Katie Pollard, PhD
Professor
Epidemiology & Biostatistics
School of Medicine

Examples of current projects are massively parallel dissection of regulatory networks and decoding cryptic variation in the human microbiome.

• Hierarchical annotation of eQTLs by H-eQTL enables identification of genes with cell type-divergent regulation.
  Genome biology 2024 Przytycki PF, Pollard KS
• De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.
  bioRxiv : the preprint server for biology 2024 Gjoni K, Ren X, Everitt A, Shen Y, Pollard KS
• An integrated view of the structure and function of the human 4D nucleome.
  bioRxiv : the preprint server for biology 2024 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 …
• Chromatin remodelling drives immune cell-fibroblast communication in heart failure.
  Nature 2024 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, …
• Exclusive enteral nutrition initiates individual protective microbiome changes to induce remission in pediatric Crohn's disease.
  Cell host & microbe 2024 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, …
• Machine learning reveals the diversity of human 3D chromatin contact patterns.
  Molecular biology and evolution 2024 Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA
• Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.
  Genome biology and evolution 2024 Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA
• Author Correction: A molecular and cellular perspective on human brain evolution and tempo.
  Nature 2024 Lindhout FW, Krienen FM, Pollard KS, Lancaster MA
• Pangenomes of human gut microbiota uncover links between genetic diversity and stress response.
  Cell host & microbe 2024 Shoer S, Reicher L, Zhao C, Pollard KS, Pilpel Y, Segal E
• Oxytocin receptor controls distinct components of pair bonding and development in prairie voles.
  bioRxiv : the preprint server for biology 2024 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, Kinkel M, Cai A, Galo D, Caamal LC, Goodwin NL, Beery A, Bales …
• Frontotemporal lobar degeneration targets brain regions linked to expression of recently evolved genes.
  Brain : a journal of neurology 2024 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, …
• Sustained mucosal colonization and fecal metabolic dysfunction by Bacteroides associates with fecal microbial transplant failure in ulcerative colitis patients.
  Scientific reports 2024 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
• Exploring the roles of RNAs in chromatin architecture using deep learning.
  Nature communications 2024 Kuang S, Pollard KS
• A molecular and cellular perspective on human brain evolution and tempo.
  Nature 2024 Lindhout FW, Krienen FM, Pollard KS, Lancaster MA
• SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models.
  Bioinformatics (Oxford, England) 2024 Gjoni K, Pollard KS
• Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells.
  Nature genetics 2024 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 …
• Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain.
  Science (New York, N.Y.) 2024 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†, …
• Massively parallel characterization of regulatory elements in the developing human cortex.
  Science (New York, N.Y.) 2024 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 …
• CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations.
  bioRxiv : the preprint server for biology 2024 Hu Z, Przytycki PF, Pollard KS
• Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements.
  mSystems 2024 Martyn C, Hayes BM, Lauko D, Midthun E, Castaneda G, Bosco-Lauth A, Salkeld DJ, Kistler A, Pollard KS, Chou S
• Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements.
  Science (New York, N.Y.) 2024 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, …
• Machine learning reveals the diversity of human 3D chromatin contact patterns.
  bioRxiv : the preprint server for biology 2023 Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA
• ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization.
  bioRxiv : the preprint server for biology 2023 Gunsalus LM, Keiser MJ, Pollard KS
• Hybrid assemblies of microbiome Blastocystis protists reveal evolutionary diversification reflecting host ecology.
  bioRxiv : the preprint server for biology 2023 Lind AL, McDonald NA, Gerrick ER, Bhatt AS, Pollard KS
• SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models.
  bioRxiv : the preprint server for biology 2023 Gjoni K, Pollard KS
• FTLD targets brain regions expressing recently evolved genes.
  medRxiv : the preprint server for health sciences 2023 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, …
• Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees.
  bioRxiv : the preprint server for biology 2023 Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA
• Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning.
  bioRxiv : the preprint server for biology 2023 Kuang S, Pollard KS
• In silico discovery of repetitive elements as key sequence determinants of 3D genome folding.
  Cell genomics 2023 Gunsalus LM, Keiser MJ, Pollard KS
• Maast: genotyping thousands of microbial strains efficiently.
