Mete Civelek

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Primary Appointment

Associate Professor, Biomedical Engineering

Education

  • BA, Molecular Biology and Genetics, Bogazici University
  • BS, Chemical Engineering, Bogazici University
  • MS, Chemical Engineering, Pennsylvania State University, University Park, PA
  • PhD, Bioengineering, University of Pennsylvania

Research Disciplines

Bioinformatics and Genomics, Biomedical Engineering, Cardiovascular Biology, Epigenetics, Experimental Pathology, Genetics, Metabolism, Metabolism, Molecular Pharmacology

Research Interests

Systems Genetics Approaches to Understand Cardiometabolic Traits

Research Description

The goal of our laboratory is to understand the genetic mechanisms that lead to increased susceptibility to cardiovascular and metabolic diseases. The interactions among hundreds of genes and gene networks along with environmental factors such as diet affect our health status. We use systems genetics to uncover this complexity. We use a range of experimental and computational methods to quantitate and integrate intermediate phenotypes, such as transcript, protein or metabolite levels, in human and mouse populations. We also test our predictions using standard biochemistry and molecular biology approaches in cell cultures and animal models. Our results provided insights into both the molecular underpinnings of complex traits and the understanding of common, complex diseases.

Training

  • Basic Cardiovascular Research Training Grant
  • Biotechnology Training Grant
  • Training in Cell and Molecular Biology
  • Training in the Pharmacological Sciences

Selected Publications

2024

Rial, S. A., You, Z., Vivoli, A., Sean, D., Al-Khoury, A., Lavoie, G., . . . Lim, G. E. (2024). 14-3-3ζ regulates adipogenesis by modulating chromatin accessibility during the early stages of adipocyte differentiation.. bioRxiv. doi:10.1101/2024.03.18.585495

Aherrahrou, R., Baig, F., Theofilatos, K., Lue, D., Beele, A., Ãrd, T., . . . Civelek, M. (2024). Secreted Protein Profiling of Human Aortic Smooth Muscle Cells Identifies Vascular Disease Associations.. Arteriosclerosis, thrombosis, and vascular biology, 44(4), 898-914. doi:10.1161/atvbaha.123.320274

2023

Aherrahrou, R., Baig, F., Theofilatos, K., Lue, D., Beele, A., Ãrd, T., . . . Civelek, M. (2023). Secreted protein profiling of human aortic smooth muscle cells identifies vascular disease associations.. medRxiv. doi:10.1101/2023.11.10.23298351

Reed, J. N., Huang, J., Li, Y., Ma, L., Banka, D., Wabitsch, M., . . . Civelek, M. (2023). Systems genetics analysis of human body fat distribution genes identifies Wnt signaling and mitochondrial activity in adipocytes.. bioRxiv. doi:10.1101/2023.09.06.556534

Benavente, E. D., Karnewar, S., Buono, M., Mili, E., Hartman, R. J. G., Kapteijn, D., . . . den Ruijter, H. M. (2023). Female gene networks are expressed in myofibroblast-like smooth muscle cells in vulnerable atherosclerotic plaques.. bioRxiv. doi:10.1101/2023.02.08.527690

Aherrahrou, R., Lue, D., Perry, R. N., Aberra, Y. T., Khan, M. D., Soh, J. Y., . . . Civelek, M. (2023). Genetic Regulation of SMC Gene Expression and Splicing Predict Causal CAD Genes. CIRCULATION RESEARCH, 132(3), 323-338. doi:10.1161/CIRCRESAHA.122.321586

Sakkers, T. R., Mokry, M., Civelek, M., Erdmann, J., Pasterkamp, G., Benavente, E. D., & den Ruijter, H. M. (2023). Sex differences in the genetic and molecular mechanisms of coronary artery disease. ATHEROSCLEROSIS, 384. doi:10.1016/j.atherosclerosis.2023.117279

Hu, P., Miller, A. E., Yeh, C. -R., Bingham, G. C., Civelek, M., & Barker, T. H. (2023). SEMA7a primes integrin α581 engagement instructing fibroblast mechanotransduction, phenotype and transcriptional programming. MATRIX BIOLOGY, 121, 179-193. doi:10.1016/j.matbio.2023.06.006

Benavente, E. D., Karnewar, S., Buono, M., Mili, E., Hartman, R. J. G., Kapteijn, D., . . . den Ruijter, H. M. (2023). Female Gene Networks Are Expressed in Myofibroblast-Like Smooth Muscle Cells in Vulnerable Atherosclerotic Plaques. ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 43(10), 1836-1850. doi:10.1161/ATVBAHA.123.319325

Perry, R. N., Albarracin, D., Aherrahrou, R., & Civelek, M. (2023). Network Preservation Analysis Reveals Dysregulated Metabolic Pathways in Human Vascular Smooth Muscle Cell Phenotypic Switching. CIRCULATION-GENOMIC AND PRECISION MEDICINE, 16(4), 372-381. doi:10.1161/CIRCGEN.122.003781

