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- ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origins
Capra JA, Williams AG, and Pollard KS.
PLoS Computational Biology, In Press, 2012.
- Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hotspots
Katzman S*, Capra JA*, Haussler D, and Pollard KS. * co-first authors
Genome Biology and Evolution, 3: 614-626, 2011.
[Paper] - SIRT1 and SIRT3 Deacetylate Homologous Substrates: AceCS1,2 and HMGCS1,2
Hirschey MD*, Shimazu T*, Capra JA*, Pollard KS, and Verdin E. * co-first authors
Aging, 3(6): 635-642, 2011.
[Paper] - Substitution patterns are GC-biased in divergent sequences across the metazoans
Capra JA and Pollard KS.
Genome Biology and Evolution, 3: 516-527, 2011.
[Paper] - DNA Replication through G-Quadruplex Motifs Is Promoted by the Saccharomyces cerevisiae Pif1 DNA Helicase
Paeschke K, Capra JA, and Zakian VA.
Cell, 145(5): 678-691, 2011. (Highlighted in Nature Reviews Molelcular Cellular Biology)
[Paper] - Novel genes exhibit distinct patterns of function acquisition and network integration
Capra JA, Pollard KS, and Singh M.
Genome Biology, 11(12): R127, 2010. (Highlighted on Genome Web)
[Paper] [Supporting Data]
- Genomics through the lens of next-generation sequencing
Capra JA, Carbone L, Riesenfeld SJ, and Wall JD.
Genome Biology, 11(6): 306, 2010.
[Paper] - G-quadruplex DNA sequences are evolutionarily conserved and associated with distinct genomic features in Saccharomyces cerevisiae.
Capra JA*, Paeschke K*, Singh M, and Zakian VA. * co-first authors
PLoS Computational Biology, 6(7): e1000861, 2010.
[Paper] - Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure
Capra JA, Laskowski RA, Thornton JM, Singh M, and Funkhouser TA.
PLoS Computational Biology, 5(12): e1000585, 2009. (Highlighted on Genome Web)
[Paper] [Supporting Code and Data] - Characterization and prediction of residues determining protein functional specificity.
Capra JA and Singh M.
Bioinformatics, 24(13): 1473-1480, 2008.
[Paper] [Supporting Code and Data]
- Predicting functionally important residues from sequence conservation.
Capra JA and Singh M.
Bioinformatics, 23(15): 1875-82, 2007.
[Paper] [Supporting Code and Data]
- Informatics center for mouse genomics: the dissection of complex traits of the nervous system.
Rosen GD, La Porte NT, Diechtiareff B, Pung CJ, Nissanov J, Gustafson C, Bertrand L, Gefen S,
Fan Y, Tretiak OJ, Manly KF, Park MR, Williams AG, Connolly MT, Capra JA, Williams RW.
Neuroinformatics, 1(4): 327-42. 2003.
[Paper]