Weirauch Lab

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; et al. 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; et al. 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; et al. Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity. Cell. 2014; 158:1431-1443.

Kottyan, LC; Davis, BP; Sherrill, JD; Liu, K; Rochman, M; Kaufman, K; Weirauch, MT; Vaughn, S; Lazaro, S; Rupert, AM; et al. Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease. Nature Genetics. 2014; 46:895-900.

Ray, D; Kazan, H; Cook, KB; Weirauch, MT; Najafabadi, HS; Li, X; Gueroussov, S; Albu, M; Zheng, H; Yang, A; et al. 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; et al. Evaluation of methods for modeling transcription factor sequence specificity. Nature Biotechnology. 2013; 31:126-134.

Weirauch, MT; Hughes, TR. Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends in Genetics. 2010; 26:66-74.

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.

Panfilio, KA; Jentzsch, IM V; Benoit, JB; Erezyilmaz, D; Suzuki, Y; Colella, S; Robertson, HM; Poelchau, MF; Waterhouse, RM; Ioannidis, P; et al. Molecular evolutionary trends and feeding ecology diversification in the Hemiptera, anchored by the milkweed bug genome. Genome Biology: biology for the post-genomic era. 2019; 20.

Burleson, JD; Siniard, D; Yadagiri, VK; Chen, X; Weirauch, MT; Ruff, BP; Brandt, EB; Hershey, GK K; Ji, H. TET1 contributes to allergic airway inflammation and regulates interferon and aryl hydrocarbon receptor signaling pathways in bronchial epithelial cells. Scientific Reports. 2019; 9.

Liu, X; Helenius, D; Skotte, L; Beaumont, RN; Wielscher, M; Geller, F; Juodakis, J; Mahajan, A; Bradfield, JP; Lin, FT; et al. Variants in the fetal genome near pro-inflammatory cytokine genes on 2q13 associate with gestational duration. Nature Communications. 2019; 10.

Attardo, GM; Abd-Alla, AM M; Acosta-Serrano, A; Allen, JE; Bateta, R; Benoit, JB; Bourtzis, K; Caers, J; Caljon, G; Christensen, MB; et al. Comparative genomic analysis of six Glossina genomes, vectors of African trypanosomes. Genome Biology: biology for the post-genomic era. 2019; 20.

Chidambaran, V; Zhang, X; Geisler, K; Stubbeman, BL; Chen, X; Weirauch, MT; Meller, J; Ji, H. Enrichment of Genomic Pathways Based on Differential DNA Methylation Associated With Chronic Postsurgical Pain and Anxiety in Children: A Prospective, Pilot Study. Journal of Pain. 2019; 20:771-785.

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.

Miller, DE; Forney, C; Rochman, M; Cranert, S; Habel, J; Rymer, J; Lynch, A; Schroeder, C; Lee, J; Sauder, A; et al. Genetic, Inflammatory, and Epithelial Cell Differentiation Factors Control Expression of Human Calpain-14. G3-Genes Genomes Genetics. 2019; 9:g3.200901.2018-g3.200901.2018.

Meibers, HE; Finch, G; Gregg, RT; Glenn, S; Assani, KD; Jennings, EC; Davies, B; Rosendale, AJ; Holmes, CJ; Gantz, JD; et al. Sex- and developmental-specific transcriptomic analyses of the Antarctic mite, Alaskozetes antarcticus, reveal transcriptional shifts underlying oribatid mite reproduction. Polar Biology. 2019; 42:357-370.

Marletaz, F; Firbas, PN; Maeso, I; Tena, JJ; Bogdanovic, O; Perry, M; Wyatt, CD R; de la Calle-Mustienes, E; Bertrand, S; Burguera, D; et al. Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. 2018; 564:64-70.

Schoville, SD; Chen, YH; Andersson, MN; Benoit, JB; Bhandari, A; Bowsher, JH; Brevik, K; Cappelle, K; Chen, MM; Childers, AK; et al. A model species for agricultural pest genomics: the genome of the Colorado potato beetle, Leptinotarsa decemlineata (Coleoptera: Chrysomelidae). Scientific Reports. 2018; 8.

Zhang, C; Seo, J; Murakami, K; Salem, ES B; Bernhard, E; Borra, VJ; Choi, K; Yuan, CL; Chan, CC; Chen, X; et al. Hepatic Ago2-mediated RNA silencing controls energy metabolism linked to AMPK activation and obesity-associated pathophysiology. Nature Communications. 2018; 9.

Valanejad, L; Cast, A; Wright, M; Bissig, K; Karns, R; Weirauch, MT; Timchenko, N. PARP1 activation increases expression of modified tumor suppressors and pathways underlying development of aggressive hepatoblastoma. Communications Biology. 2018; 1.

Modur, V; Singh, N; Mohanty, V; Chung, E; Muhammad, B; Choi, K; Chen, X; Chetal, K; Ratner, N; Salomonis, N; et al. Defective transcription elongation in a subset of cancers confers immunotherapy resistance. Nature Communications. 2018; 9.