Aberra, Y. T., Ma, L., Bjorkegren, J. L. M., & Civelek, M. (2023). Predicting mechanisms of action at genetic loci associated with discordant effects on type 2 diabetes and abdominal fat accumulation. ELIFE, 12. doi:10.7554/eLife.79834

Wong, D., Auguste, G., Lino Cardenas, C. L., Turner, A. W., Chen, Y., Song, Y., . . . Miller, C. L. (2023). FHL5 Controls Vascular Disease-Associated Gene Programs in Smooth Muscle Cells. CIRCULATION RESEARCH, 132(9), 1144-1161. doi:10.1161/CIRCRESAHA.122.321692

Xu, P., Wang, M., Sharma, N. K., Comeau, M. E., Wabitsch, M., Langefeld, C. D., . . . Das, S. K. (2023). Multi-omic integration reveals cell-type-specific regulatory networks of insulin resistance in distinct ancestry populations. CELL SYSTEMS, 14(1), 41-+. doi:10.1016/j.cels.2022.12.005

Aherrahrou, R., Lue, D., & Civelek, M. (2023). Genetic regulation of circular RNA expression in human aortic smooth muscle cells and vascular traits. HUMAN GENETICS AND GENOMICS ADVANCES, 4(1). doi:10.1016/j.xhgg.2022.100164

2022

Mokry, M., Boltjes, A., Slenders, L., Bel-Bordes, G., Cui, K., Brouwer, E., . . . Pasterkamp, G. (2022). Transcriptomic-based clustering of human atherosclerotic plaques identifies subgroups with different underlying biology and clinical presentation. NATURE CARDIOVASCULAR RESEARCH, 1(12), 1140-+. doi:10.1038/s44161-022-00171-0

Civelek, M., Fogelman, A. M., Hedrick, C. C., Lusis, A. J., Romanoski, C. E., & Witztum, J. L. (2022). In memoriam: Judith A. Berliner, Ph.D.. JOURNAL OF LIPID RESEARCH, 63(4). doi:10.1016/j.jlr.2022.100180

Slenders, L., Landsmeer, L. P. L., Cui, K., Depuydt, M. A. C., Verwer, M., Mekke, J., . . . Mokry, M. (2022). Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis.. European heart journal open, 2(1), oeab043. doi:10.1093/ehjopen/oeab043

Yang, Q., Hinkle, J., Reed, J. N., Aherrahrou, R., Xu, Z., Harris, T. E., . . . Civelek, M. (2022). Adipocyte-Specific Modulation of KLF14 Expression in Mice Leads to Sex-Dependent Impacts on Adiposity and Lipid Metabolism. DIABETES, 71(4), 677-693. doi:10.2337/db21-0674

2021

Ord, T., Ounap, K., Stolze, L. K., Aherrahrou, R., Nurminen, V., Toropainen, A., . . . Kaikkonen, M. U. (2021). Single-Cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci. CIRCULATION RESEARCH, 129(2), 240-258. doi:10.1161/CIRCRESAHA.121.318971

Innis, S. E., Reinaltt, K., Civelek, M., & Anderson, W. D. (2021). GSEAplot: A Package for Customizing Gene Set Enrichment Analysis in R. JOURNAL OF COMPUTATIONAL BIOLOGY, 28(6), 629-631. doi:10.1089/cmb.2020.0426

Hartiala, J. A., Han, Y., Jia, Q., Hilser, J. R., Huang, P., Gukasyan, J., . . . Allayee, H. (2021). Genome-wide analysis identifies novel susceptibility loci for myocardial infarction. EUROPEAN HEART JOURNAL, 42(9), 919-933. doi:10.1093/eurheartj/ehaa1040

Xu, H., Thomas, M. J., Kaul, S., Kallinger, R., Ouweneel, A. B., Maruko, E., . . . Sorci-Thomas, M. G. (2021). Pcpe2, a Novel Extracellular Matrix Protein, Regulates Adipocyte SR-BI-Mediated High-Density Lipoprotein Uptake. ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 41(11), 2708-2725. doi:10.1161/ATVBAHA.121.316615

Ke, W., Reed, J. N., Yang, C., Higgason, N., Rayyan, L., Waehlby, C., . . . O'Rourke, E. J. (2021). Genes in human obesity loci are causal obesity genes in C. elegans. PLOS GENETICS, 17(9). doi:10.1371/journal.pgen.1009736

Wierer, M., Werner, J., Wobst, J., Kastrati, A., Cepele, G., Aherrahrou, R., . . . Kessler, T. (2021). A proteomic atlas of the neointima identifies novel druggable targets for preventive therapy. EUROPEAN HEART JOURNAL, 42(18), 1773-1785. doi:10.1093/eurheartj/ehab140

Hartman, R. J. G., Owsiany, K., Ma, L., Koplev, S., Hao, K., Slenders, L., . . . den Ruijter, H. M. (2021). Sex-Stratified Gene Regulatory Networks Reveal Female Key Driver Genes of Atherosclerosis Involved in Smooth Muscle Cell Phenotype Switching. CIRCULATION, 143(7), 713-726. doi:10.1161/CIRCULATIONAHA.120.051231

