Katie Pollard, PhD

Title(s)Professor, Epidemiology & Biostatistics
SchoolSchool of Medicine
Address3333 California Street, #280L
San Francisco CA 94118
Phone415-514-8105
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    University of California, San Francisco, CA2021Diversity, Equity, and Inclusion Champion Training

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    The Pollard lab develops statistical and computational methods for the analysis of massive biomedical datasets. Our research focuses on emerging technologies for genomics, mass spectrometry, and imaging. We specialize in evolutionary and comparative approaches, including machine-learning integration of diverse types of data and longitudinal models of dynamics in disease and development. Examples of current projects are massively parallel dissection of regulatory networks and decoding cryptic variation in the human microbiome.

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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Frontotemporal lobar degeneration targets brain regions linked to expression of recently evolved genes. Brain. 2024 Jun 28. 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. PMID: 38940350.
      View in: PubMed   Mentions:    Fields:    
    2. A molecular and cellular perspective on human brain evolution and tempo. Nature. 2024 Jun; 630(8017):596-608. Lindhout FW, Krienen FM, Pollard KS, Lancaster MA. PMID: 38898293.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    3. SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. Bioinformatics. 2024 Jun 03; 40(6). Gjoni K, Pollard KS. PMID: 38796686; PMCID: PMC11153836.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    4. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nat Genet. 2024 Jun; 56(6):1156-1167. 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. PMID: 38811842; PMCID: PMC11176074.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    5. Massively parallel characterization of regulatory elements in the developing human cortex. Science. 2024 May 24; 384(6698):eadh0559. 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. PMID: 38781390.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    6. Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science. 2024 May 24; 384(6698):eadh0829. 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. PMID: 38781368.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    7. CellWalker2: multi-omic discovery of hierarchical cell type relationships and their associations with genomic annotations. bioRxiv. 2024 May 17. Hu Z, Przytycki PF, Pollard KS. PMID: 38798605; PMCID: PMC11118555.
      View in: PubMed   Mentions:
    8. Metatranscriptomic investigation of single Ixodes pacificus ticks reveals diverse microbes, viruses, and novel mRNA-like endogenous viral elements. mSystems. 2024 Jun 18; 9(6):e0032124. Martyn C, Hayes BM, Lauko D, Midthun E, Castaneda G, Bosco-Lauth A, Salkeld DJ, Kistler A, Pollard KS, Chou S. PMID: 38742892.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    9. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science. 2024 Mar 29; 383(6690):eabn3263. 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. PMID: 38422184.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    10. Machine learning reveals the diversity of human 3D chromatin contact patterns. bioRxiv. 2023 Dec 23. Gilbertson EN, Brand CM, McArthur E, Rinker DC, Kuang S, Pollard KS, Capra JA. PMID: 38187606; PMCID: PMC10769343.
      View in: PubMed   Mentions:
    11. ChromaFactor: deconvolution of single-molecule chromatin organization with non-negative matrix factorization. bioRxiv. 2023 Nov 22. Gunsalus LM, Keiser MJ, Pollard KS. PMID: 38045231; PMCID: PMC10690235.
      View in: PubMed   Mentions:
    12. Hybrid assemblies of microbiome Blastocystis protists reveal evolutionary diversification reflecting host ecology. bioRxiv. 2023 Nov 20. Lind AL, McDonald NA, Gerrick ER, Bhatt AS, Pollard KS. PMID: 38045412; PMCID: PMC10690189.
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    13. SuPreMo: a computational tool for streamlining in silico perturbation using sequence-based predictive models. bioRxiv. 2023 Nov 05. Gjoni K, Pollard KS. PMID: 37961123; PMCID: PMC10635135.
      View in: PubMed   Mentions:
    14. FTLD targets brain regions expressing recently evolved genes. medRxiv. 2023 Oct 28. 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. PMID: 37961381; PMCID: PMC10635220.
      View in: PubMed   Mentions: 1  
    15. Sequence-based machine learning reveals 3D genome differences between bonobos and chimpanzees. bioRxiv. 2023 Oct 26. Brand CM, Kuang S, Gilbertson EN, McArthur E, Pollard KS, Webster TH, Capra JA. PMID: 37961120; PMCID: PMC10634871.
      View in: PubMed   Mentions:
    16. Exploring the Roles of RNAs in Chromatin Architecture Using Deep Learning. bioRxiv. 2023 Oct 24. Kuang S, Pollard KS. PMID: 37961712; PMCID: PMC10634726.
      View in: PubMed   Mentions:
    17. In silico discovery of repetitive elements as key sequence determinants of 3D genome folding. Cell Genom. 2023 Oct 11; 3(10):100410. Gunsalus LM, Keiser MJ, Pollard KS. PMID: 37868032; PMCID: PMC10589630.
      View in: PubMed   Mentions: 4     Fields:    
    18. Maast: genotyping thousands of microbial strains efficiently. Genome Biol. 2023 08 10; 24(1):186. Shi ZJ, Nayfach S, Pollard KS. PMID: 37563669; PMCID: PMC10416524.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    19. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Mol Cell. 2023 08 03; 83(15):2624-2640. 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. PMID: 37419111; PMCID: PMC10528254.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    20. Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization. Nat Commun. 2023 06 14; 14(1):3510. Jin X, Yu FB, Yan J, Weakley AM, Dubinkina V, Meng X, Pollard KS. PMID: 37316519; PMCID: PMC10267222.
      View in: PubMed   Mentions: 4     Fields:    Translation:Humans
    21. SIMMER employs similarity algorithms to accurately identify human gut microbiome species and enzymes capable of known chemical transformations. Elife. 2023 Jun 12; 12. Bustion AE, Nayak RR, Agrawal A, Turnbaugh PJ, Pollard KS. PMID: 37306300; PMCID: PMC10289814.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansCells
    22. Comparing chromatin contact maps at scale: methods and insights. Res Sq. 2023 May 23. Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS. PMID: 37292728; PMCID: PMC10246266.
