Katherine S Pollard

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint A genome-wide approach to identifying novel-imprinted genes
    Katherine S Pollard
    UC Davis Genome Center and Department of Statistics, University of California, Davis, CA, 95616, USA
    Hum Genet 122:625-34. 2008
  2. pmc Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach
    Tiago R Magalhaes
    Programa Gulbenkian Doutoramento Biologia e Medicina, Centro Neurociências, Universidade de Coimbra, 3000 Coimbra, Portugal
    BMC Neurosci 8:59. 2007
  3. pmc Forces shaping the fastest evolving regions in the human genome
    Katherine S Pollard
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS Genet 2:e168. 2006
  4. pmc G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
    Danielle G Lemay
    Genome Center, University of California Davis, 451 Health Science Dr, Davis, CA, 95616, United States of America
    BMC Bioinformatics 13:253. 2012
  5. pmc A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes
    John A Capra
    Gladstone Institutes, University of California, San Francisco, California, United States of America
    PLoS Genet 9:e1003684. 2013
  6. pmc From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome
    Danielle G Lemay
    Genome Center, University of California Davis, Davis, California, United States of America
    PLoS ONE 8:e75030. 2013
  7. pmc Detection of nonneutral substitution rates on mammalian phylogenies
    Katherine S Pollard
    Gladstone Institutes, University of California, San Francisco, San Francisco, California 94158, USA
    Genome Res 20:110-21. 2010
  8. pmc Noncoding sequences near duplicated genes evolve rapidly
    Dennis Kostka
    Gladstone Institute for Cardiovascular Disease, Gladstone Institutes, University of California San Francisco, San Francisco, CA, USA
    Genome Biol Evol 2:518-33. 2010
  9. ncbi request reprint An RNA gene expressed during cortical development evolved rapidly in humans
    Katherine S Pollard
    Center for Biomolecular Science and Engineering, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
    Nature 443:167-72. 2006
  10. pmc ProteinHistorian: tools for the comparative analysis of eukaryote protein origin
    John A Capra
    J David Gladstone Institutes, University of California, San Francisco, California, United States of America
    PLoS Comput Biol 8:e1002567. 2012

Detail Information

Publications48

  1. ncbi request reprint A genome-wide approach to identifying novel-imprinted genes
    Katherine S Pollard
    UC Davis Genome Center and Department of Statistics, University of California, Davis, CA, 95616, USA
    Hum Genet 122:625-34. 2008
    ..With samples of mRNA from appropriate tissues and a collection of informative cSNPs, a genome-wide search using this methodology could expand the list of genes that undergo genomic imprinting in a tissue- or temporal-specific manner...
  2. pmc Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approach
    Tiago R Magalhaes
    Programa Gulbenkian Doutoramento Biologia e Medicina, Centro Neurociências, Universidade de Coimbra, 3000 Coimbra, Portugal
    BMC Neurosci 8:59. 2007
    ..We also analyzed a previously published microarray time course of Drosophila embryonic development with an axon guidance focus...
  3. pmc Forces shaping the fastest evolving regions in the human genome
    Katherine S Pollard
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS Genet 2:e168. 2006
    ..A combination of evolutionary forces has contributed to accelerated evolution of the fastest evolving elements in the human genome...
  4. pmc G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes
    Danielle G Lemay
    Genome Center, University of California Davis, 451 Health Science Dr, Davis, CA, 95616, United States of America
    BMC Bioinformatics 13:253. 2012
    ....
  5. pmc A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes
    John A Capra
    Gladstone Institutes, University of California, San Francisco, California, United States of America
    PLoS Genet 9:e1003684. 2013
    ..Together, these findings shed new light on the evolutionary, functional, and disease implications of gBGC. The phastBias program and our predicted tracts are freely available. ..