2020

Zhou, Z., Moore, T. M., Drew, B. G., Ribas, V., Wanagat, J., Civelek, M., . . . Hevener, A. L. (2020). Estrogen receptor α controls metabolism in white and brown adipocytes by regulating Polg1 and mitochondrial remodeling.. Science translational medicine, 12(555), eaax8096. doi:10.1126/scitranslmed.aax8096

Aherrahrou, R., Guo, L., Nagraj, V. P., Aguhob, A., Hinkle, J., Chen, L., . . . Civelek, M. (2020). Genetic Regulation of Atherosclerosis-Relevant Phenotypes in Human Vascular Smooth Muscle Cells. CIRCULATION RESEARCH, 127(12), 1552-1565. doi:10.1161/CIRCRESAHA.120.317415

Anderson, W. D., Soh, J. Y., Innis, S. E., Dimanche, A., Ma, L., Langefeld, C. D., . . . Civelek, M. (2020). Sex differences in human adipose tissue gene expression and genetic regulation involve adipogenesis. GENOME RESEARCH, 30(10), 1379-1392. doi:10.1101/gr.264614.120

Hartman, R. J. G., Kapteijn, D. M. C., Haitjema, S., Bekker, M. N., Mokry, M., Pasterkamp, G., . . . den Ruijter, H. M. (2020). Intrinsic transcriptomic sex differences in human endothelial cells at birth and in adults are associated with coronary artery disease targets. SCIENTIFIC REPORTS, 10(1). doi:10.1038/s41598-020-69451-8

Rodriguez, B. A. T., Bhan, A., Beswick, A., Elwood, P. C., Niiranen, T. J., Salomaa, V., . . . Johnson, A. D. (2020). A Platelet Function Modulator of Thrombin Activation Is Causally Linked to Cardiovascular Disease and Affects PAR4 Receptor Signaling. AMERICAN JOURNAL OF HUMAN GENETICS, 107(2), 211-221. doi:10.1016/j.ajhg.2020.06.008

Yang, Q., & Civelek, M. (2020). Transcription Factor KLF14 and Metabolic Syndrome. FRONTIERS IN CARDIOVASCULAR MEDICINE, 7. doi:10.3389/fcvm.2020.00091

Reifeis, S. A., Hudgens, M. G., Civelek, M., Mohlke, K. L., & Love, M. I. (2020). Assessing exposure effects on gene expression. GENETIC EPIDEMIOLOGY, 44(6), 601-610. doi:10.1002/gepi.22324

Anderson, W. D., Duarte, F. M., Civelek, M., & Guertin, M. J. (2020). Defining data-driven primary transcript annotations with primaryTranscriptAnnotation in R. BIOINFORMATICS, 36(9), 2926-2928. doi:10.1093/bioinformatics/btaa011

2019

Olin, J. W., Di Narzo, A. F., d'Escamard, V., Kadian-Dodov, D., Cheng, H., Georges, A., . . . Kovacic, J. C. (2020). A plasma proteogenomic signature for fibromuscular dysplasia. CARDIOVASCULAR RESEARCH, 116(1), 63-77. doi:10.1093/cvr/cvz219

Thibord, F., Hardy, L., Ibrahim-Kosta, M., Saut, N., Pulcrano-Nicolas, A. -S., Goumidi, L., . . . Morange, P. -E. (2019). A Genome Wide Association Study on plasma FV levels identified PLXDC2 as a new modifier of the coagulation process. JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 17(11), 1808-1814. doi:10.1111/jth.14562

Wu, Y., Broadaway, K. A., Raulerson, C. K., Scott, L. J., Pan, C., Ko, A., . . . Mohlke, K. L. (2019). Colocalization of GWAS and eQTL signals at loci with multiple signals identifies additional candidate genes for body fat distribution. HUMAN MOLECULAR GENETICS, 28(24), 4162-4173. doi:10.1093/hmg/ddz263

Helsley, R. N., Varadharajan, V., Brown, A. L., Gromovsky, A. D., Schugar, R. C., Ramachandiran, I., . . . Brown, J. M. (2019). Obesity-linked suppression of membrane-bound O-acyltransferase 7 (MBOAT7) drives non-alcoholic fatty liver disease. ELIFE, 8. doi:10.7554/eLife.49882

Raulerson, C. K., Ko, A., Kidd, J. C., Currin, K. W., Brotman, S. M., Cannon, M. E., . . . Mohlke, K. L. (2019). Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits. AMERICAN JOURNAL OF HUMAN GENETICS, 105(4), 773-787. doi:10.1016/j.ajhg.2019.09.001

Prestel, M., Prell-Schicker, C., Webb, T., Malik, R., Lindner, B., Ziesch, N., . . . Dichgans, M. (2019). The Atherosclerosis Risk Variant rs2107595 Mediates Allele-Specific Transcriptional Regulation of HDAC9 via E2F3 and Rb1. STROKE, 50(10), 2651-2660. doi:10.1161/STROKEAHA.119.026112