      View in: PubMed   Mentions:
    23. Insights into mammalian TE diversity through the curation of 248 genome assemblies. Science. 2023 04 28; 380(6643):eabn1430. 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. PMID: 37104570.
      View in: PubMed   Mentions: 9     Fields:    Translation:AnimalsCells
    24. The contribution of historical processes to contemporary extinction risk in placental mammals. Science. 2023 04 28; 380(6643):eabn5856. 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. PMID: 37104572; PMCID: PMC10184782.
      View in: PubMed   Mentions: 8     Fields:    Translation:Animals
    25. Mammalian evolution of human cis-regulatory elements and transcription factor binding sites. Science. 2023 04 28; 380(6643):eabn7930. Andrews G, Fan K, Pratt HE, Phalke N, Zoonomia Consortium§, Karlsson EK, Lindblad-Toh K, Gazal S, Moore JE, Weng Z. PMID: 37104580.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    26. A genomic timescale for placental mammal evolution. Science. 2023 04 28; 380(6643):eabl8189. 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. PMID: 37104581; PMCID: PMC10233747.
      View in: PubMed   Mentions: 19     Fields:    Translation:Animals
    27. ​Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs. Science. 2023 04 28; 380(6643):eabn5887. Moon KL, Huson HJ, Morrill K, Wang MS, Li X, Srikanth K, Zoonomia Consortium, Lindblad-Toh K, Svenson GJ, Karlsson EK, Shapiro B. PMID: 37104591; PMCID: PMC10184777.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    28. The functional and evolutionary impacts of human-specific deletions in conserved elements. Science. 2023 04 28; 380(6643):eabn2253. 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. PMID: 37104592; PMCID: PMC10202372.
      View in: PubMed   Mentions: 7     Fields:    Translation:HumansCells
    29. Evolutionary constraint and innovation across hundreds of placental mammals. Science. 2023 04 28; 380(6643):eabn3943. 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. PMID: 37104599; PMCID: PMC10250106.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansAnimalsCells
    30. Integrating gene annotation with orthology inference at scale. Science. 2023 04 28; 380(6643):eabn3107. 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. PMID: 37104600; PMCID: PMC10193443.
      View in: PubMed   Mentions: 19     Fields:    Translation:Animals
    31. Three-dimensional genome rewiring in loci with human accelerated regions. Science. 2023 04 28; 380(6643):eabm1696. 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. PMID: 37104607; PMCID: PMC10999243.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    32. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science. 2023 04 28; 380(6643):eabn2937. 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. PMID: 37104612; PMCID: PMC10259825.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansAnimals
    33. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science. 2023 04 28; 380(6643):eabm7993. 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. PMID: 37104615; PMCID: PMC10322212.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    34. Oligogenic Architecture of Rare Noncoding Variants Distinguishes 4 Congenital Heart Disease Phenotypes. Circ Genom Precis Med. 2023 06; 16(3):258-266. 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. PMID: 37026454; PMCID: PMC10330096.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    35. Genetic Determinants of the Interventricular Septum Are Linked to Ventricular Septal Defects and Hypertrophic Cardiomyopathy. Circ Genom Precis Med. 2023 06; 16(3):207-215. 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. PMID: 37017090; PMCID: PMC10293084.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    36. Comparing chromatin contact maps at scale: methods and insights. bioRxiv. 2023 Apr 04. Gunsalus LM, McArthur E, Gjoni K, Kuang S, Pittman M, Capra JA, Pollard KS. PMID: 37066196; PMCID: PMC10104037.
      View in: PubMed   Mentions:
    37. Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease. bioRxiv. 2023 Mar 10. 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. PMID: 36945512; PMCID: PMC10028973.
      View in: PubMed   Mentions:
    38. Cross-ancestry, cell-type-informed atlas of gene, isoform, and splicing regulation in the developing human brain. medRxiv. 2023 Mar 06. 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. PMID: 36945630; PMCID: PMC10029021.
      View in: PubMed   Mentions:
    39. Massively parallel characterization of psychiatric disorder-associated and cell-type-specific regulatory elements in the developing human cortex. bioRxiv. 2023 Feb 16. 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. PMID: 36824845; PMCID: PMC9949039.
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    40. An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. Genome Biol. 2023 Jan 23; 24(1):16. 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. PMID: 36691074; PMCID: PMC9869549.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    41. Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro. STAR Protoc. 2023 03 17; 4(1):101964. Shi ZJ, Nayfach S, Pollard KS. PMID: 36856771; PMCID: PMC10037184.
      View in: PubMed   Mentions:    Fields:    
    42. Pitfalls of genotyping microbial communities with rapidly growing genome collections. Cell Syst. 2023 02 15; 14(2):160-176.e3. Zhao C, Shi ZJ, Pollard KS. PMID: 36657438; PMCID: PMC9957970.
      View in: PubMed   Mentions: 3     Fields:    
    43. Machine learning dissection of human accelerated regions in primate neurodevelopment. Neuron. 2023 03 15; 111(6):857-873.e8. 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. PMID: 36640767; PMCID: PMC10023452.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansAnimalsCells
    44. Chromatin Remodeling Drives Immune-Fibroblast Crosstalk in Heart Failure Pathogenesis. bioRxiv. 2023 Jan 07. 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. PMID: 36711864; PMCID: PMC9881961.
      View in: PubMed   Mentions: 1  
    45. MIDAS2: Metagenomic Intra-species Diversity Analysis System. Bioinformatics. 2023 01 01; 39(1). Zhao C, Dimitrov B, Goldman M, Nayfach S, Pollard KS. PMID: 36321886; PMCID: PMC9805558.
      View in: PubMed   Mentions: 7     Fields:    
    46. Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables. Curr Protoc. 2022 Dec; 2(12):e604. Zhao C, Goldman M, Smith BJ, Pollard KS. PMID: 36469554; PMCID: PMC9907011.