  Genome biology 2023 Shi ZJ, Nayfach S, Pollard KS
• Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project.
  Molecular cell 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, Kalhor R, Leslie CS, Li W, Li…
• Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.
  Nature communications 2023 Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS
• SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations.
  eLife 2023 Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS
• Comparing chromatin contact maps at scale: methods and insights.
  Research square 2023 Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS
• A genomic timescale for placental mammal evolution.
  Science (New York, N.Y.) 2023 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
• Evolutionary constraint and innovation across hundreds of placental mammals.
  Science (New York, N.Y.) 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, Goodman DB, Goodman L, Keough KC, …
• Insights into mammalian TE diversity through the curation of 248 genome assemblies.
  Science (New York, N.Y.) 2023 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, …
• Integrating gene annotation with orthology inference at scale.
  Science (New York, N.Y.) 2023 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
• Leveraging base-pair mammalian constraint to understand genetic variation and human disease.
  Science (New York, N.Y.) 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, Wallerman O, Xue J, Yao S, Sun Q, …
• Mammalian evolution of human cis-regulatory elements and transcription factor binding sites.
  Science (New York, N.Y.) 2023 Andrews G, Fan K, Pratt HE, Phalke N, Zoonomia Consortium§, Karlsson EK, Lindblad-Toh K, Gazal S, Moore JE, Weng Z
• Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.
  Science (New York, N.Y.) 2023 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, …
• The contribution of historical processes to contemporary extinction risk in placental mammals.
  Science (New York, N.Y.) 2023 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, …
• The functional and evolutionary impacts of human-specific deletions in conserved elements.
  Science (New York, N.Y.) 2023 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
• Three-dimensional genome rewiring in loci with human accelerated regions.
  Science (New York, N.Y.) 2023 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
• ​Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs.
  Science (New York, N.Y.) 2023 Moon KL, Huson HJ, Morrill K, Wang MS, Li X, Srikanth K, Zoonomia Consortium, Lindblad-Toh K, Svenson GJ, Karlsson EK, Shapiro B
• Oligogenic Architecture of Rare Noncoding Variants Distinguishes 4 Congenital Heart Disease Phenotypes.
  Circulation. Genomic and precision medicine 2023 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, …
• Genetic Determinants of the Interventricular Septum Are Linked to Ventricular Septal Defects and Hypertrophic Cardiomyopathy.
  Circulation. Genomic and precision medicine 2023 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
• Comparing chromatin contact maps at scale: methods and insights.
  bioRxiv : the preprint server for biology 2023 Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS
• Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease.
  bioRxiv : the preprint server for biology 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, Xue JR, Li Y, Yao S, Sun Q, …
• Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain.
  medRxiv : the preprint server for health sciences 2023 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 …
• Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex.
  bioRxiv : the preprint server for biology 2023 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
• An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype.
  Genome biology 2023 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
• Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro.
  STAR protocols 2023 Shi ZJ, Nayfach S, Pollard KS
• Pitfalls of genotyping microbial communities with rapidly growing genome collections.
  Cell systems 2023 Zhao C, Shi ZJ, Pollard KS
• Machine learning dissection of human accelerated regions in primate neurodevelopment.
  Neuron 2023 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, …
• Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis.
  bioRxiv : the preprint server for biology 2023 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 …
• MIDAS2: Metagenomic Intra-species Diversity Analysis System.
  Bioinformatics (Oxford, England) 2023 Zhao C, Dimitrov B, Goldman M, Nayfach S, Pollard KS
• Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.
  Current protocols 2022 Zhao C, Goldman M, Smith BJ, Pollard KS
• Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism.
  Nature microbiology 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, Goga A, Pollard KS, Turnbaugh…
• Enhancer Function and Evolutionary Roles of Human Accelerated Regions.
  Annual review of genetics 2022 Whalen S, Pollard KS
• Correction to: Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons.
  Molecular psychiatry 2022 Wagle M, Zarei M, Lovett-Barron M, Poston KT, Xu J, Ramey V, Pollard KS, Prober DA, Schulkin J, Deisseroth K, Guo S
• Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors.
  Circulation 2022 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 …
• Cell Layers: uncovering clustering structure in unsupervised single-cell transcriptomic analysis.
