Publications

Selected Publications

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(1):1611.

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(1).

Liu, X; Hong, T; Parameswaran, S; Ernst, K; Marazzi, I; Weirauch, MT; Fuxman Bass, JI. Human Virus Transcriptional Regulators. Cell. 2020; 182(1):24-37.

Lambert, SA; Yang, AWH; 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(6):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(5):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(4):650-665.

Zhang, G; Feenstra, B; Bacelis, J; Liu, X; Muglia, LM; Juodakis, J; Miller, DE; Litterman, N; Jiang, P-P; Russell, L; Davey Smith, G; Melbye, M; Jacobsson, B; Muglia, LJ. Genetic Associations with Gestational Duration and Spontaneous Preterm Birth. New England Journal of Medicine. 2017; 377(12):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(8):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(6):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(7457):172-177.

Weirauch, MT; Cote, A; Norel, R; Annala, M; Zhao, Y; Riley, TR; Saez-Rodriguez, J; Cokelaer, T; Vedenko, A; Talukder, S; Bussemaker, HJ; Morris, QD; Bulyk, ML; Stolovitzky, G; Hughes, TR. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 2013; 31(2):126-134.

2025

Wheeler, MES; Takahashi, Y; Lee, J; Perez, CT; Chen, X; Lee, Y; Pope, ZS; Lu, DJ; Seldin, M; Marazzi, I; Yun, H; Weirauch, MT; Byun, M. Convergent DNA methylation abnormalities at enhancers and bivalent promoters in human growth disorders. Epigenetics and Chromatin. 2025.

Shook, MS; Lu, X; Chen, X; Edsall, LE; Granitto, M; Virolainen, SJ; Forney, C; Donmez, OA; Parameswaran, S; Fadden, C; Martin, LJ; Satish, L; Weirauch, MT; Kottyan, LC. Massively parallel analysis of genotype-dependent enhancer activity among atopic dermatitis genetic risk variants. Journal of Allergy and Clinical Immunology. 2025; 156(6):1600-1613.

Felton, JM; Edsall, LE; Troutman, TD; Mack, L; Kotliar, M; Morgenstern, NB-B; Psaila, AM; Rochman, M; Klingler, AM; Osswald, GA; Barski, A; Quinlan, KGR; Weirauch, MT; Rothenberg, ME. Epigenetic and transcriptional programming of murine eosinophils in the esophagus. Nature Communications. 2025; 16(1):10454.

Granitto, M; Parks, L; Shook, MS; Forney, C; Chen, X; Edsall, LE; Donmez, OA; Parameswaran, S; Fisher, KS; Zabeti, A; Lawson, LP; Weirauch, MT; Kottyan, LC. Genome-wide discovery of multiple sclerosis genetic risk variant allelic regulatory activity. G3: Genes, Genomes, Genetics. 2025; 15(11).

Vorontsov, IE; Kozin, I; Abramov, S; Boytsov, A; Jolma, A; Albu, M; Ambrosini, G; Faltejskova, K; Gralak, AJ; Gryzunov, N; Kolpakov, FA; Makeev, VJ; Hughes, TR; Kulakovskiy, IV. Cross-platform motif discovery and benchmarking to explore binding specificities of poorly studied human transcription factors. Communications Biology. 2025; 8(1):1545.

Fleifil, Y; Gulati, R; Jennings, K; Kycia, I; Bondoc, A; Tiao, G; Geller, J; Weirauch, M; Vakili, K; Timchenko, L; Timchenko, N. β-Catenin-Cohesin Ring-CEGRs/ALCDs Axis Activation Contributes to the Development of Hepatoblastoma and Fibrolamellar HCC. Molecular Cancer Research. 2025; 23(11):901-912.

Sayeed, K; Parameswaran, S; Beucler, MJ; Edsall, LE; Vonhandorf, A; Crowther, A; Donmez, OA; Hass, MR; Richards, S; Forney, CR; Zhao, B; Miller, WE; Kottyan, LC; Weirauch, MT. Human cytomegalovirus infection coopts chromatin organization to diminish TEAD1 transcription factor activity. eLife. 2025; 13.

Sasse, A; Ray, D; Laverty, KU; Tam, CL; Albu, M; Zheng, H; Levdansky, Y; Lyudovyk, O; Dalal, T; Nie, K; Valkov, E; Weirauch, MT; Hughes, TR; Morris, Q. A resource of RNA-binding protein motifs across eukaryotes reveals evolutionary dynamics and gene-regulatory function. Nature Biotechnology. 2025.

Secchia, S; Beilinson, V; Chen, X; Gucwa, M; Denson, LA; Miraldi, ER; Weirauch, MT; Ikegami, K. Starvation activates ECM-remodeling gene transcription and putative enhancers in fibroblasts despite inducing quiescence. Cell reports. 2025; 44(7):115896.

Lape, M; Schnell, D; Parameswaran, S; Ernst, K; O'connor, S; Salomonis, N; Martin, LJ; Harnett, BM; Kottyan, LC; Weirauch, MT. A survey of pathogenic involvement in non-communicable human diseases. Communications Medicine. 2025; 5(1):242.

Lawson, LP; Parameswaran, S; Panganiban, RA; Constantine, GM; Weirauch, MT; Kottyan, LC. Update on the genetics of allergic diseases. Journal of Allergy and Clinical Immunology. 2025; 155(6):1738-1752.

Venkatasubramanian, M; Schwartz, L; Ramachandra, N; Bennett, J; Subramanian, KR; Chen, X; Gordon-Mitchell, S; Fromowitz, A; Pradhan, K; Shechter, D; Grimes, HL; Starczynowski, DT; Verma, A; Salomonis, N. Splicing regulatory dynamics for precision analysis and treatment of heterogeneous leukemias. Science Translational Medicine. 2025; 17(797):eadr1471.

