Katie Pollard and her team develop models that enable them to decode how genomes work, evolve, and break in disease. Their analyses of massive sets of genomic and epigenomic data include investigating human genetic variation, understanding what makes humans unique compared to other species, and characterizing the genomic diversity of the human microbiome, the group of bacteria that populate our digestive system and other body sites. An evolutionary focus, coupled with rigorous statistical methods and bioinformatics tool development, gives the lab a unique perspective on human biology and disease.
Disease Areas
Areas of Expertise

Lab Focus
Research Impact
Pollard pioneered a statistical approach to identify the fastest-evolving regions of the human genome, known as Human Accelerated Regions (HARs). Her team showed that many of these correspond to non-coding sequences controlling the expression of genes important for development and associated with psychiatric disorders. The lab also used machine learning to reveal the importance of DNA shape and folding in gene regulation. These studies have generated research tools for studying human disease that are yielding novel therapeutic targets.
Pollard has also designed metagenomic-based methods to study the human microbiome at the resolution of individual genes and genetic mutations. From these studies, novel insight will arise into the relationship of the microbiome to health and disease, setting the stage for using metagenomics in precision medicine.
The Pollard Lab’s open-source code for gene expression analysis, detecting evolutionary conservation and acceleration, and quantifying genetic changes in the human microbiome is used in thousands of labs and classrooms.
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Professional Titles
L.K. Whittier Director, Gladstone Institute of Data Science and Biotechnology
Senior Investigator, Gladstone Institutes
Professor, Department of Epidemiology and Biostatistics, UC San Francisco
Director, Biomedical Informatics Graduate Program, UC San Francisco
Investigator, Chan Zuckerberg Biohub San Francisco
Bio
Computational biology, which empowers scientists to draw new insights from massive amounts of data, is Katie Pollard’s métier. She earned her PhD in biostatistics at UC Berkeley, then completed a postdoctoral fellowship at UC Santa Cruz, where she worked with David Haussler, the renowned bioinformatician who led the team that assembled the first human genome sequence. During her fellowship, Pollard discovered rapidly evolving regions in the human genome that may help explain the emergence of brain capabilities unique to humans and may also point to their vulnerability to neurological diseases. After serving as an assistant professor at UC Davis, Pollard joined Gladstone in 2008. She was appointed founding director of the Gladstone Institute of Biotechnology and Data Science in 2018.
In her work, Pollard designs computer programs that can test a million or more hypothetical experiments in a day to predict outcomes. This approach helps identify and prioritize which research avenues performed in a lab are most likely to lead to success, increasing efficiency and speeding discovery.
Her team is recognized for both its rigor to the field of genomics and for its generosity: the open-source software they create is readily shared with scientists around the world. Pollard herself is a dedicated mentor who takes pride in equipping women and other underrepresented groups in science with the skills and training to launch successful careers—and encourages them to extend the practice to the next generation.
Pollard also lends her expertise as an advisor to research programs across the country, including those at the Simons Foundation, The Rockefeller University, and Stanford University, and to biotechnology companies such as Phylagen and Tenaya Therapeutics.
What are you most excited about in your lab right now?
“It is such a thrill that we can now rapidly screen trillions of causal hypotheses about genetic diseases using AI models built in our lab This pushes us to take risks and enables us to prioritize the experiments that are most likely to yield new discoveries.”
Honors and Awards
2023 Fellow, American Association for the Advancement of Science
2022 Elected member, National Academy of Medicine
2021 Fellow, American Institute for Medical and Biological Engineering
2020 Fellow, International Society for Computational Biology
2018 Named to “San Francisco Business Times’” list of “Women Who Lead in the Life Sciences”
2018 Named to UC Berkeley School of Public Health’s list of “75 Most Influential Alumni”
2017 Named a Chan-Zuckerberg Biohub Investigator
2013 Fellow, California Academy of Sciences
2013 Alumna of the Year, UC Berkeley School of Public Health
2013 Best Scientific Visualizations of the Year, “Wired” Magazine
2009 Breakthrough Biomedical Research Award, UC San Francisco
2008 Sloan Research Fellowship, Alfred P. Sloan Foundation
2007 Faculty Development Award, UC Davis
2003 Evelyn Fix Memorial Prize, Chin Long Chiang Biostatistics Student of the Year, UC Berkeley
1998 Berkeley Fellowship, UC Berkeley
1996 Thomas J. Watson Fellowship, Watson Foundation
1995 Valedictorian, High Scholarship Prize, Math Prize, Anthropology Prize, Phi Beta Kappa Award, Pomona College
1993 Sophomore Math Prize, Pomona College
Publications
- Comparative characterization of human accelerated regions in neurons.
Cui X, Yang H, Cai C, Beaman C, Yang X, Liu H, Ren X, Amador Z, Jones IR, Keough KC, Zhang M, Fair T, Abnousi A, Mishra S, Ye Z, Hu M, Pollen AA, Pollard KS, Shen Y. Nature. 2025 Feb 26. - ChromaFactor: Deconvolution of single-molecule chromatin organization with non-negative matrix factorization.
Gunsalus LM, Keiser MJ, Pollard KS. PLoS Comput Biol. 2025 Feb; 21(2):e1012841. - Unveiling the Genetic Landscape of Coronary Artery Disease Through Common and Rare Structural Variants.
Iyer KR, Clarke SL, Guarischi-Sousa R, Gjoni K, Heath AS, Young EP, Stitziel NO, Laurie C, Broome JG, Khan AT, Lewis JP, Xu H, Montasser ME, Ashley KE, Hasbani NR, Boerwinkle E, Morrison AC, Chami N, Do R, Rocheleau G, Lloyd-Jones DM, Lemaitre RN, Bis JC, Floyd JS, Kinney GL, Bowden DW, Palmer ND, Benjamin EJ, Nayor M, Yanek LR, Kral BG, Becker LC, Kardia SLR, Smith JA, Bielak LF, Norwood AF, Min YI, Carson AP, Post WS, Rich SS, Herrington D, Guo X, Taylor KD, Manson JE, Franceschini N, Pollard KS, Mitchell BD, Loos RJF, Fornage M, Hou L, Psaty BM, Young KA, Regan EA, Freedman BI, Vasan RS, Levy D, Mathias RA, Peyser PA, Raffield LM, Kooperberg C, Reiner AP, Rotter JI, Jun G, de Vries PS, Assimes TL. J Am Heart Assoc. 2025 Feb 18; 14(4):e036499. - Artificial intelligence in molecular biology.
Kundaje A, Pollard KS, Ma J, Chang X, Chen M, Rohs R. Mol Cell. 2025 Jan 16; 85(2):193-198. - Contiguous and complete assemblies of Blastocystis gut microbiome-associated protists reveal evolutionary diversification to host ecology.
Lind AL, McDonald NA, Gerrick ER, Bhatt AS, Pollard KS. bioRxiv. 2025 Jan 15. - Cis-Regulatory Element and Transcription Factor Circuitry Required for Cell-Type Specific Expression of FOXP3.
Umhoefer JM, Arce MM, Whalen S, Dajani R, Goudy L, Kasinathan S, Belk JA, Zhang W, Zhou R, Subramanya S, Hernandez R, Tran C, Kirthivasan N, Freimer JW, Mowery CT, Nguyen V, Ota M, Gowen BG, Simeonov DR, Curie GL, Li Z, Corn JE, Chang HY, Gilbert LA, Satpathy AT, Pollard KS, Marson A. bioRxiv. 2025 Jan 14. - Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor.