  Bioinformatics advances 2022 Blair AP, Hu RK, Farah EN, Chi NC, Pollard KS, Przytycki PF, Kathiriya IS, Bruneau BG
• Differential Etv2 threshold requirement for endothelial and erythropoietic development.
  Cell reports 2022 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
• Dose adjustments of Elexacaftor/Tezacaftor/Ivacaftor in response to mental health side effects in adults with cystic fibrosis.
  Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society 2022 Spoletini G, Gillgrass L, Pollard K, Shaw N, Williams E, Etherington C, Clifton IJ, Peckham DG
• Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts.
  Frontiers in bioinformatics 2022 Smith BJ, Li X, Shi ZJ, Abate A, Pollard KS
• Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons.
  Molecular psychiatry 2022 Wagle M, Zarei M, Lovett-Barron M, Poston KT, Xu J, Ramey V, Pollard KS, Prober DA, Schulkin J, Deisseroth K, Guo S
• CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements.
  Bioinformatics (Oxford, England) 2022 Przytycki PF, Pollard KS
• Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community.
  PloS one 2022 Lyalina S, Stepanauskas R, Wu F, Sanjabi S, Pollard KS
• Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis.
  Scientific reports 2022 Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N
• Transcription factor protein interactomes reveal genetic determinants in heart disease.
  Cell 2022 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, …
• Fast and accurate metagenotyping of the human gut microbiome with GT-Pro.
  Nature biotechnology 2021 Shi ZJ, Dimitrov B, Zhao C, Nayfach S, Pollard KS
• Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes.
  Cell reports 2021 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
• Navigating the pitfalls of applying machine learning in genomics.
  Nature reviews. Genetics 2021 Whalen S, Schreiber J, Noble WS, Pollard KS
• Human gut bacterial metabolism drives Th17 activation and colitis.
  Cell host & microbe 2021 Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ
• Publisher Correction: Accelerated RNA detection using tandem CRISPR nucleases.
  Nature chemical biology 2021 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, …
• Single-cell epigenomics reveals mechanisms of human cortical development.
  Nature 2021 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
• Systematic identification of non-canonical transcription factor motifs.
  BMC molecular and cell biology 2021 Chumpitaz-Diaz L, Samee MAH, Pollard KS
• Evaluation of Le et al.: Challenges and opportunities for using data to understand equitability in science.
  Cell systems 2021 Smith BJ, Pollard KS
• Accelerated RNA detection using tandem CRISPR nucleases.
  Nature chemical biology 2021 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, …
• Genome-wide variability in recombination activity is associated with meiotic chromatin organization.
  Genome research 2021 Jin X, Fudenberg G, Pollard KS
• Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment.
  Genome research 2021 Roodgar M, Good BH, Garud NR, Martis S, Avula M, Zhou W, Lancaster SM, Lee H, Babveyh A, Nesamoney S, Pollard KS, Snyder MP
• Author Correction: lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
  Nature protocols 2021 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
• A transcriptional switch governs fibroblast activation in heart disease.
  Nature 2021 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, …
• Caloric restriction disrupts the microbiota and colonization resistance.
  Nature 2021 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, …
• The gut microbiomes of 180 species.
  Science (New York, N.Y.) 2021 Lind AL, Pollard KS
• Ultraconservation of enhancers is not ultranecessary.
  Nature genetics 2021 Pittman M, Pollard KS
• Accelerated RNA detection using tandem CRISPR nucleases.
  medRxiv : the preprint server for health sciences 2021 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…
• Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing.
  Microbiome 2021 Lind AL, Pollard KS
• CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues.
  Genome biology 2021 Przytycki PF, Pollard KS
• Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.
  Cell 2020 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, …
• Building a chemical blueprint for human blood.
  Nature 2020 Bradley PH, Pollard KS
• Molecular basis of CTCF binding polarity in genome folding.
  Nature communications 2020 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
• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms.
  Science (New York, N.Y.) 2020 Gordon DE, Hiatt J, Bouhaddou M, Rezelj VV, Ulferts S, Braberg H, Jureka AS, Obernier K, Guo JZ, Batra J, Kaake RM, Weckstein AR, Owens TW, Gupta M, Pourmal S, Titus EW, Cakir M, Soucheray M, McGregor…
• Predicting 3D genome folding from DNA sequence with Akita.
