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Katherine S. Pollard, PhD - Publications

Gladstone Institute University of California, San Francisco, San Francisco, CA 
Evolutionary Genomics, Statistics

131 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Bradley PH, Pollard KS. Building a chemical blueprint for human blood. Nature. PMID 33177685 DOI: 10.1038/d41586-020-03122-6  1
2020 Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, et al. Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature Protocols. PMID 33128032 DOI: 10.1038/s41596-020-00422-z  1
2020 Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, ... ... Pollard KS, et al. Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. Science (New York, N.Y.). PMID 33060197 DOI: 10.1126/science.abe9403  1
2020 Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks DH, Hugenholtz P, Segata N, Kyrpides NC, Finn RD. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnology. PMID 32690973 DOI: 10.1038/s41587-020-0603-3  1
2020 Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulous-Soares I, Yosef N, Ye CJ, Pollard KS, et al. lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nature Protocols. PMID 32641802 DOI: 10.1038/s41596-020-0333-5  1
2020 Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL. A Chromatin Accessibility Atlas of the Developing Human Telencephalon. Cell. PMID 32610082 DOI: 10.1016/j.cell.2020.06.002  1
2019 Hoarfrost A, Nayfach S, Ladau J, Yooseph S, Arnosti C, Dupont CL, Pollard KS. Global ecotypes in the ubiquitous marine clade SAR86. The Isme Journal. PMID 31611653 DOI: 10.1038/s41396-019-0516-7  1
2019 Bradley PH, Pollard KS. phylogenize: correcting for phylogeny reveals genes associated with microbial distributions. Bioinformatics (Oxford, England). PMID 31588499 DOI: 10.1093/bioinformatics/btz722  1
2019 Keough KC, Lyalina S, Olvera MP, Whalen S, Conklin BR, Pollard KS. AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design. Genome Biology. 20: 167. PMID 31416467 DOI: 10.1186/s13059-019-1783-3  1
2019 Lind AL, Lai YYY, Mostovoy Y, Holloway AK, Iannucci A, Mak ACY, Fondi M, Orlandini V, Eckalbar WL, Milan M, Rovatsos M, Kichigin IG, Makunin AI, Johnson Pokorná M, Altmanová M, ... ... Pollard KS, et al. Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards. Nature Ecology & Evolution. 3: 1241-1252. PMID 31358948 DOI: 10.1038/s41559-019-0945-8  1
2019 Whalen S, Pollard KS. Reply to 'Inflated performance measures in enhancer-promoter interaction-prediction methods'. Nature Genetics. 51: 1198-1200. PMID 31332377 DOI: 10.1038/s41588-019-0473-0  1
2019 Engle DD, Tiriac H, Rivera KD, Pommier A, Whalen S, Oni TE, Alagesan B, Lee EJ, Yao MA, Lucito MS, Spielman B, Da Silva B, Schoepfer C, Wright K, Creighton B, ... ... Pollard KS, et al. The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice. Science (New York, N.Y.). 364: 1156-1162. PMID 31221853 DOI: 10.1126/science.aaw3145  1
2019 Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J. Early-Career Scientists Shaping the World. Msystems. 4. PMID 31219787 DOI: 10.1128/mSystems.00196-19  1
2019 Armour CR, Nayfach S, Pollard KS, Sharpton TJ. A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome. Msystems. 4. PMID 31120034 DOI: 10.1128/mSystems.00332-18  1
2019 Armour CR, Nayfach S, Pollard KS, Sharpton TJ. A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome. Msystems. 4. PMID 31098399 DOI: 10.1128/mSystems.00332-18  1
2019 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, ... ... Pollard KS, et al. Consent insufficient for data release-Response. Science (New York, N.Y.). 364: 446. PMID 31048484 DOI: 10.1126/science.aax7509  0.4
2019 Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides N. Novel insights from uncultivated genomes of the global human gut microbiome. Nature. PMID 30867587 DOI: 10.1038/s41586-019-1058-x  1
2019 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, ... ... Pollard KS, et al. Toward unrestricted use of public genomic data. Science (New York, N.Y.). 363: 350-352. PMID 30679363 DOI: 10.1126/science.aaw1280  0.4
2019 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 Systems. PMID 30660610 DOI: 10.1016/j.cels.2018.12.001  1
2019 Whalen S, Pollard KS. Most chromatin interactions are not in linkage disequilibrium. Genome Research. PMID 30617125 DOI: 10.1101/gr.238022.118  1
2018 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. 3. PMID 30374458 DOI: 10.1128/mSystems.00167-18  1
2018 Wyman SK, Avila-Herrera A, Nayfach S, Pollard KS. A most wanted list of conserved microbial protein families with no known domains. Plos One. 13: e0205749. PMID 30332487 DOI: 10.1371/journal.pone.0205749  1