      View in: PubMed   Mentions:    Fields:    
    47. Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism. Nat Microbiol. 2022 10; 7(10):1605-1620. 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. PMID: 36138165; PMCID: PMC9530025.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    48. Enhancer Function and Evolutionary Roles of Human Accelerated Regions. Annu Rev Genet. 2022 11 30; 56:423-439. Whalen S, Pollard KS. PMID: 36070559; PMCID: PMC9712246.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimals
    49. Correction to: Brain-wide perception of the emotional valence of light is regulated by distinct hypothalamic neurons. Mol Psychiatry. 2022 Sep; 27(9):3794. Wagle M, Zarei M, Lovett-Barron M, Poston KT, Xu J, Ramey V, Pollard KS, Prober DA, Schulkin J, Deisseroth K, Guo S. PMID: 35718796; PMCID: PMC9708591.
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    50. Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors. Circulation. 2022 09 06; 146(10):770-787. 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. PMID: 35938400; PMCID: PMC9452483.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
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    53. Dose adjustments of Elexacaftor/Tezacaftor/Ivacaftor in response to mental health side effects in adults with cystic fibrosis. J Cyst Fibros. 2022 Nov; 21(6):1061-1065. Spoletini G, Gillgrass L, Pollard K, Shaw N, Williams E, Etherington C, Clifton IJ, Peckham DG. PMID: 35585012.
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    56. CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements. Bioinformatics. 2022 04 28; 38(9):2621-2623. Przytycki PF, Pollard KS. PMID: 35274675; PMCID: PMC9048661.
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    57. Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community. PLoS One. 2022; 17(4):e0261795. Lyalina S, Stepanauskas R, Wu F, Sanjabi S, Pollard KS. PMID: 35417481; PMCID: PMC9007364.
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    58. Strain-resolved analysis in a randomized trial of antibiotic pretreatment and maintenance dose delivery mode with fecal microbiota transplant for ulcerative colitis. Sci Rep. 2022 04 01; 12(1):5517. Smith BJ, Piceno Y, Zydek M, Zhang B, Syriani LA, Terdiman JP, Kassam Z, Ma A, Lynch SV, Pollard KS, El-Nachef N. PMID: 35365713; PMCID: PMC8976058.
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    59. Transcription factor protein interactomes reveal genetic determinants in heart disease. Cell. 2022 03 03; 185(5):794-814.e30. 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. PMID: 35182466; PMCID: PMC8923057.
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    60. Fast and accurate metagenotyping of the human gut microbiome with GT-Pro. Nat Biotechnol. 2022 04; 40(4):507-516. Shi ZJ, Dimitrov B, Zhao C, Nayfach S, Pollard KS. PMID: 34949778.
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    61. Autism risk gene POGZ promotes chromatin accessibility and expression of clustered synaptic genes. Cell Rep. 2021 12 07; 37(10):110089. 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. PMID: 34879283; PMCID: PMC9512081.
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    63. Human gut bacterial metabolism drives Th17 activation and colitis. Cell Host Microbe. 2022 01 12; 30(1):17-30.e9. Alexander M, Ang QY, Nayak RR, Bustion AE, Sandy M, Zhang B, Upadhyay V, Pollard KS, Lynch SV, Turnbaugh PJ. PMID: 34822777; PMCID: PMC8785648.
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    65. Single-cell epigenomics reveals mechanisms of human cortical development. Nature. 2021 10; 598(7879):205-213. 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. PMID: 34616060; PMCID: PMC8494642.
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    66. Systematic identification of non-canonical transcription factor motifs. BMC Mol Cell Biol. 2021 Aug 31; 22(1):44. Chumpitaz-Diaz L, Samee MAH, Pollard KS. PMID: 34465294; PMCID: PMC8408965.
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    67. 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. Smith BJ, Pollard KS. PMID: 34453883.
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    75. Ultraconservation of enhancers is not ultranecessary. Nat Genet. 2021 04; 53(4):429-430. Pittman M, Pollard KS. PMID: 33782604.
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    76. Accelerated RNA detection using tandem CRISPR nucleases. medRxiv. 2021 Mar 24. 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. PMID: 33791736; PMCID: PMC8010768.
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    78. CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues. Genome Biol. 2021 02 14; 22(1):61. Przytycki PF, Pollard KS. PMID: 33583425; PMCID: PMC7883575.
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    79. Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell. 2021 01 21; 184(2):323-333.e9. 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. PMID: 33306959; PMCID: PMC7834310.
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    80. Building a chemical blueprint for human blood. Nature. 2020 12; 588(7836):36-37. Bradley PH, Pollard KS. PMID: 33177685.
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    81. Molecular basis of CTCF binding polarity in genome folding. Nat Commun. 2020 11 05; 11(1):5612. 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. PMID: 33154377; PMCID: PMC7645679.
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    83. Predicting 3D genome folding from DNA sequence with Akita. Nat Methods. 2020 11; 17(11):1111-1117. Fudenberg G, Kelley DR, Pollard KS. PMID: 33046897; PMCID: PMC8211359.
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    84. Broad host range of SARS-CoV-2 predicted by comparative and structural analysis of ACE2 in vertebrates. Proc Natl Acad Sci U S A. 2020 09 08; 117(36):22311-22322. 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. PMID: 32826334; PMCID: PMC7486773.
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    86. lentiMPRA and MPRAflow for high-throughput functional characterization of gene regulatory elements. Nat Protoc. 2020 08; 15(8):2387-2412. 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. PMID: 32641802; PMCID: PMC7550205.
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    87. A Chromatin Accessibility Atlas of the Developing Human Telencephalon. Cell. 2020 08 06; 182(3):754-769.e18. Markenscoff-Papadimitriou E, Whalen S, Przytycki P, Thomas R, Binyameen F, Nowakowski TJ, Kriegstein AR, Sanders SJ, State MW, Pollard KS, Rubenstein JL. PMID: 32610082; PMCID: PMC7415678.