Muench, DE; Ferchen, K; Velu, CS; Pradhan, K; Chetal, K; Chen, X; Weirauch, MT; Colmenares, C; Verma, A; Salomonis, N; et al. SKI controls MDS-associated chronic TGF-beta signaling, aberrant splicing, and stem cell fitness. Blood. 2018; 132:e24-e34.

Bernstein, DI; Lummus, ZL; Kesavalu, B; Yao, J; Kottyan, L; Miller, D; Cartier, A; Cruz, M; Lemiere, C; Munoz, X; et al. Genetic variants with gene regulatory effects are associated with diisocyanate-induced asthma. Journal of Allergy and Clinical Immunology. 2018; 142:959-969.

Zhang, X; Chen, X; Weirauch, MT; Zhang, X; Burleson, JD; Brandt, EB; Ji, H. Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome. Environmental Epigenetics. 2018; 4.

Patel, ZH; Lu, X; Miller, D; Forney, CR; Lee, J; Lynch, A; Schroeder, C; Parks, L; Magnusen, AF; Chen, X; et al. A plausibly causal functional lupus-associated risk variant in the STAT1-STAT4 locus. Human Molecular Genetics. 2018; 27:2392-2404.

Chhipa, RR; Fan, Q; Anderson, J; Muraleedharan, R; Huang, Y; Ciraolo, G; Chen, X; Waclaw, R; Chow, LM; Khuchua, Z; et al. AMP kinase promotes glioblastoma bioenergetics and tumour growth. Nature Cell Biology. 2018; 20:823-835.

Boni, AC; Ambrosio, DL; Cupertino, FB; Montenegro-Montero, A; Virgilio, S; Freitas, FZ; Corrocher, FA; Goncalves, RD; Yang, A; Weirauch, MT; et al. Neurospora crassa developmental control mediated by the FLB-3 transcription factor. Fungal Biology. 2018; 122:570-582.

Harley, JB; Chen, X; Pujato, M; Miller, D; Maddox, A; Forney, C; Magnusen, AF; Lynch, A; Chetal, K; Yukawa, M; et al. Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity. Nature Genetics. 2018; 50:699-707.

Zhang, X; Biagini Myers, JM; Burleson, JD; Ulm, A; Bryan, KS; Chen, X; Weirauch, MT; Baker, TA; Kovacic, MS B; Ji, H. Nasal DNA methylation is associated with childhood asthma. Epigenomics. 2018; 10:629-641.

Zandvakili, A; Campbell, I; Gutzwiller, LM; Weirauch, MT; Gebelein, B. Degenerate Pax2 and Senseless binding motifs improve detection of low-affinity sites required for enhancer specificity. PLoS Genetics. 2018; 14:e1007289-e1007289.

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.

Najafabadi, HS; Garton, M; Weirauch, MT; Mnaimneh, S; Yang, A; Kim, PM; Hughes, TR. Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding. Genome Biology: biology for the post-genomic era. 2017; 18.

Tillo, D; Ray, S; Syed, K; Gaylor, MR; He, X; Wang, J; Assad, N; Durell, SR; Porollo, A; Weirauch, MT; et al. The Epstein-Barr Virus B-ZIP Protein Zta Recognizes Specific DNA Sequences Containing 5-Methylcytosine and 5-Hydroxymethylcytosine. Biochemistry. 2017; 56:6200-6210.

Zhang, X; Myers, JM B; Yadagiri, VK; Ulm, A; Chen, X; Weirauch, MT; Hershey, GK K; Ji, H. Nasal DNA methylation differentiates corticosteroid treatment response in pediatric asthma: A pilot study. PLoS ONE. 2017; 12:e0186150-e0186150.

Lander, JM; Supp, DM; He, H; Martin, LJ; Chen, X; Weirauch, MT; Boyce, ST; Kopan, R. Analysis of chromatin accessibility in human epidermis identifies putative barrier dysfunction-sensing enhancers. PLoS ONE. 2017; 12:e0184500-e0184500.

Zhang, G; Feenstra, B; Bacelis, J; Liu, X; Muglia, LM; Juodakis, J; Miller, DE; Litterman, N; Jiang, P; Russell, L; et al. Genetic Associations with Gestational Duration and Spontaneous Preterm Birth. The New England journal of medicine. 2017; 377:1156-1167.

Lin, S; Ptasinska, A; Chen, X; Shrestha, M; Assi, SA; Chin, PS; Imperato, MR; Aronow, BJ; Zhang, J; Weirauch, MT; et al. A FOXO1-induced oncogenic network defines the AML1-ETO preleukemic program. Blood. 2017; 130:1213-1222.

Johansson, E; Myers, JM B; Martin, LJ; He, H; Pilipenko, V; Mersha, T; Weirauch, M; Salomonis, N; Ryan, P; LeMasters, GK; et al. KIF3A genetic variation is associated with pediatric asthma in the presence of eczema independent of allergic rhinitis. Journal of Allergy and Clinical Immunology. 2017; 140:595-598.e5.