2018 Bradley PH, Nayfach S, Pollard KS. Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. Plos Computational Biology. 14: e1006242. PMID 30091981 DOI: 10.1371/journal.pcbi.1006242  1
2018 Kostka D, Holloway AK, Pollard KS. Developmental loci harbor clusters of accelerated regions that evolved independently in ape lineages. Molecular Biology and Evolution. PMID 29897475 DOI: 10.1093/molbev/msy109  1
2018 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, ... ... Pollard KS, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. Msystems. 3. PMID 29795809 DOI: 10.1128/mSystems.00031-18  1
2017 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. Journal of Virology. PMID 29142137 DOI: 10.1128/JVI.01413-17  1
2017 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, ... ... Pollard KS, et al. A communal catalogue reveals Earth's multiscale microbial diversity. Nature. PMID 29088705 DOI: 10.1038/nature24621  1
2017 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, ... ... Pollard KS, et al. Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk. Nature Genetics. PMID 28436984 DOI: 10.1038/ng.3841  1
2017 Bradley PH, Pollard KS. Proteobacteria explain significant functional variability in the human gut microbiome. Microbiome. 5: 36. PMID 28330508 DOI: 10.1186/s40168-017-0244-z  1
2017 Engle S, Whalen S, Joshi A, Pollard KS. Unboxing cluster heatmaps. Bmc Bioinformatics. 18: 63. PMID 28251868 DOI: 10.1186/s12859-016-1442-6  1
2017 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. PMID 28111075 DOI: 10.1016/j.cell.2016.12.021  1
2016 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. PMID 27916477 DOI: 10.1016/j.chom.2016.10.021  1
2016 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 Research. 26: 1612-1625. PMID 27803195 DOI: 10.1101/gr.201863.115  1
2016 Nayfach S, Pollard KS. Toward Accurate and Quantitative Comparative Metagenomics. Cell. 166: 1103-16. PMID 27565341 DOI: 10.1016/j.cell.2016.08.007  1
2016 Mhuireach G, Johnson BR, Altrichter AE, Ladau J, Meadow JF, Pollard KS, Green JL. Urban greenness influences airborne bacterial community composition. The Science of the Total Environment. PMID 27418518 DOI: 10.1016/j.scitotenv.2016.07.037  1
2016 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. 7. PMID 27178263 DOI: 10.1128/mBio.00714-16  1
2016 Thomas R, Thomas S, Holloway AK, Pollard KS. Features that define the best ChIP-seq peak calling algorithms. Briefings in Bioinformatics. PMID 27169896 DOI: 10.1093/bib/bbw035  1
2016 Whalen S, Truty RM, Pollard KS. Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. Nature Genetics. PMID 27064255 DOI: 10.1038/ng.3539  0.4
2016 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, et al. Transcriptomic and epigenomic characterization of the developing bat wing. Nature Genetics. PMID 27019111 DOI: 10.1038/ng.3537  1
2016 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 Genetics. 12: e1005738. PMID 27019019 DOI: 10.1371/journal.pgen.1005738  1
2016 Myers SA, Peddada S, Chatterjee N, Freidreich T, Tomoda K, Krings G, Thomas S, Broeker M, Maynard J, 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. 5. PMID 26949256 DOI: 10.7554/eLife.10647  1
2016 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. PMID 26875865 DOI: 10.1016/j.cell.2016.01.004  1
2016 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, et al. Joint mouse-human phenome-wide association to test gene function and disease risk. Nature Communications. 7: 10464. PMID 26833085 DOI: 10.1038/ncomms10464  1
2015 Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS. Accelerated evolution of enhancer hotspots in the mammal ancestor. Molecular Biology and Evolution. PMID 26715627 DOI: 10.1093/molbev/msv344  1
2015 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. Statistics and Its Interface. 8: 463-476. PMID 26709360 DOI: 10.4310/SII.2015.v8.n4.a6  1
2015 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 Computational Biology. 11: e1004573. PMID 26565399 DOI: 10.1371/journal.pcbi.1004573  1
2015 Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, et al. MICROBIOME. A unified initiative to harness Earth's microbiomes. Science (New York, N.Y.). 350: 507-8. PMID 26511287 DOI: 10.1126/science.aac8480  1
2015 Franchini LF, Pollard KS. Genomic approaches to studying human-specific developmental traits. Development (Cambridge, England). 142: 3100-12. PMID 26395139 DOI: 10.1242/dev.120048  1
2015 Haliburton GD, McKinsey GL, Pollard KS. Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development. Neurogenetics. PMID 26382291 DOI: 10.1007/s10048-015-0458-9  1
2015 Franchini LF, Pollard KS. Can a few non-coding mutations make a human brain? Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 37: 1054-61. PMID 26350501 DOI: 10.1002/bies.201500049  1
