For a summary of our main interests, see Research.

This page lists all preprints and publications from the lab. You can also follow us on Google Scholar.


Neanderthal introgression reintroduced functional alleles lost in the human out of Africa bottleneck
DC Rinker, C Simonti, E McArthur, D Shaw, E Hodges, JA Capra
bioRxiv, 533257, 2019.

Signatures of recent positive selection in enhancers across 41 human tissues
JM Moon, JA Capra, P Abbot, A Rokas
bioRxiv, 534461, 2019.

The impact of natural selection on the evolution and function of placentally expressed galectins
ZA Ely, JM Moon, GR Sliwoski, AK Sangha, XX Shen, AL LaBella, J Meiler, JA Capra, A Rokas
bioRxiv, 505339, 2018.

Genome wide association analysis uncovers variants for reproductive variation across dog breeds and links to domestication
SP Smith, JB Phillips, ML Johnson, P Abbot, JA Capra, A Rokas
bioRxiv, 285791, 2018.

Genome-wide Enhancer Maps Differ Significantly in Genomic Distribution, Evolution, and Function
Benton ML, Talipineni SC, Kostka D*, and Capra JA*
bioRxiv, 176610, 2018.


Protein structure aids predicting functional perturbation of missense variants in SCN5A and KCNQ1
Kroncke BM, Mendenhall J, Smith DK, Sanders CR, Capra JA, George AL, Blume JD, Meiler J, Roden DM
Computational and Structural Biotechnology, 2019.

Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity
Colbran LL, Chen L, and Capra JA
Genetics, 301895, 2019.

Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis
Marinko JT, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR
Chemical Reviews, 8b00532, 2019.


Genome-wide maps of distal gene regulatory regions active in the human placenta
Zhang J*, Simonti CN*, and Capra JA.
PLOS One, 13(12): e0209611, 2018.

integRATE: a desirability-based data integration framework for the prioritization of candidate genes across heterogeneous omics and its application to preterm birth
Eidem, HR, Steenwyk JL, Wisecaver JH, Capra JA, Abbot P, and Rokas A.
BMC Medical Genomics, 11: 107, 2018.

Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties
Chen L, Fish AE, and Capra JA
PLOS Comput Biol, 14(10): e100648, 2018.

Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology
Moon JM, Aronoff DM, Capra JA, Abbot P, and Rokas A.
G3 8: 1315-1325, 2018.

Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures
Sivley RM, Dou X, MeilerJ, Bush WS*, and Capra JA*
American Journal of Human Genetics, 102:415–426, 2018.

Three-dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia
Sivley RM, Sheehan JH, Kropski JA, Cogan J, Blackwell TS, Phillips JA, Bush WS, Meiler J and Capra JA*
BMC Bioinformatics, 19:18, 2018.

Local ancestry transitions modify snp-trait associations
Fish AE, Crawford DC, Capra JA*, and Bush WS*
Pacific Symposium on Biocomputing, 23:424-435, 2018. * co-corresponding authors


Gene regulatory enhancers with evolutionarily conserved-activity are more pleiotropic than those with species-specific-activity
Fish AE, Chen L, and Capra JA
Genome Biology and Evolution, evx194, 2017.

What is a placental mammal anyway?
Abbot P and Capra JA
eLife, 6:e30994, 2017.

Ancient human miRNAs are more likely to have broad functions and disease associations than young miRNAs
Patel VD and Capra JA
BMC Genomics, 18:672, 2017.

Transposable Element Exaptation into Regulatory Regions is Rare, Influenced by Evolutionary Age, and Subject to Pleiotropic Constraints
Simonti CN, Pavličev M, and Capra JA
Molecular Biology and Evolution, msx219, 2017.

Short DNA sequence patterns accurately identify broadly active human enhancers
Colbran LL, Chen L, and Capra JA
BMC Genomics, 18:536, 2017.
[Paper] [biorXiv]

The transformative potential of an integrative approach to pregnancy
Eidem HR*, McGary KL*, Capra JA, Abbot P, and Rokas A
Placenta, 57: 204–215, 2017.

Mms1 binds to G-rich regions in Saccharomyces cerevisiae and influences replication and genome stability
Wanzek K, Schindt E, Capra JA, Paeschke K
Nucleic Acids Research, gkx476, 2017.

SIRT4 Is a Lysine Deacylase that Controls Leucine Metabolism and Insulin Secretion
Anderson KA, Huynh FK, Fisher-Wellman K, Stuart JD, Peterson BS, Douros JD, Wagner GR, Thompson JW, Madsen AS, Green MF, Sivley RM, Ilkayeva OR, Stevens RD, Backos DS, Capra JA, Olsen CA, Campbell JE, Muoio DM, Grimsrud PA, Hirschey MD
Cell Metabolism, 25(4): 838–855, 2017.


Are Genetic Interactions Influencing Gene Expression Evidence for Biological Epistasis or Statistical Artifacts?
Fish A, Capra JA, Bush WS
American Journal of Human Genetics, 99(4): 817-830, 2016.
[Paper] [Supplementary Data and Methods]

Heterozygosity Ratio, a Robust Global Genomic Measure of Autozygosity and Its Association with Height and Disease Risk
Samuels DC, Wang J, Ye F, He J, Levinson RT, Sheng Q, Zhao S, Capra JA, Shyr Y, Zheng W, Guo Y.
Genetics, 204(3): 893-904, 2016.