  Nature methods 2020 Fudenberg G, Kelley DR, Pollard KS
• 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 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, Lindblad-Toh K, Teeling EC, Karlsson…
• A unified catalog of 204,938 reference genomes from the human gut microbiome.
  Nature biotechnology 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
• lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements.
  Nature protocols 2020 Gordon MG, Inoue F, Martin B, Schubach M, Agarwal V, Whalen S, Feng S, Zhao J, Ashuach T, Ziffra R, Kreimer A, Georgakopoulos-Soares I, Yosef N, Ye CJ, Pollard KS, Shendure J, Kircher M, Ahituv N
• A Chromatin Accessibility Atlas of the Developing Human Telencephalon.
  Cell 2020 Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL
• Broad Host Range of SARS-CoV-2 Predicted by Comparative and Structural Analysis of ACE2 in Vertebrates.
  bioRxiv : the preprint server for biology 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, Lindblad-Toh K, Teeling EC, Karlsson…
• Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth.
  Frontiers in microbiology 2020 Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M
• phylogenize: correcting for phylogeny reveals genes associated with microbial distributions.
  Bioinformatics (Oxford, England) 2020 Bradley PH, Pollard KS
• Early Palliative Care Consultation in the Medical ICU: A Cluster Randomized Crossover Trial.
  Critical care medicine 2019 Ma J, Chi S, Buettner B, Pollard K, Muir M, Kolekar C, Al-Hammadi N, Chen L, Kollef M, Dans M
• Population Genetics in the Human Microbiome.
  Trends in genetics : TIG 2019 Garud NR, Pollard KS
• Principles of meiotic chromosome assembly revealed in S. cerevisiae.
  Nature communications 2019 Schalbetter SA, Fudenberg G, Baxter J, Pollard KS, Neale MJ
• Global ecotypes in the ubiquitous marine clade SAR86.
  The ISME journal 2019 Hoarfrost A, Nayfach S, Ladau J, Yooseph S, Arnosti C, Dupont CL, Pollard KS
• Cooking shapes the structure and function of the gut microbiome.
  Nature microbiology 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, Northen TR, Turnbaugh PJ
• AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design.
  Genome biology 2019 Keough KC, Lyalina S, Olvera MP, Whalen S, Conklin BR, Pollard KS
• Reply to 'Inflated performance measures in enhancer-promoter interaction-prediction methods'.
  Nature genetics 2019 Whalen S, Pollard KS
• Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards.
  Nature ecology & evolution 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, Trifonov VA, Schijlen E…
• Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming.
  Cell stem cell 2019 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
• The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice.
  Science (New York, N.Y.) 2019 Engle DD, Tiriac H, Rivera KD, Pommier A, Whalen S, Oni TE, Alagesan B, Lee EJ, Yao MA, Lucito MS, Spielman B, Da Silva B, Schoepfer C, Wright K, Creighton B, Afinowicz L, Yu KH, Grützmann R, Aust D, …
• Empowering statistical methods for cellular and molecular biologists.
  Molecular biology of the cell 2019 Pollard DA, Pollard TD, Pollard KS
• Evolution of Mechanisms that Control Mating in Drosophila Males.
  Cell reports 2019 Ahmed OM, Avila-Herrera A, Tun KM, Serpa PH, Peng J, Parthasarathy S, Knapp JM, Stern DL, Davis GW, Pollard KS, Shah NM
• A Metagenomic Meta-analysis Reveals Functional Signatures of Health and Disease in the Human Gut Microbiome.
  mSystems 2019 Armour CR, Nayfach S, Pollard KS, Sharpton TJ
• Early-Career Scientists Shaping the World.
  mSystems 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
• Consent insufficient for data release-Response.
  Science (New York, N.Y.) 2019 Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, …
• New insights from uncultivated genomes of the global human gut microbiome.
  Nature 2019 Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides NC
• Toward unrestricted use of public genomic data.