2015 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. 16: 268. PMID 26303588 DOI: 10.1186/s12859-015-0677-y  1
2015 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 (Oxford, England). PMID 26104745 DOI: 10.1093/bioinformatics/btv382  1
2015 Maurice CF, Cl Knowles S, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ. Marked seasonal variation in the wild mouse gut microbiota. The Isme Journal. PMID 26023870 DOI: 10.1038/ismej.2015.53  1
2015 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 Research. 43: 5307-17. PMID 25934800 DOI: 10.1093/nar/gkv419  1
2015 Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N. Continental-scale distributions of dust-associated bacteria and fungi. Proceedings of the National Academy of Sciences of the United States of America. 112: 5756-61. PMID 25902536 DOI: 10.1073/pnas.1420815112  1
2015 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 Evolutionary Biology. 15: 35. PMID 25887984 DOI: 10.1186/s12862-015-0327-z  1
2015 Nayfach S, Pollard KS. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biology. 16: 51. PMID 25853934 DOI: 10.1186/s13059-015-0611-7  1
2015 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. 160: 1072-86. PMID 25768904 DOI: 10.1016/j.cell.2015.02.035  1
2015 Nayfach S, Pollard KS. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome Genome Biology. 16. DOI: 10.1186/s13059-015-0611-7  1
2015 Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT. Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions Molecular Biology and Evolution. 32: 1148-1160. DOI: 10.1093/molbev/msv031  1
2015 Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N. Continental-scale distributions of dust-associated bacteria and fungi Proceedings of the National Academy of Sciences of the United States of America. 112: 5756-5761. DOI: 10.1073/pnas.1420815112  1
2015 Maurice CF, CL Knowles S, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ. Marked seasonal variation in the wild mouse gut microbiota Isme Journal. DOI: 10.1038/ismej.2015.53  1
2014 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, ... ... Pollard KS, et al. Gibbon genome and the fast karyotype evolution of small apes. Nature. 513: 195-201. PMID 25209798 DOI: 10.1038/nature13679  1
2014 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. Translational Psychiatry. 4: e431. PMID 25180570 DOI: 10.1038/tp.2014.78  1
2014 Hubisz MJ, Pollard KS. Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution Current Opinion in Genetics and Development. 29: 15-21. PMID 25156517 DOI: 10.1016/j.gde.2014.07.005  1
2014 Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. Plos One. 9: e105067. PMID 25140992 DOI: 10.1371/journal.pone.0105067  1
2014 Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. Integrating diverse datasets improves developmental enhancer prediction. Plos Computational Biology. 10: e1003677. PMID 24967590 DOI: 10.1371/journal.pcbi.1003677  1
2014 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, et al. Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection. Journal of Virology. 88: 7221-34. PMID 24741080 DOI: 10.1128/JVI.00269-14  1
2014 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, ... ... Pollard KS, et al. Exome capture from saliva produces high quality genomic and metagenomic data. Bmc Genomics. 15: 262. PMID 24708091 DOI: 10.1186/1471-2164-15-262  1
2014 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. 9: e84689. PMID 24416266 DOI: 10.1371/journal.pone.0084689  1
2013 Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS. Many human accelerated regions are developmental enhancers. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 368: 20130025. PMID 24218637 DOI: 10.1098/rstb.2013.0025  1
2013 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, et al. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Molecular Cell. 52: 314-24. PMID 24207025 DOI: 10.1016/j.molcel.2013.10.009  1
2013 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 (New York, N.Y.). 342: 621-4. PMID 24179225 DOI: 10.1126/science.1243768  1
2013 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. 8. PMID 24086428 DOI: 10.1371/journal.pone.0075030  1
2013 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 Genetics. 9. PMID 23966869 DOI: 10.1371/journal.pgen.1003684  1
2013 Capra JA, Stolzer M, Durand D, Pollard KS. How old is my gene? Trends in Genetics : Tig. 29: 659-68. PMID 23915718 DOI: 10.1016/j.tig.2013.07.001  1
2013 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 Biology. 14: R72. PMID 23867016 DOI: 10.1186/gb-2013-14-7-r72  1
