Franchini LF, Pollard KS.  2015.  Genomic approaches to studying human-specific developmental traits.. Development. 142(18):3100-12.
Franchini LF, Pollard KS.  2015.  Can a few non-coding mutations make a human brain? Bioessays. 37(10):1054-61.
Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N.  2015.  Continental-scale distributions of dust-associated bacteria and fungi.. Proc Natl Acad Sci U S A. 112(18):5756-61.
Maurice CF, Knowles SCl, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ.  2015.  Marked seasonal variation in the wild mouse gut microbiota.. ISME J.
Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT.  2015.  Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions.. Mol Biol Evol. 32(5):1148-60.
Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S.  2015.  Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.. Nucleic Acids Res. 43(11):5307-17.
Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA.  2015.  Evolution of lysine acetylation in the RNA polymerase II C-terminal domain.. BMC Evol Biol. 15:35.
Carbone L, R Harris A, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B et al..  2014.  Gibbon genome and the fast karyotype evolution of small apes.. Nature. 513(7517):195-201.
Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA.  2014.  Integrating diverse datasets improves developmental enhancer prediction.. PLoS Comput Biol. 10(6):e1003677.
Roan NR, Liu H, Usmani SM, Neidleman J, Müller JA, Avila-Herrera A, Gawanbacht A, Zirafi O, Chu S, Dong M et al..  2014.  Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection.. J Virol. 88(13):7221-34.
Oksenberg N, Haliburton GDE, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N.  2014.  Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.. Transl Psychiatry. 4:e431.
Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS.  2014.  A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PLoS One. 9(1):e84689.
Kidd JM, Sharpton TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A et al..  2014.  Exome capture from saliva produces high quality genomic and metagenomic data.. BMC Genomics. 15:262.
Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL.  2014.  Profile hidden Markov models for the detection of viruses within metagenomic sequence data.. PLoS One. 9(8):e105067.
Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS.  2013.  Global marine bacterial diversity peaks at high latitudes in winter.. ISME J. 7(9):1669-77.
Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA et al..  2013.  Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells.. Mol Cell. 52(3):314-24.
Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL.  2013.  Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.. Science. 342(6158):621-4.
Capra JA, Stolzer M, Durand D, Pollard KS.  2013.  How old is my gene? Trends Genet. 29(11):659-68.
Capra JA, Erwin GD, McKinsey G, Rubenstein JLR, Pollard KS.  2013.  Many human accelerated regions are developmental enhancers.. Philos Trans R Soc Lond B Biol Sci. 368(1632):20130025.
Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N.  2013.  A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.. Genome Biol. 14(7):R72.
Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A.  2013.  A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.. PLoS Genet. 9(8):e1003684.
Lemay DG, Pollard KS, Martin WF, Zadrowski CFreeman, Hernandez J, Korf I, J German B, Rijnkels M.  2013.  From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome.. PLoS One. 8(9):e75030.
Kostka D, Hubisz MJ, Siepel A, Pollard KS.  2012.  The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.. Mol Biol Evol. 29(3):1047-57.
Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S.  2012.  Analysis of human accelerated DNA regions using archaic hominin genomes.. PLoS One. 7(3):e32877.
Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS.  2012.  Novel bacterial taxa in the human microbiome.. PLoS One. 7(6):e35294.
Capra JA, Williams AG, Pollard KS.  2012.  ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.. PLoS Comput Biol. 8(6):e1002567.
Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, J German B, Korf I, Pollard KS.  2012.  G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.. BMC Bioinformatics. 13:253.
Sharpton TJ, Jospin G, Wu D, Langille MGI, Pollard KS, Eisen JA.  2012.  Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.. BMC Bioinformatics. 13:264.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E et al..  2011.  A high-resolution map of human evolutionary constraint using 29 mammals.. Nature. 478(7370):476-82.
Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E.  2011.  SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2.. Aging (Albany NY). 3(6):635-42.