Pfh1 is an accessory replicative helicase that interacts with the replisome to facilitate fork progression and preserve genome integrity
McDonald KR, Guise AJ, Pourbozorgi-Langroudi P, Cristea IM, Zakian VA , Capra JA*, and Sabouri N*.
PLoS Genetics, 12(9): e1006238, 2016. * co- corresponding authors

XPA: A key scaffold for human nucleotide excision repair
Norie Sugitani, Robert M. Sivley, Kelly E. Perry, John A. Capra, Walter J. Chazin
DNA Repair, 44:123–135, 2016.

The phenotypic legacy of admixture between modern humans and Neandertals
Corinne N. Simonti, Benjamin Vernot, Lisa Bastarache, Erwin Bottinger, David S. Carrell, Rex L. Chisholm, David R. Crosslin, Scott J. Hebbring, Gail P. Jarvik, Iftikhar J. Kullo, Rongling Li, Jyotishman Pathak, Marylyn D. Ritchie, Dan M. Roden, Shefali S. Verma1, Gerard Tromp, Jeffrey D. Prato, William S. Bush, Joshua M. Akey, Joshua C. Denny, John A. Capra
Science, 351 (6274):737-741, 2016.

Joint mouse–human phenome-wide association to test gene function and disease risk
Xusheng Wang, Ashutosh K. Pandey, Megan K. Mulligan, Evan G. Williams, Khyobeni Mozhui, Zhengsheng Li, Virginija Jovaisaite, L. Darryl Quarles, Zhousheng Xiao, Jinsong Huang, John A. Capra, Zugen Chen, William L. Taylor, Lisa Bastarache, Xinnan Niu, Katherine S. Pollard, Daniel C. Ciobanu, Alexander O. Reznik, Artem V. Tishkov, Igor B. Zhulin, Junmin Peng, Stanley F. Nelson, Joshua C. Denny, Johan Auwerx, Lu Lu, and Robert W. Williams
Nature Communications, 7:10464, 2016.


GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes
Mara Kim, Brian A. Cooper, Rohit Venkat, Julie B. Phillips, Haley R. Eidem, Jibril Hirbo, Sashank Nutakki, Scott M. Williams, Louis J. Muglia, John A. Capra, Kenneth Petren, Patrick Abbot, Antonis Rokas, and Kriston L. McGary
Nucleic Acids Research, gkv1137, 2015.
[Paper] [GEneSTATION web site]

The evolution of the human genome
Simonti CN and Capra JA
Current Opinion in Genetics and Development, 35:9–15, 2015.

Evolution of lysine acetylation in the RNA polymerase II C-terminal domain
Simonti CN, Pollard KS, Schöder S, He D, Bruneau BG, Ott M, and Capra JA
BMC Evolutionary Biology, 15:35, 2015.

Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study
Capra JA
BMC Genomics, 16:104, 2015.


The essential Schizosaccharomyces pombe Pfh1 DNA helicase promotes fork movement past G-quadruplex motifs to prevent DNA damage
Sabouri N*, Capra JA*, and Zakian VA. * equal contribution and corresponding authors
BMC Biology, 12:101, 2014.

Log-Odds Sequence Logos
Yu YK, Capra JA, Stojmirovic A, Landsman D, and Altschul SF
Bioinformatics, 31 (3): 324-331, 2015.
[Paper] [Web Tool]

Modeling DNA methylation dynamics with approaches from phylogenetics
Capra JA* and Kostka D*. * co-corresponding authors
Bioinformatics, 30 (17): i408-i414, 2014.
[Paper] [R Package]

Integrating Diverse Datasets Improves Developmental Enhancer Prediction
Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS*, Capra JA*. * co-corresponding authors
PLoS Computational Biology, 10 (6): e1003677, 2014.
[Paper] [Predictions]


Acetylation of RNA Polymerase II Regulates Growth-Factor-Induced Gene Transcription in Mammalian Cells
Schroeder S, Herker E, Itzen F, He D, Thomas S, Gilchrist, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnoelzer M, Cole PA, Geyer M, Bruneau B, Adelman K, and Ott M.
Molecular Cell, 52(3): 314-324, 2013.

Many Human Accelerated Regions Are Developmental Enhancers
Capra JA*, Erwin GD, McKinsey G, Rubenstein JLR, Pollard KS*. * co-corresponding authors
Philosophical Transactions of the Royal Society B, 368: 20130025, 2013.

How old is my gene?
Capra JA, Stolzer M, Durand D, Pollard KS.
Trends in Genetics, 29(11): 659-668, 2013.

A Model-Based Analysis of GC-Biased Gene Conversion in the Human and Chimpanzee Genomes
Capra JA*, Hubisz MJ*, Kostka D, Pollard KS, Siepel A. * co-first authors
PLoS Genetics, 9(8): e1003684, 2013.


Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage
Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG.
Cell, 151(1): 206-220, 2012.

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origins
Capra JA*, Williams AG, and Pollard KS*. * co-corresponding authors
PLoS Computational Biology, 8(6): e1002567, 2012.
[Paper] [Web Server]


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.

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.

Substitution patterns are GC-biased in divergent sequences across the metazoans
Capra JA and Pollard KS.
Genome Biology and Evolution, 3: 516-527, 2011.

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)


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.

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.

–2009 and Earlier–

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.