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Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; de Boer, CG; Harley, JB; Weirauch, MT; Kottyan, LC. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12.

Liu, X; Hong, T; Parameswaran, S; Ernst, K; Marazzi, I; Weirauch, MT; Bass, JI F. Human Virus Transcriptional Regulators. Cell. 2020; 182:24-37.

Lambert, SA; Yang, AW H; Sasse, A; Cowley, G; Albu, M; Caddick, MX; Morris, QD; Weirauch, MT; Hughes, TR. Similarity regression predicts evolution of transcription factor sequence specificity. Nature Genetics. 2019; 51:981-989.

Harley, JB; Chen, X; Pujato, M; Miller, D; Maddox, A; Forney, C; Magnusen, AF; Lynch, A; Chetal, K; Yukawa, M; Barski, A; Salomonis, N; Kaufman, KM; Kottyan, LC; Weirauch, MT. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nature Genetics. 2018; 50:699-707.

Lambert, SA; Jolma, A; Campitelli, LF; Das, PK; Yin, Y; Albu, M; Chen, X; Taipale, J; Hughes, TR; Weirauch, MT. The Human Transcription Factors. Cell. 2018; 172:650-665.

Zhang, G; Feenstra, B; Bacelis, J; Liu, X; Muglia, LM; Juodakis, J; Miller, DE; Litterman, N; Jiang, P; Russell, L; Smith, GD; Melbye, M; Jacobsson, B; Muglia, LJ. Genetic Associations with Gestational Duration and Spontaneous Preterm Birth. The New England Journal of Medicine. 2017; 377:1156-1167.

Alipanahi, B; Delong, A; Weirauch, MT; Frey, BJ. Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning. Nature Biotechnology. 2015; 33:831-838.

Weirauch, MT; Yang, A; Albu, M; Cote, AG; Montenegro-Montero, A; Drewe, P; Najafabadi, HS; Lambert, SA; Mann, I; Cook, K; Ratsch, G; Larrondo, LF; Ecker, JR; Hughes, TR. Determination and inference of eukaryotic transcription factor sequence specificity. Cell. 2014; 158:1431-1443.

Ray, D; Kazan, H; Cook, KB; Weirauch, MT; Najafabadi, HS; Li, X; Gueroussov, S; Albu, M; Zheng, H; Yang, A; Fraser, AG; Blencowe, BJ; Morris, QD; Hughes, TR. A compendium of RNA-binding motifs for decoding gene regulation. Nature. 2013; 499:172-177.

Weirauch, MT; Cote, A; Norel, R; Annala, M; Zhao, Y; Riley, TR; Saez-Rodriguez, J; Cokelaer, T; Vedenko, A; Talukder, S; Bulyk, ML; Stolovitzky, G; Hughes, TR; Consortium, D. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 2013; 31:126-134.

Wang, Q; Kim, T; Martínez-Bonet, M; Aguiar, VR C; Sim, S; Cui, J; Sparks, JA; Chen, X; Todd, M; Wauford, B; Marion, MC; Langefeld, CD; Weirauch, MT; Gutierrez-Arcelus, M; Nigrovic, PA. High-throughput identification of functional regulatory SNPs in systemic lupus erythematosus. Nature Communications. 2024; 15:6804.

Sun, C; Swoboda, CO; Morales, FM; Calvo, C; Petrany, MJ; Parameswaran, S; VonHandorf, A; Weirauch, MT; Lepper, C; Millay, DP. Lineage tracing of nuclei in skeletal myofibers uncovers distinct transcripts and interplay between myonuclear populations. Nature Communications. 2024; 15:9372.

Viel, KC M F; Parameswaran, S; Donmez, OA; Forney, CR; Hass, MR; Yin, C; Jones, SH; Prosser, HK; Diouf, AA; Gittens, OE; Gewurz, B; Zhao, B; Kottyan, LC; Weirauch, MT. Shared and distinct interactions of type 1 and type 2 Epstein-Barr Nuclear Antigen 2 with the human genome. BMC Genomics. 2024; 25:273.