Hubisz MJ, Pollard KS, Siepel A.  2011.  PHAST and RPHAST: phylogenetic analysis with space/time models.. Brief Bioinform. 12(1):41-51.
Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS.  2011.  PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.. PLoS Comput Biol. 7(1):e1001061.
Capra JA, Pollard KS.  2011.  Substitution patterns are GC-biased in divergent sequences across the metazoans.. Genome Biol Evol. 3:516-27.
Katzman S, Capra JA, Haussler D, Pollard KS.  2011.  Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots.. Genome Biol Evol. 3:614-26.
Kembel SW, Eisen JA, Pollard KS, Green JL.  2011.  The phylogenetic diversity of metagenomes.. PLoS One. 6(8):e23214.
Takeuchi JK, Lou X, Alexander JM, Sugizaki H, Delgado-Olguin P, Holloway AK, Mori AD, Wylie JN, Munson C, Zhu Y et al..  2011.  Chromatin remodelling complex dosage modulates transcription factor function in heart development.. Nat Commun. 2:187.
Lambert N, Lambot M-A, Bilheu A, Albert V, Englert Y, Libert F, Noel J-C, Sotiriou C, Holloway AK, Pollard KS et al..  2011.  Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution.. PLoS One. 6(3):e17753.
Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH.  2010.  The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.. Mol Biol Evol. 27(10):2322-32.
Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D.  2010.  GC-biased evolution near human accelerated regions.. PLoS Genet. 6(5):e1000960.
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A.  2010.  Detection of nonneutral substitution rates on mammalian phylogenies.. Genome Res. 20(1):110-21.
Taylor SL, Pollard KS.  2010.  Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes.. Genet Res (Camb). 92(1):39-53.
Capra JA, Pollard KS, Singh M.  2010.  Novel genes exhibit distinct patterns of function acquisition and network integration.. Genome Biol. 11(12):R127.
Kostka D, Hahn MW, Pollard KS.  2010.  Noncoding sequences near duplicated genes evolve rapidly.. Genome Biol Evol. 2:518-33.
Pollard KS.  2009.  What makes us human? Sci Am. 300(5):44-9.
Berglund J, Pollard KS, Webster MT.  2009.  Hotspots of biased nucleotide substitutions in human genes.. PLoS Biol. 7(1):e26.
Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM.  2009.  Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.. J Bacteriol. 191(3):782-94.
Lemay DG, Lynn DJ, Martin WF, Neville MC, Casey TM, Rincon G, Kriventseva EV, Barris WC, Hinrichs AS, Molenaar AJ et al..  2009.  The bovine lactation genome: insights into the evolution of mammalian milk.. Genome Biol. 10(4):R43.
Holloway AK, Begun DJ, Siepel A, Pollard KS.  2008.  Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster.. Genome Res. 18(10):1592-601.
Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K.  2008.  A genome-wide approach to identifying novel-imprinted genes.. Hum Genet. 122(6):625-34.
Taylor SL, Pollard KS.  2008.  Evaluation of two methods to estimate and monitor bird populations.. PLoS One. 3(8):e3047.
Pollard KS, van der Laan MJ.  2008.  Supervised distance matrices.. Stat Appl Genet Mol Biol. 7(1):Article33.
Dreszer TR, Wall GD, Haussler D, Pollard KS.  2007.  Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion.. Genome Res. 17(10):1420-30.
Lemay DG, Neville MC, Rudolph MC, Pollard KS, J German B.  2007.  Gene regulatory networks in lactation: identification of global principles using bioinformatics.. BMC Syst Biol. 1:56.
Magalhães TR, Palmer J, Tomancak P, Pollard KS.  2007.  Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach.. BMC Neurosci. 8:59.
Pollard KS, Salama SR, Lambert N, Lambot M-A, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A et al..  2006.  An RNA gene expressed during cortical development evolved rapidly in humans.. Nature. 443(7108):167-72.
Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R et al..  2006.  Forces shaping the fastest evolving regions in the human genome.. PLoS Genet. 2(10):e168.
Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM.  2006.  The UCSC Archaeal Genome Browser.. Nucleic Acids Res. 34(Database issue):D407-10.
Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR.  2005.  Identifying genetic networks underlying myometrial transition to labor.. Genome Biol. 6(2):R12.
Dudoit S, van der Laan MJ, Pollard KS.  2004.  Multiple testing. Part I. Single-step procedures for control of general type I error rates.. Stat Appl Genet Mol Biol. 3:Article13.
van der Laan MJ, Dudoit S, Pollard KS.  2004.  Multiple testing. Part II. Step-down procedures for control of the family-wise error rate.. Stat Appl Genet Mol Biol. 3:Article14.
Pollard KS, van der Laan MJ.  2002.  Statistical inference for simultaneous clustering of gene expression data.. Math Biosci. 176(1):99-121.

Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides N. Novel insights from uncultivated genomes of the global human gut microbiome. Nature. 2019 Mar 13.

Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, Hugenholtz P, Ioannidis JPA, Jansson JK, Kim JF, Klenk HP, Klotz MG, Knight R, Konstantinidis KT, Kyrpides NC, Mason CE, McHardy AC, Meyer F, Ouzounis CA, Patrinos AAN, Podar M, Pollard KS, Ravel J, Muñoz AR, Roberts RJ, Rosselló-Móra R, Sansone SA, Schloss PD, Schriml LM, Setubal JC, Sorek R, Stevens RL, Tiedje JM, Turjanski A, Tyson GW, Ussery DW, Weinstock GM, White O, Whitman WB, Xenarios I. Toward unrestricted use of public genomic data. Science. 2019 Jan 25; 363(6425):350-352.

Garud NR, Good BH, Hallatschek O, Pollard KS. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol. 2019 Jan 23; 17(1):e3000102.

Fudenberg G, Pollard KS. Chromatin features constrain structural variation across evolutionary timescales. Proc Natl Acad Sci U S A. 2019 Jan 18.

Samee MAH, Bruneau BG, Pollard KS. A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs. Cell Syst. 2019 Jan 23; 8(1):27-42.e6.

Whalen S, Pollard KS. Most chromatin interactions are not in linkage disequilibrium. Genome Res. 2019 Jan 07.

Shah PS, Link N, Jang GM, Sharp PP, Zhu T, Swaney DL, Johnson JR, Von Dollen J, Ramage HR, Satkamp L, Newton B, Hüttenhain R, Petit MJ, Baum T, Everitt A, Laufman O, Tassetto M, Shales M, Stevenson E, Iglesias GN, Shokat L, Tripathi S, Balasubramaniam V, Webb LG, Aguirre S, Willsey AJ, Garcia-Sastre A, Pollard KS, Cherry S, Gamarnik AV, Marazzi I, Taunton J, Fernandez-Sesma A, Bellen HJ, Andino R, Krogan NJ. Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell. 2018 Dec 13; 175(7):1931-1945.e18.

Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, Jauregui A, Malcolm K, Lyden A, Khan L, Vessel K, Quan J, Zinter M, Chiu CY, Chow ED, Wilson J, Miller S, Matthay MA, Pollard KS, Christenson S, Calfee CS, DeRisi JL. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A. 2018 Dec 26; 115(52):E12353-E12362.

Ladau J, Shi Y, Jing X, He JS, Chen L, Lin X, Fierer N, Gilbert JA, Pollard KS, Chu H. Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes. mSystems. 2018 Sep-Oct; 3(5).

Wyman SK, Avila-Herrera A, Nayfach S, Pollard KS. A most wanted list of conserved microbial protein families with no known domains. PLoS One. 2018; 13(10):e0205749.

Bradley PH, Nayfach S, Pollard KS. Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. PLoS Comput Biol. 2018 08; 14(8):e1006242.

Kostka D, Holloway AK, Pollard KS. Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages. Mol Biol Evol. 2018 Aug 01; 35(8):2034-2045.

McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G, Green JL, Hugenholtz P, Humphrey G, Huttenhower C, Jackson MA, Janssen S, Jeste DV, Jiang L, Kelley ST, Knights D, Kosciolek T, Ladau J, Leach J, Marotz C, Meleshko D, Melnik AV, Metcalf JL, Mohimani H, Montassier E, Navas-Molina J, Nguyen TT, Peddada S, Pevzner P, Pollard KS, Rahnavard G, Robbins-Pianka A, Sangwan N, Shorenstein J, Smarr L, Song SJ, Spector T, Swafford AD, Thackray VG, Thompson LR, Tripathi A, Vázquez-Baeza Y, Vrbanac A, Wischmeyer P, Wolfe E, Zhu Q, Knight R. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3).

