Drive Adipogenesis. Science, accepted.
Raval K, Jamshidi N, Seyran B, Salwinski L, Pillai R, Yang L, Ma F, Pellegrini M, Shin J, Yang X, Tudzarova S. Dysfunctional β-cell longevity in diabetes relies on high energy conservation and positive epistasis. Life Science Alliances, accepted.
Brownstein A, Mura M, Ruffenach G, Channick R, Saggar R, Kim A, Umar S, Eghbali M, Yang X, Hong J. Dissecting the Lung Transcriptome of Pulmonary Fibrosis-associated Pulmonary Hypertension. American Journal of Physiology-Lung Cellular and Molecular Physiology, online ahead of print, 2024.
Hong J, Medzikovic L, Sun W, Wong B, Ruffenach G, Rhodes C, Brownstein A, Liang L, Aryan L, Li M, Vadgama A, Kurt Z, Schwantes-An TH, Mickler E, Gräf S, Eyries M, Lutz K, Pauciulo M, Trembath R, Perros, Montani D, Morrell N, Soubrier F, Wilkins M, Nichols W, Aldred M, Desai A, Tregouet DA, Umar S, Saggar R, Channick R, Tuder R, Geraci M, Stearman R, Yang X, EghbaliM. Integrative Multiomics in the Lung Reveals a Protective Role of Asporin in Pulmonary Arterial Hypertension. Circulation, accepted.
Zhang G, Diamante G, Ahn IS, Palafox-Sanchez V, Cheng J, Cheng M, Ying; Z, Wang SS; Abuhanna KD, Phi N, Arneson D, Cely I, Arellano K, Wang N, Zhang S, Peng C, Gomez-Pinilla F, Yang, X. Thyroid Hormone T4 Mitigates Traumatic Brain Injury in Mice by Dynamically Remodeling Cell Type Specific Genes, Pathways, and Networks in Hippocampus and Frontal Cortex. BBA – Molecular Mechanisms of Disease, advanced online. [link]
Bhetraratana M, Orozco L, Bennet B, Karla L, Yang X, Lusis AJ, Araujo J. Diesel exhaust particle extract elicits an oxPAPC-like transcriptomic profile in macrophages across multiple mouse strains. Environment Pollution 358:124415. [link]
Gurlo T, Liu R, Wang Z, Hoang J, Ryazantsev S, Daval M, Butler AE, Yang X, Blencowe M*, Butler PC*. Dysregulation of cholesterol homeostasis is an early signal of beta cell proteotoxicity characteristic of type 2 diabetes. Physiological Genomics [link]
Diamante G+, Ha S+, Wijaya D, Yang X. Single Cell Multiomics Systems Biology in Molecular Toxicology. Current Opinion in Toxicology, 100477. [link]
Thapak P, Ying Z, Palafox-Sanchez V, Zhang G, Yang X, Gómez-Pinilla F. Humanin ameliorates TBI-related cognitive impairment by attenuating mitochondrial dysfunction and inflammation. BBA – Molecular Mechanisms of Disease, 1870 (2): 166937. [link]
Zamora Z, Wang S, Chen YW, Diamante G*, Yang X*. Systematic Transcriptome-wide Meta-Analysis across Endocrine Disrupting Chemicals Reveals Shared and Unique Liver Pathways, Gene Networks, and Disease Associations. Environment International, 183, 108339. [link]
2023
Levenson MT, Barrere-Cain R, Truong L, Chen Y-W, Shuck K, Panter B, E, Reich E, Yang X, Allard P. Protocol for nuclear dissociation of the adult C. elegans for single-nucleus RNA sequencing and its application for mapping environmental responses. STAR Protocols, 4:102756. [link]
Cheng J+, Cheng M+, Lusis AJ*, Yang X*. Gene regulatory networks in coronary artery disease. Current Atherosclerosis Reports, 1-11. [link]
Verdikt R, Armstrong AA, Cheng J, Yang X, Allard P. Metabolic memory of Δ9-tetrahydrocannabinol exposure in pluripotent stem cells and primordial germ cells-like cells. eLife. [link]
Lum GR, Ha S, Olson CA, Blencowe M, Paramo J, Reyes B, Matsumoto J, Yang X, Hsiao EY. Ketogenic diet therapy for pediatric epilepsy is associated with alterations in the human gut microbiome that confer seizure resistance in mice. Cell Reports, 42 (12), 113521. [link]
Kurt Z, Cheng J, McQuillen C.N, Saleem Z, Hsu N, Jiang, N, Barrere-Cain R, Pan C, Franzen O, Koplev S,Wang, S., Bjorkegren J, Lusis AJ, Blencowe M, Yang X*. Shared and distinct pathways and networks genetically linked to coronary artery disease between human and mouse. elife. [link]
Hui S, Gong L, Swichkow C, Blencowe M, Kaminska D, Diamante G, Pan C, Dalsania M, French S, Magyar C, Pajukanta P, Pihlajamäki J, Boström K, Yang X, and Lusis A. Role of Matrix Gla Protein in Transforming Growth Factor-β Signaling and Non-Alcoholic Steatohepatitis in Mice. Cellular and Molecular Gastroenterology and Hepatology. Cell Mol Gastroenterol Hepatol, 16 (6), 943-960. [link]
Littman R, Cheng M, Wang N, Peng C, Yang X. SCING: Single Cell INtegrative Gene regulatory network inference elucidates robust, interpretable gene regulatory networks. iScience 26 (7): 107124. [link]
Moore TM, Lee S, Olsen T, Morselli M, Strumwasser AR, Lin AJ, Zhou Z, Abrishami A,…Ahn IS, Diamante G, Blencowe M, Yang X,…Lusis AJ, Hevener A. Conserved multitissue transcriptomic adaptations to exercise training in humans and mice. Cell Reports, 42(5), 112499. [link].