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    89. Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth. Front Microbiol. 2020; 11:476. Kosti I, Lyalina S, Pollard KS, Butte AJ, Sirota M. PMID: 32322240; PMCID: PMC7156768.
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    91. Early Palliative Care Consultation in the Medical ICU: A Cluster Randomized Crossover Trial. Crit Care Med. 2019 12; 47(12):1707-1715. Ma J, Chi S, Buettner B, Pollard K, Muir M, Kolekar C, Al-Hammadi N, Chen L, Kollef M, Dans M. PMID: 31609772; PMCID: PMC6861688.
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    92. Population Genetics in the Human Microbiome. Trends Genet. 2020 01; 36(1):53-67. Garud NR, Pollard KS. PMID: 31780057.
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    93. Principles of meiotic chromosome assembly revealed in S. cerevisiae. Nat Commun. 2019 10 22; 10(1):4795. Schalbetter SA, Fudenberg G, Baxter J, Pollard KS, Neale MJ. PMID: 31641121; PMCID: PMC6805904.
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    94. Global ecotypes in the ubiquitous marine clade SAR86. ISME J. 2020 01; 14(1):178-188. Hoarfrost A, Nayfach S, Ladau J, Yooseph S, Arnosti C, Dupont CL, Pollard KS. PMID: 31611653; PMCID: PMC6908720.
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    95. Cooking shapes the structure and function of the gut microbiome. Nat Microbiol. 2019 12; 4(12):2052-2063. 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. PMID: 31570867; PMCID: PMC6886678.
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    96. AlleleAnalyzer: a tool for personalized and allele-specific sgRNA design. Genome Biol. 2019 Aug 15; 20(1):167. Keough KC, Lyalina S, Olvera MP, Whalen S, Conklin BR, Pollard KS. PMID: 31416467; PMCID: PMC6694686.
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    100. The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice. Science. 2019 06 21; 364(6446):1156-1162. 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. PMID: 31221853; PMCID: PMC6705393.
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    102. Evolution of Mechanisms that Control Mating in Drosophila Males. Cell Rep. 2019 05 28; 27(9):2527-2536.e4. Ahmed OM, Avila-Herrera A, Tun KM, Serpa PH, Peng J, Parthasarathy S, Knapp JM, Stern DL, Davis GW, Pollard KS, Shah NM. PMID: 31141679; PMCID: PMC6646047.
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    104. Early-Career Scientists Shaping the World. mSystems. 2019 May 07; 4(3). Cristea IM, Dorrestein PC, Eisen JA, Gilbert JA, Huber JA, Jansson JK, Knight R, Pollard KS, Raes J, Silver PA, Webster NS, Xu J. PMID: 31219787; PMCID: PMC6533378.
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    105. Consent insufficient for data release-Response. Science. 2019 05 03; 364(6439):446. 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. PMID: 31048484.
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    106. New insights from uncultivated genomes of the global human gut microbiome. Nature. 2019 04; 568(7753):505-510. Nayfach S, Shi ZJ, Seshadri R, Pollard KS, Kyrpides NC. PMID: 30867587; PMCID: PMC6784871.
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    107. Toward unrestricted use of public genomic data. Science. 2019 01 25; 363(6425):350-352. 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. PMID: 30679363.
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    108. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol. 2019 01; 17(1):e3000102. Garud NR, Good BH, Hallatschek O, Pollard KS. PMID: 30673701; PMCID: PMC6361464.
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    109. Chromatin features constrain structural variation across evolutionary timescales. Proc Natl Acad Sci U S A. 2019 02 05; 116(6):2175-2180. Fudenberg G, Pollard KS. PMID: 30659153; PMCID: PMC6369792.
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    110. A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs. Cell Syst. 2019 01 23; 8(1):27-42.e6. Samee MAH, Bruneau BG, Pollard KS. PMID: 30660610; PMCID: PMC6368855.
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    111. Most chromatin interactions are not in linkage disequilibrium. Genome Res. 2019 03; 29(3):334-343. Whalen S, Pollard KS. PMID: 30617125; PMCID: PMC6396425.
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    112. Comparative Flavivirus-Host Protein Interaction Mapping Reveals Mechanisms of Dengue and Zika Virus Pathogenesis. Cell. 2018 12 13; 175(7):1931-1945.e18. 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. PMID: 30550790; PMCID: PMC6474419.
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    113. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci U S A. 2018 12 26; 115(52):E12353-E12362. 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. PMID: 30482864; PMCID: PMC6310811.
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    114. Existing Climate Change Will Lead to Pronounced Shifts in the Diversity of Soil Prokaryotes. mSystems. 2018 Sep-Oct; 3(5). Ladau J, Shi Y, Jing X, He JS, Chen L, Lin X, Fierer N, Gilbert JA, Pollard KS, Chu H. PMID: 30374458; PMCID: PMC6199470.
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    115. A most wanted list of conserved microbial protein families with no known domains. PLoS One. 2018; 13(10):e0205749. Wyman SK, Avila-Herrera A, Nayfach S, Pollard KS. PMID: 30332487; PMCID: PMC6192648.
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    116. Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. PLoS Comput Biol. 2018 08; 14(8):e1006242. Bradley PH, Nayfach S, Pollard KS. PMID: 30091981; PMCID: PMC6084841.
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    117. Developmental Loci Harbor Clusters of Accelerated Regions That Evolved Independently in Ape Lineages. Mol Biol Evol. 2018 08 01; 35(8):2034-2045. Kostka D, Holloway AK, Pollard KS. PMID: 29897475; PMCID: PMC6063267.
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    118. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018 May-Jun; 3(3). 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. PMID: 29795809; PMCID: PMC5954204.
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    119. The Epstein-Barr Virus Episome Maneuvers between Nuclear Chromatin Compartments during Reactivation. J Virol. 2018 02 01; 92(3). Moquin SA, Thomas S, Whalen S, Warburton A, Fernandez SG, McBride AA, Pollard KS, Miranda JL. PMID: 29142137; PMCID: PMC5774889.