Kim, T; Martínez-Bonet, M; Wang, Q; Hackert, N; Sparks, JA; Baglaenko, Y; Koh, B; Darbousset, R; Laza-Briviesca, R; Chen, X; Weirauch, MT; Raychaudhuri, S; Rao, DA; Nigrovic, PA. Non-coding autoimmune risk variant defines role for ICOS in T peripheral helper cell development. Nature Communications. 2024; 15:2150.

Shook, MS; Lu, X; Chen, X; Edsall, LE; Granitto, M; Virolainen, SJ; Forney, C; Donmez, OA; Parameswaran, S; Fadden, C; Martin, L; Satish, L; Weirauch, MT; Kottyan, LC. Massively Parallel Analysis of Genotype-Dependent Enhancer Activity Among Atopic Dermatitis Genetic Risk Variants. 2024.

Dourson, AJ; Fadaka, AO; Warshak, AM; Paranjpe, A; Weinhaus, B; Queme, LF; Hofmann, MC; Evans, HM; Donmez, OA; Forney, C; Weirauch, MT; Kottyan, LC; Lucas, D; Deepe, GS; Jankowski, MP. Macrophage memories of early-life injury drive neonatal nociceptive priming. Cell Reports. 2024; 43:114129.

Virolainen, SJ; Satish, L; Biagini, JM; Chaib, H; Chang, WC; Dexheimer, PJ; Dixon, MR; Dunn, K; Fletcher, D; Forney, C; Shook, M; Weirauch, MT; Khurana Hershey, GK; Kottyan, LC. Filaggrin loss-of-function variants are associated with atopic dermatitis phenotypes in a diverse, early-life prospective cohort. JCI insight. 2024; 9:e178258.

Shook, MS; Lu, X; Chen, X; Parameswaran, S; Edsall, L; Trimarchi, MP; Ernst, K; Granitto, M; Forney, C; Donmez, OA; Diouf, AA; VonHandorf, A; Rothenberg, ME; Weirauch, MT; Kottyan, LC. Systematic identification of genotype-dependent enhancer variants in eosinophilic esophagitis. The American Journal of Human Genetics. 2024; 111:280-294.

Dai, D; Gu, S; Han, X; Ding, H; Jiang, Y; Zhang, X; Yao, C; Hong, S; Zhang, J; Shen, Y; Kottyan, LC; Weirauch, MT; Vinuesa, CG; Shen, N. The transcription factor ZEB2 drives the formation of age-associated B cells. Science. 2024; 383:413-421.

Li, G; Mahajan, S; Ma, S; Jeffery, ED; Zhang, X; Bhattacharjee, A; Venkatasubramanian, M; Weirauch, MT; Miraldi, ER; Grimes, HL; Sheynkman, GM; Tilburgs, T; Salomonis, N. Splicing neoantigen discovery with SNAF reveals shared targets for cancer immunotherapy. Science Translational Medicine. 2024; 16:eade2886.

Torre, D; Fstkchyan, YS; Ho, JS Y; Cheon, Y; Patel, RS; Degrace, EJ; Mzoughi, S; Schwarz, M; Mohammed, K; Seo, JS; Rosenberg, BR; Benner, C; Guccione, E; Marazzi, I. Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Molecular Cell. 2023; 83:4255-4271.e9.

Wang, C; Liu, X; Liang, J; Narita, Y; Ding, W; Li, D; Zhang, L; Wang, H; Leong, MM L; Hou, I; Zeng, MS; Jiang, S; Teng, M; Zhao, B. A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth. Nature Communications. 2023; 14:1598.

Wang, L; Rossi, RM; Chen, X; Chen, J; Runyon, J; Chawla, M; Miller, D; Forney, C; Lynch, A; Zhang, X; Kottyan, LC; Weirauch, MT; Zhang, G; Muglia, LJ. A functional mechanism for a non-coding variant near AGTR2 associated with risk for preterm birth. BMC Medicine. 2023; 21:258.

Fu, H; Zheng, H; Chen, X; Weirauch, MT; Muglia, LJ; Wang, L; Liu, Y. NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. Genome Biology: biology for the post-genomic era. 2023; 24:50.

