Selected Publications

*denotes equal contribution


Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations

Toropainen A, Stolze LK, Ord T, Whalen MB, Torrell PM, Link VM, Kaikkonen MU, Romanoski CE. Genome Res. Feb 22. doi: 10.1101/gr.276064.121.

Systematic analysis of naturally occurring insertions and deletions that alter transcription factor spaving identifies tolerant and sensitive transcription factor pairs

Shen Z, Li RZ, Prohaska TA, Hoeksema MA, Spann NJ, Tao J, Fonseca GJ, Le T, Stolze LK, Sakai M, Romanoski CE, Glass CK. Elife 2022 Jan 20;11:e70878. doi: 10.7554/eLife.70878.

Biological heterogeneity in idiopathic pulmonary arterial hypertension identified through unsupervised transcriptomic profiling of whole blood

Kariotis S, Jammeh E, Swietlik EM, Pickworth JA, Rhodes CJ, Otero P, Wharton J, Iremonger J, Dunning MJ, Pandya D, Mascarenhas TS, Errington N, Thompson AR, Romansoki CE, Rischard F, Garcia JGN, Yuan JX, An TS, Desai AA, Coghlan G, Lordan J, Corris PA, Howard LS, Condliffe R, Kiley DG, Church C, Pepke-Zaba J, Toshner M, Wort S, Graf S, Morrell NW, Wilkins MR, Lawrie A, Wang D, UK National PAH Cohort Study Consortium. Nat Commun. 2021 Dec 7;12(1):7104. doi: 10.1038/241467-021-27326-0.

Sex-specific genetic regulation of adipose mitochondria and metabolic syndrome by Ndufv2

Krishnan KC, Vergnes L, Acin-Perez R, Stiles L, Shum M, Ma L, Mouisel E, Pan C, Moore TM, Peterfy M, Romanoski CE, Reue K, Bjorkegren JLM, Laakso M, Liese M, Lusis AJ. Nat. Metab. 2021 Nov;3(11):1552-1568. doi: 10.1038/s42255-021-00481-w. Epub 2021 Oct 25.

Functional non-coding SNPs in human endothelial cells fine-map vascular trait associations

Toropainen A, Stolze LK, Ord T, Whalen M, Torrell PM, Link VM, Kaikkonen MU, Romanoski CE.

Breast Tumor stiffness instructs bone metastasis via maintenance of mechnaical conditioning

Watson AW, Grant AD, Parker SS, Hill S, Whalen MB, Chakrabarti J, Harman MW, Roman MR, Forte BL, Gowan CC, Castro-Portuguez R, Stolze LK, Franck C, Cusanovich DA, Zavros Y, Padi M, Romanoski CE*, Mouneimne G* (*co-corresponding authors)

Meta-Analysis of Smooth Muscle Lineage Transcriptomes in Atherosclerosis and Their Relationships to In Vitro Models

Conklin AC, Nishi H, Schlamp F, Ord T, Ounap K, Kaikkonen MU, Fisher EA, Romanoski CE. Immunometabolism. doi: 10.20900/immunometab20210022. Epub 2021 May 21. PMID:34178388

Single-cell Epigenomics and Functional Fine-Mapping of Atherosclerosis GWAS Loci

Ord T, Ounap K, Stolze L, Aherrahrou R, Nurminen V, Selvarajan I, Toropainen A, Lonnberg T, Aavik E, Yla-Herttuala S, Civelek M, Romanoski CE, Kaikkonen MU. Circ Res. 2021 May 24: doi: 10.1161/CIRCRESAHA.121.318971. PMID: 34024118

Integrative analysis of liver-specific non-coding regulatory SNPs associated with the risk of coronary artery disease

Selvarajan, I, Toropainen A, Garske KM, Rodeiguez ML, Ko A, Miao Z, Kaminska D, Ounap K, Ord T, Ravindran A, Liu OH, Moreau PR, Deen AJ, Mannistro V, Pan C, Levonen A-L, Lusis AJ, Heikkinen S, Romanoski CE, Pihlajamaki J, Pajukanta P, Kaikkonen MU. Am J Hum Genet. 2021 Feb 18;S0002-9297(21)00048-3. doi: 10.1016/j.ajhg.2021.02.006. PMID: 33626337