  Science (New York, N.Y.) 2019 Amann RI, Baichoo S, Blencowe BJ, Bork P, Borodovsky M, Brooksbank C, Chain PSG, Colwell RR, Daffonchio DG, Danchin A, de Lorenzo V, Dorrestein PC, Finn RD, Fraser CM, Gilbert JA, Hallam SJ, …
• Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.
  PLoS biology 2019 Garud NR, Good BH, Hallatschek O, Pollard KS
• Chromatin features constrain structural variation across evolutionary timescales.
  Proceedings of the National Academy of Sciences of the United States of America 2019 Fudenberg G, Pollard KS
• A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs.
  Cell systems 2019 Samee MAH, Bruneau BG, Pollard KS
• Most chromatin interactions are not in linkage disequilibrium.
  Genome research 2019 Whalen S, Pollard KS
• Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis.
  Cell 2018 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,…
• 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 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, Quan J, Zinter M, Chiu CY, Chow ED, …
• Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes.
  mSystems 2018 Ladau J, Shi Y, Jing X, He JS, Chen L, Lin X, Fierer N, Gilbert JA, Pollard KS, Chu H
• A most wanted list of conserved microbial protein families with no known domains.
  PloS one 2018 Wyman SK, Avila-Herrera A, Nayfach S, Pollard KS
• Phylogeny-corrected identification of microbial gene families relevant to human gut colonization.
  PLoS computational biology 2018 Bradley PH, Nayfach S, Pollard KS
• Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages.
  Molecular biology and evolution 2018 Kostka D, Holloway AK, Pollard KS
• American Gut: an Open Platform for Citizen Science Microbiome Research.
  mSystems 2018 McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A, Ackermann G, Aksenov AA, Behsaz B, Brennan C, Chen Y, DeRight Goldasich L, Dorrestein PC, Dunn RR, Fahimipour AK, Gaffney J, Gilbert JA, Gogul G…
• The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation.
  Journal of virology 2018 Moquin SA, Thomas S, Whalen S, Warburton A, Fernandez SG, McBride AA, Pollard KS, Miranda JL
• A communal catalogue reveals Earth's multiscale microbial diversity.
  Nature 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, Morton JT, Mirarab S…
• Human evolution: the non-coding revolution.
  BMC biology 2017 Franchini LF, Pollard KS
• Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice.
  mSystems 2017 Sharpton T, Lyalina S, Luong J, Pham J, Deal EM, Armour C, Gaulke C, Sanjabi S, Pollard KS
• 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.
  Journal of dentistry 2017 Milgrom P, Horst JA, Ludwig S, Rothen M, Chaffee BW, Lyalina S, Pollard KS, DeRisi JL, Mancl L
• Features that define the best ChIP-seq peak calling algorithms.
  Briefings in bioinformatics 2017 Thomas R, Thomas S, Holloway AK, Pollard KS
• Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk.
  Nature genetics 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, Demerath E, Giri A, He C, Hottenga …
• Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites.
  Development (Cambridge, England) 2017 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
• Proteobacteria explain significant functional variability in the human gut microbiome.
  Microbiome 2017 Bradley PH, Pollard KS
• Unboxing cluster heatmaps.
  BMC bioinformatics 2017 Engle S, Whalen S, Joshi A, Pollard KS
• Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases.
  Cell 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
• Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota.
  Cell host & microbe 2016 Devlin AS, Marcobal A, Dodd D, Nayfach S, Plummer N, Meyer T, Pollard KS, Sonnenburg JL, Fischbach MA
• An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography.
  Genome research 2016 Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS
• Toward Accurate and Quantitative Comparative Metagenomics.
  Cell 2016 Nayfach S, Pollard KS
• Urban greenness influences airborne bacterial community composition.
  The Science of the total environment 2016 Mhuireach G, Johnson BR, Altrichter AE, Ladau J, Meadow JF, Pollard KS, Green JL
• Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges.
  mBio 2016 Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL
• Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin.
  Nature genetics 2016 Whalen S, Truty RM, Pollard KS
• Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus.
  PLoS genetics 2016 Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N
• Transcriptomic and epigenomic characterization of the developing bat wing.
  Nature genetics 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, Wall JD, Illing N, …
• SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells.
  eLife 2016 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
• Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis.