Kalliora, C., Kyriazis, I. D., Oka, S. -I., Lieu, M. J., Yue, Y., Area-Gomez, E., . . . Drosatos, K. (2019). Dua PPARα/γ activation inhibits SIRT1-PGC1α axis and causes cardiac dysfunction. JCI INSIGHT, 4(17). doi:10.1172/jci.insight.129556

Malik, R., Chauhan, G., Traylor, M., Sargurupremraj, M., Okada, Y., Mishra, A., . . . Dichgans, M. (2019). Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes (vol 50, pg 524, 2018). NATURE GENETICS, 51(7), 1192-1193. doi:10.1038/s41588-019-0449-0

Civelek, M., & Erdmann, J. (2019). MicroRNAs and regulation of cardiometabolic phenotypes: novel insights into the complexity of genome-wide association studies loci. CARDIOVASCULAR RESEARCH, 115(11), 1570-1571. doi:10.1093/cvr/cvz120

Sharma, N. K., Key, C. -C. C., Civelek, M., Wabitsch, M., Comeau, M. E., Langefeld, C. D., . . . Das, S. K. (2019). Genetic Regulation of Enoyl-CoA Hydratase Domain-Containing 3 in Adipose Tissue Determines Insulin Sensitivity in African Americans and Europeans. DIABETES, 68(7), 1508-1522. doi:10.2337/db18-1229

Bond, S. T., Moody, S. C., Liu, Y., Civelek, M., Villanueva, C. J., Gregorevic, P., . . . Drew, B. G. (2019). The E3 ligase MARCH5 is a PPARγ target gene that regulates mitochondria and metabolism in adipocytes. AMERICAN JOURNAL OF PHYSIOLOGY-ENDOCRINOLOGY AND METABOLISM, 316(2), E293-E304. doi:10.1152/ajpendo.00394.2018

2018

Small, K. S., TodorÄeviÄ, M., Civelek, M., El-Sayed Moustafa, J. S., Wang, X., Simon, M. M., . . . McCarthy, M. I. (2018). Author Correction: Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition.. Nature genetics, 50(9), 1342. doi:10.1038/s41588-018-0180-2

Fang, Y., Krause, M., Civelek, M., & Romanoski, C. (2018). Abstract 217: Coronary Artery Disease Locus 1p32.2 Harbors a Flow-Sensitive Endothelial Enhancer that Regulates PLPP3. Arteriosclerosis, Thrombosis, and Vascular Biology, 38(Suppl_1). doi:10.1161/atvb.38.suppl_1.217

Xu, H., Kaul, S., Proudfoot, S., Schill, R. L., Fatema, K., Thomas, M. J., . . . Sorci-Thomas, M. G. (2018). Abstract 045: SR-BI and PCPE2 Modulate Lipid Trafficking in Adipocytes. Arteriosclerosis, Thrombosis, and Vascular Biology, 38(Suppl_1). doi:10.1161/atvb.38.suppl_1.045

Seldin, M. M., Koplev, S., Rajbhandari, P., Vergnes, L., Rosenberg, G. M., Meng, Y., . . . Lusis, A. J. (2018). A Strategy for Discovery of Endocrine Interactions with Application to Whole-Body Metabolism. CELL METABOLISM, 27(5), 1138-+. doi:10.1016/j.cmet.2018.03.015

Small, K. S., Todorcevic, M., Civelek, M., Moustafa, J. S. E. -S., Wang, X., Simon, M. M., . . . McCarthy, M. I. (2018). Regulatory variants at KLF14 influence type 2 diabetes risk via a female-specific effect on adipocyte size and body composition. NATURE GENETICS, 50(4), 572-+. doi:10.1038/s41588-018-0088-x

Malik, R., Chauhan, G., Traylor, M., Sargurupremraj, M., Okada, Y., Mishra, A., . . . Dichgans, M. (2018). Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes. NATURE GENETICS, 50(4), 524-+. doi:10.1038/s41588-018-0058-3

Sallam, T., Jones, M., Thomas, B. J., Wu, X., Gilliland, T., Qian, K., . . . Tontonoz, P. (2018). Transcriptional regulation of macrophage cholesterol efflux and atherogenesis by a long noncoding RNA. NATURE MEDICINE, 24(3), 304-+. doi:10.1038/nm.4479

Krause, M. D., Huang, R. -T., Wu, D., Shentu, T. -P., Harrison, D. L., Whalen, M. B., . . . Fang, Y. (2018). Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 115(48), E11349-E11358. doi:10.1073/pnas.1810568115

Dusart, P., Fagerberg, L., Perisic, L., Civelek, M., Struck, E., Hedin, U., . . . Butler, L. M. (2018). A systems-approach reveals human nestin is an endothelial-enriched, angiogenesis-independent intermediate filament protein. SCIENTIFIC REPORTS, 8. doi:10.1038/s41598-018-32859-4