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    120. A communal catalogue reveals Earth's multiscale microbial diversity. Nature. 2017 11 23; 551(7681):457-463. 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. PMID: 29088705; PMCID: PMC6192678.
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    121. Human evolution: the non-coding revolution. BMC Biol. 2017 10 02; 15(1):89. Franchini LF, Pollard KS. PMID: 28969617; PMCID: PMC5625771.
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    122. Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice. mSystems. 2017 Sep-Oct; 2(5). Sharpton T, Lyalina S, Luong J, Pham J, Deal EM, Armour C, Gaulke C, Sanjabi S, Pollard KS. PMID: 28904997; PMCID: PMC5585689.
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    123. Topical silver diamine fluoride for dental caries arrest in preschool children: A randomized controlled trial and microbiological analysis of caries associated microbes and resistance gene expression. J Dent. 2018 01; 68:72-78. Milgrom P, Horst JA, Ludwig S, Rothen M, Chaffee BW, Lyalina S, Pollard KS, DeRisi JL, Mancl L. PMID: 28866468; PMCID: PMC5748247.
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    124. Features that define the best ChIP-seq peak calling algorithms. Brief Bioinform. 2017 05 01; 18(3):441-450. Thomas R, Thomas S, Holloway AK, Pollard KS. PMID: 27169896; PMCID: PMC5429005.
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    125. Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk. Nat Genet. 2017 Jun; 49(6):834-841. 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. PMID: 28436984; PMCID: PMC5841952.
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    126. Cooperative activation of cardiac transcription through myocardin bridging of paired MEF2 sites. Development. 2017 04 01; 144(7):1235-1241. 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. PMID: 28351867; PMCID: PMC5399617.
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    127. Proteobacteria explain significant functional variability in the human gut microbiome. Microbiome. 2017 03 23; 5(1):36. Bradley PH, Pollard KS. PMID: 28330508; PMCID: PMC5363007.
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    128. Unboxing cluster heatmaps. BMC Bioinformatics. 2017 Feb 15; 18(Suppl 2):63. Engle S, Whalen S, Joshi A, Pollard KS. PMID: 28251868; PMCID: PMC5333167.
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    129. Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases. Cell. 2017 01 26; 168(3):517-526.e18. 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. PMID: 28111075; PMCID: PMC5302092.
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    130. Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota. Cell Host Microbe. 2016 Dec 14; 20(6):709-715. Devlin AS, Marcobal A, Dodd D, Nayfach S, Plummer N, Meyer T, Pollard KS, Sonnenburg JL, Fischbach MA. PMID: 27916477; PMCID: PMC5159218.
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    131. An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. Genome Res. 2016 11; 26(11):1612-1625. Nayfach S, Rodriguez-Mueller B, Garud N, Pollard KS. PMID: 27803195; PMCID: PMC5088602.
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    132. Toward Accurate and Quantitative Comparative Metagenomics. Cell. 2016 Aug 25; 166(5):1103-1116. Nayfach S, Pollard KS. PMID: 27565341; PMCID: PMC5080976.
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    133. Urban greenness influences airborne bacterial community composition. Sci Total Environ. 2016 Nov 15; 571:680-7. Mhuireach G, Johnson BR, Altrichter AE, Ladau J, Meadow JF, Pollard KS, Green JL. PMID: 27418518.
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    134. Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. mBio. 2016 05 13; 7(3). Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL. PMID: 27178263; PMCID: PMC4895116.
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    135. Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. Nat Genet. 2016 05; 48(5):488-96. Whalen S, Truty RM, Pollard KS. PMID: 27064255; PMCID: PMC4910881.
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    136. Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus. PLoS Genet. 2016 Mar; 12(3):e1005738. Booker BM, Friedrich T, Mason MK, VanderMeer JE, Zhao J, Eckalbar WL, Logan M, Illing N, Pollard KS, Ahituv N. PMID: 27019019; PMCID: PMC4809552.
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    137. Transcriptomic and epigenomic characterization of the developing bat wing. Nat Genet. 2016 05; 48(5):528-36. 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. PMID: 27019111; PMCID: PMC4848140.
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    138. SOX2 O-GlcNAcylation alters its protein-protein interactions and genomic occupancy to modulate gene expression in pluripotent cells. Elife. 2016 Mar 07; 5:e10647. 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. PMID: 26949256; PMCID: PMC4841768.
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    139. Complex Interdependence Regulates Heterotypic Transcription Factor Distribution and Coordinates Cardiogenesis. Cell. 2016 Feb 25; 164(5):999-1014. 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. PMID: 26875865; PMCID: PMC4769693.
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    140. Joint mouse-human phenome-wide association to test gene function and disease risk. Nat Commun. 2016 Feb 02; 7:10464. 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. PMID: 26833085; PMCID: PMC4740880.
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    141. Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor. Mol Biol Evol. 2016 Apr; 33(4):1008-18. Holloway AK, Bruneau BG, Sukonnik T, Rubenstein JL, Pollard KS. PMID: 26715627; PMCID: PMC4776709.
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    142. Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. PLoS Comput Biol. 2015 Nov; 11(11):e1004573. Nayfach S, Bradley PH, Wyman SK, Laurent TJ, Williams A, Eisen JA, Pollard KS, Sharpton TJ. PMID: 26565399; PMCID: PMC4643905.
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    143. MICROBIOME. A unified initiative to harness Earth's microbiomes. Science. 2015 Oct 30; 350(6260):507-8. 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. PMID: 26511287.
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    144. Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development. Neurogenetics. 2016 Jan; 17(1):1-9. Haliburton GD, McKinsey GL, Pollard KS. PMID: 26382291; PMCID: PMC4701781.
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    145. Genomic approaches to studying human-specific developmental traits. Development. 2015 Sep 15; 142(18):3100-12. Franchini LF, Pollard KS. PMID: 26395139.