Bedard, MC; Chihanga, T; Carlile, A; Jackson, R; Brusadelli, MG; Lee, D; VonHandorf, A; Rochman, M; Dexheimer, PJ; Chalmers, J; Lambert, PF; Adam, M; Steven Potter, S; Wells, SI. Single cell transcriptomic analysis of HPV16-infected epithelium identifies a keratinocyte subpopulation implicated in cancer. Nature Communications. 2023; 14:1975.

Wang, Q; Martínez-Bonet, M; Kim, T; Sparks, JA; Ishigaki, K; Chen, X; Sudman, M; Aguiar, V; Sim, S; Hernandez, MC; Weirauch, MT; Langefeld, CD; Thompson, SD; Nigrovic, PA. Identification of a regulatory pathway governing TRAF1 via an arthritis-associated non-coding variant. Cell Genomics. 2023; 3:100420.

Meibers, HE; Warrick, KA; VonHandorf, A; Vallez, CN; Kawarizadeh, K; Saha, I; Donmez, O; Jain, VG; Kottyan, LC; Weirauch, MT; Pasare, C. Effector memory T cells induce innate inflammation by triggering DNA damage and a non-canonical STING pathway in dendritic cells. Cell Reports. 2023; 42:113180.

Dexheimer, PJ; Pujato, M; Roskin, KM; Weirauch, MT. VExD: a curated resource for human gene expression alterations following viral infection. Editor, McIntyre L. G3-Genes Genomes Genetics. 2023; 13:jkad176.

Cain, B; Webb, J; Yuan, Z; Cheung, D; Lim, HW; Kovall, RA; Weirauch, MT; Gebelein, B. Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data. Nucleic Acids Research (NAR). 2023; 51:6055-6072.

Kiryluk, K; Sanchez-Rodriguez, E; Zhou, XJ; Zanoni, F; Liu, L; Mladkova, N; Khan, A; Marasa, M; Zhang, JY; Balderes, O; Savoldi, S; Spotti, D; Zamboli, P; Izzi, C. Genome-wide association analyses define pathogenic signaling pathways and prioritize drug targets for IgA nephropathy. Nature Genetics. 2023; 55:1091-1105.

Brusilovsky, M; Rochman, M; Shoda, T; Kotliar, M; Caldwell, JM; Mack, LE; Besse, JA; Chen, X; Weirauch, MT; Barski, A; Rothenberg, ME. Vitamin D receptor and STAT6 interactome governs oesophageal epithelial barrier responses to IL-13 signalling. Gut. 2023; 72:834-845.

Virolainen, SJ; VonHandorf, A; Viel, KC M F; Weirauch, MT; Kottyan, LC. Gene-environment interactions and their impact on human health. Genes and Immunity. 2023; 24:1-11.

Cazares, TA; Rizvi, FW; Iyer, B; Chen, X; Kotliar, M; Bejjani, AT; Wayman, JA; Donmez, O; Wronowski, B; Parameswaran, S; Kottyan, LC; Barski, A; Weirauch, MT; Surya Prasath, VB; Miraldi, ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. Editor, Przytycka TM. PLoS Computational Biology. 2023; 19:e1010863.

Zhou, T; Zhu, X; Ye, Z; Wang, YF; Yao, C; Xu, N; Zhou, M; Ma, J; Qin, Y; Shen, Y; Kottyan, LC; Weirauch, MT; Hou, G; Shen, N. Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery. Nature Communications. 2022; 13:1855.

Namjou, B; Lape, M; Malolepsza, E; DeVore, SB; Weirauch, MT; Dikilitas, O; Jarvik, GP; Kiryluk, K; Kullo, IJ; Liu, C; Biagini, JM; Khurana Hershey, GK; Martin, LJ; Kottyan, L. Multiancestral polygenic risk score for pediatric asthma. Journal of Allergy and Clinical Immunology. 2022; 150:1086-1096.

Sawyer, RP; Stone, HK; Salim, H; Lu, X; Weirauch, MT; Kottyan, L. Frontotemporal degeneration genetic risk loci and transcription regulation as a possible mechanistic link to disease risk. Medicine; analytical reviews of general medicine, neurology, psychiatry, dermatology, and pediatries. 2022; 101:e31078.

