Katherine S. Pollard, PhD - Publications

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

121 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
2023 Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, ... ... Pollard KS, et al. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Molecular Cell. PMID 37419111 DOI: 10.1016/j.molcel.2023.06.018  0.491
2023 Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, ... ... Pollard KS, ... ... Pollard KS, et al. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science (New York, N.Y.). 380: eabn2937. PMID 37104612 DOI: 10.1126/science.abn2937  0.31
2023 Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Nowakowski T, Ahituv N, Pollen A, Pollard KS, Andrews G, ... ... Pollard KS, et al. Three-dimensional genome rewiring in loci with human accelerated regions. Science (New York, N.Y.). 380: eabm1696. PMID 37104607 DOI: 10.1126/science.abm1696  0.318
2023 Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, ... ... Pollard KS, ... ... Pollard KS, et al. Evolutionary constraint and innovation across hundreds of placental mammals. Science (New York, N.Y.). 380: eabn3943. PMID 37104599 DOI: 10.1126/science.abn3943  0.322
2023 Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wallerman O, ... ... Pollard KS, et al. Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease. Biorxiv : the Preprint Server For Biology. PMID 36945512 DOI: 10.1101/2023.03.10.531987  0.312
2022 Spanogiannopoulos P, Kyaw TS, Guthrie BGH, Bradley PH, Lee JV, Melamed J, Malig YNA, Lam KN, Gempis D, Sandy M, Kidder W, Van Blarigan EL, Atreya CE, Venook A, Gerona RR, ... ... Pollard KS, et al. Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism. Nature Microbiology. PMID 36138165 DOI: 10.1038/s41564-022-01226-5  0.729
2022 Whalen S, Pollard KS. Enhancer Function and Evolutionary Roles of Human Accelerated Regions. Annual Review of Genetics. PMID 36070559 DOI: 10.1146/annurev-genet-071819-103933  0.343
2022 Lyalina S, Stepanauskas R, Wu F, Sanjabi S, Pollard KS. Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community. Plos One. 17: e0261795. PMID 35417481 DOI: 10.1371/journal.pone.0261795  0.325
2021 Whalen S, Schreiber J, Noble WS, Pollard KS. Navigating the pitfalls of applying machine learning in genomics. Nature Reviews. Genetics. PMID 34837041 DOI: 10.1038/s41576-021-00434-9  0.472
2020 Bradley PH, Pollard KS. Building a chemical blueprint for human blood. Nature. PMID 33177685 DOI: 10.1038/d41586-020-03122-6  0.724
2020 Damas J, Hughes GM, Keough KC, Painter CA, Persky NS, Corbo M, Hiller M, Koepfli KP, Pfenning AR, Zhao H, Genereux DP, Swofford R, Pollard KS, Ryder OA, Nweeia MT, et al. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proceedings of the National Academy of Sciences of the United States of America. PMID 32826334 DOI: 10.1073/Pnas.2010146117  0.335
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  0.459
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  0.392
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  0.356
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  0.361
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  0.79
2019 Carmody RN, Bisanz JE, Bowen BP, Maurice CF, Lyalina S, Louie KB, Treen D, Chadaideh KS, Maini Rekdal V, Bess EN, Spanogiannopoulos P, Ang QY, Bauer KC, Balon TW, Pollard KS, et al. Cooking shapes the structure and function of the gut microbiome. Nature Microbiology. PMID 31570867 DOI: 10.1038/S41564-019-0569-4  0.314
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  0.353
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  0.405
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  0.493
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  0.727
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  0.727
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  0.442
2019 Garud NR, Good BH, Hallatschek O, Pollard KS. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. Plos Biology. 17: e3000102. PMID 30673701 DOI: 10.1371/Journal.Pbio.3000102  0.36
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  0.338
2019 Fudenberg G, Pollard KS. Chromatin features constrain structural variation across evolutionary timescales. Proceedings of the National Academy of Sciences of the United States of America. PMID 30659153 DOI: 10.1073/Pnas.1808631116  0.365
2019 Whalen S, Pollard KS. Most chromatin interactions are not in linkage disequilibrium. Genome Research. PMID 30617125 DOI: 10.1101/Gr.238022.118  0.376
2018 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, ... ... Pollard KS, et al. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proceedings of the National Academy of Sciences of the United States of America. PMID 30482864 DOI: 10.1073/Pnas.1809700115  0.316
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  0.359
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  0.782
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  0.443
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  0.379
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  0.405
2017 Franchini LF, Pollard KS. Human evolution: the non-coding revolution. Bmc Biology. 15: 89. PMID 28969617 DOI: 10.1186/S12915-017-0428-9  0.431
2017 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. 2. PMID 28904997 DOI: 10.1128/mSystems.00036-17  0.721
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  0.315
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  0.777
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  0.344
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  0.315
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  0.349
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  0.367
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  0.329
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  0.314
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  0.309
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  0.362
