John A. Capra

Publication Activity (10 Years)

Years Active: 2003-2023
Publications (10 Years): 6

Top Topics

Gene Regulatory

Spatial Analysis

Top Venues

PLoS Comput. Biol.

Publications

Abin Abraham, Abigail L. Labella, Mary Lauren Benton, Antonis Rokas, John A. Capra
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions. Bioinform. 39 (1) (2023)
Ling Chen, John A. Capra
Learning and interpreting the gene regulatory grammar in a deep learning framework. PLoS Comput. Biol. 16 (11) (2020)
Bian Li, Yucheng T. Yang, John A. Capra, Mark B. Gerstein
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks. PLoS Comput. Biol. 16 (11) (2020)
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
Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia. BMC Bioinform. 19 (1) (2018)
Alexandra E. Fish, Dana C. Crawford, John A. Capra, William S. Bush
Local ancestry transitions modify snp-trait associations. PSB (2018)
Ling Chen, Alexandra E. Fish, John A. Capra
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PLoS Comput. Biol. 14 (10) (2018)
Yi-Kuo Yu, John A. Capra, Aleksandar Stojmirovic, David Landsman, Stephen F. Altschul
Log-odds sequence logos. Bioinform. 31 (3) (2015)
Genevieve D. Erwin, Nir Oksenberg, Rebecca M. Truty, Dennis Kostka, Karl K. Murphy, Nadav Ahituv, Katherine S. Pollard, John A. Capra
Integrating Diverse Datasets Improves Developmental Enhancer Prediction. PLoS Comput. Biol. 10 (6) (2014)
John A. Capra, Dennis Kostka
Modeling DNA methylation dynamics with approaches from phylogenetics. Bioinform. 30 (17) (2014)
John A. Capra, Alexander G. Williams, Katherine S. Pollard
ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin. PLoS Comput. Biol. 8 (6) (2012)
John A. Capra, Katrin Paeschke, Mona Singh, Virginia A. Zakian
. PLoS Comput. Biol. 6 (7) (2010)
Xusheng Wang, Richa Agarwala, John A. Capra, Zugen Chen, Deanna M. Church, Daniel C. Ciobanu, Zhengsheng Li, Lu Lu, Khyobeni Mozhui, Megan K. Mulligan, Stanley F. Nelson, Katherine S. Pollard, William Taylor, Donald B. Thomason, Robert W. Williams
High-throughput sequencing of the DBA/2J mouse genome. BMC Bioinform. 11 (S-4) (2010)
John A. Capra, Roman A. Laskowski, Janet M. Thornton, Mona Singh, Thomas A. Funkhouser
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure. PLoS Comput. Biol. 5 (12) (2009)
John A. Capra, Mona Singh
Characterization and prediction of residues determining protein functional specificity. Bioinform. 24 (13) (2008)
John A. Capra, Mona Singh
Predicting functionally important residues from sequence conservation. Bioinform. 23 (15) (2007)
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, Alexander G. Williams, Michael T. Connolly, John A. Capra, Robert W. Williams
: Informatics center for mouse genomics - The dissection of complex traits of the nervous system. Neuroinformatics 1 (4) (2003)