Gulati, R; Johnston, M; Rivas, M; Cast, A; Kumbaji, M; Hanlon, MA; Lee, S; Zhou, P; Lake, C; Schepers, E; Geller, J; Tiao, G; Shin, S; Timchenko, N. β-catenin cancer-enhancing genomic regions axis is involved in the development of fibrolamellar hepatocellular carcinoma. Hepatology Communications. 2022; 6:2950-2963.

Zhao, Y; Vartak, SV; Conte, A; Wang, X; Garcia, DA; Stevens, E; Kyoung Jung, S; Kieffer-Kwon, KR; Vian, L; Stodola, T; Upadhyaya, A; Weirauch, MT; Hager, G; Casellas, R. "Stripe " transcription factors provide accessibility to co-binding partners in mammalian genomes. Molecular Cell. 2022; 82:3398-3411.e11.

Fagg, WS; Liu, N; Braunschweig, U; de Castro, KL P; Chen, X; Ditmars, FS; Widen, SG; Donohue, JP; Modis, K; Russell, WK; Fair, JH; Weirauch, MT; Blencowe, BJ; Garcia-Blanco, MA. Definition of germ layer cell lineage alternative splicing programs reveals a critical role for Quaking in specifying cardiac cell fate. Nucleic Acids Research (NAR). 2022; 50:5313-5334.

Eapen, AA; Parameswaran, S; Forney, C; Edsall, LE; Miller, D; Donmez, O; Dunn, K; Lu, X; Granitto, M; Rowden, H; Devonshire, AL; Rothenberg, ME; Weirauch, MT; Kottyan, LC. Epigenetic and transcriptional dysregulation in CD4+ T cells in patients with atopic dermatitis. Editor, Absher DM. PLoS Genetics. 2022; 18:e1009973.

Kim, E; Forney, C; Viel, K; O'Brien, M; Nelson, C; Gecaine, P; Zabeti, A; Weirauch, M; Kottyan, L. Enrichment of Epstein Barr Virus in patients with Multiple Sclerosis. Journal of immunology (Baltimore, Md. : 1950). 2022; 208:104.09.

Fu, H; Zheng, H; Chen, X; Weirauch, M; Muglia, L; Wang, L; Liu, Y. NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. 2022; 2022.03.29.486102.

Barreyro, L; Sampson, AM; Ishikawa, C; Hueneman, KM; Choi, K; Pujato, MA; Chutipongtanate, S; Wyder, M; Haffey, WD; O'Brien, E; Greis, KD; Nurmemmedov, E; Seibel, WL; Starczynowski, DT. Blocking UBE2N abrogates oncogenic immune signaling in acute myeloid leukemia. Science Translational Medicine. 2022; 14:eabb7695.

Bray, D; Hook, H; Zhao, R; Keenan, JL; Penvose, A; Osayame, Y; Mohaghegh, N; Chen, X; Parameswaran, S; Kottyan, LC; Weirauch, MT; Siggers, T. CASCADE: high-throughput characterization of regulatory complex binding altered by non-coding variants. Cell Genomics. 2022; 2:100098.

Murrison, LB; Ren, X; Preusse, K; He, H; Kroner, J; Chen, X; Jenkins, S; Johansson, E; Biagini, JM; Weirauch, MT; Kopan, R; Martin, LJ; Khurana Hershey, GK. TSLP disease-associated genetic variants combined with airway TSLP expression influence asthma risk. Journal of Allergy and Clinical Immunology. 2022; 149:79-88.

Hou, G; Harley, IT W; Lu, X; Zhou, T; Xu, N; Yao, C; Qin, Y; Ouyang, Y; Ma, J; Zhu, X; Weirauch, MT; Kottyan, LC; Harley, JB; Shen, N. SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression. Nature Communications. 2021; 12:135.

Alizada, A; Khyzha, N; Wang, L; Antounians, L; Chen, X; Khor, M; Liang, M; Rathnakumar, K; Weirauch, MT; Medina-Rivera, A; Fish, JE; Wilson, MD. Conserved regulatory logic at accessible and inaccessible chromatin during the acute inflammatory response in mammals. Nature Communications. 2021; 12:567.

