John A. Capra

16 papers Misc 1Journal 15
YearRankTypeTitle / Venue / Authors
2023 J jnl
GSEL: a fast, flexible python package for detecting signatures of diverse evolutionary forces on genomic regions.
Bioinform.
Abin Abraham, Abigail L. Labella, Mary Lauren Benton, Antonis Rokas, John A. Capra
2020 J jnl
Learning and interpreting the gene regulatory grammar in a deep learning framework.
PLoS Comput. Biol.
Ling Chen, John A. Capra
2020 J jnl
Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks.
PLoS Comput. Biol.
Bian Li, Yucheng T. Yang, John A. Capra, Mark B. Gerstein
2018 Misc conf
Local ancestry transitions modify snp-trait associations.
PSB
Alexandra E. Fish, Dana C. Crawford, John A. Capra, William S. Bush
2018 J jnl
Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties.
PLoS Comput. Biol.
Ling Chen, Alexandra E. Fish, John A. Capra
2018 J jnl
Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia.
BMC Bioinform.
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
2015 J jnl
Log-odds sequence logos.
Bioinform.
Yi-Kuo Yu, John A. Capra, Aleksandar Stojmirovic, David Landsman, Stephen F. Altschul
2014 J jnl
Integrating Diverse Datasets Improves Developmental Enhancer Prediction.
PLoS Comput. Biol.
Genevieve D. Erwin, Nir Oksenberg, Rebecca M. Truty, Dennis Kostka, Karl K. Murphy, Nadav Ahituv, Katherine S. Pollard, John A. Capra
2014 J jnl
Modeling DNA methylation dynamics with approaches from phylogenetics.
Bioinform.
John A. Capra, Dennis Kostka
2012 J jnl
ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin.
PLoS Comput. Biol.
John A. Capra, Alexander G. Williams, Katherine S. Pollard
2010 J jnl
G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in
PLoS Comput. Biol.
John A. Capra, Katrin Paeschke, Mona Singh, Virginia A. Zakian
2010 J jnl
High-throughput sequencing of the DBA/2J mouse genome.
BMC Bioinform.
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
2009 J jnl
Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure.
PLoS Comput. Biol.
John A. Capra, Roman A. Laskowski, Janet M. Thornton, Mona Singh, Thomas A. Funkhouser
2008 J jnl
Characterization and prediction of residues determining protein functional specificity.
Bioinform.
John A. Capra, Mona Singh
2007 J jnl
Predicting functionally important residues from sequence conservation.
Bioinform.
John A. Capra, Mona Singh
2003 J jnl
: Informatics center for mouse genomics - The dissection of complex traits of the nervous system.
Neuroinformatics
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