, Alvarsson A, , Duesman SJ, Centonze A, Hathaway E, , , , Cho CH, Talari NK, Rajbhandari AK, Goedeke L, Wang P, , Blanpain C, Chella , , , Mammary duct luminal epithelium controls adipocyte thermogenic programme. Nature, 620(7972):192-199. [link]
Adlam D, Berrandou TE, Georges A, Nelson CP, Giannoulatou E, Henry J, Ma L, Blencowe M,… Cheng J,… Yang X, Ganesh S, Olson T, Kovacic J, Graham R, Samani NJ, Bouatia-Naji N. Genome-wide association meta-analysis of spontaneous coronary artery dissection reveals common variants and genes related to artery integrity and tissue-mediated coagulation. Nature Genetics, 55(6), 964–972. [link]
Truong L+, Chen Y-W+, Barrere-Cain R, Shuck K, Xiao W, Levenson MT, da Veiga Beltrame E, Panter B, E, Reich E, Sternberg PW, Yang X, Allard P. Single-nucleus resolution mapping of the adult C. elegansand its application to elucidate inter- and trans-generational response to alcohol. Cell Reports, 42(6), 112535. [link]
Sharma S+, Littman R+, Tompkins J, Arneson D, Contreras J, Dajani A, Ang K, Tsanhani A, Sun X, Jay PY, Herzog H, Yang X, Ajijola OA. Tiered Sympathetic Control of Cardiac Function Revealed by Viral Tracing and Single Cell Transcriptome Profiling. eLife, 12, e86295.[link].
Venugopal S, Ghulam-Jhelani Z, Ahn IS, Yang X, Wiedau M, Simmons D, Chandler SH. Early deficits in GABA inhibition parallels an increase in L-type Ca2+ currents in the jaw motor neurons of SOD1G93A mouse model for ALS. Neurobiology of Disease. 177:155992, 2023. [link]
2022
Guma E, Beauchamp A, Liu S, Levitis E, Clasen L, Torres E, Blumenthal J, Lalonde F, Qiu L, Hrncir H, MacKenzie-Graham A, Yang X, Arnold A, Lerch J, and Raznahan A cross-species neuroimaging study of sex chromosome dosage effects on human and mouse brain anatomy. Journal of Neuroscience, 43(8), 1321–1333. [link]
Hong J*, Wong B, Huynh C, Tang B, Ruffenach G, Li M, Umar S, Yang X*, Eghbali M*. Tm4sf1-marked Endothelial Subpopulation Is Dysregulated in Pulmonary Arterial Hypertension. American Journal of Respiratory Cell & Molecular Biology, 68(4), 381–394. [link]
Li J+, Diamante G+, Ahn IS, Wijaya D, Wang X, Chang CH, Ha S, Immadisetty K, Meng H, Nel AE*, Yang X*, Tian X*. Determination of the Nanoparticle- and Cell-Specific Toxicological Mechanisms in 3D Liver Spheroids Using scRNAseq Analysis. Nano Today, 47, 101652. [link]
Tsan L, Chometton S, Zuo Y, Sun S, Hayes AMR, Klug ME, Bridi L, Lam R, Fodor A, Noble E, Yang X, Kanoski S, Schier L. Early life low-calorie sweetener consumption disrupts glucose regulation, sugar-motivated behavior, and memory function in rats. JCI Insights, 7(24), e167266, 2022 [link]
Blencowe M, Chen X, Zhao Y, Itoh Y, McQuillen CN, Han Y, Shou BL, McClusky R, Reue K, Arnold AP*, Yang X*. Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation. Genome Research, 32(5), 807-824, 2022 [link]
Chen Y-W+, Diamante G+, Ding J+, Nghiem TX, Ha S, Cohn P, Arneson D, Blencowe M, Garcia J, Zaghari N, Patel P, Yang J, Yang X. PharmOmics: A Species- and Tissue-specific Drug Signature Database and Online Tool for Drug Repurposing. iScience, 25(4):104052, 2022 [link]
Arneson D+, Zhang G+, Ahn IS, Ying Z, Diamante G, Cely I, Palafox-Sanchez V, Gomez-Pinilla F*, Yang X*. Systems spatiotemporal dynamics of traumatic brain injury at single cell resolution reveals humanin as a therapeutic target. Cellular and Molecular Life Sciences, 79(9):480, 2022 [link]
Zuo Y, Iemolo A, Montilla-Perez A, Li H, Yang X, Telese F. Chronic adolescent exposure to cannabis in mice leads to long-term sex-biased changes in gene expression networks across brain regions. Neuropsychopharmacology, 2022. [link]
He Q, Bennett AN, Liu J, Fan B, Han X, Cheng L, Chen Y, Yang X, Chan KHK. Exploring Lead Loci shared Between Schizophrenia and Cardiometabolic Traits. BMC Genomics 23:617, 2022. [link]
Zhang F, Yang X, Bao Z. Bioinformatics network analyses of growth differentiation factor 11. Open Life Sciences, 17 (1), 426-437, 2022. [link]
2021
Blencowe M, Yang X. Found in Translation – core network preservation across liver diseases and species. Cell Reports Medicine, 2:7, 2021. [link]
Zuo Y, Wei D, Zhu C, Naveed O, Hong W, Yang X. Unveiling the pathogenesis of psychiatric disorders using network models. Genes, 12(7):1101, 2021. [link]
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. 65, 173–187, 2021. [link].