Olafson, PU; Aksoy, S; Attardo, GM; Buckmeier, G; Chen, X; Coates, CJ; Davis, M; Dykema, J; Emrich, SJ; Friedrich, M; Werren, JH; Wilson, RK; Zdobnov, EM; Benoit, JB. The genome of the stable fly, Stomoxys calcitrans, reveals potential mechanisms underlying reproduction, host interactions, and novel targets for pest control. BMC Biology. 2021; 19:41.

Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; de Boer, CG; Harley, JB; Weirauch, MT; Kottyan, LC. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12:1611.

Herman, EK; Greninger, A; van der Giezen, M; Ginger, ML; Ramirez-Macias, I; Miller, HC; Morgan, MJ; Tsaousis, AD; Velle, K; Vargová, R; Puzon, GJ; Walsh, T; Chiu, C; Dacks, JB. Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri. BMC Biology. 2021; 19:142.

Singh, B; Maiti, GP; Zhou, X; Fazel-Najafabadi, M; Bae, SC; Sun, C; Terao, C; Okada, Y; Heng Chua, K; Kochi, Y; Harley, JB; Varshney, GK; Looger, LL; Nath, SK. Lupus Susceptibility Region Containing CDKN1B rs34330 Mechanistically Influences Expression and Function of Multiple Target Genes, Also Linked to Proliferation and Apoptosis. Arthritis and Rheumatology. 2021; 73:2303-2313.

Hong, T; Parameswaran, S; Donmez, OA; Miller, D; Forney, C; Lape, M; Ribeiro, MS J; Liang, J; Edsall, LE; Magnusen, AF; Harley, JB; Zhao, B; Kottyan, LC; Weirauch, MT. Epstein-Barr virus nuclear antigen 2 extensively rewires the human chromatin landscape at autoimmune risk loci. Genome research. 2021; 31:2185-2198.

Kiryluk, K; Sanchez-Rodriguez, E; Zhou, X; Zanoni, F; Liu, L; Mladkova, N; Khan, A; Marasa, M; Zhang, J; Balderes, O; Novak, J; Scolari, F; Zhang, H; Gharavi, A. GWAS defines pathogenic signaling pathways and prioritizes drug targets for IgA nephropathy. 2021; 2021.11.19.21265383.

Felton, JM; Bouffi, C; Schwartz, JT; Schollaert, KL; Malik, A; Vallabh, S; Wronowski, B; Magier, AZ; Merlin, L; Barski, A; Weirauch, MT; Fulkerson, PC; Rothenberg, ME. Aiolos regulates eosinophil migration into tissues. Mucosal Immunology. 2021; 14:1271-1281.

Johnston, ME; Rivas, MP; Nicolle, D; Gorse, A; Gulati, R; Kumbaji, M; Weirauch, MT; Bondoc, A; Cairo, S; Geller, J; Tiao, G; Timchenko, N. Olaparib Inhibits Tumor Growth of Hepatoblastoma in Patient-Derived Xenograft Models. Hepatology. 2021; 74:2201-2215.

Kuang, Y; Pyo, A; Eafergan, N; Cain, B; Gutzwiller, LM; Axelrod, O; Gagliani, EK; Weirauch, MT; Kopan, R; Kovall, RA; Sprinzak, D; Gebelein, B. Enhancers with cooperative Notch binding sites are more resistant to regulation by the Hairless co-repressor. Editor, Aster JC. PLoS Genetics. 2021; 17:e1009039.

Felton, JM; Vallabh, S; Parameswaran, S; Edsall, LE; Ernst, K; Wronowski, B; Malik, A; Kotliar, M; Weirauch, MT; Barski, A; Fulkerson, PC; Rothenberg, ME. Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. Journal of immunology (Baltimore, Md. : 1950). 2021; 207:1044-1054.

Korinfskaya, S; Parameswaran, S; Weirauch, MT; Barski, A. Runx Transcription Factors in T Cells-What Is Beyond Thymic Development?. Frontiers in Immunology. 2021; 12:701924.