2013 Riesenfeld SJ, Pollard KS. Beyond classification: Gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis Bmc Genomics. 14. PMID 23799973 DOI: 10.1186/1471-2164-14-419  1
2013 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. The Isme Journal. 7: 1669-77. PMID 23514781 DOI: 10.1038/ismej.2013.37  1
2012 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. 13: 264. PMID 23061897 DOI: 10.1186/1471-2105-13-264  1
2012 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. 13. PMID 23020263 DOI: 10.1186/1471-2105-13-253  1
2012 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, et al. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 151: 206-20. PMID 22981692 DOI: 10.1016/j.cell.2012.07.035  1
2012 Capra JA, Williams AG, Pollard KS. Proteinhistorian: Tools for the comparative analysis of eukaryote protein origin Plos Computational Biology. 8. PMID 22761559 DOI: 10.1371/journal.pcbi.1002567  1
2012 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. 7: e35294. PMID 22719826 DOI: 10.1371/journal.pone.0035294  1
2012 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. 7: e32877. PMID 22412940 DOI: 10.1371/journal.pone.0032877  1
2012 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 Molecular Biology and Evolution. 29: 1047-1057. PMID 22075116 DOI: 10.1093/molbev/msr279  1
2011 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, ... ... Pollard KS, et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 478: 476-82. PMID 21993624 DOI: 10.1038/nature10530  1
2011 Kembel SW, Eisen JA, Pollard KS, Green JL. The phylogenetic diversity of metagenomes. Plos One. 6: e23214. PMID 21912589 DOI: 10.1371/journal.pone.0023214  1
2011 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. American Journal of Human Genetics. 89: 382-97. PMID 21855840 DOI: 10.1016/j.ajhg.2011.07.023  1
2011 Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E. SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2 Aging. 3: 635-642. PMID 21701047  1
2011 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 Biology and Evolution. 3: 614-626. PMID 21697099 DOI: 10.1093/gbe/evr058  1
2011 Capra JA, Pollard KS. Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biology and Evolution. 3: 516-27. PMID 21670083 DOI: 10.1093/gbe/evr051  0.32
2011 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. 6: e17753. PMID 21445258 DOI: 10.1371/journal.pone.0017753  1
2011 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, ... ... Pollard KS, et al. Chromatin remodelling complex dosage modulates transcription factor function in heart development. Nature Communications. 2: 187. PMID 21304516 DOI: 10.1038/ncomms1187  1
2011 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 Computational Biology. 7: e1001061. PMID 21283775 DOI: 10.1371/journal.pcbi.1001061  1
2011 Capra JA, Pollard KS. Substitution patterns are GC-biased in divergent sequences across the metazoans Genome Biology and Evolution. 3: 516-527. DOI: 10.1093/gbe/evr051  1
2011 Hubisz MJ, Pollard KS, Siepel A. Phastand Rphast: Phylogenetic analysis with space/time models Briefings in Bioinformatics. 12: 41-51. DOI: 10.1093/bib/bbq072  1
2010 Capra JA, Pollard KS, Singh M. Novel genes exhibit distinct patterns of function acquisition and network integration Genome Biology. 11. PMID 21187012 DOI: 10.1186/gb-2010-11-12-r127  1
2010 Kostka D, Hahn MW, Pollard KS. Noncoding sequences near duplicated genes evolve rapidly Genome Biology and Evolution. 2: 518-533. PMID 20660939 DOI: 10.1093/gbe/evq037  1
2010 Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. GC-biased evolution near human accelerated regions. Plos Genetics. 6: e1000960. PMID 20502635 DOI: 10.1371/journal.pgen.1000960  1
2010 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. Molecular Biology and Evolution. 27: 2322-32. PMID 20494938 DOI: 10.1093/molbev/msq128  1
2010 Taylor SL, Pollard KS. Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes Genetics Research. 92: 39-53. PMID 20196895 DOI: 10.1017/S0016672310000042  1
2010 Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies Genome Research. 20: 110-121. PMID 19858363 DOI: 10.1101/gr.097857.109  1
2009 Hsieh F, Chen SC, Pollard K. A Nearly exhaustive search for cpg islands on whole chromosomes International Journal of Biostatistics. 5. PMID 20148132 DOI: 10.2202/1557-4679.1158  1
2009 Pollard KS. What makes us human? Comparisons of the genomes of humans and chimpanzees are revealing those rare stretches of DNA that are ours alone Scientific American. 300: 44-49. PMID 19438048 DOI: 10.1038/scientificamerican0509-44  1
2009 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, et al. The bovine lactation genome: insights into the evolution of mammalian milk. Genome Biology. 10: R43. PMID 19393040 DOI: 10.1186/gb-2009-10-4-r43  1