Ahn IS, Yoon J, Diamante G, Cohn P, Jang C, Yang X. Disparate metabolomic responses to fructose consumption between different mouse strains and the role of gut microbiota. Metabolites, 11:342, 2021. [link]
Littman R, Hemminger Z, Foreman R, Arneson D, Zhang G, Gomez-Pinilla F, Yang X*, Wollman R*. JSTA: joint cell segmentation and cell type annotation for spatial transcriptomics. Molecular Systems Biology 17:e10108, 2021. [link]
Ding J+, Blencowe M+, Nghiem TX+, Ha S, Chen Y-W, 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 49: W375-387, 2021. [link]
Li J, Pan L, Godoy MI, Pembroke WG, Rexach JE, Condro MC, Alvarado AG, Harteni M, Chen Y-W, 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 12: 3958, 2021. [link]
Noble EE, Olson CA, Davis E, Tsan L, Chen Y-W, 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, 11:194, 2021. [link]
von Scheidt M+, Zhao Y+, Vallim Q, Che N, Franzén O, Kurt Z, Yamamoto M, Edwards PA, Ruusalepp A, Kovacic J, Björkegren JLM, Lusis AJ, Yang X, Schunkert H. The transcription factor MAFF regulates an atherosclerosis relevant gene network connecting inflammation and cholesterol metabolism. Circulation, 143:1809–1823, 2021. [link]
Zhang Z, Park JW, Ahn IS, Diamante G, Sivakumar N, Arneson D, Yang X, van Veen JE, Correa SM. Hypothalamic estrogen receptor alpha mediate key side effects of tamoxifen therapy in mice. eLife, 10:e63333, 2021. [link]
Van Weperen V, Littman R, Arneson D, Contreras J, Yang X, Ajijola O. Single-cell transcriptomic profiling of satellite glial cells in stellate ganglia reveals developmental and functional axial dynamics. Glia, 69(5):1281-1291, 2021. [link]
Blencowe M+, Ahn IS+, Saleem Z, Luk H, Cely I, Makinen VP, Zhao Y*, Yang X*. Gene networks and pathways for plasma lipid traits via multi-tissue multi-omics systems analysis. Journal of Lipid Research, 62: 100019, 2021. [link]
2020
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 146: 106260, 2020. [link]
Hong J, Arneson D, Umar S, Ruffenach G, Cunningham CM, Ahn IS, Diamante G, Bhetraratana M, Park JF, Said E, Huynh C, Le T, 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 203(8): 1006-1022, 2020, 2020. [link]
Haynes K, Yau C, Bild A, Laughney A, Morsut L, Yang X, Zaugg J, Hsu P, Pancaldi V, Iyer-Biswas S. How Has the Covid1-9 Pandemic Changed How You Will Approach Research and Lab Work in the Future? Cell Systems 11(6): 550-554, 2020. (Invited Voices) [link]
Zhang G, Meng Q, Blencowe M, Agrawal R, Gomez-Pinilla F, Yang X. Multi-tissue Multi-omics Nutrigenomics Indicates Context Specific Effects of DHA on Rat Brain. Molecular Nutrition and Food Research 64(23):2000788, 2020. [link]
Ahn IS, Lang J, Olsen C, Diamante G, Zhang G, Ying Z, Byun HR, Cely I, Ding J, Cohn P, Kurtz I, Gomez-Pinilla F, Lusis AJ, Hsiao E, Yang X. Host Genetic Background and Gut Microbiota Contribute to Differential Metabolic Responses to High Fructose Consumption in Mice. Journal of Nutrition 150(10): 2716-2728, 2020. [link]
Ruffenach G, O’Connor E, Vaillancourt M, Hong J, Cao N, Sarji S, Moazeni S, Papesh J, Grijalva V, Cunningham CM, Shu L, Tiwari S, Mercier O, Perros F, Umar S, Fogelman A, Yang X, Gomes AV, Reddy ST, Eghbali M. Oral 15-HETE Induces Pulmonary Hypertension in Mice by Triggering T-cell Dependent Endothelial Cell Apoptosis. Hypertension 76:985-996, 2020. [link]
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. The FASEB Journal 34(8): 9982-9994, 2020. [link]
Arneson D, Yang X, Wang K. MethylResolver – A Method for Deconvoluting Bulk Tissue DNA Methylation Profiles into Known and Unknown Cell Contents. Communications Biology, 3:422, 2020. [link]
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, 141: 104877, 2020. [link] [Data available at: GSE178693]
Yang X. Multi-tissue Multi-omics Systems Biology of Complex Diseases. Trends in Molecular Medicine, 26:718-728, 2020. [link]
Zhang G, Byun HR, Ying Z, Blencowe M, Zhao Y, Hong J, Shu L, Gomez-Pinilla F, Yang X. Differential Metabolic and Multi-tissue Transcriptomic Responses to Fructose Consumption among Genetically Diverse Mice. BBA – Molecular Basis of Disease, 1866: 165569, 2020. [link]
van Veen JE, Kammel LG, Bunda PC, Shum M, Reid MS, Park JW, Zhang Z, Massa MG, Arneson D, Hrncir H, Liesa M, Arnold AP, Yang X, Correa SM. Hypothalamic oestrogen receptor alpha establishes a sexually dimorphic regulatory node of energy expenditure. Nature Metabolism, 2:351-363, 2020. [link]
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.