Grant ZL, Kuang S, Zhang S, Horrillo AJ, Rao KS, Kameswaran V, Joubran C, Lau PK, Dong K, Yang B, Bartosik WM, Zemke NR, Ren B, Kathiriya IS, Pollard KS, Bruneau BG. bioRxiv. 2025 Jan 12. - Oxytocin receptor controls promiscuity and development in prairie voles.
Sharma R, Berendzen KM, Everitt A, Wang B, Williams G, Wang S, Quine K, Larios RD, Long KLP, Hoglen N, Sulaman BA, Heath MC, Sherman M, Klinkel R, Cai A, Galo D, Caamal LC, Goodwin NL, Beery A, Bales KL, Pollard KS, Willsey AJ, Manoli DS. bioRxiv. 2024 Dec 02. - Hierarchical annotation of eQTLs by H-eQTL enables identification of genes with cell type-divergent regulation.
Przytycki PF, Pollard KS. Genome Biol. 2024 Nov 25; 25(1):299. - De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.
Gjoni K, Ren X, Everitt A, Shen Y, Pollard KS. bioRxiv. 2024 Nov 07. - Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees.
Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA. Genome Biol Evol. 2024 Nov 01; 16(11). - An integrated view of the structure and function of the human 4D nucleome.
4D Nucleome Consortium, Dekker J, Oksuz BA, Zhang Y, Wang Y, Minsk MK, Kuang S, Yang L, Gibcus JH, Krietenstein N, Rando OJ, Xu J, Janssens DH, Henikoff S, Kukalev A, Willemin A, Winick-Ng W, Kempfer R, Pombo A, Yu M, Kumar P, Zhang L, Belmont AS, Sasaki T, van Schaik T, Brueckner L, Peric-Hupkes D, van Steensel B, Wang P, Chai H, Kim M, Ruan Y, Zhang R, Quinodoz SA, Bhat P, Guttman M, Zhao W, Chien S, Liu Y, Venev SV, Plewczynski D, Azcarate II, Szabó D, Thieme CJ, Szczepinska T, Chilinski M, Sengupta K, Conte M, Esposito A, Abraham A, Zhang R, Wang Y, Wen X, Wu Q, Yang Y, Liu J, Boninsegna L, Yildirim A, Zhan Y, Chiariello AM, Bianco S, Lee L, Hu M, Li Y, Barnett RJ, Cook AL, Emerson DJ, Marchal C, Zhao P, Park P, Alver BH, Schroeder A, Navelkar R, Bakker C, Ronchetti W, Ehmsen S, Veit A, Gehlenborg N, Wang T, Li D, Wang X, Nicodemi M, Ren B, Zhong S, Phillips-Cremins JE, Gilbert DM, Pollard KS, Alber F, Ma J, Noble WS, Yue F. bioRxiv. 2024 Oct 27. - Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease.
Häcker D, Siebert K, Smith BJ, Köhler N, Riva A, Mahapatra A, Heimes H, Nie J, Metwaly A, Hölz H, Manz Q, De Zen F, Heetmeyer J, Socas K, Le Thi G, Meng C, Kleigrewe K, Pauling JK, Neuhaus K, List M, Pollard KS, Schwerd T, Haller D. Cell Host Microbe. 2024 Nov 13; 32(11):2019-2034.e8. - Chromatin remodelling drives immune cell-fibroblast communication in heart failure.
Alexanian M, Padmanabhan A, Nishino T, Travers JG, Ye L, Pelonero A, Lee CY, Sadagopan N, Huang Y, Auclair K, Zhu A, An Y, Ekstrand CA, Martinez C, Teran BG, Flanigan WR, Kim CK, Lumbao-Conradson K, Gardner Z, Li L, Costa MW, Jain R, Charo I, Combes AJ, Haldar SM, Pollard KS, Vagnozzi RJ, McKinsey TA, Przytycki PF, Srivastava D. Nature. 2024 Nov; 635(8038):434-443. - Machine Learning Reveals the Diversity of Human 3D Chromatin Contact Patterns.
Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA. Mol Biol Evol. 2024 Oct 04; 41(10). - Author Correction: A molecular and cellular perspective on human brain evolution and tempo.
Lindhout FW, Krienen FM, Pollard KS, Lancaster MA. Nature. 2024 Oct; 634(8034):E9. - Pangenomes of human gut microbiota uncover links between genetic diversity and stress response.
Shoer S, Reicher L, Zhao C, Pollard KS, Pilpel Y, Segal E. Cell Host Microbe. 2024 Oct 09; 32(10):1744-1757.e2. - Frontotemporal lobar degeneration targets brain regions linked to expression of recently evolved genes.
Pasquini L, Pereira FL, Seddighi S, Zeng Y, Wei Y, Illán-Gala I, Vatsavayai SC, Friedberg A, Lee AJ, Brown JA, Spina S, Grinberg LT, Sirkis DW, Bonham LW, Yokoyama JS, Boxer AL, Kramer JH, Rosen HJ, Humphrey J, Gitler AD, Miller BL, Pollard KS, Ward ME, Seeley WW. Brain. 2024 Sep 03; 147(9):3032-3047. - Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients.
Zhang B, Magnaye KM, Stryker E, Moltzau-Anderson J, Porsche CE, Hertz S, McCauley KE, Smith BJ, Zydek M, Pollard KS, Ma A, El-Nachef N, Lynch SV. Sci Rep. 2024 08 09; 14(1):18558. - Exploring the roles of RNAs in chromatin architecture using deep learning.
Kuang S, Pollard KS. Nat Commun. 2024 Jul 29; 15(1):6373. - A molecular and cellular perspective on human brain evolution and tempo.
Lindhout FW, Krienen FM, Pollard KS, Lancaster MA. Nature. 2024 Jun; 630(8017):596-608. - SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models.
Gjoni K, Pollard KS. Bioinformatics. 2024 06 03; 40(6). - Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells.
Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A. Nat Genet. 2024 Jun; 56(6):1156-1167. - Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain.
Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H, PsychENCODE Consortium†, Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ, PsychENCODE Consortium. Science. 2024 May 24; 384(6698):eadh0829. - Massively parallel characterization of regulatory elements in the developing human cortex.
Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, PsychENCODE Consortium‡, Pollen AA, Nowakowski TJ, Ahituv N, Pollard KS, PsychENCODE Consortium. Science. 2024 May 24; 384(6698):eadh0559. - CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations.
Hu Z, Przytycki PF, Pollard KS. bioRxiv. 2024 May 17. - Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements.
Martyn C, Hayes BM, Lauko D, Midthun E, Castaneda G, Bosco-Lauth A, Salkeld DJ, Kistler A, Pollard KS, Chou S. mSystems. 2024 Jun 18; 9(6):e0032124. - Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.
Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E, Zoonomia Consortium, Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Science. 2024 Mar 29; 383(6690):eabn3263. - Machine learning reveals the diversity of human 3D chromatin contact patterns.
Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA. bioRxiv. 2023 Dec 23. - ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization.
Gunsalus LM, Keiser MJ, Pollard KS. bioRxiv. 2023 Nov 22. - SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models.
