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    Katie Pollard, PhD

    TitleProfessor
    SchoolUCSF School of Medicine
    DepartmentEpidemiology & Biostatistics
    Address550 16th Street
    San Francisco CA 94158
    Phone415-734-2711
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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.
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      1. Haliburton GD, McKinsey GL, Pollard KS. Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development. Neurogenetics. 2016 Jan; 17(1):1-9. PMID: 26382291.
        View in: PubMed
      2. Franchini LF, Pollard KS. Genomic approaches to studying human-specific developmental traits. Development. 2015 Sep 15; 142(18):3100-12. PMID: 26395139.
        View in: PubMed
      3. Franchini LF, Pollard KS. Can a few non-coding mutations make a human brain? Bioessays. 2015 Oct; 37(10):1054-61. PMID: 26350501.
        View in: PubMed
      4. Avila-Herrera A, Pollard KS. Coevolutionary analyses require phylogenetically deep alignments and better null models to accurately detect inter-protein contacts within and between species. BMC Bioinformatics. 2015; 16:268. PMID: 26303588; PMCID: PMC4549020.
      5. Nayfach S, Fischbach MA, Pollard KS. MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome. Bioinformatics. 2015 Oct 15; 31(20):3368-70. PMID: 26104745; PMCID: PMC4595903.
      6. Maurice CF, Cl Knowles S, Ladau J, Pollard KS, Fenton A, Pedersen AB, Turnbaugh PJ. Marked seasonal variation in the wild mouse gut microbiota. ISME J. 2015 Nov; 9(11):2423-34. PMID: 26023870; PMCID: PMC4611506.
      7. Smith KS, Yadav VK, Pedersen BS, Shaknovich R, Geraci MW, Pollard KS, De S. Signatures of accelerated somatic evolution in gene promoters in multiple cancer types. Nucleic Acids Res. 2015 Jun 23; 43(11):5307-17. PMID: 25934800; PMCID: PMC4477653.
      8. Barberán A, Ladau J, Leff JW, Pollard KS, Menninger HL, Dunn RR, Fierer N. Continental-scale distributions of dust-associated bacteria and fungi. Proc Natl Acad Sci U S A. 2015 May 5; 112(18):5756-61. PMID: 25902536; PMCID: PMC4426398.
      9. Nayfach S, Pollard KS. Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. Genome Biol. 2015; 16:51. PMID: 25853934; PMCID: PMC4389708.
      10. Theodoris CV, Li M, White MP, Liu L, He D, Pollard KS, Bruneau BG, Srivastava D. Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency. Cell. 2015 Mar 12; 160(6):1072-86. PMID: 25768904; PMCID: PMC4359747 [Available on 03/12/16].
      11. Simonti CN, Pollard KS, Schröder S, He D, Bruneau BG, Ott M, Capra JA. Evolution of lysine acetylation in the RNA polymerase II C-terminal domain. BMC Evol Biol. 2015; 15:35. PMID: 25887984; PMCID: PMC4362643.
      12. Xu K, Schadt EE, Pollard KS, Roussos P, Dudley JT. Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. Mol Biol Evol. 2015 May; 32(5):1148-60. PMID: 25681384; PMCID: PMC4408416 [Available on 05/01/16].
      13. 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. Gibbon genome and the fast karyotype evolution of small apes. Nature. 2014 Sep 11; 513(7517):195-201. PMID: 25209798; PMCID: PMC4249732.
      14. Oksenberg N, Haliburton GD, Eckalbar WL, Oren I, Nishizaki S, Murphy K, Pollard KS, Birnbaum RY, Ahituv N. Genome-wide distribution of Auts2 binding localizes with active neurodevelopmental genes. Transl Psychiatry. 2014; 4:e431. PMID: 25180570; PMCID: PMC4199417.
      15. Hubisz MJ, Pollard KS. 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. PMID: 25156517.
        View in: PubMed
      16. Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL. Profile hidden Markov models for the detection of viruses within metagenomic sequence data. PLoS One. 2014; 9(8):e105067. PMID: 25140992; PMCID: PMC4139300.
      17. Erwin GD, Oksenberg N, Truty RM, Kostka D, Murphy KK, Ahituv N, Pollard KS, Capra JA. Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol. 2014 Jun; 10(6):e1003677. PMID: 24967590; PMCID: PMC4072507.