Shi J, Lu J, Chen H, Wei C, Xu X, Li H, Bai Q, Xia F, Lam SM, Zhang H, Shi Y, Cao D, Chen L, Hui G, Yang X, Lu Y, Chen R, Zhang WJ. Liver ChREBP Protects Against Fructose-induced Glycogenic Hepatotoxicity by Regulating L-type Pyruvate Kinase. Diabetes, , 2020. [link]
2019
Blencowe M, Karunanayake T, Wier J, Hsu N, Yang X. Network Modeling Approaches and Applications to Unraveling Non-Alcoholic Fatty Liver Disease. Genes, 10(12), 966, 2019. [link]
Rajbhandari P+, Arneson D+, Feng AC, Ahn IS, Diamante G, Zaghari N, Thomas BJ, Vergnes L, Lee SD, Reue K, Smale ST, Yang X, Tontonoz P. Single Cell Analysis Reveals Immune Cell-Adipocyte Crosstalk Regulating the Transcription of Thermogenic Adipocytes. eLife, 8:e49501, 2019. [link]
Seldin M, Yang X, & Lusis A. J. Systems genetics applications in metabolism research. Nature Metabolism, 1: 1038–1050, 2019. [link]
Lee SD, Priest C, Bjursell M, Gao J, Arneson DV, Ahn IS, Diamante G, Calkin A, Kim J, Andersén H, Porritt M, Carreras A, Jörjesson J, Ahnmark A, Seeliger F, Maxvall I, Eliasson P, Althage M, Åkerblad P, Lindén D, Cole TA, Lee R, Boyd H, Bohlooly-Y M, Yang X, Tontonoz P. IDOL Regulates Systemic Energy Balance through Control of CNS VLDLR Expression. Nature Metabolism, 1: 1089–1100, 2019. [link]
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, 678: 108116, 2019. [link][limited free access]
Blencowe M, Arneson D, Ding J, Chen Y-W, Saleem Z, Yang X. Network Modeling of Single Cell Omics Data: Challenges, Opportunities, and Progresses. Emerging Topics in Life Sciences 3 (4): 379-398, 2019. [link]
Zhou M+, Shao J+, Wu C-Y+, Shu L+, Dong W, Liu Y, Chen M, Wynn RM, Wang J, Wang J, Gui W-J, Qi X, Lusis AJ, Li Z, Wang W, Ning G, Yang X, Chuang DT, Wang Y, Sun H. Targeting BCAA Catabolism to Treat Obesity-Associated Insulin Resistance. Diabetes, , 2019. [Link]
, , , , , , , , , Prenatal Bisphenol A Exposure in Mice Induces Multi-tissue Multi-omics Disruptions Linking to Cardiometabolic Disorders. Endocrinology 160: 409-429, 2019. [link]
Zhao Y, Jhamb D, Shu L, Arneson D, Rajpal D, Yang X. Multi-omics Integration Reveals Molecular Networks and Regulators of Psoriasis. BMC Systems Biology, 13:8, 2019. [link]
Zhao Y, Blencowe M, Shi X, Shu L, Levian C, Ahn IS, ICBP consortium, Kim SK, Huan T, Levy D, Yang X. Integrative Genomics Analysis Unravels Tissue-Specific Pathways, Networks, and Key Regulators of Blood Pressure Regulation. Frontiers in Cardiovascular Medicine, 6:21, 2019. [link]
Rege S, Royes L, Tsai B, Zhang G, Yang X, Gomez-Pinilla. Brain Trauma Disrupts Hepatic Lipid Metabolism: Blame It on Fructose? Molecular Nutrition and Food Research 63: 1801054, 2019. [link]
2018
Martin LJ, Meng Q, Blencowe M, Lagarrigue S, Xiao S, Pan C, Wier J, Temple WC, Devaskar SU, Lusis AJ, Yang X. Maternal High-protein and Low-protein Diets Perturb Hypothalamus and Liver Transcriptome and Metabolic Homeostasis in Adult Mouse Offspring. Frontiers in Genetics 9:642, 2018 [link]
, , , ,, , , Single Cell Molecular Alterations Reveal Target Cells and Pathways of Concussive Brain Injury. Nature Communications, 9:3894, 2018 [link]
News releases about the Arneson et al. study:
UCLA Newsroom, NIH, NINDS, Science Daily, MedicalXpress, EurekAlert!UCLA Health, ReliaWire, Technology, The Medical News, Technology Networks, Wellness Destination India, Asian News International/Gulf Daily News, ScienceCodex, Business Standard, The Health Site, News Medical, Times Now News
Ying Z, Byun HR, Meng Q, Noble E, Zhang G, Yang X*, Gomez-Pinilla F*. Biglycan Gene Connects Metabolic Dysfunction with Brain Disorder. BBA – Molecular Basis of Disease, 1864(12):3679-3687, 2018. [link]
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, 9:46, 2018. [link]
Biomedical Central features the Kurt et al. study: Do Sex Differences play a role in non-alcoholic fatty liver disease
Emilsson V, llkov M, Lamb JR, Finkel N, Gudmundsson EF, Pitts R, Hoover H, Jennings LL, Horman SR, Aspelund T, Shu L, Trifonov V, Gudmundsdottir V, Sigurdsson S, Manolescu A, Zhu J,Lesley SA, To J, Zhang J, Harris TB, Launer LJ, Zhang B, Eiriksdottir G, Yang X, Smith AV, Orth AP, Gudnason V. Coregulatory Networks of Human Serum Proteins Link Genetics to Disease. Science, 361:769-773, 2018 [link].