  6. pmc From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome
    Danielle G Lemay
    Genome Center, University of California Davis, Davis, California, United States of America
    PLoS ONE 8:e75030. 2013
    ..Genes essential to the mammary gland's uniqueness are isolated from neighbors, and likely have less tolerance for variation in expression, properties they share with genes responsible for an organism's survival. ..
  7. pmc Detection of nonneutral substitution rates on mammalian phylogenies
    Katherine S Pollard
    Gladstone Institutes, University of California, San Francisco, San Francisco, California 94158, USA
    Genome Res 20:110-21. 2010
    ..We also describe new "Conservation" tracks in the UCSC Genome Browser that display both phyloP and phastCons scores for genome-wide alignments of 44 vertebrate species...
  8. pmc Noncoding sequences near duplicated genes evolve rapidly
    Dennis Kostka
    Gladstone Institute for Cardiovascular Disease, Gladstone Institutes, University of California San Francisco, San Francisco, CA, USA
    Genome Biol Evol 2:518-33. 2010
    ..Our findings support the hypothesis that adaptive evolution of the regulation of duplicated genes has played a significant role in human evolution...
  9. ncbi request reprint An RNA gene expressed during cortical development evolved rapidly in humans
    Katherine S Pollard
    Center for Biomolecular Science and Engineering, Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California 95064, USA
    Nature 443:167-72. 2006
    ..HAR1 and the other human accelerated regions provide new candidates in the search for uniquely human biology...
  10. pmc ProteinHistorian: tools for the comparative analysis of eukaryote protein origin
    John A Capra
    J David Gladstone Institutes, University of California, San Francisco, California, United States of America
    PLoS Comput Biol 8:e1002567. 2012
    ..The ProteinHistorian web server, source code, and pre-computed ages for 32 eukaryotic genomes are freely available under the GNU public license at http://lighthouse.ucsf.edu/ProteinHistorian/...
  11. pmc The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome
    Dennis Kostka
    Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, USA
    Mol Biol Evol 29:1047-57. 2012
    ....
  12. pmc The bovine lactation genome: insights into the evolution of mammalian milk
    Danielle G Lemay
    Department of Food Science and Technology, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
    Genome Biol 10:R43. 2009
    ..The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes...
  13. pmc Substitution patterns are GC-biased in divergent sequences across the metazoans
    John A Capra
    Gladstone Institutes, University of California, San Francisco, USA
    Genome Biol Evol 3:516-27. 2011
    ....
  14. pmc Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spots
    Sol Katzman
    Center for Biomolecular Science and Engineering, University of California, Santa Cruz, USA
    Genome Biol Evol 3:614-26. 2011
    ..These findings demonstrate the presence of ongoing fixation bias favoring G and C alleles throughout the human genome and suggest that the bias is caused by a recombination-associated process, such as GC-biased gene conversion...
  15. pmc GC-biased evolution near human accelerated regions
    Sol Katzman
    Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
    PLoS Genet 6:e1000960. 2010
    ....
  16. pmc Many human accelerated regions are developmental enhancers
    John A Capra
    Gladstone Institutes, University of California, San Francisco, CA 94158, USA
    Philos Trans R Soc Lond B Biol Sci 368:20130025. 2013
    ....
  17. pmc Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster
    Alisha K Holloway
    Department of Evolution and Ecology and Center for Population Biology, University of California, Davis, California 95691, USA
    Genome Res 18:1592-601. 2008
    ..Our analysis also highlights interesting noncoding genomic regions, such as regulatory regions in the gene gooseberry-neuro and a putative novel miRNA...
  18. pmc Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion
    Timothy R Dreszer
    Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
    Genome Res 17:1420-30. 2007
    ..These observations support the hypothesis that biased gene conversion (BGC), specifically in the male germline, played a significant role in the evolution of the human genome...
  19. pmc Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis
    Samantha J Riesenfeld
    Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, CA 94158, USA
    BMC Genomics 14:419. 2013
    ..But the accuracy of gene-family phylogenies that characterize evolutionary relationships among short, non-overlapping sequencing reads has not been thoroughly evaluated...