Pan, D. Z., Garske, K. M., Alvarez, M., Bhagat, Y. V., Boocock, J., Nikkola, E., . . . Ko, A. (2018). Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS (vol 9, 1512, 2018). NATURE COMMUNICATIONS, 9. doi:10.1038/s41467-018-05849-3

Orozco, L. D., Farrell, C., Hale, C., Rubbi, L., Rinaldi, A., Civelek, M., . . . Pellegrini, M. (2018). Epigenome-wide association in adipose tissue from the METSIM cohort (vol 27, pg 1830, 2018). HUMAN MOLECULAR GENETICS, 27(14), 2586. doi:10.1093/hmg/ddy205

Pan, D. Z., Garske, K. M., Alvarez, M., Bhagat, Y. V., Boocock, J., Nikkola, E., . . . Ko, A. (2018). Integration of human adipocyte chromosomal interactions with adipose gene expression prioritizes obesity-related genes from GWAS. NATURE COMMUNICATIONS, 9. doi:10.1038/s41467-018-03554-9

Wang, Z., Civelek, M., Miller, C. L., Sheffield, N. C., Guertin, M. J., & Zang, C. (2018). BART: a transcription factor prediction tool with query gene sets or epigenomic profiles. BIOINFORMATICS, 34(16), 2867-2869. doi:10.1093/bioinformatics/bty194

Orozco, L. D., Farrell, C., Hale, C., Rubbi, L., Rinaldi, A., Civelek, M., . . . Pellegrini, M. (2018). Epigenome-wide association in adipose tissue from the METSIM cohort. HUMAN MOLECULAR GENETICS, 27(10), 1830-1846. doi:10.1093/hmg/ddy093

2017

Kessler, T., Wobst, J., Wolf, B., Eckhold, J., Vilne, B., Hollstein, R., . . . Schunkert, H. (2017). P4471The 4q32.1 coronary artery disease locus influences disease risk via differential transcription factor binding. European Heart Journal, 38(suppl_1). doi:10.1093/eurheartj/ehx504.p4471

Schugar, R. C., Shih, D. M., Warrier, M., Helsley, R. N., Burrows, A., Ferguson, D., . . . Brown, J. M. (2017). The TMAO-Producing Enzyme Flavin-Containing Monooxygenase 3 Regulates Obesity and the Beiging of White Adipose Tissue.. Cell reports, 20(1), 279. doi:10.1016/j.celrep.2017.06.053

Wu, D., Huang, R. -T., Hamanaka, R. B., Krause, M., Oh, M. -J., Kuo, C. -H., . . . Mutlu, G. M. (2017). HIF-1α is required for disturbed flow-induced metabolic reprogramming in human and porcine vascular endothelium. ELIFE, 6. doi:10.7554/eLife.25217

Kessler, T., Wobst, J., Wolf, B., Eckhold, J., Vilne, B., Hollstein, R., . . . Schunkert, H. (2017). Functional Characterization of the GUCY1A3 Coronary Artery Disease Risk Locus. CIRCULATION, 136(5), 476-+. doi:10.1161/CIRCULATIONAHA.116.024152

Civelek, M. (2017). A Smoking-Associated miRNA-mRNA Coexpression Network. CIRCULATION-CARDIOVASCULAR GENETICS, 10(5). doi:10.1161/CIRCGENETICS.117.001914

Liu, Y., Walavalkar, N. M., Dozmorov, M. G., Rich, S. S., Civelek, M., & Guertin, M. J. (2017). Identification of breast cancer associated variants that modulate transcription factor binding. PLOS GENETICS, 13(9). doi:10.1371/journal.pgen.1006761

Cannon, M. E., Duan, Q., Wu, Y., Zeynalzadeh, M., Xu, Z., Kangas, A. J., . . . Mohlke, K. L. (2017). Trans-ancestry Fine Mapping and Molecular Assays Identify Regulatory Variants at the ANGPTL8 HDL-C GWAS Locus. G3-GENES GENOMES GENETICS, 7(9), 3217-3227. doi:10.1534/g3.117.300088

Civelek, M., Wu, Y., Pan, C., Raulerson, C. K., Ko, A., He, A., . . . Lusis, A. J. (2017). Genetic Regulation of Adipose Gene Expression and Cardio-Metabolic Traits. AMERICAN JOURNAL OF HUMAN GENETICS, 100(3), 428-443. doi:10.1016/j.ajhg.2017.01.027

2016

Rau, C. D., Civelek, M., Pan, C., & Lusis, A. J. (2017). A Suite of Tools for Biologists That Improve Accessibility and Visualization of Large Systems Genetics Datasets: Applications to the Hybrid Mouse Diversity Panel. SYSTEMS GENETICS: METHODS AND PROTOCOLS, 1488, 153-188. doi:10.1007/978-1-4939-6427-7_7