Moquin SA, Thomas S, Whalen S, Warburton A, Fernandez SG, McBride AA, Pollard KS, Miranda JJL. The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation. J Virol. 2017 Nov 15.

Thompson LR, Sanders JG, McDonald D, Amir A, Ladau J, Locey KJ, Prill RJ, Tripathi A, Gibbons SM, Ackermann G, Navas-Molina JA, Janssen S, Kopylova E, Vázquez-Baeza Y, González A, Morton JT, Mirarab S, Zech Xu Z, Jiang L, Haroon MF, Kanbar J, Zhu Q, Jin Song S, Kosciolek T, Bokulich NA, Lefler J, Brislawn CJ, Humphrey G, Owens SM, Hampton-Marcell J, Berg-Lyons D, McKenzie V, Fierer N, Fuhrman JA, Clauset A, Stevens RL, Shade A, Pollard KS, Goodwin KD, Jansson JK, Gilbert JA, Knight R. A communal catalogue reveals Earth's multiscale microbial diversity. Nature. 2017 11 23; 551(7681):457-463.

Franchini LF, Pollard KS. Human evolution: the non-coding revolution. BMC Biol. 2017 10 02; 15(1):89.

Sharpton T, Lyalina S, Luong J, Pham J, Deal EM, Armour C, Gaulke C, Sanjabi S, Pollard KS. Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice. mSystems. 2017 Sep-Oct; 2(5).

Milgrom P, Horst JA, Ludwig S, Rothen M, Chaffee BW, Lyalina S, Pollard KS, DeRisi JL, Mancl L. Topical silver diamine fluoride for dental caries arrest in preschool children: A randomized controlled trial and microbiological analysis of caries associated microbes and resistance gene expression. J Dent. 2018 01; 68:72-78.

Thomas R, Thomas S, Holloway AK, Pollard KS. Features that define the best ChIP-seq peak calling algorithms. Brief Bioinform. 2017 05 01; 18(3):441-450.

Day FR, Thompson DJ, Helgason H, Chasman DI, Finucane H, Sulem P, Ruth KS, Whalen S, Sarkar AK, Albrecht E, Altmaier E, Amini M, Barbieri CM, Boutin T, Campbell A, Demerath E, Giri A, He C, Hottenga JJ, Karlsson R, Kolcic I, Loh PR, Lunetta KL, Mangino M, Marco B, McMahon G, Medland SE, Nolte IM, Noordam R, Nutile T, Paternoster L, Perjakova N, Porcu E, Rose LM, Schraut KE, Segrè AV, Smith AV, Stolk L, Teumer A, Andrulis IL, Bandinelli S, Beckmann MW, Benitez J, Bergmann S, Bochud M, Boerwinkle E, Bojesen SE, Bolla MK, Brand JS, Brauch H, Brenner H, Broer L, Brüning T, Buring JE, Campbell H, Catamo E, Chanock S, Chenevix-Trench G, Corre T, Couch FJ, Cousminer DL, Cox A, Crisponi L, Czene K, Davey Smith G, de Geus EJCN, de Mutsert R, De Vivo I, Dennis J, Devilee P, Dos-Santos-Silva I, Dunning AM, Eriksson JG, Fasching PA, Fernández-Rhodes L, Ferrucci L, Flesch-Janys D, Franke L, Gabrielson M, Gandin I, Giles GG, Grallert H, Gudbjartsson DF, Guénel P, Hall P, Hallberg E, Hamann U, Harris TB, Hartman CA, Heiss G, Hooning MJ, Hopper JL, Hu F, Hunter DJ, Ikram MA, Im HK, Järvelin MR, Joshi PK, Karasik D, Kellis M, Kutalik Z, LaChance G, Lambrechts D, Langenberg C, Launer LJ, Laven JSE, Lenarduzzi S, Li J, Lind PA, Lindstrom S, Liu Y, Luan J, Mägi R, Mannermaa A, Mbarek H, McCarthy MI, Meisinger C, Meitinger T, Menni C, Metspalu A, Michailidou K, Milani L, Milne RL, Montgomery GW, Mulligan AM, Nalls MA, Navarro P, Nevanlinna H, Nyholt DR, Oldehinkel AJ, O'Mara TA, Padmanabhan S, Palotie A, Pedersen N, Peters A, Peto J, Pharoah PDP, Pouta A, Radice P, Rahman I, Ring SM, Robino A, Rosendaal FR, Rudan I, Rueedi R, Ruggiero D, Sala CF, Schmidt MK, Scott RA, Shah M, Sorice R, Southey MC, Sovio U, Stampfer M, Steri M, Strauch K, Tanaka T, Tikkanen E, Timpson NJ, Traglia M, Truong T, Tyrer JP, Uitterlinden AG, Edwards DRV, Vitart V, Völker U, Vollenweider P, Wang Q, Widen E, van Dijk KW, Willemsen G, Winqvist R, Wolffenbuttel BHR, Zhao JH, Zoledziewska M, Zygmunt M, Alizadeh BZ, Boomsma DI, Ciullo M, Cucca F, Esko T, Franceschini N, Gieger C, Gudnason V, Hayward C, Kraft P, Lawlor DA, Magnusson PKE, Martin NG, Mook-Kanamori DO, Nohr EA, Polasek O, Porteous D, Price AL, Ridker PM, Snieder H, Spector TD, Stöckl D, Toniolo D, Ulivi S, Visser JA, Völzke H, Wareham NJ, Wilson JF, Spurdle AB, Thorsteindottir U, Pollard KS, Easton DF, Tung JY, Chang-Claude J, Hinds D, Murray A, Murabito JM, Stefansson K, Ong KK, Perry JRB. Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk. Nat Genet. 2017 Jun; 49(6):834-841.