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    146. Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. BMC Bioinformatics. 2015 Aug 25; 16:268. Avila-Herrera A, Pollard KS. PMID: 26303588; PMCID: PMC4549020.
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    147. Can a few non-coding mutations make a human brain? Bioessays. 2015 Oct; 37(10):1054-61. Franchini LF, Pollard KS. PMID: 26350501; PMCID: PMC5054932.
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    148. MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. Bioinformatics. 2015 Oct 15; 31(20):3368-70. Nayfach S, Fischbach MA, Pollard KS. PMID: 26104745; PMCID: PMC4595903.
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    149. Fungal contamination of nebuliser devices used by people with cystic fibrosis. J Cyst Fibros. 2016 Jan; 15(1):74-7. Peckham D, Williams K, Wynne S, Denton M, Pollard K, Barton R. PMID: 26104996.
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    150. Marked seasonal variation in the wild mouse gut microbiota. ISME J. 2015 Nov; 9(11):2423-34. Maurice CF, Knowles SC, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ. PMID: 26023870; PMCID: PMC4611506.
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    151. Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Nucleic Acids Res. 2015 Jun 23; 43(11):5307-17. Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S. PMID: 25934800; PMCID: PMC4477653.
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    152. Continental-scale distributions of dust-associated bacteria and fungi. Proc Natl Acad Sci U S A. 2015 May 05; 112(18):5756-61. Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N. PMID: 25902536; PMCID: PMC4426398.
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    153. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 2015 Mar 25; 16:51. Nayfach S, Pollard KS. PMID: 25853934; PMCID: PMC4389708.
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    154. Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency. Cell. 2015 Mar 12; 160(6):1072-86. Theodoris CV, Li M, White MP, Liu L, He D, Pollard KS, Bruneau BG, Srivastava D. PMID: 25768904; PMCID: PMC4359747.
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    155. Evolution of lysine acetylation in the RNA polymerase II C-terminal domain. BMC Evol Biol. 2015 Mar 10; 15:35. Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA. PMID: 25887984; PMCID: PMC4362643.
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    156. Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. Mol Biol Evol. 2015 May; 32(5):1148-60. Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT. PMID: 25681384; PMCID: PMC4408416.
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    157. motifDiverge: a model for assessing the statistical significance of gene regulatory motif divergence between two DNA sequences. Stat Interface. 2015; 8(4):463-476. Kostka D, Friedrich T, Holloway AK, Pollard KS. PMID: 26709360; PMCID: PMC4689439.
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    158. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 Sep 11; 513(7517):195-201. 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. PMID: 25209798; PMCID: PMC4249732.
      View in: PubMed   Mentions: 138     Fields:    Translation:HumansAnimalsCells
    159. Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes. Transl Psychiatry. 2014 Sep 02; 4:e431. Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N. PMID: 25180570; PMCID: PMC4199417.
      View in: PubMed   Mentions: 30     Fields:    Translation:Animals
    160. Exploring the genesis and functions of Human Accelerated Regions sheds light on their role in human evolution. Curr Opin Genet Dev. 2014 Dec; 29:15-21. Hubisz MJ, Pollard KS. PMID: 25156517.
      View in: PubMed   Mentions: 56     Fields:    Translation:HumansAnimalsCells
    161. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One. 2014; 9(8):e105067. Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. PMID: 25140992; PMCID: PMC4139300.
      View in: PubMed   Mentions: 84     Fields:    Translation:HumansCells
    162. Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol. 2014 Jun; 10(6):e1003677. Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. PMID: 24967590; PMCID: PMC4072507.
      View in: PubMed   Mentions: 74     Fields:    Translation:HumansAnimalsCells
    163. Protective role of HO-1 and carbon monoxide in ethanol-induced hepatocyte cell death and liver injury in mice. J Hepatol. 2014 Nov; 61(5):1029-37. Bakhautdin B, Das D, Mandal P, Roychowdhury S, Danner J, Bush K, Pollard K, Kaspar JW, Li W, Salomon RG, McMullen MR, Nagy LE. PMID: 24946281; PMCID: PMC4203703.
      View in: PubMed   Mentions: 43     Fields:    Translation:AnimalsCells
    164. Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection. J Virol. 2014 Jul; 88(13):7221-34. 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. PMID: 24741080; PMCID: PMC4054457.
      View in: PubMed   Mentions: 37     Fields:    Translation:HumansCells
    165. Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genomics. 2014 Apr 04; 15:262. 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. PMID: 24708091; PMCID: PMC4051168.
      View in: PubMed   Mentions: 16     Fields:    Translation:Humans
    166. A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PLoS One. 2014; 9(1):e84689. Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. PMID: 24416266; PMCID: PMC3885756.
      View in: PubMed   Mentions: 149     Fields:    Translation:HumansCells
    167. Many human accelerated regions are developmental enhancers. Philos Trans R Soc Lond B Biol Sci. 2013 Dec 19; 368(1632):20130025. Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS. PMID: 24218637; PMCID: PMC3826498.
      View in: PubMed   Mentions: 100     Fields:    Translation:HumansAnimalsCells
    168. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell. 2013 Nov 07; 52(3):314-24. 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. PMID: 24207025; PMCID: PMC3936344.
      View in: PubMed   Mentions: 60     Fields:    Translation:HumansAnimalsCells
    169. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 2013 Nov 01; 342(6158):621-4. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. PMID: 24179225.
      View in: PubMed   Mentions: 144     Fields:    Translation:AnimalsCellsPHPublic Health
    170. From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. PLoS One. 2013; 8(9):e75030. Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M. PMID: 24086428; PMCID: PMC3784412.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansAnimalsCells
    171. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genet. 2013; 9(8):e1003684. Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. PMID: 23966869; PMCID: PMC3744432.
      View in: PubMed   Mentions: 39     Fields:    Translation:HumansAnimalsCells
    172. How old is my gene? Trends Genet. 2013 Nov; 29(11):659-68. Capra JA, Stolzer M, Durand D, Pollard KS. PMID: 23915718; PMCID: PMC3812327.
