A photo of Matthew Weirauch.

Associate Professor, UC Department of Pediatrics


Biography & Affiliation


Dr. Weirauch is a computational biologist. His lab seeks to understand the mechanisms of gene transcriptional regulation. Current projects focus on characterizing transcription factor binding specificities, and developing methods for modeling their interactions with DNA, both in vitro and in vivo. His lab applies insights from basic research on transcription factor-DNA interactions to study the mechanisms underlying complex diseases.

Academic Affiliation

Associate Professor, UC Department of Pediatrics


Biomedical Informatics, Developmental Biology

Blog Posts

‘Mono’ Virus Linked to Seven Serious Diseases

Autoimmune Disorders

‘Mono’ Virus Linked to Seven Serious Diseases

Matthew T. Weirauch, PhD, John B. Harley, MD, PhD ...6/30/2019


Postdoctoral Fellow: University of Toronto (Donnelly Center for Cellular and Biomolecular Research), Toronto, Ontario, Canada.

PhD: Bioinformatics, University of California Santa Cruz, Santa Cruz, California.

BSc: Computer Science, Pennsylvania State University, University Park, PA.


Selected Publication

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

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

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

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

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

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity. Weirauch, MT; Yang, A; Albu, M; Cote, AG; Montenegro-Montero, A; Drewe, P; Najafabadi, HS; Lambert, SA; Mann, I; Cook, K; et al. Cell. 2014; 158:1431-1443.

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

A compendium of RNA-binding motifs for decoding gene regulation. Ray, D; Kazan, H; Cook, KB; Weirauch, MT; Najafabadi, HS; Li, X; Gueroussov, S; Albu, M; Zheng, H; Yang, A; et al. Nature. 2013; 499:172-177.

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

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