Genome-wide analysis identifies novel susceptibility loci for myocardial infarction

Hartiala JA, Han Y, Jia Q, Hilser JR, Huang P, Gukasyan J, Schwartzman WS, Cai Z, Biswas S, Tregouet DA, Smith NL, INVENT Consortium, CHARGE Consortium Hemostasis Working Group, GENIUS-CHD Consortium, Seldin M, Pan C, Mehrabian M, Lusis AJ, Bazeley P, Sun YV, Liu C, Quyyumi AA, Scholz M, Thiery J, Delgado GE, Kleber ME, Marz W, Howe LJ, Asselbergs FW, Vugt MV, Vlachojannis GJ, Patel RS, Lyytikainen LP, Kahonen M, Lehtimaki T, Nieminen TVM, Kuukasjarvi P, Laurikka JO, Chang X, Heng CK, Jiang R, Kraus WE, Hauser ER, Ferguson JF, Reilly MP, Ito K, Koyama S, Kamatani Y, Komuro I, Biobank Japan, Stolze LK, Romanoski CE, Khan MD, Turner AW, Miller CL, Aherrahrou R, Civelek M, Ma L, Bjorkeren JLM, Kumar SR, Tang WHW, Hazen SL, Allayee H. Eur Heart J. 2021 Feb 3;ehaa1040. doi: 10.1093/eurheartj/ehaa1040. PMID: 33532862

CC16 Binding to α4β1 Integrin (VLA-4) Protects Against Mycoplasma pneumoniae Infection

Johnson MD, Younis US, Menghani SV, Addison KJ, Whalen M, Pilon AL, Cress AE, Polverino F, Romanoski CE, Kraft M, Martinez FD, Guerra S, Ledford JG. Am J Respir Crit Card Med. 2020 Dec 16. doi:10.1164/rccm.202006-2576OC. PMID: 33326355.

Transcriptomic profiles in pulmonary arterial hypertension associates with disease severity and identify novel candidate genes

Romanoski CE, Qi X, Sangam S, Vanderpool RR, Stearman RS, Conklin A, Gonzalez-Garay M, Rischard F, Ayon RJ, Wang J, Simonson T, Babicheva A, Shi Y, Tang H, Makino A, Kanthi Y, Geraci MW, Garcia JGN, Yuan JX, Desai AA. Pulm Circ. 2020 Dec 7; 10(4):2045894020968531. doi:10.1177/2045894020968531. PMID: 33343881.

Transcriptional Profiling Suggests T Cells CLuster around Neurons Injected with Toxoplasma gondii Proteins.

Merritt EF, Johnson HJ, Wong ZS, Buntzman AS, Conklin AC, Cabral CM, Romanoski CE, Boyle JP, Koshy AA. mSphere. 2020 Sep 2;5(5):e00538-20. doi:10.1128/mSphere.00538-20. PMID: 32878927; PMCID: PMC7471001.

RV Infections in Asthmatics Increase ACE2 Expression and Cytokine Pathways Implicated in COVID-19.

Chang EH, Willis AL, Romanoski CE, Cusanovich DA, Pouladi N, Li J, Lussier YA, Martinez FD. Am J Respir Crit Care Med. 2020 Jul 10. doi:10.1164/rccm.202004-1343LE.

Systems genetics in human endothelial cells identifies non-coding variants modifying enhancers, expression, and complex disease traits.

Stolze LK, Conklin AC, Whalen MB, Rodriguez ML, Ounap K, Selvarajan I, Toropainen A, Ord T, Li J, Eshgi A, Solomon AE, Fang Y, Kaikkonen MU, Romanoski CE. American Journal of Human Genetics June 2020.

Transcriptomic and epigenetic mechanisms underlying myeloid diversity in the lung.

Sajti E, Link VM, Ouyang Z, Spann NJ, Romanoski CE, Fonesca GJ, Prince LS, Glass CK. Nat Immunol. 2020 Feb;21(2):221-231. doi: 10.1038/s41590-019-0582-z. Epub 2020 Jan 20.

Breast tumor stiffness instructs bone metastasis via mechanical memory.

Watson AW, Grant A, Parker SS, Harman MW, Roman MR, Forte BL, Gowan CC, Castro-Portuguez R, Franck C, Cusanovich D, Padi M, Romanoski CE, Mouneimne G. bioRxiv Nov 20 2019 doi: https://doi.org/10.1101/847699.