      18. 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. Liquefaction of semen generates and later degrades a conserved semenogelin peptide that enhances HIV infection. J Virol. 2014 Jul; 88(13):7221-34. PMID: 24741080; PMCID: PMC4054457.
      19. 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. Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genomics. 2014; 15:262. PMID: 24708091; PMCID: PMC4051168.
      20. Finucane MM, Sharpton TJ, Laurent TJ, Pollard KS. A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter. PLoS One. 2014; 9(1):e84689. PMID: 24416266; PMCID: PMC3885756.
      21. Capra JA, Erwin GD, McKinsey G, Rubenstein JL, Pollard KS. Many human accelerated regions are developmental enhancers. Philos Trans R Soc Lond B Biol Sci. 2013 Dec 19; 368(1632):20130025. PMID: 24218637; PMCID: PMC3826498.
      22. 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. Acetylation of RNA polymerase II regulates growth-factor-induced gene transcription in mammalian cells. Mol Cell. 2013 Nov 7; 52(3):314-24. PMID: 24207025; PMCID: PMC3936344.
      23. Fierer N, Ladau J, Clemente JC, Leff JW, Owens SM, Pollard KS, Knight R, Gilbert JA, McCulley RL. Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States. Science. 2013 Nov 1; 342(6158):621-4. PMID: 24179225.
        View in: PubMed
      24. Lemay DG, Pollard KS, Martin WF, Freeman Zadrowski C, Hernandez J, Korf I, German JB, Rijnkels M. From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. PLoS One. 2013; 8(9):e75030. PMID: 24086428; PMCID: PMC3784412.
      25. Capra JA, Hubisz MJ, Kostka D, Pollard KS, Siepel A. A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes. PLoS Genet. 2013; 9(8):e1003684. PMID: 23966869; PMCID: PMC3744432.
      26. Capra JA, Stolzer M, Durand D, Pollard KS. How old is my gene? Trends Genet. 2013 Nov; 29(11):659-68. PMID: 23915718; PMCID: PMC3812327.
      27. Smith RP, Riesenfeld SJ, Holloway AK, Li Q, Murphy KK, Feliciano NM, Orecchia L, Oksenberg N, Pollard KS, Ahituv N. A compact, in vivo screen of all 6-mers reveals drivers of tissue-specific expression and guides synthetic regulatory element design. Genome Biol. 2013; 14(7):R72. PMID: 23867016; PMCID: PMC4054837.
      28. Riesenfeld SJ, Pollard KS. Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis. BMC Genomics. 2013; 14:419. PMID: 23799973; PMCID: PMC3701559.
      29. Ladau J, Sharpton TJ, Finucane MM, Jospin G, Kembel SW, O'Dwyer J, Koeppel AF, Green JL, Pollard KS. Global marine bacterial diversity peaks at high latitudes in winter. ISME J. 2013 Sep; 7(9):1669-77. PMID: 23514781; PMCID: PMC3749493.
      30. Sharpton TJ, Jospin G, Wu D, Langille MG, Pollard KS, Eisen JA. Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. BMC Bioinformatics. 2012; 13:264. PMID: 23061897; PMCID: PMC3481395.
      31. Lemay DG, Martin WF, Hinrichs AS, Rijnkels M, German JB, Korf I, Pollard KS. G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. BMC Bioinformatics. 2012; 13:253. PMID: 23020263; PMCID: PMC3575404.
      32. 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. Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage. Cell. 2012 Sep 28; 151(1):206-20. PMID: 22981692; PMCID: PMC3462286.
      33. Capra JA, Williams AG, Pollard KS. ProteinHistorian: tools for the comparative analysis of eukaryote protein origin. PLoS Comput Biol. 2012; 8(6):e1002567. PMID: 22761559; PMCID: PMC3386163.
      34. Wylie KM, Truty RM, Sharpton TJ, Mihindukulasuriya KA, Zhou Y, Gao H, Sodergren E, Weinstock GM, Pollard KS. Novel bacterial taxa in the human microbiome. PLoS One. 2012; 7(6):e35294. PMID: 22719826; PMCID: PMC3374617.