Zhou, T; Zhu, X; Ye, Z; Wang, Y; Yao, C; Xu, N; Zhou, M; Ma, J; Qin, Y; Shen, Y; Kottyan, L; Weirauch, M; Hou, G; Shen, N. CRISPRa screen on a genetic risk locus shared by multiple autoimmune diseases identifies a dysfunctional enhancer that affects IRF8 expression through cooperative lncRNA and DNA methylation machinery. 2021; 2021.06.11.448156.

Hass, MR; Brissette, D; Parameswaran, S; Pujato, M; Donmez, O; Kottyan, LC; Weirauch, MT; Kopan, R. Runx1 shapes the chromatin landscape via a cascade of direct and indirect targets. Editor, Greally JM. PLoS Genetics. 2021; 17:e1009574.

Moreno-Fernandez, ME; Giles, DA; Oates, JR; Chan, CC; Damen, MS M A; Doll, JR; Stankiewicz, TE; Chen, X; Chetal, K; Karns, R; Inge, TH; Deshmukh, H; Salomonis, N; Divanovic, S. PKM2-dependent metabolic skewing of hepatic Th17 cells regulates pathogenesis of non-alcoholic fatty liver disease. Cell Metabolism. 2021; 33:1187-1204.e9.

Johansson, E; Martin, LJ; He, H; Chen, X; Weirauch, MT; Kroner, JW; Khurana Hershey, GK; Biagini, JM. Second-hand smoke and NFE2L2 genotype interaction increases paediatric asthma risk and severity. Clinical and Experimental Allergy. 2021; 51:801-810.

Zhu, T; Zhang, X; Chen, X; Brown, AP; Weirauch, MT; Guilbert, TW; Khurana Hershey, GK; Biagini, JM; Ji, H. Nasal DNA methylation differentiates severe from non-severe asthma in African-American children. Allergy: European Journal of Allergy and Clinical Immunology. 2021; 76:1836-1845.

Ho, JS Y; Mok, BW Y; Campisi, L; Jordan, T; Yildiz, S; Parameswaran, S; Wayman, JA; Gaudreault, NN; Meekins, DA; Indran, SV; Chen, H; Benner, C; Richt, JA; Marazzi, I. TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation. Cell. 2021; 184:2618-2632.e17.

Yin, X; Kim, K; Suetsugu, H; Bang, SY; Wen, L; Koido, M; Ha, E; Liu, L; Sakamoto, Y; Jo, S; Zhang, X; Terao, C; Cui, Y; Bae, SC. Meta-analysis of 208370 East Asians identifies 113 susceptibility loci for systemic lupus erythematosus. Annals of the Rheumatic Diseases. 2021; 80:632-640.

Schott, G; Munoz, GG; Trevino, N; Chen, X; Weirauch, MT; Gregory, SG; Bradrick, SS; Blanco, MA G. U2AF2 binds IL7R exon 6 ectopically and represses its inclusion. RNA: A publication of the RNA Society. 2021; 27:571-583.

Chidambaran, V; Zhang, X; Pilipenko, V; Chen, X; Wronowski, B; Geisler, K; Martin, LJ; Barski, A; Weirauch, MT; Ji, H. Methylation quantitative trait locus analysis of chronic postsurgical pain uncovers epigenetic mediators of genetic risk. Epigenomics. 2021; 13:613-630.

Santiago, IJ; Zhang, D; Saras, A; Pontillo, N; Xu, C; Chen, X; Weirauch, MT; Mistry, M; Ginty, DD; Pecot, MY; Peng, J. Drosophila Fezf functions as a transcriptional repressor to direct layer-specific synaptic connectivity in the fly visual system. Proceedings of the National Academy of Sciences of USA. 2021; 118:e2025530118.

Song, R; Gao, Y; Dozmorov, I; Malladi, V; Saha, I; McDaniel, MM; Parameswaran, S; Liang, C; Arana, C; Zhang, B; Weirauch, MT; Kottyan, LC; Wakeland, EK; Pasare, C. IRF1 governs the differential interferon-stimulated gene responses in human monocytes and macrophages by regulating chromatin accessibility. Cell Reports. 2021; 34:108891.