Uscategui Calderon, M; Spaeth, ML; Granitto, M; Gonzalez, BA; Weirauch, MT; Kottyan, LC; Yutzey, KE. GDF10 promotes rodent cardiomyocyte maturation during the postnatal period. Journal of Molecular and Cellular Cardiology. 2025; 201:16-31.

Bedard, MC; Rivera-Cruz, CM; Chihanga, T; Vonhandorf, A; Tang, AL; Zender, C; Weirauch, MT; Ferris, R; Wise-Draper, TM; Adam, M; Wells, SI. A Single-Cell Transcriptome Atlas of Epithelial Subpopulations in HPV-Positive and HPV-Negative Head and Neck Cancers. Viruses. 2025; 17(4).

Yoneyama, Y; Zhang, R-R; Maezawa, M; Masaki, H; Kimura, M; Cai, Y; Adam, M; Parameswaran, S; Mizuno, N; Bhadury, J; Nakauchi, H; Potter, SS; Weirauch, MT; Takebe, T. Intercellular mRNA transfer alters the human pluripotent stem cell state. Proceedings of the National Academy of Sciences of the United States of America. 2025; 122(4):e2413351122.

Brown, AP; Parameswaran, S; Cai, L; Elston, S; Pham, C; Barski, A; Weirauch, MT; Ji, H. Silencing TET1 expression alters the epigenomic landscape and amplifies transcriptomic responses to allergen in airway epithelial cells. Environmental Epigenetics. 2025; 11(1):dvaf007.

2024

Koritala, BSC; Parameswaran, S; Donmez, OA; Forney, C; Rowden, H; Moore, CA; Duggins, AL; Sestito, A; Leader, BA; Weirauch, MT; Kottyan, LC; Smith, DF. Genome-wide epigenetic profiling and transcriptome analysis in pediatric Obstructive Sleep Apnea: A focus on Black female children. Heliyon. 2024; 10(23):e40830.

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(1):9372.

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.

Wang, Q; Kim, T; Martínez-Bonet, M; Aguiar, VRC; 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(1):6804.

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(5):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(9).

Viel, KCMF; 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(1):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(1):2150.

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. American Journal of Human Genetics. 2024; 111(2):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(6681):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(730):eade2886.

Shippy, TD; Hosmani, PS; Flores-Gonzalez, M; Mann, M; Miller, S; Weirauch, MT; Vosberg, C; Massimino, C; Tank, W; De Oliveira, L; Mueller, LA; Brown, SJ; D'elia, T; Saha, S. Diaci v3.0: chromosome-level assembly, de novo transcriptome, and manual annotation of Diaphorina citri, insect vector of Huanglongbing. GigaScience. 2024; 13.

2023

Torre, D; Fstkchyan, YS; Ho, JSY; Cheon, Y; Patel, RS; Degrace, EJ; Mzoughi, S; Schwarz, M; Mohammed, K; Seo, J-S; Rosenberg, BR; Benner, C; Guccione, E; Marazzi, I. Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Molecular Cell. 2023; 83(23):4255-4271.e9.

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(11):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(10):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(10).

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(1):258.

Cain, B; Webb, J; Yuan, Z; Cheung, D; Lim, H-W; Kovall, RA; Weirauch, MT; Gebelein, B. Prediction of cooperative homeodomain DNA binding sites from high-throughput-SELEX data. Nucleic Acids Research (NAR). 2023; 51(12):6055-6072.

Kiryluk, K; Sanchez-Rodriguez, E; Zhou, X-J; Zanoni, F; Liu, L; Mladkova, N; Khan, A; Marasa, M; Zhang, JY; Balderes, O; Novak, J; Scolari, F; Zhang, H; Gharavi, AG. Genome-wide association analyses define pathogenic signaling pathways and prioritize drug targets for IgA nephropathy. Nature Genetics. 2023; 55(7):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(5):834-845.

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(1):1975.

Wang, C; Liu, X; Liang, J; Narita, Y; Ding, W; Li, D; Zhang, L; Wang, H; Leong, MML; Hou, I; Zeng, M-S; Jiang, S; Teng, M; Zhao, B. A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth. Nature Communications. 2023; 14(1):1598.

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. 2023; 24(1):50.

Virolainen, SJ; Vonhandorf, A; Viel, KCMF; Weirauch, MT; Kottyan, LC. Gene-environment interactions and their impact on human health. Genes and Immunity. 2023; 24(1):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; Prasath, VBS; Miraldi, ER. maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. PLoS Computational Biology. 2023; 19(1):e1010863.

2022

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(5):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 (United Kingdom). 2022; 101(41):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(10):2950-2963.

Zhao, Y; Vartak, SV; Conte, A; Wang, X; Garcia, DA; Stevens, E; Kyoung Jung, S; Kieffer-Kwon, K-R; 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(18):3398-3411.e11.

Fagg, WS; Liu, N; Braunschweig, U; Pereira De Castro, KL; 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(9):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. PLoS Genetics. 2022; 18(5):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. 2022; 208(Supplement_1):104.09-104.09.

Zhou, T; Zhu, X; Ye, Z; Wang, Y-F; 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(1):1855.

Fu, H; Zheng, H; Chen, X; Weirauch, MT; Muglia, LJ; Wang, L; Liu, Y. NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. bioRxiv. 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(635):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(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(1):79-88.

Weirauch Research LabPublications

Connect With Us

Weirauch Research Lab
Publications