An upstream enhancer regulates Gpihbp1 expression in a tissue-specific manner.

Allan CM, Heizer PJ, Tu Y, Sandoval NP, Jung RS, Morales JE, Sajti E, Troutman TD, Saunders TL, Cusanovich DA, Beigneux AP, Romanoski CE, Fong LG, Young SG. J Lipid Res. 2019 Apr;60(4):869-879. 2018 Dec. doi: 10.1194/jlr.M091322.

Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics.

Krause MD, Huang RT, Wu D, Shentu TP, Harrison DL, Whalen MB, Stolze LK, Di Rienzo A, Moskowitz IP, Romanoski CE, Fang Y. PNAS USA, 2018 Nov. pii: 201810568. doi: 10.1073/pnas.1810568115.

Oxidized phospholipids regulate amino acid metabolism through MTHFD2 to facilitate nucleotide release in endothelial cells.

Hitzel J, Lee E, Bibli SI, Li X, Zukunft S, Pflüger B, Hu J, Schürmann C, Vasconez AE, Oo JA, Kratzer A, Kumar S, Rezende F, Josipovic I, Thomas D, Giral H, Schreiber Y, Geisslinger G, Fork C, Yang X, Sigala F, Romanoski CE, Kyoll J, Jo H, Landmesser U, Lusis AJ, Namgaladze D, Fleming I, Leisegana MS, Zhu J, Brandes RP. Nat Commun, 2018 Jun 12;9(1):2292. doi: 10. 1038/s41467-018-04602-0. PMID: 29895827.

MMARGE:Motif Mutation Analysis for Regulatory Genomic Elements.

Link VM, Romanoski CE, Metzler D, Glass CK. Nucleic Acids Res. 2018 Jun 9. doi: 10.1093/nar/gky491. PMID: 29893919.

Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function.

Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, Spann NJ, Strid T, Sakai M, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK. Cell 2018 May 5. pii: S0092-8674(18)30511-7. doi: 10.1016/j.cell.2018.04.018. PMID: 29779944.

Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells

Hogan NT, Whalen MB, Stolze LK, Hadeli NK, Lam MT, Springstead JR, Glass CK, Romanoski CE. eLIFE. 2017 Jun:eLife.22536

Exploiting genomics and natural genetic variation to decode macrophage enhancers

Romanoski CE, Link VM, Heinz S, Glass CK. Trends Immunology. 2015 Sep;36(9):507-18. PMID26298065; PMC4548828.

Epigenomics: Roadmap for regulation

Romanoski CE, Glass CK, Stunnenberg HG, Wilson L, Almouzni G. Nature. 2015 Feb 19;518(7539):314-6. doi: 10.1038/518314a. No abstract available. PMID:25693562

Environment drives selection and function of enhancers controlling tissue-specific macrophage identities

Gosselin DO*, Link V*, Romanoski CE*, Fonseca GJ, Eichenfield DJ, Spann NJ, Stender JD, Chun HB, Garner H, Geissmann F, Glass CK. Cell. 2014 Dec 4;159(6):1327-40. PMID25480297; PMC4364385

Effect of Natural Genetic Variation on Enhancer Selection and Function

Heinz S*, Romanoski CE*, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK. Nature. 2013 Nov 28;503(7477):487-92. PMID24121437; PMC3994126

Network for Activation of Human Endothelial Cells by Oxidized Phospholipids: A Critical Role of Heme Oxygenase 1

Romanoski CE, Che N, Yin F, Mai N, Pouldar D, Civelek M, Pan C, Lee S, Vakili L, Yang W, Kayne PS, Araujo JA, Berliner JA, and Lusis AJ. Circulation Research. 2011 Aug 19;109(5):e27-41. PMID21737788; PMC3163234

Systems Genetics Analysis of Gene-by-Environment Interactions in Human Cells

Romanoski CE, Lee S, Kim MJ, Ingram-Drake L., Plaisier CL, Yordanova R, Tilford C, Guan B, He A, Gargalovic PS, Kirchgessner TG, Berliner JA, Lusis AJ. American Journal of Human Genetics. 2010 Mar 12;86, 399-410. PMID20170901; PMC2833388


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