Touat-Hamici, Z., Weidmann, H., Blum, Y., Proust, C., Durand, H., Iannacci, F., . . . Ninio, E. (2016). Role of lipid phosphate phosphatase 3 in human aortic endothelial cell function. CARDIOVASCULAR RESEARCH, 112(3), 702-713. doi:10.1093/cvr/cvw217

Kojima, Y., Volkmer, J. -P., McKenna, K., Civelek, M., Lusis, A. J., Miller, C. L., . . . Leeper, N. J. (2016). CD47-blocking antibodies restore phagocytosis and prevent atherosclerosis. NATURE, 536(7614), 86-+. doi:10.1038/nature18935

Gusev, A., Ko, A., Shi, H., Bhatia, G., Chung, W., Penninx, B. W. J. H., . . . Pasaniuc, B. (2016). Integrative approaches for large-scale transcriptome-wide association studies. NATURE GENETICS, 48(3), 245-252. doi:10.1038/ng.3506

Codoni, V., Blum, Y., Civelek, M., Proust, C., Franzen, O., Bjorkegren, J. L. M., . . . Tregouet, D. -A. (2016). Preservation Analysis of Macrophage Gene Coexpression Between Human and Mouse Identifies PARK2 as a Genetically Controlled Master Regulator of Oxidative Phosphorylation in Humans. G3-GENES GENOMES GENETICS, 6(10), 3361-3371. doi:10.1534/g3.116.033894

Dennis, J., Truong, V., Aissi, D., Medina-Rivera, A., Blankenberg, S., Germain, M., . . . Gagnon, F. (2016). Single nucleotide polymorphisms in an intergenic chromosome 2q region associated with tissue factor pathway inhibitor plasma levels and venous thromboembolism. JOURNAL OF THROMBOSIS AND HAEMOSTASIS, 14(10), 1960-1970. doi:10.1111/jth.13431

Talukdar, H. A., Asl, H. F., Jain, R. K., Ermel, R., Ruusalepp, A., Franzen, O., . . . Bjorkegren, J. L. M. (2016). Cross-Tissue Regulatory Gene Networks in Coronary Artery Disease. CELL SYSTEMS, 2(3), 196-208. doi:10.1016/j.cels.2016.02.002

Lusis, A. J., Seldin, M. M., Allayee, H., Bennett, B. J., Civelek, M., Davis, R. C., . . . Wang, J. (2016). The Hybrid Mouse Diversity Panel: a resource for systems genetics analyses of metabolic and cardiovascular traits. JOURNAL OF LIPID RESEARCH, 57(6), 925-942. doi:10.1194/jlr.R066944

Kenagy, R. D., Civelek, M., Kikuchi, S., Chen, L., Grieff, A., Sobel, M., . . . Clowes, A. W. (2016). Scavenger receptor class A member 5 (SCARA5) and suprabasin (SBSN) are hub genes of coexpression network modules associated with peripheral vein graft patency. JOURNAL OF VASCULAR SURGERY, 64(1), 202-+. doi:10.1016/j.jvs.2014.12.052

2015

Briot, A., Civelek, M., Seki, A., Hoi, K., Mack, J. J., Lee, S. D., . . . Iruela-Arispe, L. (2015). Endothelial NOTCH1 is suppressed by circulating lipids and antagonizes inflammation during atherosclerosis. The Journal of Cell Biology, 211(4), 2114OIA269. doi:10.1083/jcb.2114oia269

Germain, M., Chasman, D. I., de Haan, H., Tang, W., Lindstroem, S., Weng, L. -C., . . . Morange, P. -E. (2015). Meta-analysis of 65,734 Individuals Identifies TSPAN15 and SLC44A2 as Two Susceptibility Loci for Venous Thromboembolism. AMERICAN JOURNAL OF HUMAN GENETICS, 96(4), 532-542. doi:10.1016/j.ajhg.2015.01.019

Bennett, B. J., Davis, R. C., Civelek, M., Orozco, L., Wu, J., Qi, H., . . . Lusis, A. J. (2015). Genetic Architecture of Atherosclerosis in Mice: A Systems Genetics Analysis of Common Inbred Strains. PLOS GENETICS, 11(12). doi:10.1371/journal.pgen.1005711

Roman, T. S., Marvelle, A. F., Fogarty, M. P., Vadlamudi, S., Gonzalez, A. J., Buchkovich, M. L., . . . Mohlke, K. L. (2015). Multiple Hepatic Regulatory Variants at the GALNT2 GWAS Locus Associated with High-Density Lipoprotein Cholesterol. AMERICAN JOURNAL OF HUMAN GENETICS, 97(6), 801-815. doi:10.1016/j.ajhg.2015.10.016

Briot, A., Civelek, M., Seki, A., Hoi, K., Mack, J. J., Lee, S. D., . . . Iruela-Arispe, M. L. (2015). Endothelial NOTCH1 is suppressed by circulating lipids and antagonizes inflammation during atherosclerosis. JOURNAL OF EXPERIMENTAL MEDICINE, 212(12), 2147-2163. doi:10.1084/jem.20150603