      View in: PubMed   Mentions: 30     Fields:    
    173. A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. Genome Biol. 2013 Jul 18; 14(7):R72. Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. PMID: 23867016; PMCID: PMC4054837.
      View in: PubMed   Mentions: 11     Fields:    Translation:AnimalsCells
    174. Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis. BMC Genomics. 2013 Jun 22; 14:419. Riesenfeld SJ, Pollard KS. PMID: 23799973; PMCID: PMC3701559.
      View in: PubMed   Mentions: 3     Fields:    
    175. Global marine bacterial diversity peaks at high latitudes in winter. ISME J. 2013 Sep; 7(9):1669-77. Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS. PMID: 23514781; PMCID: PMC3749493.
      View in: PubMed   Mentions: 72     Fields:    Translation:HumansCellsPHPublic Health
    176. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics. 2012 Oct 13; 13:264. Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA. PMID: 23061897; PMCID: PMC3481395.
      View in: PubMed   Mentions: 12     Fields:    
    177. G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. BMC Bioinformatics. 2012 Sep 28; 13:253. Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS. PMID: 23020263; PMCID: PMC3575404.
      View in: PubMed   Mentions: 9     Fields:    Translation:HumansAnimalsCells
    178. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28; 151(1):206-20. 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. PMID: 22981692; PMCID: PMC3462286.
      View in: PubMed   Mentions: 357     Fields:    Translation:HumansAnimalsCells
    179. ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. PLoS Comput Biol. 2012; 8(6):e1002567. Capra JA, Williams AG, Pollard KS. PMID: 22761559; PMCID: PMC3386163.
      View in: PubMed   Mentions: 45     Fields:    Translation:HumansAnimals
    180. Novel bacterial taxa in the human microbiome. PLoS One. 2012; 7(6):e35294. Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS. PMID: 22719826; PMCID: PMC3374617.
      View in: PubMed   Mentions: 44     Fields:    Translation:Humans
    181. Analysis of human accelerated DNA regions using archaic hominin genomes. PLoS One. 2012; 7(3):e32877. Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S. PMID: 22412940; PMCID: PMC3296746.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimals
    182. The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol. 2012 Mar; 29(3):1047-57. Kostka D, Hubisz MJ, Siepel A, Pollard KS. PMID: 22075116; PMCID: PMC3278478.
      View in: PubMed   Mentions: 51     Fields:    Translation:HumansCells
    183. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 12; 478(7370):476-82. 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. PMID: 21993624; PMCID: PMC3207357.
      View in: PubMed   Mentions: 591     Fields:    Translation:HumansAnimals
    184. Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet. 2011 Sep 09; 89(3):382-97. Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF. PMID: 21855840; PMCID: PMC3169815.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansCells
    185. The phylogenetic diversity of metagenomes. PLoS One. 2011; 6(8):e23214. Kembel SW, Eisen JA, Pollard KS, Green JL. PMID: 21912589; PMCID: PMC3166145.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    186. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biol Evol. 2011; 3:614-26. Katzman S, Capra JA, Haussler D, Pollard KS. PMID: 21697099; PMCID: PMC3157837.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    187. Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biol Evol. 2011; 3:516-27. Capra JA, Pollard KS. PMID: 21670083; PMCID: PMC3138425.
      View in: PubMed   Mentions: 23     Fields:    Translation:HumansAnimalsCells
    188. SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2. Aging (Albany NY). 2011 Jun; 3(6):635-42. Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E. PMID: 21701047; PMCID: PMC3164371.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansAnimalsCells
    189. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PLoS One. 2011 Mar 18; 6(3):e17753. Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P. PMID: 21445258; PMCID: PMC3060818.
      View in: PubMed   Mentions: 34     Fields:    Translation:HumansCells
    190. Chromatin remodelling complex dosage modulates transcription factor function in heart development. Nat Commun. 2011 Feb 08; 2:187. 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. PMID: 21304516; PMCID: PMC3096875.
      View in: PubMed   Mentions: 113     Fields:    Translation:AnimalsCells
    191. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol. 2011 Jan 20; 7(1):e1001061. Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. PMID: 21283775; PMCID: PMC3024254.
      View in: PubMed   Mentions: 42     Fields:    
    192. Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol. 2010; 11(12):R127. Capra JA, Pollard KS, Singh M. PMID: 21187012; PMCID: PMC3046487.
      View in: PubMed   Mentions: 47     Fields:    Translation:AnimalsCells
    193. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 2011 Jan; 12(1):41-51. Hubisz MJ, Pollard KS, Siepel A. PMID: 21278375; PMCID: PMC3030812.
      View in: PubMed   Mentions: 252     Fields:    
    194. Noncoding sequences near duplicated genes evolve rapidly. Genome Biol Evol. 2010; 2:518-33. Kostka D, Hahn MW, Pollard KS. PMID: 20660939; PMCID: PMC2942038.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansAnimalsCells
    195. The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. Mol Biol Evol. 2010 Oct; 27(10):2322-32. Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH. PMID: 20494938; PMCID: PMC3107594.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansAnimalsCells
    196. GC-biased evolution near human accelerated regions. PLoS Genet. 2010 May 20; 6(5):e1000960. Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. PMID: 20502635; PMCID: PMC2873926.
      View in: PubMed   Mentions: 16     Fields:    Translation:HumansCells
    197. Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes. Genet Res (Camb). 2010 Feb; 92(1):39-53. Taylor SL, Pollard KS. PMID: 20196895.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    198. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan; 20(1):110-21. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. PMID: 19858363; PMCID: PMC2798823.