Gjoni K, Pollard KS. bioRxiv. 2023 Nov 05. - FTLD targets brain regions expressing recently evolved genes.
Pasquini L, Pereira FL, Seddighi S, Zeng Y, Wei Y, Illán-Gala I, Vatsavayai SC, Friedberg A, Lee AJ, Brown JA, Spina S, Grinberg LT, Sirkis DW, Bonham LW, Yokoyama JS, Boxer AL, Kramer JH, Rosen HJ, Humphrey J, Gitler AD, Miller BL, Pollard KS, Ward ME, Seeley WW. medRxiv. 2023 Oct 28. - Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.
Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA. bioRxiv. 2023 Oct 26. - Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning.
Kuang S, Pollard KS. bioRxiv. 2023 Oct 24. - In silico discovery of repetitive elements as key sequence determinants of 3D genome folding.
Gunsalus LM, Keiser MJ, Pollard KS. Cell Genom. 2023 Oct 11; 3(10):100410. - Maast: genotyping thousands of microbial strains efficiently.
Shi ZJ, Nayfach S, Pollard KS. Genome Biol. 2023 08 10; 24(1):186. - Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.
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, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Mol Cell. 2023 08 03; 83(15):2624-2640. - Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.
Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS. Nat Commun. 2023 06 14; 14(1):3510. - SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations.
Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS. Elife. 2023 Jun 12; 12. - Comparing chromatin contact maps at scale: methods and insights.
Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS. Res Sq. 2023 May 23. - A genomic timescale for placental mammal evolution.
Foley NM, Mason VC, Harris AJ, Bredemeyer KR, Damas J, Lewin HA, Eizirik E, Gatesy J, Karlsson EK, Lindblad-Toh K, Zoonomia Consortium‡, Springer MS, Murphy WJ. Science. 2023 04 28; 380(6643):eabl8189. - Evolutionary constraint and innovation across hundreds of placental mammals.
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, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR, Zoonomia Consortium§, Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Science. 2023 04 28; 380(6643):eabn3943. - Insights into mammalian TE diversity through the curation of 248 genome assemblies.
Osmanski AB, Paulat NS, Korstian J, Grimshaw JR, Halsey M, Sullivan KAM, Moreno-Santillán DD, Crookshanks C, Roberts J, Garcia C, Johnson MG, Densmore LD, Stevens RD, Zoonomia Consortium†, Rosen J, Storer JM, Hubley R, Smit AFA, Dávalos LM, Karlsson EK, Lindblad-Toh K, Ray DA. Science. 2023 04 28; 380(6643):eabn1430. - Integrating gene annotation with orthology inference at scale.
Kirilenko BM, Munegowda C, Osipova E, Jebb D, Sharma V, Blumer M, Morales AE, Ahmed AW, Kontopoulos DG, Hilgers L, Lindblad-Toh K, Karlsson EK, Zoonomia Consortium‡, Hiller M. Science. 2023 04 28; 380(6643):eabn3107. - Leveraging base-pair mammalian constraint to understand genetic variation and human disease.
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, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler A, Keough KC, Zheng Z, Zeng J, Wray NR, Li Y, Johnson J, Chen J, Zoonomia Consortium§, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Science. 2023 04 28; 380(6643):eabn2937. - Mammalian evolution of human cis-regulatory elements and transcription factor binding sites.
Andrews G, Fan K, Pratt HE, Phalke N, Zoonomia Consortium§, Karlsson EK, Lindblad-Toh K, Gazal S, Moore JE, Weng Z. Science. 2023 04 28; 380(6643):eabn7930. - Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.
Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP, Zoonomia Consortium**, Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR. Science. 2023 04 28; 380(6643):eabm7993. - The contribution of historical processes to contemporary extinction risk in placental mammals.
Wilder AP, Supple MA, Subramanian A, Mudide A, Swofford R, Serres-Armero A, Steiner C, Koepfli KP, Genereux DP, Karlsson EK, Lindblad-Toh K, Marques-Bonet T, Munoz Fuentes V, Foley K, Meyer WK, Zoonomia Consortium‡, Ryder OA, Shapiro B. Science. 2023 04 28; 380(6643):eabn5856. - The functional and evolutionary impacts of human-specific deletions in conserved elements.
Xue JR, Mackay-Smith A, Mouri K, Garcia MF, Dong MX, Akers JF, Noble M, Li X, Zoonomia Consortium†, Lindblad-Toh K, Karlsson EK, Noonan JP, Capellini TD, Brennand KJ, Tewhey R, Sabeti PC, Reilly SK. Science. 2023 04 28; 380(6643):eabn2253. - Three-dimensional genome rewiring in loci with human accelerated regions.
Keough KC, Whalen S, Inoue F, Przytycki PF, Fair T, Deng C, Steyert M, Ryu H, Lindblad-Toh K, Karlsson E, Zoonomia Consortium§, Nowakowski T, Ahituv N, Pollen A, Pollard KS. Science. 2023 04 28; 380(6643):eabm1696. - Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs.
Moon KL, Huson HJ, Morrill K, Wang MS, Li X, Srikanth K, Zoonomia Consortium, Lindblad-Toh K, Svenson GJ, Karlsson EK, Shapiro B. Science. 2023 04 28; 380(6643):eabn5887. - Oligogenic Architecture of Rare Noncoding Variants Distinguishes 4 Congenital Heart Disease Phenotypes.
Yu M, Aguirre M, Jia M, Gjoni K, Cordova-Palomera A, Munger C, Amgalan D, Rosa Ma X, Pereira A, Tcheandjieu C, Seidman C, Seidman J, Tristani-Firouzi M, Chung W, Goldmuntz E, Srivastava D, Loos RJF, Chami N, Cordell H, Dreßen M, Mueller-Myhsok B, Lahm H, Krane M, Pollard KS, Engreitz JM, Gagliano Taliun SA, Gelb BD, Priest JR. Circ Genom Precis Med. 2023 06; 16(3):258-266. - Genetic Determinants of the Interventricular Septum Are Linked to Ventricular Septal Defects and Hypertrophic Cardiomyopathy.
Yu M, Harper AR, Aguirre M, Pittman M, Tcheandjieu C, Amgalan D, Grace C, Goel A, Farrall M, Xiao K, Engreitz J, Pollard KS, Watkins H, Priest JR. Circ Genom Precis Med. 2023 06; 16(3):207-215. - Comparing chromatin contact maps at scale: methods and insights.
Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS. bioRxiv. 2023 Apr 04. - Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease.
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, Xue JR, Li Y, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler AJ, Keough KC, Zheng Z, Zeng J, Wray NR, Johnson J, Chen J, Zoonomia Consortium, Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. bioRxiv. 2023 Mar 10. - Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain.
Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, Chatzinakos C, Clarke D, Pratt H, Consortium P, Peters MA, Gerstein M, Daskalakis NP, Weng Z, Jaffe AE, Kleinman JE, Hyde TM, Weinberger DR, Bray NJ, Sestan N, Geschwind DH, Roeder K, Gusev A, Pasaniuc B, Stein JL, Love MI, Pollard KS, Liu C, Gandal MJ. medRxiv. 2023 Mar 06. - Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex.
Deng C, Whalen S, Steyert M, Ziffra R, Przytycki PF, Inoue F, Pereira DA, Capauto D, Norton S, Vaccarino FM, Pollen A, Nowakowski TJ, Ahituv N, Pollard KS. bioRxiv. 2023 Feb 16. - An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype.
Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R. Genome Biol. 2023 01 23; 24(1):16. - Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro.
Shi ZJ, Nayfach S, Pollard KS. STAR Protoc. 2023 03 17; 4(1):101964. - Pitfalls of genotyping microbial communities with rapidly growing genome collections.
Zhao C, Shi ZJ, Pollard KS. Cell Syst. 2023 02 15; 14(2):160-176.e3. - Machine learning dissection of human accelerated regions in primate neurodevelopment.
Whalen S, Inoue F, Ryu H, Fair T, Markenscoff-Papadimitriou E, Keough K, Kircher M, Martin B, Alvarado B, Elor O, Laboy Cintron D, Williams A, Hassan Samee MA, Thomas S, Krencik R, Ullian EM, Kriegstein A, Rubenstein JL, Shendure J, Pollen AA, Ahituv N, Pollard KS. Neuron. 2023 03 15; 111(6):857-873.e8. - Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis.
Alexanian M, Padmanabhan A, Nishino T, Travers JG, Ye L, Lee CY, Sadagopan N, Huang Y, Pelonero A, Auclair K, Zhu A, Teran BG, Flanigan W, Kim CK, Lumbao-Conradson K, Costa M, Jain R, Charo I, Haldar SM, Pollard KS, Vagnozzi RJ, McKinsey TA, Przytycki PF, Srivastava D. bioRxiv. 2023 Jan 07. - MIDAS2: Metagenomic Intra-species Diversity Analysis System.
Zhao C, Dimitrov B, Goldman M, Nayfach S, Pollard KS. Bioinformatics. 2023 01 01; 39(1). - Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.
Zhao C, Goldman M, Smith BJ, Pollard KS. Curr Protoc. 2022 Dec; 2(12):e604. - Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism.
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, Goga A, Pollard KS, Turnbaugh PJ. Nat Microbiol. 2022 10; 7(10):1605-1620. - Enhancer Function and Evolutionary Roles of Human Accelerated Regions.
Whalen S, Pollard KS. Annu Rev Genet. 2022 11 30; 56:423-439. - Correction to: Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons.
Wagle M, Zarei M, Lovett-Barron M, Poston KT, Xu J, Ramey V, Pollard KS, Prober DA, Schulkin J, Deisseroth K, Guo S. Mol Psychiatry. 2022 Sep; 27(9):3794. - Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors.
Zhu L, Choudhary K, Gonzalez-Teran B, Ang YS, Thomas R, Stone NR, Liu L, Zhou P, Zhu C, Ruan H, Huang Y, Jin S, Pelonero A, Koback F, Padmanabhan A, Sadagopan N, Hsu A, Costa MW, Gifford CA, van Bemmel JG, Hüttenhain R, Vedantham V, Conklin BR, Black BL, Bruneau BG, Steinmetz L, Krogan NJ, Pollard KS, Srivastava D. Circulation. 2022 09 06; 146(10):770-787. - Cell Layers: uncovering clustering structure in unsupervised single-cell transcriptomic analysis.
Blair AP, Hu RK, Farah EN, Chi NC, Pollard KS, Przytycki PF, Kathiriya IS, Bruneau BG. Bioinform Adv. 2022; 2(1):vbac051. - Differential Etv2 threshold requirement for endothelial and erythropoietic development.
Sinha T, Lammerts van Bueren K, Dickel DE, Zlatanova I, Thomas R, Lizama CO, Xu SM, Zovein AC, Ikegami K, Moskowitz IP, Pollard KS, Pennacchio LA, Black BL. Cell Rep. 2022 05 31; 39(9):110881. - Dose adjustments of Elexacaftor/Tezacaftor/Ivacaftor in response to mental health side effects in adults with cystic fibrosis.
Spoletini G, Gillgrass L, Pollard K, Shaw N, Williams E, Etherington C, Clifton IJ, Peckham DG. J Cyst Fibros. 2022 11; 21(6):1061-1065. - Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts.
Smith BJ, Li X, Shi ZJ, Abate A, Pollard KS. Front Bioinform. 2022; 2:867386. - Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons.
Wagle M, Zarei M, Lovett-Barron M, Poston KT, Xu J, Ramey V, Pollard KS, Prober DA, Schulkin J, Deisseroth K, Guo S. Mol Psychiatry. 2022 09; 27(9):3777-3793. - CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements.
Przytycki PF, Pollard KS. Bioinformatics. 2022 04 28; 38(9):2621-2623. - Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community.
Lyalina S, Stepanauskas R, Wu F, Sanjabi S, Pollard KS. PLoS One. 2022; 17(4):e0261795. - Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis.
Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N. Sci Rep. 2022 04 01; 12(1):5517. - Transcription factor protein interactomes reveal genetic determinants in heart disease.
Gonzalez-Teran B, Pittman M, Felix F, Thomas R, Richmond-Buccola D, Hüttenhain R, Choudhary K, Moroni E, Costa MW, Huang Y, Padmanabhan A, Alexanian M, Lee CY, Maven BEJ, Samse-Knapp K, Morton SU, McGregor M, Gifford CA, Seidman JG, Seidman CE, Gelb BD, Colombo G, Conklin BR, Black BL, Bruneau BG, Krogan NJ, Pollard KS, Srivastava D. Cell. 2022 03 03; 185(5):794-814.e30. - Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.
Shi ZJ, Dimitrov B, Zhao C, Nayfach S, Pollard KS. Nat Biotechnol. 2022 04; 40(4):507-516. - Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes.
Markenscoff-Papadimitriou E, Binyameen F, Whalen S, Price J, Lim K, Ypsilanti AR, Catta-Preta R, Pai EL, Mu X, Xu D, Pollard KS, Nord AS, State MW, Rubenstein JL. Cell Rep. 2021 12 07; 37(10):110089. - Navigating the pitfalls of applying machine learning in genomics.
Whalen S, Schreiber J, Noble WS, Pollard KS. Nat Rev Genet. 2022 03; 23(3):169-181. - Human gut bacterial metabolism drives Th17 activation and colitis.
Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ. Cell Host Microbe. 2022 01 12; 30(1):17-30.e9. - Publisher Correction: Accelerated RNA detection using tandem CRISPR nucleases.
Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim S, Dugan EJ, IGI Testing Consortium, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. Nat Chem Biol. 2021 Nov; 17(11):1210. - Single-cell epigenomics reveals mechanisms of human cortical development.
Ziffra RS, Kim CN, Ross JM, Wilfert A, Turner TN, Haeussler M, Casella AM, Przytycki PF, Keough KC, Shin D, Bogdanoff D, Kreimer A, Pollard KS, Ament SA, Eichler EE, Ahituv N, Nowakowski TJ. Nature. 2021 10; 598(7879):205-213. - Systematic identification of non-canonical transcription factor motifs.
Chumpitaz-Diaz L, Samee MAH, Pollard KS. BMC Mol Cell Biol. 2021 Aug 31; 22(1):44. - Evaluation of Le et al.: Challenges and opportunities for using data to understand equitability in science.
Smith BJ, Pollard KS. Evaluation of Le et al.: Challenges and opportunities for using data to understand equitability in science. Cell Syst. 2021 09 22; 12(9):839-841. - Accelerated RNA detection using tandem CRISPR nucleases.
Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, Díaz de León Derby M, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim S, Dugan EJ, IGI Testing Consortium, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. Nat Chem Biol. 2021 09; 17(9):982-988. - Genome-wide variability in recombination activity is associated with meiotic chromatin organization.
Jin X, Fudenberg G, Pollard KS. Genome Res. 2021 09; 31(9):1561-1572. - Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment.
Roodgar M, Good BH, Garud NR, Martis S, Avula M, Zhou W, Lancaster SM, Lee H, Babveyh A, Nesamoney S, Pollard KS, Snyder MP. Genome Res. 2021 08; 31(8):1433-1446. - Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
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, Shendure J, Kircher M, Ahituv N. Nat Protoc. 2021 Jul; 16(7):3736. - A transcriptional switch governs fibroblast activation in heart disease.
Alexanian M, Przytycki PF, Micheletti R, Padmanabhan A, Ye L, Travers JG, Gonzalez-Teran B, Silva AC, Duan Q, Ranade SS, Felix F, Linares-Saldana R, Li L, Lee CY, Sadagopan N, Pelonero A, Huang Y, Andreoletti G, Jain R, McKinsey TA, Rosenfeld MG, Gifford CA, Pollard KS, Haldar SM, Srivastava D. Nature. 2021 07; 595(7867):438-443. - Caloric restriction disrupts the microbiota and colonization resistance.
von Schwartzenberg RJ, Bisanz JE, Lyalina S, Spanogiannopoulos P, Ang QY, Cai J, Dickmann S, Friedrich M, Liu SY, Collins SL, Ingebrigtsen D, Miller S, Turnbaugh JA, Patterson AD, Pollard KS, Mai K, Spranger J, Turnbaugh PJ. Nature. 2021 07; 595(7866):272-277. - The gut microbiomes of 180 species.
Lind AL, Pollard KS. Science. 2021 04 16; 372(6539):238-239. - Ultraconservation of enhancers is not ultranecessary.
Pittman M, Pollard KS. Nat Genet. 2021 04; 53(4):429-430. - Accelerated RNA detection using tandem CRISPR nucleases.
Liu TY, Knott GJ, Smock DCJ, Desmarais JJ, Son S, Bhuiya A, Jakhanwal S, Prywes N, Agrawal S, de León Derby MD, Switz NA, Armstrong M, Harris AR, Charles EJ, Thornton BW, Fozouni P, Shu J, Stephens SI, Kumar GR, Zhao C, Mok A, Iavarone AT, Escajeda AM, McIntosh R, Kim SE, Dugan EJ, IGI Testing Consortium, Pollard KS, Tan MX, Ott M, Fletcher DA, Lareau LF, Hsu PD, Savage DF, Doudna JA. medRxiv. 2021 Mar 24. - Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing.
Lind AL, Pollard KS. Microbiome. 2021 03 03; 9(1):58. - CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues.
Przytycki PF, Pollard KS. Genome Biol. 2021 02 14; 22(1):61. - Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.
Fozouni P, Son S, Díaz de León Derby M, Knott GJ, Gray CN, D'Ambrosio MV, Zhao C, Switz NA, Kumar GR, Stephens SI, Boehm D, Tsou CL, Shu J, Bhuiya A, Armstrong M, Harris AR, Chen PY, Osterloh JM, Meyer-Franke A, Joehnk B, Walcott K, Sil A, Langelier C, Pollard KS, Crawford ED, Puschnik AS, Phelps M, Kistler A, DeRisi JL, Doudna JA, Fletcher DA, Ott M. Cell. 2021 01 21; 184(2):323-333.e9. - Building a chemical blueprint for human blood.
Bradley PH, Pollard KS. Nature. 2020 12; 588(7836):36-37. - Molecular basis of CTCF binding polarity in genome folding.
Nora EP, Caccianini L, Fudenberg G, So K, Kameswaran V, Nagle A, Uebersohn A, Hajj B, Saux AL, Coulon A, Mirny LA, Pollard KS, Dahan M, Bruneau BG. Nat Commun. 2020 11 05; 11(1):5612. - Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
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, Titus EW, Cakir M, Soucheray M, McGregor M, Cakir Z, Jang G, O'Meara MJ, Tummino TA, Zhang Z, Foussard H, Rojc A, Zhou Y, Kuchenov D, Hüttenhain R, Xu J, Eckhardt M, Swaney DL, Fabius JM, Ummadi M, Tutuncuoglu B, Rathore U, Modak M, Haas P, Haas KM, Naing ZZC, Pulido EH, Shi Y, Barrio-Hernandez I, Memon D, Petsalaki E, Dunham A, Marrero MC, Burke D, Koh C, Vallet T, Silvas JA, Azumaya CM, Billesbølle C, Brilot AF, Campbell MG, Diallo A, Dickinson MS, Diwanji D, Herrera N, Hoppe N, Kratochvil HT, Liu Y, Merz GE, Moritz M, Nguyen HC, Nowotny C, Puchades C, Rizo AN, Schulze-Gahmen U, Smith AM, Sun M, Young ID, Zhao J, Asarnow D, Biel J, Bowen A, Braxton JR, Chen J, Chio CM, Chio US, Deshpande I, Doan L, Faust B, Flores S, Jin M, Kim K, Lam VL, Li F, Li J, Li YL, Li Y, Liu X, Lo M, Lopez KE, Melo AA, Moss FR, Nguyen P, Paulino J, Pawar KI, Peters JK, Pospiech TH, Safari M, Sangwan S, Schaefer K, Thomas PV, Thwin AC, Trenker R, Tse E, Tsui TKM, Wang F, Whitis N, Yu Z, Zhang K, Zhang Y, Zhou F, Saltzberg D, QCRG Structural Biology Consortium, Hodder AJ, Shun-Shion AS, Williams DM, White KM, Rosales R, Kehrer T, Miorin L, Moreno E, Patel AH, Rihn S, Khalid MM, Vallejo-Gracia A, Fozouni P, Simoneau CR, Roth TL, Wu D, Karim MA, Ghoussaini M, Dunham I, Berardi F, Weigang S, Chazal M, Park J, Logue J, McGrath M, Weston S, Haupt R, Hastie CJ, Elliott M, Brown F, Burness KA, Reid E, Dorward M, Johnson C, Wilkinson SG, Geyer A, Giesel DM, Baillie C, Raggett S, Leech H, Toth R, Goodman N, Keough KC, Lind AL, Zoonomia Consortium, Klesh RJ, Hemphill KR, Carlson-Stevermer J, Oki J, Holden K, Maures T, Pollard KS, Sali A, Agard DA, Cheng Y, Fraser JS, Frost A, Jura N, Kortemme T, Manglik A, Southworth DR, Stroud RM, Alessi DR, Davies P, Frieman MB, Ideker T, Abate C, Jouvenet N, Kochs G, Shoichet B, Ott M, Palmarini M, Shokat KM, García-Sastre A, Rassen JA, Grosse R, Rosenberg OS, Verba KA, Basler CF, Vignuzzi M, Peden AA, Beltrao P, Krogan NJ. Science. 2020 12 04; 370(6521). - Predicting 3D genome folding from DNA sequence with Akita.
Fudenberg G, Kelley DR, Pollard KS. Nat Methods. 2020 11; 17(11):1111-1117. - Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates.