  Cell 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
• Joint mouse-human phenome-wide association to test gene function and disease risk.
  Nature communications 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, Ciobanu DC, Reznik AO, Tishkov AV,…
• Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor.
  Molecular biology and evolution 2015 Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS
• Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes.
  PLoS computational biology 2015 Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ
• MICROBIOME. A unified initiative to harness Earth's microbiomes.
  Science (New York, N.Y.) 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, Ruby EG, Taha SA, Unified…
• Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development.
  Neurogenetics 2015 Haliburton GD, McKinsey GL, Pollard KS
• Can a few non-coding mutations make a human brain?
  BioEssays : news and reviews in molecular, cellular and developmental biology 2015 Franchini LF, Pollard KS
• Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species.
  BMC bioinformatics 2015 Avila-Herrera A, Pollard KS
• Fungal contamination of nebuliser devices used by people with cystic fibrosis.
  Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society 2015 Peckham D, Williams K, Wynne S, Denton M, Pollard K, Barton R
• Marked seasonal variation in the wild mouse gut microbiota.
  The ISME journal 2015 Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ
• Signatures of accelerated somatic evolution in gene promoters in multiple cancer types.
  Nucleic acids research 2015 Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S
• Continental-scale distributions of dust-associated bacteria and fungi.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N
• Evolution of lysine acetylation in the RNA polymerase II C-terminal domain.
  BMC evolutionary biology 2015 Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA
• Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions.
  Molecular biology and evolution 2015 Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT
• motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences.
  Statistics and its interface 2015 Kostka D, Friedrich T, Holloway AK, Pollard KS
• Gibbon genome and the fast karyotype evolution of small apes.
  Nature 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, Beal K, Blancher A, …
• Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes.
  Translational psychiatry 2014 Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N
• Profile hidden Markov models for the detection of viruses within metagenomic sequence data.
  PloS one 2014 Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL
• Protective role of HO-1 and carbon monoxide in ethanol-induced hepatocyte cell death and liver injury in mice.
  Journal of hepatology 2014 Bakhautdin B, Das D, Mandal P, Roychowdhury S, Danner J, Bush K, Pollard K, Kaspar JW, Li W, Salomon RG, McMullen MR, Nagy LE
• Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection.
  Journal of virology 2014 Roan NR, Liu H, Usmani SM, Neidleman J, Müller JA, Avila-Herrera A, Gawanbacht A, Zirafi O, Chu S, Dong M, Kumar ST, Smith JF, Pollard KS, Fändrich M, Kirchhoff F, Münch J, Witkowska HE, Greene WC
• Exome capture from saliva produces high quality genomic and metagenomic data.
  BMC genomics 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, Parham P, Hoal EG, Feldman MW, Pollard KS, …
• Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells.
  Molecular cell 2013 Schröder S, Herker E, Itzen F, He D, Thomas S, Gilchrist DA, Kaehlcke K, Cho S, Pollard KS, Capra JA, Schnölzer M, Cole PA, Geyer M, Bruneau BG, Adelman K, Ott M
• Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States.
  Science (New York, N.Y.) 2013 Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL
• From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome.
  PloS one 2013 Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M
• A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.
  PLoS genetics 2013 Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A
• How old is my gene?
  Trends in genetics : TIG 2013 Capra JA, Stolzer M, Durand D, Pollard KS
• Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.
  BMC genomics 2013 Riesenfeld SJ, Pollard KS
• Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.
  BMC bioinformatics 2012 Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA
• G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes.
  BMC bioinformatics 2012 Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS
• Novel bacterial taxa in the human microbiome.
  PloS one 2012 Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS
• Analysis of human accelerated DNA regions using archaic hominin genomes.
  PloS one 2012 Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S
• The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.
  Molecular biology and evolution 2011 Kostka D, Hubisz MJ, Siepel A, Pollard KS
• A high-resolution map of human evolutionary constraint using 29 mammals.
  Nature 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, Alföldi J, Beal K, Chang J, Clawson H, …
• Chromosomal haplotypes by genetic phasing of human families.
  American journal of human genetics 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
• The phylogenetic diversity of metagenomes.
  PloS one 2011 Kembel SW, Eisen JA, Pollard KS, Green JL
• Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots.