2009 Taylor S, Pollard K. Hypothesis tests for point-mass mixture data with application to 'omics data with many zero values Statistical Applications in Genetics and Molecular Biology. 8. PMID 19222391 DOI: 10.2202/1544-6115.1425  1
2009 Berglund J, Pollard KS, Webster MT. Hotspots of biased nucleotide substitutions in human genes Plos Biology. 7. PMID 19175294 DOI: 10.1371/journal.pbio.1000026  1
2009 Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM. Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum Journal of Bacteriology. 191: 782-794. PMID 19047344 DOI: 10.1128/JB.00965-08  1
2008 Pollard KS, van der Laan MJ. Supervised distance matrices. Statistical Applications in Genetics and Molecular Biology. 7: Article 33. PMID 19049489 DOI: 10.2202/1544-6115.1404  1
2008 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. 9: 494. PMID 18937867 DOI: 10.1186/1471-2164-9-494  1
2008 Taylor SL, Pollard KS. Evaluation of two methods to estimate and monitor bird populations Plos One. 3. PMID 18728775 DOI: 10.1371/journal.pone.0003047  1
2008 Holloway AK, Begun DJ, Siepel A, Pollard KS. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Research. 18: 1592-601. PMID 18583644 DOI: 10.1101/gr.077131.108  1
2008 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 Human Genetics. 122: 625-634. PMID 17955261 DOI: 10.1007/s00439-007-0440-1  1
2007 Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB. Gene regulatory networks in lactation: identification of global principles using bioinformatics. Bmc Systems Biology. 1: 56. PMID 18039394 DOI: 10.1186/1752-0509-1-56  1
2007 Dreszer TR, Wall GD, Haussler D, Pollard KS. Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion Genome Research. 17: 1420-1430. PMID 17785536 DOI: 10.1101/gr.6395807  1
2007 Magalhães TR, Palmer J, Tomancak P, Pollard KS. Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach. Bmc Neuroscience. 8: 59. PMID 17672901 DOI: 10.1186/1471-2202-8-59  1
2006 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 Genetics. 2: e168. PMID 17040131 DOI: 10.1371/journal.pgen.0020168  1
2006 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, et al. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 443: 167-72. PMID 16915236 DOI: 10.1038/nature05113  1
2006 Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. The UCSC Archaeal Genome Browser. Nucleic Acids Research.. 34: D407-410. PMID 16381898  1
2006 Siepel A, Pollard KS, Haussler D. New methods for detecting lineage-specific selection Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 190-205. DOI: 10.1007/11732990_17  1
2005 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 Biology. 6: R12. PMID 15693941 DOI: 10.1186/gb-2005-6-2-r12  1
2004 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. Statistical Applications in Genetics and Molecular Biology. 3: Article15. PMID 16646793 DOI: 10.2202/1544-6115.1042  1
2004 van der Laan MJ, Dudoit S, Pollard KS. Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Statistical Applications in Genetics and Molecular Biology. 3: Article14. PMID 16646792 DOI: 10.2202/1544-6115.1041  1
2004 Dudoit S, van der Laan MJ, Pollard KS. Multiple testing. Part I. Single-step procedures for control of general type I error rates. Statistical Applications in Genetics and Molecular Biology. 3: Article13. PMID 16646791 DOI: 10.2202/1544-6115.1040  1
2004 Pollard KS, van der Laan MK. Choice of a null distribution in resampling-based multiple testing Journal of Statistical Planning and Inference. 125: 85-100. DOI: 10.1016/j.jspi.2003.07.019  1
2003 Van der Laan MJ, Pollard KS, Bryan J. A new partitioning around medoids algorithm Journal of Statistical Computation and Simulation. 73: 575-584. DOI: 10.1080/0094965031000136012  1
2003 van der Laan MJ, Pollard KS. A new algorithm for hybrid hierarchical clustering with visualization and the bootstrap Journal of Statistical Planning and Inference. 117: 275-303. DOI: 10.1016/S0378-3758(02)00388-9  1
2003 Pollard KS, Van der Laan MJ. Multiple testing for gene expression data: An investigation of null distributions with consequences for the permutation test Proceedings of the International Conference On Mathematics and Engineering Techniques in Medicine and Biological Sciences. 3-9.  1
2002 Pollard KS, van der Laan MJ. Statistical inference for simultaneous clustering of gene expression data. Mathematical Biosciences. 176: 99-121. PMID 11867086  1
2002 Bryan J, Pollard KS, Van der Laan MJ. Paired and unpaired comparison and clustering with gene expression data Statistica Sinica. 12: 87-110.  1
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