: Informatics center for mouse genomics - The dissection of complex traits of the nervous system. - Glenn D. Rosen; Nathan T. La Porte; Boris Diechtiareff; Christopher J. Pung; Jonathan Nissanov; Carl Gustafson; Louise Bertrand; Smadar Gefen; Yingli Fan; Oleh J. Tretiak; Kenneth F. Manly; Melburn R. Park; et al. (Neuroinformatics, 2003)

Predicting functionally important residues from sequence conservation. - John A. Capra; Mona Singh 001 (Bioinform., 2007)

Characterization and prediction of residues determining protein functional specificity. - John A. Capra; Mona Singh 001 (Bioinform., 2008)

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. - John A. Capra; Roman A. Laskowski; Janet M. Thornton; Mona Singh 001; Thomas A. Funkhouser (PLoS Comput. Biol., 2009)

High-throughput sequencing of the DBA/2J mouse genome. - Xusheng Wang; Richa Agarwala; John A. Capra; Zugen Chen; Deanna M. Church; Daniel C. Ciobanu; Zhengsheng Li; Lu Lu 004; Khyobeni Mozhui; Megan K. Mulligan; Stanley F. Nelson; Katherine S. Pollard; et al. (BMC Bioinform., 2010)

G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae. - John A. Capra; Katrin Paeschke; Mona Singh 001; Virginia A. Zakian (PLoS Comput. Biol., 2010)

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin. - John A. Capra; Alexander G. Williams; Katherine S. Pollard (PLoS Comput. Biol., 2012)

Modeling DNA methylation dynamics with approaches from phylogenetics. - John A. Capra; Dennis Kostka (Bioinform., 2014)

Integrating Diverse Datasets Improves Developmental Enhancer Prediction. - Genevieve D. Erwin; Nir Oksenberg; Rebecca M. Truty; Dennis Kostka; Karl K. Murphy; Nadav Ahituv; Katherine S. Pollard; John A. Capra (PLoS Comput. Biol., 2014)

Log-odds sequence logos. - Yi-Kuo Yu; John A. Capra; Aleksandar Stojmirovic; David Landsman; Stephen F. Altschul (Bioinform., 2015)

Local ancestry transitions modify snp-trait associations. - Alexandra E. Fish; Dana C. Crawford; John A. Capra; William S. Bush (PSB, 2018)

Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. - R. Michael Sivley; Jonathan H. Sheehan; Jonathan A. Kropski; Joy D. Cogan; Timothy S. Blackwell; John A. Phillips; William S. Bush; Jens Meiler; John A. Capra (BMC Bioinform., 2018)

Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. - Ling Chen; Alexandra E. Fish; John A. Capra (PLoS Comput. Biol., 2018)

Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. - Bian Li; Yucheng T. Yang; John A. Capra; Mark B. Gerstein (PLoS Comput. Biol., 2020)

Learning and interpreting the gene regulatory grammar in a deep learning framework. - Ling Chen; John A. Capra (PLoS Comput. Biol., 2020)

GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. - Abin Abraham; Abigail L. Labella; Mary Lauren Benton; Antonis Rokas; John A. Capra (Bioinform., 2023)