Anderson CM, Hu J, Thomas R, Gainous TB, Celona B, Sinha T, Dickel DE, Heidt AB, Xu SM, Bruneau BG, Pollard KS, Pennacchio LA, Black BL. Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites. Development. 2017 04 01; 144(7):1235-1241.

Bradley PH, Pollard KS. Proteobacteria explain significant functional variability in the human gut microbiome. Microbiome. 2017 03 23; 5(1):36.

Engle S, Whalen S, Joshi A, Pollard KS. Unboxing cluster heatmaps. BMC Bioinformatics. 2017 Feb 15; 18(Suppl 2):63.

Guo CJ, Chang FY, Wyche TP, Backus KM, Acker TM, Funabashi M, Taketani M, Donia MS, Nayfach S, Pollard KS, Craik CS, Cravatt BF, Clardy J, Voigt CA, Fischbach MA. Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell. 2017 01 26; 168(3):517-526.e18.

Devlin AS, Marcobal A, Dodd D, Nayfach S, Plummer N, Meyer T, Pollard KS, Sonnenburg JL, Fischbach MA. Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota. Cell Host Microbe. 2016 Dec 14; 20(6):709-715.

Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 2016 11; 26(11):1612-1625.

Nayfach S, Pollard KS. Toward Accurate and Quantitative Comparative Metagenomics. Cell. 2016 Aug 25; 166(5):1103-1116.

Mhuireach G, Johnson BR, Altrichter AE, Ladau J, Meadow JF, Pollard KS, Green JL. Urban greenness influences airborne bacterial community composition. Sci Total Environ. 2016 Nov 15; 571:680-7.

Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL. Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. MBio. 2016 05 13; 7(3).

Whalen S, Truty RM, Pollard KS. Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. Nat Genet. 2016 05; 48(5):488-96.

Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N. Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus. PLoS Genet. 2016 Mar; 12(3):e1005738.

Eckalbar WL, Schlebusch SA, Mason MK, Gill Z, Parker AV, Booker BM, Nishizaki S, Muswamba-Nday C, Terhune E, Nevonen KA, Makki N, Friedrich T, VanderMeer JE, Pollard KS, Carbone L, Wall JD, Illing N, Ahituv N. Transcriptomic and epigenomic characterization of the developing bat wing. Nat Genet. 2016 05; 48(5):528-36.

Myers SA, Peddada S, Chatterjee N, Friedrich T, Tomoda K, Krings G, Thomas S, Maynard J, Broeker M, Thomson M, Pollard K, Yamanaka S, Burlingame AL, Panning B. SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells. Elife. 2016 Mar 07; 5:e10647.

