John A. Capra

According to our database, John A. Capra authored at least 16 papers between 2003 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2023

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., January, 2023

2020

Learning and interpreting the gene regulatory grammar in a deep learning framework.

Ling Chen, John A. Capra

PLoS Comput. Biol., November, 2020

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

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

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

Local ancestry transitions modify snp-trait associations.

Alexandra E. Fish, Dana C. Crawford, John A. Capra, William S. Bush

Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

2015

Log-odds sequence logos.

Yi-Kuo Yu, John A. Capra, Aleksandar Stojmirovic, David Landsman, Stephen F. Altschul

Bioinform., 2015

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

Modeling DNA methylation dynamics with approaches from phylogenetics.

John A. Capra, Dennis Kostka

Bioinform., 2014

2012

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin.

John A. Capra, Alexander G. Williams, Katherine S. Pollard

PLoS Comput. Biol., 2012

2010

G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in <i>Saccharomyces cerevisiae</i>.

John A. Capra, Katrin Paeschke, Mona Singh, Virginia A. Zakian

PLoS Comput. Biol., 2010

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, Khyobeni Mozhui, Megan K. Mulligan, Stanley F. Nelson, Katherine S. Pollard, William Taylor, Donald B. Thomason, Robert W. Williams

BMC Bioinform., 2010

2009

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure.

John A. Capra, Roman A. Laskowski, Janet M. Thornton, Mona Singh, Thomas A. Funkhouser

PLoS Comput. Biol., 2009

2008

Characterization and prediction of residues determining protein functional specificity.

John A. Capra, Mona Singh

Bioinform., 2008

2007

Predicting functionally important residues from sequence conservation.

John A. Capra, Mona Singh

Bioinform., 2007

2003

: 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, Alexander G. Williams, Michael T. Connolly, John A. Capra, Robert W. Williams

Neuroinformatics, 2003