  Genome biology and evolution 2011 Katzman S, Capra JA, Haussler D, Pollard KS
• Substitution patterns are GC-biased in divergent sequences across the metazoans.
  Genome biology and evolution 2011 Capra JA, Pollard KS
• SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2.
  Aging 2011 Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E
• Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution.
  PloS one 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
• Chromatin remodelling complex dosage modulates transcription factor function in heart development.
  Nature communications 2011 Takeuchi JK, Lou X, Alexander JM, Sugizaki H, Delgado-Olguín P, Holloway AK, Mori AD, Wylie JN, Munson C, Zhu Y, Zhou YQ, Yeh RF, Henkelman RM, Harvey RP, Metzger D, Chambon P, Stainier DY, Pollard KS…
• Novel genes exhibit distinct patterns of function acquisition and network integration.
  Genome biology 2010 Capra JA, Pollard KS, Singh M
• PHAST and RPHAST: phylogenetic analysis with space/time models.
  Briefings in bioinformatics 2010 Hubisz MJ, Pollard KS, Siepel A
• Noncoding sequences near duplicated genes evolve rapidly.
  Genome biology and evolution 2010 Kostka D, Hahn MW, Pollard KS
• The importance of being cis: evolution of orthologous fish and mammalian enhancer activity.
  Molecular biology and evolution 2010 Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH
• GC-biased evolution near human accelerated regions.
  PLoS genetics 2010 Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D
• Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes.
  Genetics research 2010 Taylor SL, Pollard KS
• A nearly exhaustive search for CpG islands on whole chromosomes.
  The international journal of biostatistics 2009 Hsieh F, Chen SC, Pollard K
• The bovine lactation genome: insights into the evolution of mammalian milk.
  Genome biology 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, Tellam RL, Medrano JF, German …
• Student engagement in interprofessional working in practice placement settings.
  Journal of clinical nursing 2009 Pollard K
• Hypothesis tests for point-mass mixture data with application to 'omics data with many zero values.
  Statistical applications in genetics and molecular biology 2009 Taylor S, Pollard K
• Hotspots of biased nucleotide substitutions in human genes.
  PLoS biology 2009 Berglund J, Pollard KS, Webster MT
• Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum.
  Journal of bacteriology 2008 Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM
• Supervised distance matrices.
  Statistical applications in genetics and molecular biology 2008 Pollard KS, van der Laan MJ
• Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients.
  BMC genomics 2008 Walker WL, Liao IH, Gilbert DL, Wong B, Pollard KS, McCulloch CE, Lit L, Sharp FR
• Evaluation of two methods to estimate and monitor bird populations.
  PloS one 2008 Taylor SL, Pollard KS
• Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster.
  Genome research 2008 Holloway AK, Begun DJ, Siepel A, Pollard KS
• Gene regulatory networks in lactation: identification of global principles using bioinformatics.
  BMC systems biology 2007 Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB
• Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion.
  Genome research 2007 Dreszer TR, Wall GD, Haussler D, Pollard KS
• Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach.
  BMC neuroscience 2007 Magalhães TR, Palmer J, Tomancak P, Pollard KS
• Forces shaping the fastest evolving regions in the human genome.
  PLoS genetics 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
• Discovery of a cool planet of 5.5 Earth masses through gravitational microlensing.
  Nature 2006 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…
• The UCSC Archaeal Genome Browser.
  Nucleic acids research 2006 Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM
• Identifying genetic networks underlying myometrial transition to labor.
  Genome biology 2005 Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR
• 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 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 2004 van der Laan MJ, Dudoit S, Pollard KS
• Multiple testing. Part I. Single-step procedures for control of general type I error rates.
  Statistical applications in genetics and molecular biology 2004 Dudoit S, van der Laan MJ, Pollard KS
• Stenotrophomonas maltophilia contamination of nebulizers used to deliver aerosolized therapy to inpatients with cystic fibrosis.
  The Journal of hospital infection 2003 Denton M, Rajgopal A, Mooney L, Qureshi A, Kerr KG, Keer V, Pollard K, Peckham DG, Conway SP
• Statistical inference for simultaneous clustering of gene expression data.
  Mathematical biosciences 2002 Pollard KS, van der Laan MJ