      35. Burbano HA, Green RE, Maricic T, Lalueza-Fox C, de la Rasilla M, Rosas A, Kelso J, Pollard KS, Lachmann M, Pääbo S. Analysis of human accelerated DNA regions using archaic hominin genomes. PLoS One. 2012; 7(3):e32877. PMID: 22412940; PMCID: PMC3296746.
      36. Kostka D, Hubisz MJ, Siepel A, Pollard KS. The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome. Mol Biol Evol. 2012 Mar; 29(3):1047-57. PMID: 22075116; PMCID: PMC3278478.
      37. 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, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA, 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, 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. A high-resolution map of human evolutionary constraint using 29 mammals. Nature. 2011 Oct 27; 478(7370):476-82. PMID: 21993624; PMCID: PMC3207357.
      38. Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF. Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet. 2011 Sep 9; 89(3):382-97. PMID: 21855840; PMCID: PMC3169815.
      39. Kembel SW, Eisen JA, Pollard KS, Green JL. The phylogenetic diversity of metagenomes. PLoS One. 2011; 6(8):e23214. PMID: 21912589; PMCID: PMC3166145.
      40. Katzman S, Capra JA, Haussler D, Pollard KS. Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots. Genome Biol Evol. 2011; 3:614-26. PMID: 21697099; PMCID: PMC3157837.
      41. Capra JA, Pollard KS. Substitution patterns are GC-biased in divergent sequences across the metazoans. Genome Biol Evol. 2011; 3:516-27. PMID: 21670083; PMCID: PMC3138425.
      42. Hirschey MD, Shimazu T, Capra JA, Pollard KS, Verdin E. SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2. Aging (Albany NY). 2011 Jun; 3(6):635-42. PMID: 21701047; PMCID: PMC3164371.
      43. Lambert N, Lambot MA, Bilheu A, Albert V, Englert Y, Libert F, Noel JC, Sotiriou C, Holloway AK, Pollard KS, Detours V, Vanderhaeghen P. Genes expressed in specific areas of the human fetal cerebral cortex display distinct patterns of evolution. PLoS One. 2011; 6(3):e17753. PMID: 21445258; PMCID: PMC3060818.
      44. 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. Chromatin remodelling complex dosage modulates transcription factor function in heart development. Nat Commun. 2011; 2:187. PMID: 21304516; PMCID: PMC3096875.
      45. Sharpton TJ, Riesenfeld SJ, Kembel SW, Ladau J, O'Dwyer JP, Green JL, Eisen JA, Pollard KS. PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data. PLoS Comput Biol. 2011; 7(1):e1001061. PMID: 21283775; PMCID: PMC3024254.
      46. Capra JA, Pollard KS, Singh M. Novel genes exhibit distinct patterns of function acquisition and network integration. Genome Biol. 2010; 11(12):R127. PMID: 21187012; PMCID: PMC3046487.
      47. Hubisz MJ, Pollard KS, Siepel A. PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform. 2011 Jan; 12(1):41-51. PMID: 21278375; PMCID: PMC3030812.
      48. Kostka D, Hahn MW, Pollard KS. Noncoding sequences near duplicated genes evolve rapidly. Genome Biol Evol. 2010; 2:518-33. PMID: 20660939; PMCID: PMC2942038.
      49. Ritter DI, Li Q, Kostka D, Pollard KS, Guo S, Chuang JH. The importance of being cis: evolution of orthologous fish and mammalian enhancer activity. Mol Biol Evol. 2010 Oct; 27(10):2322-32. PMID: 20494938; PMCID: PMC3107594.
      50. Katzman S, Kern AD, Pollard KS, Salama SR, Haussler D. GC-biased evolution near human accelerated regions. PLoS Genet. 2010 May; 6(5):e1000960. PMID: 20502635; PMCID: PMC2873926.
      51. Taylor SL, Pollard KS. Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes. Genet Res (Camb). 2010 Feb; 92(1):39-53. PMID: 20196895.
        View in: PubMed
      52. Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan; 20(1):110-21. PMID: 19858363; PMCID: PMC2798823.
      53. Pollard KS. What makes us human? Sci Am. 2009 May; 300(5):44-9. PMID: 19438048.
        View in: PubMed
      54. 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. The bovine lactation genome: insights into the evolution of mammalian milk. Genome Biol. 2009; 10(4):R43. PMID: 19393040; PMCID: PMC2688934.