Germain, M., Pezzolesi, M. G., Sandholm, N., McKnight, A. J., Susztak, K., Lajer, M., . . . Hadjadj, S. (2015). SORBS1 gene, a new candidate for diabetic nephropathy: results from a multi-stage genome-wide association study in patients with type 1 diabetes. DIABETOLOGIA, 58(3), 543-548. doi:10.1007/s00125-014-3459-6

Bahn, J. H., Ahn, J., Lin, X., Zhang, Q., Lee, J. -H., Civelek, M., & Xiao, X. (2015). Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways. NATURE COMMUNICATIONS, 6. doi:10.1038/ncomms7355

Soccio, R. E., Chen, E. R., Rajapurkar, S. R., Safabakhsh, P., Marinis, J. M., Dispirito, J. R., . . . Lazar, M. A. (2015). Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo. CELL, 162(1), 33-44. doi:10.1016/j.cell.2015.06.025

Wu, C., Huang, R. -T., Kuo, C. -H., Kumar, S., Kim, C. W., Lin, Y. -C., . . . Fang, Y. (2015). Mechanosensitive PPAP2B Regulates Endothelial Responses to Atherorelevant Hemodynamic Forces. CIRCULATION RESEARCH, 117(4), E41-E53. doi:10.1161/CIRCRESAHA.117.306457

Braenne, I., Civelek, M., Vilne, B., Di Narzo, A., Johnson, A. D., Zhao, Y., . . . Lusis, A. J. (2015). Prediction of Causal Candidate Genes in Coronary Artery Disease Loci. ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 35(10), 2207-2217. doi:10.1161/ATVBAHA.115.306108

2014

Romay, M. C., Che, N., Becker, S. N., Pouldar, D., Hagopian, R., Xiao, X., . . . Civelek, M. (2015). Regulation of NF-κB signaling by oxidized glycerophospholipid and IL-1β induced miRs-21-3p and-27a-5p in human aortic endothelial cells. JOURNAL OF LIPID RESEARCH, 56(1), 38-50. doi:10.1194/jlr.M052670

Iatan, I., Choi, H. Y., Ruel, I., Reddy, M. V. P. L., Kil, H., Lee, J., . . . Genest, J. (2014). The WWOX Gene Modulates High-Density Lipoprotein and Lipid Metabolism. CIRCULATION-CARDIOVASCULAR GENETICS, 7(4). doi:10.1161/CIRCGENETICS.113.000248

Makinen, V. -P., Civelek, M., Meng, Q., Zhang, B., Zhu, J., Levian, C., . . . Assimes, T. L. (2014). Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease. PLOS GENETICS, 10(7). doi:10.1371/journal.pgen.1004502

Civelek, M., & Lusis, A. J. (2014). From Hairballs to an Understanding of Transendothelial Migration of Monocytes in Atherosclerosis. ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY, 34(9), 1809-1810. doi:10.1161/ATVBAHA.114.304151

2013

Civelek, M., & Lusis, A. J. (2014). Systems genetics approaches to understand complex traits. NATURE REVIEWS GENETICS, 15(1), 34-48. doi:10.1038/nrg3575

Civelek, M., Hagopian, R., Pan, C., Che, N., Yang, W. -P., Kayne, P. S., . . . Lusis, A. J. (2013). Genetic regulation of human adipose microRNA expression and its consequences for metabolic traits. HUMAN MOLECULAR GENETICS, 22(15), 3023-3037. doi:10.1093/hmg/ddt159

Parks, B. W., Nam, E., Org, E., Kostem, E., Norheim, F., Hui, S. T., . . . Lusis, A. J. (2013). Genetic Control of Obesity and Gut Microbiota Composition in Response to High-Fat, High-Sucrose Diet in Mice. CELL METABOLISM, 17(1), 141-152. doi:10.1016/j.cmet.2012.12.007

Vallim, T. Q. D. A., Tarling, E. J., Kim, T., Civelek, M., Baldan, A., Esau, C., & Edwards, P. A. (2013). MicroRNA-144 Regulates Hepatic ATP Binding Cassette Transporter A1 and Plasma High-Density Lipoprotein After Activation of the Nuclear Receptor Farnesoid X Receptor. CIRCULATION RESEARCH, 112(12), 1602-+. doi:10.1161/CIRCRESAHA.112.300648

Mahendran, Y., Vangipurapu, J., Cederberg, H., Stancakova, A., Pihlajamaki, J., Soininen, P., . . . Laakso, M. (2013). Association of Ketone Body Levels With Hyperglycemia and Type 2 Diabetes in 9,398 Finnish Men. DIABETES, 62(10), 3618-3626. doi:10.2337/db12-1363

Davies, P. F., Civelek, M., Fang, Y., & Fleming, I. (2013). The atherosusceptible endothelium: endothelial phenotypes in complex haemodynamic shear stress regions in vivo. CARDIOVASCULAR RESEARCH, 99(2), 315-327. doi:10.1093/cvr/cvt101