The Scientist features this proteomics study: Serum Survey Reveals Protein Patterns of Ill Health
Gomez-Pinilla F, Yang X. Systems Biology Approach Intersecting Diet and Cell Metabolism with Pathogenesis of Brain disorders. Progress in Neurobiology, 169: 76-90, 2018. [link]
Li H, Li Q, Zhang Y, Liu W, Gu B, Narumi T, Siu KL, Youn JY, Liu P, Yang X, Cai HL. Novel Treatment of Hypertension by Specifically Targeting E2F for the Restoration of Endothelial Dihydrofolate Reductase and eNOS Function Under Oxidative Stress. Hypertension, 73:179–189, 2018. [link]
Shu L, Blencowe M, Yang X. Translating GWAS Findings to Novel Therapeutic Targets for Coronary Artery Disease. Frontiers in Cardiovascular Medicine, 5:56, 2018. [link]
Hui S, Kurt Z, Tuominen L, Norheim F, Davis RC, Pan C, Dirks DL, Magyar CE, French SW, Krishnan KC, Sabir S, Campos-Pérez F, Sánchez NM, Macías-Kauffer L, León-Mimila P, Canizales-Quinteros S, Yang X, Beaven SW, Huertas-Vazquez A, Lusis AJ. The Genetic Architecture of Diet-induced Hepatic Fibrosis in Mice. Hepatology, 68: 2182-2196, 2018. [link]
Editorial by David A. Brenner in Hepatology: Of mice and men and NASH.
Plubell DL, Fenton AM, Wilmarth PA, Bergstrom P, Zhao Y, Minnier J, Heinecke JW, Yang X, Pamir N. Diet-independent proteome-wide alterations in adipose tissue link dendritic cells to 2-aminoadipoate associated insulin sensitivity. Scientific Reports, 8:11485, 2018. [link]
Hitzel J, Lee EJ, Zhang Y, Bibli S, Li X, Zukunft S, Pfluger B, Hu J, Schürmann C, Vasconez A, Oo J, Kratzer A, Kumar S, de Rezende F, Josipovic I, Thomas D, Giral H, Schreiber Y, Geisslinger G, Fork C, Yang X, Sigala F, Romanoski C, Kroll J, Jo H, Landmesser U, Lusis A, Namgaladze D, Fleming I, Leisegang MS, Zhu J, Brandes R. Oxidized phospholipids regulate amino acid metabolism through MTHFD2 to facilitate nucleotide release in endothelial cells. Nature Communications, 9:2292, 2018. [link]
Jones PD, Kaiser MA, Najafabadi MG,Koplev S, Zhao Y, Douglas G, Kyriakou T, Andrews S, Rajmohan R, Watkins H, Channon KM, Ye S, Yang X, Björkegren J, Samani NJ, Webb TR. The JCAD gene at the 10p11 coronary artery disease locus regulates Hippo signaling in endothelial cells. ATVB, 38:1711–1722, 2018. [link]
Arneson D, Zhang Y, Yang X*, Narayanan M*. Shared mechanisms among neurodegenerative diseases: from genetic factors to gene networks. Journal of Genetics 97: 795-806, 2018. [link]
The memory of environmental chemical exposure in C. elegans is dependent on the Jumonji demethylases jmjd-2 and jmjd-3/utx-1. Cell Reports 23:2392-2404, 2018. [link].
Batchu SN, Dugbartey JG, Wadosky KM, Mickelsen DM, Ko KA, Wood RW, Zhao Y, Yang X, Fowell DJ, Korshunov VA. Role of Innate Immunity in Development of Salt-dependent Hypertension: AXL, A Tyrosine Kinase Receptor the Key Regulator. American Journal of Pathology 188:1794-1806, 2018. [link].
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 6:1-13, 2018. [link][temporary free text link]
F1000Prime Recommended. Commentary on Chella Krishnan et al. study by Mardinoglu et al. in Cell Systems: Broad Views of Non-alcoholic Fatty Liver Disease
Shu L, Arneson D, Yang X. Bioinformatics Principles for Deciphering Cardiovascular Diseases. In: Vasan R., Sawyer, D.(eds.) The Encyclopedia of Cardiovascular Research and Medicine, vol.[1], pp. 273-292. Oxford: Elsevier. 2018 [Book chapter]
2017
Shu L, Chen KHK, Zhang G, Huan T, Kurt Z, Zhao Y, Codoni V, Tregouet DA, Yang J, Wilson JG, Luo X, Levy D, Lusis AJ, Liu S, Yang X. Shared genetic regulatory networks for cardiovascular disease and type 2 diabetes in multiple populations of diverse ethnicities in the United States. PLOS Genetics 3(9): e1007040, 2017. [link].
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 16:184-194, 2017. [link].
News coverage on Meng et al. study: UCLA Newsroom, University of California News, Science Daily, EurekAlert, UPI, UCLA Health, MSN, News Medical, MedicalExpress, TechTimes, MDmag, LaboratoryEquipment, Youtube, Healthcanal, iTechPost, Inquisitr, SF Gate; more at the publication site.