      55. Berglund J, Pollard KS, Webster MT. Hotspots of biased nucleotide substitutions in human genes. PLoS Biol. 2009 Jan 27; 7(1):e26. PMID: 19175294; PMCID: PMC2631073.
      56. Cozen AE, Weirauch MT, Pollard KS, Bernick DL, Stuart JM, Lowe TM. Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum. J Bacteriol. 2009 Feb; 191(3):782-94. PMID: 19047344; PMCID: PMC2632070.
      57. Pollard KS, van der Laan MJ. Supervised distance matrices. Stat Appl Genet Mol Biol. 2008; 7(1):Article 33. PMID: 19049489.
        View in: PubMed
      58. Walker WL, Liao IH, Gilbert DL, Wong B, Pollard KS, McCulloch CE, Lit L, Sharp FR. Empirical Bayes accomodation of batch-effects in microarray data using identical replicate reference samples: application to RNA expression profiling of blood from Duchenne muscular dystrophy patients. BMC Genomics. 2008; 9:494. PMID: 18937867; PMCID: PMC2576259.
      59. Taylor SL, Pollard KS. Evaluation of two methods to estimate and monitor bird populations. PLoS One. 2008; 3(8):e3047. PMID: 18728775; PMCID: PMC2516598.
      60. Holloway AK, Begun DJ, Siepel A, Pollard KS. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res. 2008 Oct; 18(10):1592-601. PMID: 18583644; PMCID: PMC2556263.
      61. Lemay DG, Neville MC, Rudolph MC, Pollard KS, German JB. Gene regulatory networks in lactation: identification of global principles using bioinformatics. BMC Syst Biol. 2007; 1:56. PMID: 18039394; PMCID: PMC2225983.
      62. Pollard KS, Serre D, Wang X, Tao H, Grundberg E, Hudson TJ, Clark AG, Frazer K. A genome-wide approach to identifying novel-imprinted genes. Hum Genet. 2008 Jan; 122(6):625-34. PMID: 17955261.
        View in: PubMed
      63. Dreszer TR, Wall GD, Haussler D, Pollard KS. Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion. Genome Res. 2007 Oct; 17(10):1420-30. PMID: 17785536; PMCID: PMC1987345.
      64. Magalhães TR, Palmer J, Tomancak P, Pollard KS. Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach. BMC Neurosci. 2007; 8:59. PMID: 17672901; PMCID: PMC1950096.
      65. Pollard KS, Salama SR, King B, Kern AD, Dreszer T, Katzman S, Siepel A, Pedersen JS, Bejerano G, Baertsch R, Rosenbloom KR, Kent J, Haussler D. Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2006 Oct 13; 2(10):e168. PMID: 17040131; PMCID: PMC1599772.
      66. 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. An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 2006 Sep 14; 443(7108):167-72. PMID: 16915236.
        View in: PubMed
      67. Schneider KL, Pollard KS, Baertsch R, Pohl A, Lowe TM. The UCSC Archaeal Genome Browser. Nucleic Acids Res. 2006 Jan 1; 34(Database issue):D407-10. PMID: 16381898; PMCID: PMC1347496.
      68. Salomonis N, Cotte N, Zambon AC, Pollard KS, Vranizan K, Doniger SW, Dolganov G, Conklin BR. Identifying genetic networks underlying myometrial transition to labor. Genome Biol. 2005; 6(2):R12. PMID: 15693941; PMCID: PMC551532.
      69. van der Laan MJ, Dudoit S, Pollard KS. Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives. Stat Appl Genet Mol Biol. 2004; 3:Article15. PMID: 16646793.
        View in: PubMed
      70. van der Laan MJ, Dudoit S, Pollard KS. Multiple testing. Part II. Step-down procedures for control of the family-wise error rate. Stat Appl Genet Mol Biol. 2004; 3:Article14. PMID: 16646792.
        View in: PubMed
      71. Dudoit S, van der Laan MJ, Pollard KS. Multiple testing. Part I. Single-step procedures for control of general type I error rates. Stat Appl Genet Mol Biol. 2004; 3:Article13. PMID: 16646791.
        View in: PubMed
      72. Pollard KS, van der Laan MJ. Statistical inference for simultaneous clustering of gene expression data. Math Biosci. 2002 Mar; 176(1):99-121. PMID: 11867086.
        View in: PubMed
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