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  0.356
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  0.362
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  0.314
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  0.407
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  0.417
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  0.414
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  0.783
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  0.335
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  0.444
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  0.363
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  0.408
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  0.376
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  0.346
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  0.334
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  0.304
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  0.376
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  0.406
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  0.381
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  0.37
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  0.451
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  0.742
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  0.419
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  0.766
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  0.713
2014 Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. The between-study variability in the relative abundance of Bacteroidetes and Firmicutes is greater than the within-study differences between lean and obese individuals. Plos One. DOI: 10.1371/Journal.Pone.0084689.G003  0.689
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  0.429
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  0.356
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  0.678
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  0.328
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  0.339
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  0.391
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  0.727
2013 Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS. Erratum: Global marine bacterial diversity peaks at high latitudes in winter The Isme Journal. 7: 1876-1876. DOI: 10.1038/Ismej.2013.76  0.698
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  0.786
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  0.353
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  0.309
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  0.315
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  0.771
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  0.458
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  0.668
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  0.793
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  0.655
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  0.318
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  0.716
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  0.419
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  0.363
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  0.791
2011 Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space/time models. Briefings in Bioinformatics. 12: 41-51. PMID 21278375 DOI: 10.1093/Bib/Bbq072  0.614
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  0.5
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  0.363
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  0.444
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  0.792
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  0.36
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  0.641
2010 Wang X, Agarwala R, Capra JA, Chen Z, Church DM, Ciobanu DC, Li Z, Lu L, Mozhui K, Mulligan MK, Nelson SF, Pollard KS, Taylor WL, Thomason DB, Williams RW. High-throughput sequencing of the DBA/2J mouse genome Bmc Bioinformatics. 11. DOI: 10.1186/1471-2105-11-S4-O7  0.356
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  0.318
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  0.355
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  0.425
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  0.422
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  0.367
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  0.53
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  0.311
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  0.67
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  0.385
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  0.535
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  0.794
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  0.772
2006 Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. The UCSC Archaeal Genome Browser. Nucleic Acids Research.. 34: D407-410. PMID 16381898 DOI: 10.1093/Nar/Gkj134  0.689
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  0.514
2005 Mikkelsen TS, Hillier LW, Eichler EE, Zody MC, Jaffe DB, Yang S, Enard W, Hellmann I, Lindblad-Toh K, Altheide TK, Archidiacono N, Bork P, Butler J, Chang JL, Cheng Z, ... ... Pollard KS, et al. Initial sequence of the chimpanzee genome and comparison with the human genome Nature. 437: 69-87. PMID 16136131 DOI: 10.1038/Nature04072  0.406
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  0.312
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  0.742
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  0.75
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  0.752
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  0.492
2002 Pollard KS, van der Laan MJ. Statistical inference for simultaneous clustering of gene expression data. Mathematical Biosciences. 176: 99-121. PMID 11867086 DOI: 10.1016/S0025-5564(01)00116-X  0.528
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