Anderson, JL; Muraleedharan, R; Oatman, N; Klotter, A; Sengupta, S; Waclaw, RR; Wu, J; Drissi, R; Miles, L; Raabe, EH; et al. The transcription factor Olig2 is important for the biology of diffuse intrinsic pontine gliomas. Neuro-Oncology. 2017; 19:1068-1078.

Endale, M; Ahlfeld, S; Bao, E; Chen, X; Green, J; Bess, Z; Weirauch, M; Xu, Y; Perl, AK. Dataset on transcriptional profiles and the developmental characteristics of PDGFRα expressing lung fibroblasts. Data in Brief. 2017; 13:415-431.

Gu, Z; Kalamboglas, J; Yoshioka, S; Han, W; Li, Z; Kawasawa, YI; Pochareddy, S; Li, Z; Liu, F; Xu, X; et al. Control of species-dependent cortico-motoneuronal connections underlying manual dexterity. Science. 2017; 357:400-404.

Endale, M; Ahlfeld, S; Bao, E; Chen, X; Green, J; Bess, Z; Weirauch, MT; Xu, Y; Perl, AK. Temporal, spatial, and phenotypical changes of PDGFR alpha expressing fibroblasts during late lung development. Developmental Biology. 2017; 425:161-175.

Chidambaran, V; Zhang, X; Martin, LJ; Ding, L; Weirauch, MT; Geisler, K; Stubbeman, BL; Sadhasivam, S; Ji, H. DNA methylation at the mu-1 opioid receptor gene (OPRM1) promoter predicts preoperative, acute, and chronic postsurgical pain after spine fusion. Pharmacogenomics and Personalized Medicine. 2017; Volume 10:157-168.

Merkel, PA; Xie, G; Monach, PA; Ji, X; Ciavatta, DJ; Byun, J; Pinder, BD; Zhao, A; Zhang, J; Tadesse, Y; et al. Identification of Functional and Expression Polymorphisms Associated With Risk for Antineutrophil Cytoplasmic Autoantibody-Associated Vasculitis. Arthritis and Rheumatology. 2017; 69:1054-1066.

Dauber, A; Cunha-Silva, M; Macedo, DB; Brito, VN; Abreu, AP; Roberts, SA; Montenegro, LR; Andrew, M; Kirby, A; Weirauch, MT; et al. Paternally Inherited DLK1 Deletion Associated With Familial Central Precocious Puberty. Journal of Clinical Endocrinology and Metabolism. 2017; 102:1557-1567.

Vander Lugt, B; Riddell, J; Khan, AA; Hackney, JA; Lesch, J; DeVoss, J; Weirauch, MT; Singh, H; Mellman, I. Transcriptional determinants of tolerogenic and immunogenic states during dendritic cell maturation. The Journal of Cell Biology. 2017; 216:779-792.

Fang, J; Bolanos, LC; Choi, K; Liu, X; Christie, S; Akunuru, S; Kumar, R; Wang, D; Chen, X; Greis, KD; et al. Ubiquitination of hnRNPA1 by TRAF6 links chronic innate immune signaling with myelodysplasia. Nature Immunology. 2017; 18:236-245.

Imai, F; Chen, X; Weirauch, MT; Yoshida, Y. Requirement for Dicer in Maintenance of Monosynaptic Sensory-Motor Circuits in the Spinal Cord. Cell Reports. 2016; 17:2163-2172.

Khund-Sayeed, S; He, X; Holzberg, T; Wang, J; Rajagopal, D; Upadhyay, S; Durell, SR; Mukherjee, S; Weirauch, MT; Rose, R; et al. 5-Hydroxymethylcytosine in E-box motifs ACAT|GTG and ACAC|GTG increases DNA-binding of the B-HLH transcription factor TCF4. Integrative Biology: interdisciplinary approaches for molecular and cellular life sciences. 2016; 8:936-945.

Miller, DE; Patel, ZH; Lu, X; Lynch, AT; Weirauch, MT; Kottyan, LC. Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA). Jove-Journal of Visualized Experiments. 2016; 2016.

Mao, A; Constantinides, MG; Mathew, R; Zuo, Z; Chen, X; Weirauch, MT; Bendelac, A. Multiple layers of transcriptional regulation by PLZF in NKT-cell development. Proceedings of the National Academy of Sciences of USA. 2016; 113:7602-7607.

Rialdi, A; Campisi, L; Zhao, N; Lagda, AC; Pietzsch, C; Ho, JS Y; Martinez-Gil, L; Fenouil, R; Chen, X; Edwards, M; et al. Topoisomerase 1 inhibition suppresses inflammatory genes and protects from death by inflammation. Science. 2016; 352:aad7993-aad7993.

Benoit, JB; Adelman, ZN; Reinhardt, K; Dolan, A; Poelchau, M; Jennings, EC; Szuter, EM; Hagan, RW; Gujar, H; Shukla, JN; et al. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome. Nature Communications. 2016; 7.

Cokelaer, T; Bansal, M; Bare, C; Bilal, E; Bot, BM; Chaibub Neto, E; Eduati, F; de la Fuente, A; Gönen, M; Hill, SM; et al. DREAMTools: A Python package for scoring collaborative challenges. F1000Research. 2016; 4:1030-1030.