      View in: PubMed   Mentions: 1127     Fields:    Translation:HumansAnimalsCells
    199. A nearly exhaustive search for CpG islands on whole chromosomes. Int J Biostat. 2009; 5(1). Hsieh F, Chen SC, Pollard K. PMID: 20148132; PMCID: PMC2818740.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    200. What makes us human? Sci Am. 2009 May; 300(5):44-9. Pollard KS. PMID: 19438048.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    201. The bovine lactation genome: insights into the evolution of mammalian milk. Genome Biol. 2009; 10(4):R43. 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. PMID: 19393040; PMCID: PMC2688934.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansAnimalsCells
    202. Student engagement in interprofessional working in practice placement settings. J Clin Nurs. 2009 Oct; 18(20):2846-56. Pollard K. PMID: 19220612.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    203. Hypothesis tests for point-mass mixture data with application to 'omics data with many zero values. Stat Appl Genet Mol Biol. 2009; 8:Article 8. Taylor S, Pollard K. PMID: 19222391.
      View in: PubMed   Mentions: 15     Fields:    Translation:Animals
    204. Hotspots of biased nucleotide substitutions in human genes. PLoS Biol. 2009 Jan 27; 7(1):e26. Berglund J, Pollard KS, Webster MT. PMID: 19175294; PMCID: PMC2631073.
      View in: PubMed   Mentions: 86     Fields:    Translation:HumansAnimals
    205. Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. J Bacteriol. 2009 Feb; 191(3):782-94. Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM. PMID: 19047344; PMCID: PMC2632070.
      View in: PubMed   Mentions: 25     Fields:    Translation:Cells
    206. Supervised distance matrices. Stat Appl Genet Mol Biol. 2008; 7(1):Article 33. Pollard KS, van der Laan MJ. PMID: 19049489.
      View in: PubMed   Mentions: 1     Fields:    Translation:Humans
    207. Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients. BMC Genomics. 2008 Oct 20; 9:494. Walker WL, Liao IH, Gilbert DL, Wong B, Pollard KS, McCulloch CE, Lit L, Sharp FR. PMID: 18937867; PMCID: PMC2576259.
      View in: PubMed   Mentions: 26     Fields:    Translation:Humans
    208. Evaluation of two methods to estimate and monitor bird populations. PLoS One. 2008 Aug 27; 3(8):e3047. Taylor SL, Pollard KS. PMID: 18728775; PMCID: PMC2516598.
      View in: PubMed   Mentions: 1     Fields:    Translation:AnimalsPHPublic Health
    209. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res. 2008 Oct; 18(10):1592-601. Holloway AK, Begun DJ, Siepel A, Pollard KS. PMID: 18583644; PMCID: PMC2556263.
      View in: PubMed   Mentions: 16     Fields:    Translation:AnimalsCells
    210. Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Syst Biol. 2007 Nov 27; 1:56. Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB. PMID: 18039394; PMCID: PMC2225983.
      View in: PubMed   Mentions: 59     Fields:    Translation:HumansCells
    211. A genome-wide approach to identifying novel-imprinted genes. Hum Genet. 2008 Jan; 122(6):625-34. Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K. PMID: 17955261.
      View in: PubMed   Mentions: 38     Fields:    Translation:HumansCells
    212. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res. 2007 Oct; 17(10):1420-30. Dreszer TR, Wall GD, Haussler D, Pollard KS. PMID: 17785536; PMCID: PMC1987345.
      View in: PubMed   Mentions: 52     Fields:    Translation:HumansAnimalsCells
    213. Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach. BMC Neurosci. 2007 Jul 31; 8:59. Magalhães TR, Palmer J, Tomancak P, Pollard KS. PMID: 17672901; PMCID: PMC1950096.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    214. Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2006 Oct 13; 2(10):e168. 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. PMID: 17040131; PMCID: PMC1599772.
      View in: PubMed   Mentions: 220     Fields:    Translation:HumansAnimalsCells
    215. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14; 443(7108):167-72. 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. PMID: 16915236.
      View in: PubMed   Mentions: 391     Fields:    Translation:HumansAnimalsCells
    216. Discovery of a cool planet of 5.5 Earth masses through gravitational microlensing. Nature. 2006 Jan 26; 439(7075):437-40. 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. PMID: 16437108.
      View in: PubMed   Mentions: 9     Fields:    
    217. The UCSC Archaeal Genome Browser. Nucleic Acids Res. 2006 Jan 01; 34(Database issue):D407-10. Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. PMID: 16381898; PMCID: PMC1347496.
      View in: PubMed   Mentions: 69     Fields:    
    218. Identifying genetic networks underlying myometrial transition to labor. Genome Biol. 2005; 6(2):R12. Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. PMID: 15693941; PMCID: PMC551532.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    219. Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Stat Appl Genet Mol Biol. 2004; 3:Article15. van der Laan MJ, Dudoit S, Pollard KS. PMID: 16646793.
      View in: PubMed   Mentions: 18     Fields:    
    220. Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Stat Appl Genet Mol Biol. 2004; 3:Article14. van der Laan MJ, Dudoit S, Pollard KS. PMID: 16646792.
      View in: PubMed   Mentions: 16     Fields:    
    221. Multiple testing. Part I. Single-step procedures for control of general type I error rates. Stat Appl Genet Mol Biol. 2004; 3:Article13. Dudoit S, van der Laan MJ, Pollard KS. PMID: 16646791.
      View in: PubMed   Mentions: 38     Fields:    
    222. Stenotrophomonas maltophilia contamination of nebulizers used to deliver aerosolized therapy to inpatients with cystic fibrosis. J Hosp Infect. 2003 Nov; 55(3):180-3. Denton M, Rajgopal A, Mooney L, Qureshi A, Kerr KG, Keer V, Pollard K, Peckham DG, Conway SP. PMID: 14572484.
      View in: PubMed   Mentions: 14     Fields:    Translation:HumansCellsPHPublic Health
    223. Statistical inference for simultaneous clustering of gene expression data. Math Biosci. 2002 Mar; 176(1):99-121. Pollard KS, van der Laan MJ. PMID: 11867086.
      View in: PubMed   Mentions: 3     Fields:    Translation:Humans
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