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2020 – today
- 2023
[j15]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)- 2020
- [j14]Ling Chen, John A. Capra:
Learning and interpreting the gene regulatory grammar in a deep learning framework. PLoS Comput. Biol. 16(11): 1008334 (2020) - [j13]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)
2010 – 2019
- 2018
- [j12]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): 18:1-18:10 (2018) - [j11]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) - [c1]Alexandra E. Fish, Dana C. Crawford, John A. Capra, William S. Bush:
Local ancestry transitions modify snp-trait associations. PSB 2018: 424-435 - 2015
- [j10]Yi-Kuo Yu, John A. Capra, Aleksandar Stojmirovic, David Landsman, Stephen F. Altschul:
Log-odds sequence logos. Bioinform. 31(3): 324-331 (2015) - 2014
- [j9]John A. Capra, Dennis Kostka:
Modeling DNA methylation dynamics with approaches from phylogenetics. Bioinform. 30(17): 408-414 (2014) - [j8]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) - 2012
- [j7]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) - 2010
- [j6]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): O7 (2010) - [j5]John A. Capra, Katrin Paeschke, Mona Singh, Virginia A. Zakian:
G-Quadruplex DNA Sequences Are Evolutionarily Conserved and Associated with Distinct Genomic Features in Saccharomyces cerevisiae. PLoS Comput. Biol. 6(7) (2010)
2000 – 2009
- 2009
- [j4]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) - 2008
- [j3]John A. Capra, Mona Singh:
Characterization and prediction of residues determining protein functional specificity. Bioinform. 24(13): 1473-1480 (2008) - 2007
- [j2]John A. Capra, Mona Singh:
Predicting functionally important residues from sequence conservation. Bioinform. 23(15): 1875-1882 (2007) - 2003
- [j1]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): 327-342 (2003)
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