Lu, X; Chen, X; Forney, C; Donmez, O; Miller, D; Parameswaran, S; Hong, T; Huang, Y; Pujato, M; Cazares, T; de Boer, CG; Harley, JB; Weirauch, MT; Kottyan, LC. Global discovery of lupus genetic risk variant allelic enhancer activity. Nature Communications. 2021; 12.

Miraldi, ER; Chen, X; Weirauch, MT. Deciphering cis-regulatory grammar with deep learning. Nature Genetics. 2021; 53:266-268.

Oatman, N; Dasgupta, N; Arora, P; Choi, K; Gawali, MV; Gupta, N; Parameswaran, S; Salomone, J; Reisz, JA; Lawler, S; Weirauch, MT; D'Alessandro, A; Komurov, K; Dasgupta, B. Mechanisms of stearoyl CoA desaturase inhibitor sensitivity and acquired resistance in cancer. Science Advances. 2021; 7:eabd7459.

Stone, HK; Parameswaran, S; Eapen, AA; Chen, X; Harley, JB; Devarajan, P; Weirauch, MT; Kottyan, L. Comprehensive Review of Steroid-Sensitive Nephrotic Syndrome Genetic Risk Loci and Transcriptional Regulation as a Possible Mechanistic Link to Disease Risk. Kidney International Reports. 2021; 6:187-195.

Kottyan, LC; Trimarchi, MP; Lu, X; Caldwell, JM; Maddox, A; Parameswaran, S; Lape, M; D'Mello, RJ; Bonfield, M; Ballaban, A; Eapen, AA; Wen, T; Weirauch, MT; Rothenberg, ME. Replication and meta-analyses nominate numerous eosinophilic esophagitis risk genes. Journal of Allergy and Clinical Immunology. 2021; 147:255-266.

Petrany, MJ; Swoboda, CO; Sun, C; Chetal, K; Chen, X; Weirauch, MT; Salomonis, N; Millay, DP. Single-nucleus RNA-seq identifies transcriptional heterogeneity in multinucleated skeletal myofibers. Nature Communications. 2020; 11:6374.

Sirvent, S; Vallejo, AF; Davies, J; Clayton, K; Wu, Z; Woo, J; Riddell, J; Chaudhri, VK; Stumpf, P; Nazlamova, LA; Friedmann, PS; Weirauch, MT; Singh, H; Polak, ME. Genomic programming of IRF4-expressing human Langerhans cells. Nature Communications. 2020; 11:313.

Sparks, ME; Bansal, R; Benoit, JB; Blackburn, MB; Chao, H; Chen, M; Cheng, S; Childers, C; Dinh, H; Doddapaneni, HV; Werren, JH; Worley, KC; Zdobnov, EM; Gundersen-Rindal, DE. Brown marmorated stink bug, Halyomorpha halys (Stål), genome: putative underpinnings of polyphagy, insecticide resistance potential and biology of a top worldwide pest. BMC Genomics. 2020; 21:227.

Rotenberg, D; Baumann, AA; Ben-Mahmoud, S; Christiaens, O; Dermauw, W; Ioannidis, P; Jacobs, CG C; Vargas Jentzsch, IM; Oliver, JE; Poelchau, MF; Whitfield, AE; Zdobnov, EM; Gibbs, RA; Richards, S. Genome-enabled insights into the biology of thrips as crop pests. BMC Biology. 2020; 18:142.

Finch, G; Nandyal, S; Perretta, C; Davies, B; Rosendale, AJ; Holmes, CJ; Gantz, JD; Spacht, DE; Bailey, ST; Chen, X; Matter, SF; Attardo, GM; Weirauch, MT; Benoit, JB. Multi-level analysis of reproduction in an Antarctic midge identifies female and male accessory gland products that are altered by larval stress and impact progeny viability. Scientific Reports. 2020; 10:19791.

Scott, MJ; Benoit, JB; Davis, RJ; Bailey, ST; Varga, V; Martinson, EO; Hickner, PV; Syed, Z; Cardoso, GA; Torres, TT; Sagel, A; Vasquez, M; Quintero, G; Skoda, SR. Genomic analyses of a livestock pest, the New World screwworm, find potential targets for genetic control programs. Communications Biology. 2020; 3:424.