Arneson D+, Shu L+, Tsai B, Barrere-Cain R, Sun C, Yang X. Multi-dimensional Integrative Genomics Approaches to Dissecting Cardiovascular Disease. Frontiers in Cardiovascular Medicine 4:8, 2017. [link].
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 25: 248-261, 2017. [link].
Axelsson AS, Mahdi T, Nenonen HA, Singh T, Hänzelmann S, Wendt A, Bagge A, Reinbothe TM, Millstein J, Yang X, Zhang B, Gusmao EG, Shu L, Szabat M, Tang Y, Wang J, Salö S, Eliasson L, Artner I, Fex M, Johnson JD, Wollheim CB, Derry JMJ, Mecham B, Spégel P, Mulder H, Gesteira Costa Filho I, Zhang E, Rosengren AH. Sox5 Regulates Beta-cell Phenotype And Is Reduced in Type 2 Diabetes. Nature Communications. 8: 15652, 2017. [link]
Plubell DL, Wilmarch PA, Zhao Y, Fenton AM, Minnier J, Reddy AP, Klimek J, Yang X, David L, Pamir N. Extended multiplexing of TMT labeling reveals age and high fat diet specific proteome changes in mouse epididymal adipose tissue. Molecular and Cellular Proteomics. 16(5):873-890, 2017. [link].
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, Makinen VP, Yang X. Mergeomics: Integration of Diverse Genomics Resources to Identify Pathogenic Perturbations to Biological Systems. BMC Genomics 17:874, 2016. [link to paper; link to R package at Mergeomics web server; link to R package at R Bioconductor].
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 to paper; link to Mergeomics web server].
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].
Zhao Y, Forst CV, Sayegh CE, Wang I*, Yang X*, Zhang B*. Molecular and Genetic Inflammation Networks in Major Human Diseases. (Invited Review). Molecular BioSystems. 12(8):2318-41, 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].
This study was honored the Popular Mechanics 2016 Breakthrough Award for “making the world a little better this year”. More news coverage on Meng et al. study: UCLA newsroom, Science Daily, EurekAlert (American Association for the Advancement of Science), Forbes, Elle, UPI, UCLA Health, ScienMag, Medical News Today, MedicalExpress, Healthline News, Health Newsline, Science2.0, BioscienceTechnology, GEN News Highlights, BreitBart, LaboratoryEquipment, Sydney Morning Herald, The Science Explorer, News-Medical.net, Bangalore Mirror, diabetes.co.uk, The Telegraph, The Sun, The Age, ScienTecDaily, Asia News International, HealthCanal.com, The Times of India, AOL News, Yahoo News, UC news, National Radio of Slovenia, more at the publication site.
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]
2015
Branne I+, Civelek M+, Vilne B+, Di Narzo A, Johnson AD, Zhao Y, Reiz B, Codoni V, Webb TR, Asl HF, Hamby SE, Zeng L, Tregouet DA, Hao K, Topol EJ, Schadt EE, Yang X, Samani NJ, Bjorkegren JLM, Erdmann J, Schunkert H, Lusis AJ on behalf of the Leducq Consortium CADGenomics. Prediction of Causal Candidate Genes in Coronary Artery Disease Loci. Arteriosclerosis, Thrombosis, and Vascular Biology. 35(10):2207-17, 2015. [link]
Zhao Y, Barrere-Cain R,Yang X. Nutritional Systems Biology of Type 2 Diabetes. (Invited Review). Genes & Nutrition 10:31, 2015. [link]
Sazonova O+, Zhao Y+, Nurnberg ST+, Miller C, Castano VG, Kim JB, Salfati ELI, Kundaje AB, Bejerano G, Assimes T, Yang X, Quertermous T. Characterization of TCF21 Downstream Target Regions Identifies A Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci. PLOS Genetics 11:e1005202, 2015. [link]
Ghosh S, Vivar J, Nelson CP, Willenborg C, Segre AV, Mäkinen VP, Nikpay M, Erdmann J, Blankenberg S, O’Donnell C, März W, Laaksonen R, Stewart AFR, Epstein SE, Shah SH, Granger CB, Hazen SL, Kathiresan S, Reilly MP, CARDIoGRAM consortium, Yang X, Quertermous T, Samani NJ, Schunkert H, Assimes TL, McPherson R. Systems Genetics Analysis of GWAS reveals Novel Associations between Key Biological Processes and Coronary Artery Disease. Arteriosclerosis, Thrombosis, and Vascular Biology. 35: 1712-1722, 2015. [link]
Huan T, Meng Q, Saleh MA, Norlander AE, Joehanes R, Zhu J, Chen BH, Zhang B, Wang Z, 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*. Integration of Transcriptomic Profiling, Genome-wide Association, and Network Biology Reveals Molecular Mechanisms Underlying Blood Pressure Regulation. Molecular Systems Biology 11:799, 2015. [link]
Knowles J, Hao K, Xie W, Zhang Z, Assimes TL, Paananen J, et al. Genome-wide Identification and Functional Validation of NAT2 as a Human Insulin Sensitivity Gene. Journal of Clinical Investigation 125: 1739-1751, 2015. [link]
Huan T, Esko T, Peters MJ, Pilling LC, Chen B, Liu C,…, Yang X*, Prokisch H*, Volker U*, van Meurs J*, Ferrucci L*, Levy D*. Transcriptome-wide Association Study of Gene Expression Signatures of Blood Pressure and Hypertension. PLOS Genetics 11:e1005035, 2015. [link]
Huan T, Rong J, Tanriverdi K, Meng Q, Bhattacharya A, McManus D,…, Levy D, Yang X. Dissecting the Roles of microRNAs in Coronary Heart Disease via Integrative Genomics Analyses. Arteriosclerosis, Thrombosis, and Vascular Biology. 35: 1011-21, 2015. [link]
Zhu J, Chen C, Yang B, Guo Y, Ai H, Ren J, et al. A Systems Genetics Study of Swine Illustrates Mechanisms Underlying Human Phenotypic Traits. BMC Genomics. 16:88, 2015. [link]
2014
Chan KHK, Huang Y, Meng Q, Wu C, Reiner A, Sobel EM,…Yang X*, Liu S*. Shared Molecular Pathways and Gene Networks for Cardiovascular Disease and Type 2 Diabetes in Women across Diverse Ethnicities. Circulation: Cardiovascular Genetics. 7:911-919, 2014. [link] (Multiple media reports by Science Daily, Medical Xpress etc. See Lab News).
