MultiPipMaker and supporting tools: alignments and analysis of multiple genomic DNA sequences. - Scott Schwartz; Laura Elnitski; Mei Li; Matthew T. Weirauch; Cathy Riemer; Arian Smit; Eric D. Green; Ross C. Hardison; Webb Miller (Nucleic Acids Res., 2003)

Discovering Functional Transcription Factor Binding from Superimposed Gene Networks. - Matthew T. Weirauch; Joshua M. Stuart (CSB Workshops, 2005)

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results. - Laura Elnitski; Belinda Giardine; Prachi Shah; Yi Zhang; Cathy Riemer; Matthew T. Weirauch; Richard Burhans; Webb Miller; Ross C. Hardison (Nucleic Acids Res., 2005)

Rapid knot detection and application to protein structure prediction. - Firas Khatib; Matthew T. Weirauch; Carol A. Rohl (ISMB (Supplement of Bioinformatics), 2006)

A search engine to identify pathway genes from expression data on multiple organisms. - Chunnuan Chen; Matthew T. Weirauch; Corey Powell; Alexander C. Zambon; Joshua M. Stuart (BMC Syst. Biol., 2007)

Information-based methods for predicting gene function from systematic gene knock-downs. - Matthew T. Weirauch; Christopher K. Wong; Alexandra B. Byrne; Joshua M. Stuart (BMC Bioinform., 2008)

Identification of Conserved Regulatory Elements in Mammalian Promoter Regions: A Case Study Using the PCK1 Promoter. - George E. Liu; Matthew T. Weirauch; Curtis P. Van Tassell; Robert W. Li; Tad S. Sonstegard; Lakshmi K. Matukumalli; Erin E. Connor; Richard W. Hanson; Jianqi Yang (Genom. Proteom. Bioinform., 2008)

A compendium of RNA-binding motifs for decoding gene regulation. - Debashish Ray; Hilal Kazan; Kate B. Cook; Matthew T. Weirauch; Hamed S. Najafabadi; Xiao Li; Serge Gueroussov; Mihai Albu; Hong Zheng; Ally Yang; Hong Na; Manuel Irimia; et al. (Nat., 2013)

Meta-Analysis of Differential Gene Co-Expression: Application to Lupus. - Sumit B. Makashir; Leah C. Kottyan; Matthew T. Weirauch (Pacific Symposium on Biocomputing, 2015)

DREAMTools: a Python package for scoring collaborative challenges. - Thomas Cokelaer; Mukesh Bansal; Christopher Bare; Erhan Bilal; Brian M. Bot; Elias Chaibub Neto; Federica Eduati; Mehmet Gönen; Steven M. Hill; Bruce R. Hoff; Jonathan R. Karr; Robert Küffner; et al. (F1000Research, 2015)

maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks. - Tareian A. Cazares; Faiz W. Rizvi; Balaji Iyer; Xiaoting Chen; Michael Kotliar; Anthony T. Bejjani; Joseph A. Wayman; Omer Donmez; Benjamin Wronowski; Sreeja Parameswaran; Leah C. Kottyan; Artem Barski; et al. (PLoS Comput. Biol., 2023)