Luna-Zurita L, Stirnimann CU, Glatt S, Kaynak BL, Thomas S, Baudin F, Samee MA, He D, Small EM, Mileikovsky M, Nagy A, Holloway AK, Pollard KS, Müller CW, Bruneau BG. Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. Cell. 2016 Feb 25; 164(5):999-1014.

Wang X, Pandey AK, Mulligan MK, Williams EG, Mozhui K, Li Z, Jovaisaite V, Quarles LD, Xiao Z, Huang J, Capra JA, Chen Z, Taylor WL, Bastarache L, Niu X, Pollard KS, Ciobanu DC, Reznik AO, Tishkov AV, Zhulin IB, Peng J, Nelson SF, Denny JC, Auwerx J, Lu L, Williams RW. Joint mouse-human phenome-wide association to test gene function and disease risk. Nat Commun. 2016 Feb 02; 7:10464.

Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS. Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor. Mol Biol Evol. 2016 Apr; 33(4):1008-18.

Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PLoS Comput Biol. 2015 Nov; 11(11):e1004573.

Haliburton GD, McKinsey GL, Pollard KS. Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development. Neurogenetics. 2016 Jan; 17(1):1-9.

Franchini LF, Pollard KS. Genomic approaches to studying human-specific developmental traits. Development. 2015 Sep 15; 142(18):3100-12.

Franchini LF, Pollard KS. Can a few non-coding mutations make a human brain? Bioessays. 2015 Oct; 37(10):1054-61.

Avila-Herrera A, Pollard KS. Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. BMC Bioinformatics. 2015 Aug 25; 16:268.

Nayfach S, Fischbach MA, Pollard KS. MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. Bioinformatics. 2015 Oct 15; 31(20):3368-70.

Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ. Marked seasonal variation in the wild mouse gut microbiota. ISME J. 2015 Nov; 9(11):2423-34.

Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S. Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Nucleic Acids Res. 2015 Jun 23; 43(11):5307-17.

Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N. Continental-scale distributions of dust-associated bacteria and fungi. Proc Natl Acad Sci U S A. 2015 May 05; 112(18):5756-61.

Nayfach S, Pollard KS. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 2015 Mar 25; 16:51.

Theodoris CV, Li M, White MP, Liu L, He D, Pollard KS, Bruneau BG, Srivastava D. Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency. Cell. 2015 Mar 12; 160(6):1072-86.

Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA. Evolution of lysine acetylation in the RNA polymerase II C-terminal domain. BMC Evol Biol. 2015 Mar 10; 15:35.

Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT. Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. Mol Biol Evol. 2015 May; 32(5):1148-60.

Kostka D, Friedrich T, Holloway AK, Pollard KS. motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences. Stat Interface. 2015; 8(4):463-476.

Carbone L, Harris RA, Gnerre S, Veeramah KR, Lorente-Galdos B, Huddleston J, Meyer TJ, Herrero J, Roos C, Aken B, Anaclerio F, Archidiacono N, Baker C, Barrell D, Batzer MA, Beal K, Blancher A, Bohrson CL, Brameier M, Campbell MS, Capozzi O, Casola C, Chiatante G, Cree A, Damert A, de Jong PJ, Dumas L, Fernandez-Callejo M, Flicek P, Fuchs NV, Gut I, Gut M, Hahn MW, Hernandez-Rodriguez J, Hillier LW, Hubley R, Ianc B, Izsvák Z, Jablonski NG, Johnstone LM, Karimpour-Fard A, Konkel MK, Kostka D, Lazar NH, Lee SL, Lewis LR, Liu Y, Locke DP, Mallick S, Mendez FL, Muffato M, Nazareth LV, Nevonen KA, O'Bleness M, Ochis C, Odom DT, Pollard KS, Quilez J, Reich D, Rocchi M, Schumann GG, Searle S, Sikela JM, Skollar G, Smit A, Sonmez K, ten Hallers B, Terhune E, Thomas GW, Ullmer B, Ventura M, Walker JA, Wall JD, Walter L, Ward MC, Wheelan SJ, Whelan CW, White S, Wilhelm LJ, Woerner AE, Yandell M, Zhu B, Hammer MF, Marques-Bonet T, Eichler EE, Fulton L, Fronick C, Muzny DM, Warren WC, Worley KC, Rogers J, Wilson RK, Gibbs RA. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 Sep 11; 513(7517):195-201.

Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N. Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes. Transl Psychiatry. 2014 Sep 02; 4:e431.

Hubisz MJ, Pollard KS. Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution. Curr Opin Genet Dev. 2014 Dec; 29:15-21.

Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One. 2014; 9(8):e105067.

Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol. 2014 Jun; 10(6):e1003677.

Bakhautdin B, Das D, Mandal P, Roychowdhury S, Danner J, Bush K, Pollard K, Kaspar JW, Li W, Salomon RG, McMullen MR, Nagy LE. Protective role of HO-1 and carbon monoxide in ethanol-induced hepatocyte cell death and liver injury in mice. J Hepatol. 2014 Nov; 61(5):1029-37.

Roan NR, Liu H, Usmani SM, Neidleman J, Müller JA, Avila-Herrera A, Gawanbacht A, Zirafi O, Chu S, Dong M, Kumar ST, Smith JF, Pollard KS, Fändrich M, Kirchhoff F, Münch J, Witkowska HE, Greene WC. Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection. J Virol. 2014 Jul; 88(13):7221-34.

Kidd JM, Sharpton TJ, Bobo D, Norman PJ, Martin AR, Carpenter ML, Sikora M, Gignoux CR, Nemat-Gorgani N, Adams A, Guadalupe M, Guo X, Feng Q, Li Y, Liu X, Parham P, Hoal EG, Feldman MW, Pollard KS, Wall JD, Bustamante CD, Henn BM. Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genomics. 2014 Apr 04; 15:262.

Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PLoS One. 2014; 9(1):e84689.

Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS. Many human accelerated regions are developmental enhancers. Philos Trans R Soc Lond B Biol Sci. 2013 Dec 19; 368(1632):20130025.

Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell. 2013 Nov 07; 52(3):314-24.

Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 2013 Nov 01; 342(6158):621-4.

Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M. From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. PLoS One. 2013; 8(9):e75030.

Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genet. 2013; 9(8):e1003684.

Capra JA, Stolzer M, Durand D, Pollard KS. How old is my gene? Trends Genet. 2013 Nov; 29(11):659-68.

Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. Genome Biol. 2013 Jul 18; 14(7):R72.

Riesenfeld SJ, Pollard KS. Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis. BMC Genomics. 2013 Jun 22; 14:419.

Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS. Global marine bacterial diversity peaks at high latitudes in winter. ISME J. 2013 Sep; 7(9):1669-77.

Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics. 2012 Oct 13; 13:264.

Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS. G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. BMC Bioinformatics. 2012 Sep 28; 13:253.

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. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28; 151(1):206-20.

Capra JA, Williams AG, Pollard KS. ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. PLoS Comput Biol. 2012; 8(6):e1002567.

Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS. Novel bacterial taxa in the human microbiome. PLoS One. 2012; 7(6):e35294.

Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S. Analysis of human accelerated DNA regions using archaic hominin genomes. PLoS One. 2012; 7(3):e32877.

Kostka D, Hubisz MJ, Siepel A, Pollard KS. The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol. 2012 Mar; 29(3):1047-57.

Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12; 478(7370):476-82.

Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF. Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet. 2011 Sep 09; 89(3):382-97.

Kembel SW, Eisen JA, Pollard KS, Green JL. The phylogenetic diversity of metagenomes. PLoS One. 2011; 6(8):e23214.

Katzman S, Capra JA, Haussler D, Pollard KS. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biol Evol. 2011; 3:614-26.

Capra JA, Pollard KS. Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biol Evol. 2011; 3:516-27.

Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E. SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2. Aging (Albany NY). 2011 Jun; 3(6):635-42.

Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PLoS One. 2011 Mar 18; 6(3):e17753.

Takeuchi JK, Lou X, Alexander JM, Sugizaki H, Delgado-Olguín P, Holloway AK, Mori AD, Wylie JN, Munson C, Zhu Y, Zhou YQ, Yeh RF, Henkelman RM, Harvey RP, Metzger D, Chambon P, Stainier DY, Pollard KS, Scott IC, Bruneau BG. Chromatin remodelling complex dosage modulates transcription factor function in heart development. Nat Commun. 2011 Feb 08; 2:187.

Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol. 2011 Jan 20; 7(1):e1001061.

Capra JA, Pollard KS, Singh M. Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol. 2010; 11(12):R127.

Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 2011 Jan; 12(1):41-51.

Kostka D, Hahn MW, Pollard KS. Noncoding sequences near duplicated genes evolve rapidly. Genome Biol Evol. 2010; 2:518-33.

Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH. The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. Mol Biol Evol. 2010 Oct; 27(10):2322-32.

Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. GC-biased evolution near human accelerated regions. PLoS Genet. 2010 May 20; 6(5):e1000960.

Taylor SL, Pollard KS. Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes. Genet Res (Camb). 2010 Feb; 92(1):39-53.

Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan; 20(1):110-21.

Hsieh F, Chen SC, Pollard K. A nearly exhaustive search for CpG islands on whole chromosomes. Int J Biostat. 2009; 5(1).

Pollard KS. What makes us human? Sci Am. 2009 May; 300(5):44-9.

Lemay DG, Lynn DJ, Martin WF, Neville MC, Casey TM, Rincon G, Kriventseva EV, Barris WC, Hinrichs AS, Molenaar AJ, Pollard KS, Maqbool NJ, Singh K, Murney R, Zdobnov EM, Tellam RL, Medrano JF, German JB, Rijnkels M. The bovine lactation genome: insights into the evolution of mammalian milk. Genome Biol. 2009; 10(4):R43.

Taylor S, Pollard K. Hypothesis tests for point-mass mixture data with application to 'omics data with many zero values. Stat Appl Genet Mol Biol. 2009; 8:Article 8.

Berglund J, Pollard KS, Webster MT. Hotspots of biased nucleotide substitutions in human genes. PLoS Biol. 2009 Jan 27; 7(1):e26.

Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM. Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. J Bacteriol. 2009 Feb; 191(3):782-94.

Pollard KS, van der Laan MJ. Supervised distance matrices. Stat Appl Genet Mol Biol. 2008; 7(1):Article 33.

Walker WL, Liao IH, Gilbert DL, Wong B, Pollard KS, McCulloch CE, Lit L, Sharp FR. Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients. BMC Genomics. 2008 Oct 20; 9:494.

Taylor SL, Pollard KS. Evaluation of two methods to estimate and monitor bird populations. PLoS One. 2008 Aug 27; 3(8):e3047.

Holloway AK, Begun DJ, Siepel A, Pollard KS. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res. 2008 Oct; 18(10):1592-601.

Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB. Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Syst Biol. 2007 Nov 27; 1:56.

Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K. A genome-wide approach to identifying novel-imprinted genes. Hum Genet. 2008 Jan; 122(6):625-34.

Dreszer TR, Wall GD, Haussler D, Pollard KS. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res. 2007 Oct; 17(10):1420-30.

Magalhães TR, Palmer J, Tomancak P, Pollard KS. Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach. BMC Neurosci. 2007 Jul 31; 8:59.

Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D. Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2006 Oct 13; 2(10):e168.

Pollard KS, Salama SR, Lambert N, Lambot MA, Coppens S, Pedersen JS, Katzman S, King B, Onodera C, Siepel A, Kern AD, Dehay C, Igel H, Ares M, Vanderhaeghen P, Haussler D. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14; 443(7108):167-72.

Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. The UCSC Archaeal Genome Browser. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D407-10.

Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Identifying genetic networks underlying myometrial transition to labor. Genome Biol. 2005; 6(2):R12.

van der Laan MJ, Dudoit S, Pollard KS. Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Stat Appl Genet Mol Biol. 2004; 3:Article15.

van der Laan MJ, Dudoit S, Pollard KS. Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Stat Appl Genet Mol Biol. 2004; 3:Article14.

Dudoit S, van der Laan MJ, Pollard KS. Multiple testing. Part I. Single-step procedures for control of general type I error rates. Stat Appl Genet Mol Biol. 2004; 3:Article13.

Pollard KS, van der Laan MJ. Statistical inference for simultaneous clustering of gene expression data. Math Biosci. 2002 Mar; 176(1):99-121.