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, Lindblad-Toh K, Teeling EC, Karlsson EK, Lewin HA. Proc Natl Acad Sci U S A. 2020 09 08; 117(36):22311-22322. - A unified catalog of 204,938 reference genomes from the human gut microbiome.
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. Nat Biotechnol. 2021 01; 39(1):105-114. - lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
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, Shendure J, Kircher M, Ahituv N. Nat Protoc. 2020 08; 15(8):2387-2412. - A Chromatin Accessibility Atlas of the Developing Human Telencephalon.
Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL. Cell. 2020 08 06; 182(3):754-769.e18. - Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates.
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, Lindblad-Toh K, Teeling EC, Karlsson EK, Lewin HA. bioRxiv. 2020 Apr 18. - Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth.
Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M. Front Microbiol. 2020; 11:476. - phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.
Bradley PH, Pollard KS. Bioinformatics. 2020 02 15; 36(4):1289-1290. - Early Palliative Care Consultation in the Medical ICU: A Cluster Randomized Crossover Trial.
Ma J, Chi S, Buettner B, Pollard K, Muir M, Kolekar C, Al-Hammadi N, Chen L, Kollef M, Dans M. Crit Care Med. 2019 12; 47(12):1707-1715. - Population Genetics in the Human Microbiome.
Garud NR, Pollard KS. Trends Genet. 2020 01; 36(1):53-67. - Principles of meiotic chromosome assembly revealed in S. cerevisiae.
Schalbetter SA, Fudenberg G, Baxter J, Pollard KS, Neale MJ. Nat Commun. 2019 10 22; 10(1):4795. - Global ecotypes in the ubiquitous marine clade SAR86.
Hoarfrost A, Nayfach S, Ladau J, Yooseph S, Arnosti C, Dupont CL, Pollard KS. ISME J. 2020 01; 14(1):178-188. - Cooking shapes the structure and function of the gut microbiome.
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, Northen TR, Turnbaugh PJ. Nat Microbiol. 2019 12; 4(12):2052-2063. - AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design.
Keough KC, Lyalina S, Olvera MP, Whalen S, Conklin BR, Pollard KS. Genome Biol. 2019 Aug 15; 20(1):167. - Reply to 'Inflated performance measures in enhancer-promoter interaction-prediction methods'.
Whalen S, Pollard KS. Nat Genet. 2019 08; 51(8):1198-1200. - Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards.
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, Trifonov VA, Schijlen E, Kratochvíl L, Fani R, Velenský P, Rehák I, Patarnello T, Jessop TS, Hicks JW, Ryder OA, Mendelson JR, Ciofi C, Kwok PY, Pollard KS, Bruneau BG. Nat Ecol Evol. 2019 08; 3(8):1241-1252. - Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming.
Stone NR, Gifford CA, Thomas R, Pratt KJB, Samse-Knapp K, Mohamed TMA, Radzinsky EM, Schricker A, Ye L, Yu P, van Bemmel JG, Ivey KN, Pollard KS, Srivastava D. Cell Stem Cell. 2019 07 03; 25(1):87-102.e9. - The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice.
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, Afinowicz L, Yu KH, Grützmann R, Aust D, Gimotty PA, Pollard KS, Hruban RH, Goggins MG, Pilarsky C, Park Y, Pappin DJ, Hollingsworth MA, Tuveson DA. Science. 2019 06 21; 364(6446):1156-1162. - Empowering statistical methods for cellular and molecular biologists.
Pollard DA, Pollard TD, Pollard KS. Mol Biol Cell. 2019 06 01; 30(12):1359-1368. - Evolution of Mechanisms that Control Mating in Drosophila Males.
Ahmed OM, Avila-Herrera A, Tun KM, Serpa PH, Peng J, Parthasarathy S, Knapp JM, Stern DL, Davis GW, Pollard KS, Shah NM. Cell Rep. 2019 05 28; 27(9):2527-2536.e4. - A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome.
Armour CR, Nayfach S, Pollard KS, Sharpton TJ. mSystems. 2019 Jul-Aug; 4(4). - Early-Career Scientists Shaping the World.
Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J. mSystems. 2019 May 07; 4(3). - Consent insufficient for data release-Response.
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. Science. 2019 05 03; 364(6439):446. - New insights from uncultivated genomes of the global human gut microbiome.
Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides NC. Nature. 2019 04; 568(7753):505-510. - Toward unrestricted use of public genomic data.
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. Science. 2019 01 25; 363(6425):350-352. - Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.
Garud NR, Good BH, Hallatschek O, Pollard KS. PLoS Biol. 2019 01; 17(1):e3000102. - Chromatin features constrain structural variation across evolutionary timescales.
Fudenberg G, Pollard KS. Proc Natl Acad Sci U S A. 2019 02 05; 116(6):2175-2180. - A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs.
Samee MAH, Bruneau BG, Pollard KS. Cell Syst. 2019 01 23; 8(1):27-42.e6. - Most chromatin interactions are not in linkage disequilibrium.
Whalen S, Pollard KS. Genome Res. 2019 03; 29(3):334-343. - Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis.
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. Cell. 2018 12 13; 175(7):1931-1945.e18. - Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults.
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. Proc Natl Acad Sci U S A. 2018 12 26; 115(52):E12353-E12362. - Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes.
Ladau J, Shi Y, Jing X, He JS, Chen L, Lin X, Fierer N, Gilbert JA, Pollard KS, Chu H. mSystems. 2018 Sep-Oct; 3(5). - A most wanted list of conserved microbial protein families with no known domains.
Wyman SK, Avila-Herrera A, Nayfach S, Pollard KS. PLoS One. 2018; 13(10):e0205749. - Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.
Bradley PH, Nayfach S, Pollard KS. PLoS Comput Biol. 2018 08; 14(8):e1006242. - Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages.
Kostka D, Holloway AK, Pollard KS. Mol Biol Evol. 2018 08 01; 35(8):2034-2045. - American Gut: an Open Platform for Citizen Science Microbiome Research.
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, American Gut Consortium , Knight R. mSystems. 2018 May-Jun; 3(3). - The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation.
Moquin SA, Thomas S, Whalen S, Warburton A, Fernandez SG, McBride AA, Pollard KS, Miranda JL. J Virol. 2018 02 01; 92(3). - A communal catalogue reveals Earth's multiscale microbial diversity.
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, Earth Microbiome Project Consortium. Nature. 2017 11 23; 551(7681):457-463. - Human evolution: the non-coding revolution.
Franchini LF, Pollard KS. BMC Biol. 2017 10 02; 15(1):89. - Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice.
Sharpton T, Lyalina S, Luong J, Pham J, Deal EM, Armour C, Gaulke C, Sanjabi S, Pollard KS. mSystems. 2017 Sep-Oct; 2(5). - 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.
Milgrom P, Horst JA, Ludwig S, Rothen M, Chaffee BW, Lyalina S, Pollard KS, DeRisi JL, Mancl L. J Dent. 2018 01; 68:72-78. - Features that define the best ChIP-seq peak calling algorithms.
Thomas R, Thomas S, Holloway AK, Pollard KS. Brief Bioinform. 2017 05 01; 18(3):441-450. - Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk.