Narayanan M, Huynh JL, Wang K, Yang X, Yoo S, McElwee J, et al. Commom Dysrelation Network in the Human Prefrontal cortex Underlies Two Neurodegenrative Diseases. Molecular Systems Biology. 10 (7):743, 2014. [link]
Mäkinen V, Civelek M, Meng Q, Zhang B, Zhu J, Levian C,…Yang X*, Assimes T*. Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease. PLoS Genetics. 10(7):e1004502, 2014. [link] (Highlighed by Nature Reviews Genetics in “Piecing together the puzzle of cronary artery disease“).
Levian C,+ Ruiz E,+ Yang X. The Pathogenesis of Obesity from A Genomic and Systems Biology Perspective. (Invited Review). Yale Journal of Biology and Medicine. 87:113-126, 2014. [link]
2013
Dimas AS, Lagou V, Barker A, Knowles JW, Magi R, et al. Impact of Type 2 Diabetes Susceptibility Variants on Quantitative Glycemic Traits Reveals Mechanistic Heterogeneity. Diabetes 63(6):2158-71, 2013. [link]
Chaudhry AJ, Thirumaran RK, Yasuda K, Yang X, Fan Y, et al. Genetic Variation in Aldo-keto Reductase 1D1 (AKR1D1) Affects the Expression and Activity of Multiple Cytochrome P450s (CYPs). Drug Metabolism and Disposition 41(8):1538-47, 2013. [link]
He X, Fuller K, Song Y, Meng Q, Zhang B, Yang X, Li H. Sherlock: Detecting Gene-Disease Associations by Matching Patterns of Expression QTL and GWAS. American Journal of Human Genetics. 92(5):667-80, 2013. [link].
Huan T, Zhang B, Joehanes R, Wang Z, Zhu J,…, Meng Q,… Yang X*, Levy D* A Systems Biology Framework Identifies Molecular Underpinnings of Coronary Heart Disease. Arteriosclerosis, Thrombosis, and Vascular Biology. 33: 1427-1434, 2013. [link]
Meng Q, Maekinen V, Luk H, Yang X. Systems Biology Approaches and Applications in Obesity, Diabetes, and Cardiovascular Diseases. (Invited Review). Current Cardiovascular Risk Reports. 7:73-83, 2013 [link]
Lou M, Thieringer R, Springer MS, Wright SD, Hermanowski-Vosatka A, et al. 11 β-HSD1 Inhibition Reduces Atherosclerosis in Mice by Altering Proinflammatory Gene Expression in the Vasculature. Physiological Genomics. 45:47-57, 2013. [link]
2012
Tu, Z., Keller, M.P., Zhang, C., Rabaglia, M.E., Greenawalt, D.M. et al. Integrative Analysis of a Cross-loci Regulation Network Identifies App as a Gene Regulating Insulin Secretion from Pancreatic Islets. PLoS Genetics. 8:e1003107, 2012. [link]
Gaedigk, A., Yang, X. Genetic Concepts of Pharmacogenomics: Analytical Methods to Identify Genetic Variations and Bioinformatics. Book chapter for Textbook of Pharmacogenomics: An Introduction and Clinical Perspective (ed. Joe Bertino). The McCraw-Hill Companies 2012.[link]
Wang, I.*+, Zhang, B.*+, Yang, X.*+, Zhu, J., Stepaniants, S. et al. Systems Analysis of Eleven Rodent Disease Models Reveals an Inflammatome Signature and Key Drivers. Molecular Systems Biology 8:594, 2012. [link]
Greenawalt, D., Sieberts, S., Cornelis, M.C., Girman, C.J., Zhong, H., et al. Integrating SNP association, genetics of gene expression and SNP set analysis to identify susceptibility loci for type 2 diabetes. American Journal of Epidemiology 176(5):423-30, 2012. [link]
Yang, X.*, Zhang, B., Zhu, J. Functional Genomics- and Network-driven Systems Biology Approaches for Pharmacogenomics and Toxicogenomics. Current Drug Metabolism. 13(7):952-67, 2012 . [link]
Kang, P., Yang, X., Chen, R., Zhang, B., Corona, E., Schadt, E.E., Butte, A. Integration of Disease-specific SNPs, Expression Quantitative Trait Loci, and Coexpression Networks Reveals Novel Candidate Genes for Type 2 Diabetes. Diabetologia 55:2205-2213, 2012. [link]
Salm, M., Horswell, D., Hutchison, C., Ringham, H., Yang, X., et al. The Origin, Global Distribution and Functional Impact of the Human 8p23Inversion Polymorphism. Genome Research 22(6):1144-53, 2012. [link]
Yang, X.* Use of Functional Genomics to Identify Candidate Genes Underlying Human Genetic Association Studies of Vascular Diseases.Arteriosclerosis, Thrombosis, and Vascular Biology 32:216-222, 2012. [link].