Stevens, ML; Zhang, Z; Johansson, E; Ray, S; Jagpal, A; Ruff, BP; Kothari, A; He, H; Martin, LJ; Ji, H; Wikenheiser-Brokamp, K; Weirauch, MT; Supp, DM; Myers, JM B; Hershey, GK K. Disease-associated KIF3A variants alter gene methylation and expression impacting skin barrier and atopic dermatitis risk. Nature Communications. 2020; 11:4092.

Elliott, KH; Chen, X; Salomone, J; Chaturvedi, P; Schultz, PA; Balchand, SK; Servetas, JD; Zuniga, A; Zeller, R; Gebelein, B; Weirauch, MT; Peterson, KA; Brugmann, SA. Gli3 utilizes Hand2 to synergistically regulate tissue-specific transcriptional networks. eLife. 2020; 9:e56450.

Maezawa, S; Sakashita, A; Yukawa, M; Chen, X; Takahashi, K; Alavattam, KG; Nakata, I; Weirauch, MT; Barski, A; Namekawa, SH. Super-enhancer switching drives a burst in gene expression at the mitosis-to-meiosis transition. Nature Structural and Molecular Biology. 2020; 27:978-988.

Mukherjee, S; Chaturvedi, P; Rankin, SA; Fish, MB; Wlizla, M; Paraiso, KD; MacDonald, M; Chen, X; Weirauch, MT; Blitz, IL; Cho, KW Y; Zorn, AM. Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endoderm gene regulatory network. eLife. 2020; 9:e58029.

Liu, X; Hong, T; Parameswaran, S; Ernst, K; Marazzi, I; Weirauch, MT; Bass, JI F. Human Virus Transcriptional Regulators. Cell. 2020; 182:24-37.

Rajaram, S; Canaday, LM; Ochayon, DE; Rangel, KM; Ali, A; Gyurova, IE; Krishnamurthy, D; Fletcher, JS; Reighard, SD; Cox, A; Deshmukh, H; Zacharias, WJ; Borchers, MT; Waggoner, SN. The Promise and Peril of Natural Killer Cell Therapies in Pulmonary Infection. Immunity. 2020; 52:887-889.

Moncrieffe, H; Dunn, K; Huang, Y; Chen, X; Langefeld, CD; Weirauch, MT; Harley, JB; Kottyan, LC; Thompson, SD. 4277 Functional consequences of the juvenile idiopathic arthritis risk variant at 1q24.3. Journal of Clinical and Translational Science. 2020; 4:95-96.

Laurynenka, V; Ho, D; Huang, Y; Parameswaran, S; Kottyan, LC; Weirauch, MT; Perentesis, J; Kaufman, KM; Mizukawa, B; Harley, JB. The Ikaros1, IKZF1 , risk locus for Acute Lymphoblastic Leukemia (ALL) at chromosome 7p12.2 regulates the expression of the FIGNL1 gene. Journal of immunology (Baltimore, Md. : 1950). 2020; 204:163.15.

Jennings, EC; Korthauer, MW; Hendershot, JM; Bailey, ST; Weirauch, MT; Ribeiro, JM C; Benoit, JB. Molecular mechanisms underlying milk production and viviparity in the cockroach, Diploptera punctata. Insect Biochemistry and Molecular Biology. 2020; 120:103333.

Laurynenka, V; Chen, X; Carter, M; Parameswaran, S; Eswar, S; Kaufman, KM; Namjou, B; Weirauch, MT; Kottyan, LC; Harley, JB. Latency III gene products of Epstein-Barr Virus (EBV) are associated with Systemic Lupus Erythematosus (SLE) genetic risk loci. Journal of immunology (Baltimore, Md. : 1950). 2020; 204:141.2.

Yukawa, M; Jagannathan, S; Vallabh, S; Kartashov, AV; Chen, X; Weirauch, MT; Barski, A. AP-1 activity induced by co-stimulation is required for chromatin opening during T cell activation. The Journal of Experimental Medicine. 2020; 217:e20182009.

Kottyan, LC; Parameswaran, S; Weirauch, MT; Rothenberg, ME; Martin, LJ. The genetic etiology of eosinophilic esophagitis. Journal of Allergy and Clinical Immunology. 2020; 145:9-15.