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, LifeLines Cohort Study, InterAct Consortium, kConFab/AOCS Investigators, Endometrial Cancer Association Consortium, Ovarian Cancer Association Consortium, PRACTICAL consortium, 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. Nat Genet. 2017 Jun; 49(6):834-841. - Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites.
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. Development. 2017 04 01; 144(7):1235-1241. - Proteobacteria explain significant functional variability in the human gut microbiome.
Bradley PH, Pollard KS. Microbiome. 2017 03 23; 5(1):36. - Unboxing cluster heatmaps.
Engle S, Whalen S, Joshi A, Pollard KS. BMC Bioinformatics. 2017 Feb 15; 18(Suppl 2):63. - Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.
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. Cell. 2017 01 26; 168(3):517-526.e18. - Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota.
Devlin AS, Marcobal A, Dodd D, Nayfach S, Plummer N, Meyer T, Pollard KS, Sonnenburg JL, Fischbach MA. Cell Host Microbe. 2016 Dec 14; 20(6):709-715. - An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.
Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS. Genome Res. 2016 11; 26(11):1612-1625. - Toward Accurate and Quantitative Comparative Metagenomics.
Nayfach S, Pollard KS. Cell. 2016 Aug 25; 166(5):1103-1116. - Urban greenness influences airborne bacterial community composition.
Mhuireach G, Johnson BR, Altrichter AE, Ladau J, Meadow JF, Pollard KS, Green JL. Sci Total Environ. 2016 Nov 15; 571:680-7. - Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges.
Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL. mBio. 2016 05 13; 7(3). - Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.
Whalen S, Truty RM, Pollard KS. Nat Genet. 2016 05; 48(5):488-96. - Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus.
Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N. PLoS Genet. 2016 Mar; 12(3):e1005738. - Transcriptomic and epigenomic characterization of the developing bat wing.
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. Nat Genet. 2016 05; 48(5):528-36. - SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells.
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. Elife. 2016 Mar 07; 5:e10647. - Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.
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. Cell. 2016 Feb 25; 164(5):999-1014. - Joint mouse-human phenome-wide association to test gene function and disease risk.
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. Nat Commun. 2016 Feb 02; 7:10464. - Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor.
Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS. Mol Biol Evol. 2016 Apr; 33(4):1008-18. - Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.
Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. PLoS Comput Biol. 2015 Nov; 11(11):e1004573. - MICROBIOME. A unified initiative to harness Earth's microbiomes.
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, Ruby EG, Taha SA, Unified Microbiome Initiative Consortium. Science. 2015 Oct 30; 350(6260):507-8. - Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development.
Haliburton GD, McKinsey GL, Pollard KS. Neurogenetics. 2016 Jan; 17(1):1-9. - Genomic approaches to studying human-specific developmental traits.
Franchini LF, Pollard KS. Development. 2015 Sep 15; 142(18):3100-12. - Can a few non-coding mutations make a human brain?
Franchini LF, Pollard KS. Bioessays. 2015 Oct; 37(10):1054-61. - Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species.
Avila-Herrera A, Pollard KS. BMC Bioinformatics. 2015 Aug 25; 16:268. - MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome.
Nayfach S, Fischbach MA, Pollard KS. Bioinformatics. 2015 Oct 15; 31(20):3368-70. - Fungal contamination of nebuliser devices used by people with cystic fibrosis.
Peckham D, Williams K, Wynne S, Denton M, Pollard K, Barton R. J Cyst Fibros. 2016 Jan; 15(1):74-7. - Marked seasonal variation in the wild mouse gut microbiota.
Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ. ISME J. 2015 Nov; 9(11):2423-34. - Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.
Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S. Nucleic Acids Res. 2015 Jun 23; 43(11):5307-17. - Continental-scale distributions of dust-associated bacteria and fungi.
Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N. Proc Natl Acad Sci U S A. 2015 May 05; 112(18):5756-61. - Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome.
Nayfach S, Pollard KS. Genome Biol. 2015 Mar 25; 16:51. - Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency.
Theodoris CV, Li M, White MP, Liu L, He D, Pollard KS, Bruneau BG, Srivastava D. Cell. 2015 Mar 12; 160(6):1072-86. - Evolution of lysine acetylation in the RNA polymerase II C-terminal domain.
Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA. BMC Evol Biol. 2015 Mar 10; 15:35. - Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions.
Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT. Mol Biol Evol. 2015 May; 32(5):1148-60. - motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences.
Kostka D, Friedrich T, Holloway AK, Pollard KS. Stat Interface. 2015; 8(4):463-476. - Gibbon genome and the fast karyotype evolution of small apes.
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. Nature. 2014 Sep 11; 513(7517):195-201. - Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.
Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N. Transl Psychiatry. 2014 Sep 02; 4:e431. - Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution.
Hubisz MJ, Pollard KS. Curr Opin Genet Dev. 2014 Dec; 29:15-21. - Profile hidden Markov models for the detection of viruses within metagenomic sequence data.
Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. PLoS One. 2014; 9(8):e105067. - Integrating diverse datasets improves developmental enhancer prediction.
Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. PLoS Comput Biol. 2014 Jun; 10(6):e1003677. - Protective role of HO-1 and carbon monoxide in ethanol-induced hepatocyte cell death and liver injury in mice.
Bakhautdin B, Das D, Mandal P, Roychowdhury S, Danner J, Bush K, Pollard K, Kaspar JW, Li W, Salomon RG, McMullen MR, Nagy LE. J Hepatol. 2014 Nov; 61(5):1029-37. - Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection.
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. J Virol. 2014 Jul; 88(13):7221-34. - Exome capture from saliva produces high quality genomic and metagenomic data.
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. BMC Genomics. 2014 Apr 04; 15:262. - A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter.
Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. PLoS One. 2014; 9(1):e84689. - Many human accelerated regions are developmental enhancers.
Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS. Philos Trans R Soc Lond B Biol Sci. 2013 Dec 19; 368(1632):20130025. - Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells.
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. Mol Cell. 2013 Nov 07; 52(3):314-24. - Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.
Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. Science. 2013 Nov 01; 342(6158):621-4. - From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome.
Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M. PLoS One. 2013; 8(9):e75030. - A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.
Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. PLoS Genet. 2013; 9(8):e1003684. - How old is my gene?
Capra JA, Stolzer M, Durand D, Pollard KS. Trends Genet. 2013 Nov; 29(11):659-68. - A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design.
Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. Genome Biol. 2013 Jul 18; 14(7):R72. - Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.
Riesenfeld SJ, Pollard KS. BMC Genomics. 2013 Jun 22; 14:419. - Global marine bacterial diversity peaks at high latitudes in winter.
Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS. ISME J. 2013 Sep; 7(9):1669-77. - Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.
Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA. BMC Bioinformatics. 2012 Oct 13; 13:264. - G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.
Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS. BMC Bioinformatics. 2012 Sep 28; 13:253. - Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.
Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG. Cell. 2012 Sep 28; 151(1):206-20. - ProteinHistorian: tools for the comparative analysis of eukaryote protein origin.
Capra JA, Williams AG, Pollard KS. PLoS Comput Biol. 2012; 8(6):e1002567. - Novel bacterial taxa in the human microbiome.
Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS. PLoS One. 2012; 7(6):e35294. - Analysis of human accelerated DNA regions using archaic hominin genomes.
Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S. PLoS One. 2012; 7(3):e32877. - The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.
