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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.

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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. G3-Genes Genomes Genetics. 2023; 13.

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.

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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.

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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.

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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.

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.

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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.

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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.

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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.

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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.

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.

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.

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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.

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.

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.

Ji, H; Zhang, X; Myers, JB; Chen, X; Weirauch, M; Guilbert, T; Hershey, GK. DNA methylation Variation Associated with the Severity of Childhood Asthma. Journal of Allergy and Clinical Immunology. 2020; 145:ab344.

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.

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.