Erbilgin, A., Civelek, M., Romanoski, C. E., Pan, C., Hagopian, R., Berliner, J. A., & Lusis, A. J. (2013). Identification of CAD candidate genes in GWAS loci and their expression in vascular cells. JOURNAL OF LIPID RESEARCH, 54(7), 1894-1905. doi:10.1194/jlr.M037085

2012

Ghazalpour, A., Rau, C. D., Farber, C. R., Bennett, B. J., Orozco, L. D., van Nas, A., . . . LeBoeuf, R. C. (2012). Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits. MAMMALIAN GENOME, 23(9-10), 680-692. doi:10.1007/s00335-012-9411-5

Stancakova, A., Civelek, M., Saleem, N. K., Soininen, P., Kangas, A. J., Cederberg, H., . . . Laakso, M. (2012). Hyperglycemia and a Common Variant of GCKR Are Associated With the Levels of Eight Amino Acids in 9,369 Finnish Men. DIABETES, 61(7), 1895-1902. doi:10.2337/db11-1378

Kim, J. B., Deluna, A., Mungrue, I. N., Vu, C., Pouldar, D., Civelek, M., . . . Lusis, A. J. (2012). Effect of 9p21.3 Coronary Artery Disease Locus Neighboring Genes on Atherosclerosis in Mice. CIRCULATION, 126(15), 1896-U294. doi:10.1161/CIRCULATIONAHA.111.064881

Haas, B. E., Horvath, S., Pietilainen, K. H., Cantor, R. M., Nikkola, E., Weissglas-Volkov, D., . . . Pajukanta, P. (2012). Adipose Co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes. BMC MEDICAL GENOMICS, 5. doi:10.1186/1755-8794-5-61

2011

Romanoski, C. E., Che, N., Yin, F., Nguyen, M., Pouldar, D., Civelek, M., . . . Lusis, A. J. (2011). Network for Activation of Human Endothelial Cells by Oxidized Phospholipids. CIRCULATION RESEARCH, 109(5), E27-U52. doi:10.1161/CIRCRESAHA.111.241869

Civelek, M., & Lusis, A. J. (2011). Conducting the metabolic syndrome orchestra. NATURE GENETICS, 43(6), 506-508. doi:10.1038/ng.842

Davies, P. F., & Civelek, M. (2011). Endoplasmic Reticulum Stress, Redox, and a Proinflammatory Environment in Athero-Susceptible Endothelium In Vivo at Sites of Complex Hemodynamic Shear Stress. ANTIOXIDANTS & REDOX SIGNALING, 15(5), 1427-1432. doi:10.1089/ars.2010.3741

Civelek, M., Manduchi, E., Riley, R. J., Stoeckert, C. J. J., & Davies, P. F. (2011). Coronary Artery Endothelial Transcriptome In Vivo Identification of Endoplasmic Reticulum Stress and Enhanced Reactive Oxygen Species by Gene Connectivity Network Analysis. CIRCULATION-CARDIOVASCULAR GENETICS, 4(3), 243-252. doi:10.1161/CIRCGENETICS.110.958926

Civelek, M., Manduchi, E., Grant, G. R., Stoeckert, C. J. J., & Davies, P. F. (2011). DISCOVERY APPROACHES TO UPR IN ATHERO-SUSCEPTIBLE ENDOTHELIUM IN VIVO. METHODS IN ENZYMOLOGY: UNFOLDED PROTEIN RESPONSE AND CELLULAR STRESS, VOL 489, PT A, 489, 109-126. doi:10.1016/B978-0-12-385116-1.00007-8

2010

Fang, Y., Shi, C., Manduchi, E., Civelek, M., & Davies, P. F. (2010). MicroRNA-10a regulation of proinflammatory phenotype in athero-susceptible endothelium in vivo and in vitro. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 107(30), 13450-13455. doi:10.1073/pnas.1002120107

Davies, P. F., Civelek, M., Fang, Y., Guerraty, M. A., & Passerini, A. G. (2010). Endothelial heterogeneity associated with regional athero-susceptibility and adaptation to disturbed blood flow in vivo.. Seminars in thrombosis and hemostasis, 36(3), 265-275. doi:10.1055/s-0030-1253449

Civelek, M., Grant, G. R., Irolla, C. R., Shi, C., Riley, R. J., Chiesa, O. A., . . . Davies, P. F. (2010). Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivo. AMERICAN JOURNAL OF PHYSIOLOGY-HEART AND CIRCULATORY PHYSIOLOGY, 298(1), H163-H170. doi:10.1152/ajpheart.00652.2009

Civelek, M., Grant, G. R., Irolla, C. R., Shi, C., Riley, R. J., Chiesa, O. A., . . . Davies, P. F. (2010). Prelesional arterial endothelial phenotypes in hypercholesterolemia: universal ABCA1 upregulation contrasts with region-specific gene expression in vivo.. American journal of physiology. Heart and circulatory physiology, 298(1), H163-H170. doi:10.1152/ajpheart.00652.2009