Kostka D, Hubisz MJ, Siepel A, Pollard KS. Mol Biol Evol. 2012 Mar; 29(3):1047-57. - A high-resolution map of human evolutionary constraint using 29 mammals.
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, Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, 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, Genome Institute at Washington University, 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. Nature. 2011 Oct 12; 478(7370):476-82. - Chromosomal haplotypes by genetic phasing of human families.
Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF. Am J Hum Genet. 2011 Sep 09; 89(3):382-97. - The phylogenetic diversity of metagenomes.
Kembel SW, Eisen JA, Pollard KS, Green JL. PLoS One. 2011; 6(8):e23214. - Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots.
Katzman S, Capra JA, Haussler D, Pollard KS. Genome Biol Evol. 2011; 3:614-26. - Substitution patterns are GC-biased in divergent sequences across the metazoans.
Capra JA, Pollard KS. Genome Biol Evol. 2011; 3:516-27. - SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2.
Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E. Aging (Albany NY). 2011 Jun; 3(6):635-42. - Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution.
Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P. PLoS One. 2011 Mar 18; 6(3):e17753. - Chromatin remodelling complex dosage modulates transcription factor function in heart development.
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. Nat Commun. 2011 Feb 08; 2:187. - PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data.
Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. PLoS Comput Biol. 2011 Jan 20; 7(1):e1001061. - Novel genes exhibit distinct patterns of function acquisition and network integration.
Capra JA, Pollard KS, Singh M. Genome Biol. 2010; 11(12):R127. - PHAST and RPHAST: phylogenetic analysis with space/time models.
Hubisz MJ, Pollard KS, Siepel A. Brief Bioinform. 2011 Jan; 12(1):41-51. - Noncoding sequences near duplicated genes evolve rapidly.
Kostka D, Hahn MW, Pollard KS. Genome Biol Evol. 2010; 2:518-33. - The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.
Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH. Mol Biol Evol. 2010 Oct; 27(10):2322-32. - GC-biased evolution near human accelerated regions.
Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. PLoS Genet. 2010 May 20; 6(5):e1000960. - Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes.
Taylor SL, Pollard KS. Genet Res (Camb). 2010 Feb; 92(1):39-53. - Detection of nonneutral substitution rates on mammalian phylogenies.
Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Genome Res. 2010 Jan; 20(1):110-21. - A nearly exhaustive search for CpG islands on whole chromosomes.
Hsieh F, Chen SC, Pollard K. Int J Biostat. 2009; 5(1). - What makes us human?
Pollard KS. Sci Am. 2009 May; 300(5):44-9. - The bovine lactation genome: insights into the evolution of mammalian milk.
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. Genome Biol. 2009; 10(4):R43. - Student engagement in interprofessional working in practice placement settings.
Pollard K. J Clin Nurs. 2009 Oct; 18(20):2846-56. - Hypothesis tests for point-mass mixture data with application to 'omics data with many zero values.
Taylor S, Pollard K. Stat Appl Genet Mol Biol. 2009; 8:Article 8. - Hotspots of biased nucleotide substitutions in human genes.
Berglund J, Pollard KS, Webster MT. PLoS Biol. 2009 Jan 27; 7(1):e26. - Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.
Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM. J Bacteriol. 2009 Feb; 191(3):782-94. - Supervised distance matrices.
Pollard KS, van der Laan MJ. Stat Appl Genet Mol Biol. 2008; 7(1):Article 33. - 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.
Walker WL, Liao IH, Gilbert DL, Wong B, Pollard KS, McCulloch CE, Lit L, Sharp FR. BMC Genomics. 2008 Oct 20; 9:494. - Evaluation of two methods to estimate and monitor bird populations.
Taylor SL, Pollard KS. PLoS One. 2008 Aug 27; 3(8):e3047. - Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster.
Holloway AK, Begun DJ, Siepel A, Pollard KS. Genome Res. 2008 Oct; 18(10):1592-601. - Gene regulatory networks in lactation: identification of global principles using bioinformatics.
Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB. BMC Syst Biol. 2007 Nov 27; 1:56. - A genome-wide approach to identifying novel-imprinted genes.
Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K. Hum Genet. 2008 Jan; 122(6):625-34. - Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion.
Dreszer TR, Wall GD, Haussler D, Pollard KS. Genome Res. 2007 Oct; 17(10):1420-30. - Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach.
Magalhães TR, Palmer J, Tomancak P, Pollard KS. BMC Neurosci. 2007 Jul 31; 8:59. - Forces shaping the fastest evolving regions in the human genome.
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. PLoS Genet. 2006 Oct 13; 2(10):e168. - An RNA gene expressed during cortical development evolved rapidly in humans.
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. Nature. 2006 Sep 14; 443(7108):167-72. - Discovery of a cool planet of 5.5 Earth masses through gravitational microlensing.
Beaulieu JP, Bennett DP, Fouqué P, Williams A, Dominik M, Jørgensen UG, Kubas D, Cassan A, Coutures C, Greenhill J, Hill K, Menzies J, Sackett PD, Albrow M, Brillant S, Caldwell JA, Calitz JJ, Cook KH, Corrales E, Desort M, Dieters S, Dominis D, Donatowicz J, Hoffman M, Kane S, Marquette JB, Martin R, Meintjes P, Pollard K, Sahu K, Vinter C, Wambsganss J, Woller K, Horne K, Steele I, Bramich DM, Burgdorf M, Snodgrass C, Bode M, Udalski A, Szymanski MK, Kubiak M, Wieckowski T, Pietrzynski G, Soszynski I, Szewczyk O, Wyrzykowski L, Paczynski B, Abe F, Bond IA, Britton TR, Gilmore AC, Hearnshaw JB, Itow Y, Kamiya K, Kilmartin PM, Korpela AV, Masuda K, Matsubara Y, Motomura M, Muraki Y, Nakamura S, Okada C, Ohnishi K, Rattenbury NJ, Sako T, Sato S, Sasaki M, Sekiguchi T, Sullivan DJ, Tristram PJ, Yock PC, Yoshioka T. Nature. 2006 Jan 26; 439(7075):437-40. - The UCSC Archaeal Genome Browser.
Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D407-10. - Identifying genetic networks underlying myometrial transition to labor.
Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Genome Biol. 2005; 6(2):R12. - Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives.
van der Laan MJ, Dudoit S, Pollard KS. Stat Appl Genet Mol Biol. 2004; 3:Article15. - Multiple testing. Part II. Step-down procedures for control of the family-wise error rate.
van der Laan MJ, Dudoit S, Pollard KS. Stat Appl Genet Mol Biol. 2004; 3:Article14. - Multiple testing. Part I. Single-step procedures for control of general type I error rates.
Dudoit S, van der Laan MJ, Pollard KS. Stat Appl Genet Mol Biol. 2004; 3:Article13. - Stenotrophomonas maltophilia contamination of nebulizers used to deliver aerosolized therapy to inpatients with cystic fibrosis.
Denton M, Rajgopal A, Mooney L, Qureshi A, Kerr KG, Keer V, Pollard K, Peckham DG, Conway SP. J Hosp Infect. 2003 Nov; 55(3):180-3. - Statistical inference for simultaneous clustering of gene expression data.
Pollard KS, van der Laan MJ. Math Biosci. 2002 Mar; 176(1):99-121.
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Katie Pollard
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415.734.2743
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415.734.4827
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