2011 and earlier
Yang, X., Tu, Z., Zhu, J. Systems Biology Approaches to Study Diet x Genome Interactions. Book Chapter for Nutritional Genomics: The Impact of Dietary Regulation of Gene Function on Human Diseases (eds Wayne R. Ridlack and Raymond Rodriguez). Taylor and Francis 2011. [article] [book]
Kasarskis, A.+, Yang, X.+, Schadt, EE. Integrative Genomics Strategies to Elucidate the Complexity of Drug Response. Pharmacogenomics12:1695-715, 2011. [link]
Yang, X.*, Peterson, L., Stepaniants, S., Deignan, J., Wang, X., et al. Identification and Validation of Genes Affecting Aortic Lesions in Mice.The Journal of Clinical Investigation 120:2414-22, 2010. [link]
Zhong, H., Yang, X., Kaplan, L., Molony, C., Schadt, E.E. Integrating Pathway Analysis and Genetics of Gene Expression for Genome-wide Association Studies. American Journal of Human Genetics 86:581-591, 2010. [link]
Yang, X.*+, Zhang, B+., Molony, C., Chudin, E., Ulrich, R., et al. Systematic Genetic and Genomic Analysis of Cytochrome P450 Enzyme Activities in Human Liver. Genome Research 20(8):1020-36, 2010. [link]
Zhong, H., Beaulaurier, J., Lum, P., Molony, C., Yang X., et al. Liver and Adipose Expression Associated SNPs Are Enriched for Association to Type 2 Diabetes. PLoS Genetics 6:e1000932, 2010. [link]
Stoltz, D.A., Ozer, E.A., Recker, T.J., Estin, M., Yang, X., et al. Common Mutation in Paraoxonase-2 Results in Impaired Lactonase Activity. Journal of Biological Chemistry 284(51): 35564–35571, 2009. [link]
Loboda, A., Kraft, W.K., Joseph, J., Fine, B., Neboahyn, M., et al., Diurnal Variation in Human Adipose Tissue: Link to Metabolic Diseases. BMC Medical Genomics 2:7, 2009. [link]
Yang, X., Deignan, J.L., Qi, H., Zhu, J., Qian, S., et al. Validation of Candidate Causal Genes for Obesity Which Affect Shared Metabolic Pathways and Networks. Nature Genetics 41: 415-423, 2009. [link] (Featured by Nature Medicine, Nature Biotechnology, and SciBX)
Chen, Y., Zhu, J., Lum, P.Y., Yang, X., Pinto, S., et al. Variations in DNA Elucidate Molecular Networks that Cause Disease. Nature 452: 429-435, 2008. [link] (Featured by ~20 journals, magazines, and newspapers such as Nature News, Forbes, Reuters)
Schadt, E.E., Molony, C., Chudin, E., Hao, K., Yang, X., et al. Mapping the Genetic Architecture of Gene Expression in Human Liver. PLoS Biology 6: e107, 2008. [link] (Feathered by Bio-IT World and The Scientist)
Bhattacharyya, T., Nicholls, S.J., Topol, E.J., Zhang, R., Yang, X., et al. Relationship of Paraoxonase 1 (PON1) Gene Polymorphisms and Functional Activity with Systemic Oxidative Stress and Cardiovascular Risk. Journal of American Medical Association 299: 1265-1276, 2008. [link]
Itoh, Y., Melamed, E., Yang, X., Kampf, K., Wang, S., et al. Dosage Compensation Is Less Effective in Birds than in Mammals. Journal of Biology 6:2, 2007. [link] (Featured by ScienceNow, Physorg, Innovations-report, Alphagalileo, and Softpedia)
Yang, X., Schadt, E.E., Wang, S., Ingram-Drake, L., Arnold, A., et al. Tissue-Specific Expression and Regulation of Sexually Dimorphic Genes in Mice. Genome Research 16:95-1004, 2006. [link] (Featured by ~40 journals, magazines, newspapers, TV shows, and radio stations such as Science News, Nature News, Discover magazine, CNN news)
Schadt, E.E., Lamb, J. Yang, X., Zhu, J., Edwards, S., et al. An Integrative Genomics Approach to Infer Causal Associations between Gene Expression and Disease. Nature Genetics 37:710-717, 2005. [link] (Nominated as “Breakthrough of the Year 2005 – The Runners Up” byScience)
Ghazalpour, A., Doss, S., Yang, X., Aten, J., Toomey, E. M., et al. Thematic Review Series: The Pathogenesis of Atherosclerosis. Toward a Biological Network for Atherosclerosis. Journal of Lipid Research 45: 1793-1805, 2004. [link]
Yang, X., Grant, K.B. Chemical Sequencing of Restriction Fragments 3-end-labeled with [35S]dATPαS. Journal of Biochemical and Biophysical Methods. 50: 123-128, 2002.