  20. pmc Global marine bacterial diversity peaks at high latitudes in winter
    Joshua Ladau
    The Gladstone Institutes, University of California, San Francisco, CA 94158, USA
    ISME J 7:1669-77. 2013
    ..Our maps provide the first picture of bacterial distributions at a global scale and suggest important differences between the diversity patterns of bacteria compared with other organisms. ..
  21. pmc Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilum
    Aaron E Cozen
    Department of Ocean Sciences, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
    J Bacteriol 191:782-94. 2009
    ..The complete gene expression data set can be viewed in genomic context with the Archaeal Genome Browser at archaea.ucsc.edu...
  22. pmc Evaluation of two methods to estimate and monitor bird populations
    Sandra L Taylor
    Department of Statistics, University of California Davis, Davis, California, USA
    PLoS ONE 3:e3047. 2008
    ..Two population estimation methods, double observer (DO) and double sampling (DS), have been advocated for avian population studies and the relative merits and short-comings of these methods remain an area of debate...
  23. pmc Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes
    Stephen Nayfach
    Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America
    PLoS Comput Biol 11:e1004573. 2015
    ....
  24. pmc Integrating diverse datasets improves developmental enhancer prediction
    Genevieve D Erwin
    Gladstone Institute of Cardiovascular Disease, San Francisco, California, United States of America Institute for Human Genetics, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 10:e1003677. 2014
    ..Our genome-wide developmental enhancer predictions are freely available as a UCSC Genome Browser track, which we hope will enable researchers to further investigate questions in developmental biology. ..
  25. pmc PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic data
    Thomas J Sharpton
    The J David Gladstone Institutes, University of California San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 7:e1001061. 2011
    ..Taken together, these results suggest that PhylOTU enables characterization of part of the biosphere currently hidden from PCR-based surveys of diversity?..
  26. ncbi request reprint Statistical inference for simultaneous clustering of gene expression data
    Katherine S Pollard
    Division of Biostatistics, School of Public Health, University of California, Earl Warren Hall 7360, Berkeley, CA 94720 7360, USA
    Math Biosci 176:99-121. 2002
    ..We present results of simulations designed to assess the asymptotic validity of different bootstrap methods for estimating the distribution of Phi(P(n)). The method is illustrated on a publicly available data set...
  27. pmc Transcriptomic and epigenomic characterization of the developing bat wing
    Walter L Eckalbar
    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA
    Nat Genet 48:528-36. 2016
    ..In combination, our work outlines multiple genetic components that likely contribute to bat wing formation, providing insights into this morphological innovation. ..
  28. ncbi request reprint Augmentation procedures for control of the generalized family-wise error rate and tail probabilities for the proportion of false positives
    Mark J Van Der Laan
    Division of Biostatistics, School of Public Health, University of California, Berkeley, USA
    Stat Appl Genet Mol Biol 3:Article15. 2004
    ..Finally, two simple conservative procedures are proposed for controlling the false discovery rate...
  29. ncbi request reprint Multiple testing. Part II. Step-down procedures for control of the family-wise error rate
    Mark J Van Der Laan
    Division of Biostatistics, School of Public Health, University of California, Berkeley, USA
    Stat Appl Genet Mol Biol 3:Article14. 2004
    ..A general bootstrap algorithm is supplied to conveniently obtain consistent estimators of the null distribution...
  30. pmc A taxonomic signature of obesity in the microbiome? Getting to the guts of the matter
    Mariel M Finucane
    The J David Gladstone Institutes, San Francisco, California, United States of America
    PLoS ONE 9:e84689. 2014
    ..Differences between studies are likely due to a combination of technical and clinical factors. We conclude that there is no simple taxonomic signature of obesity in the microbiota of the human gut. ..
  31. pmc Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource
    Thomas J Sharpton
    The J David Gladstone Institutes, University of California San Francisco, San Francisco, CA 94158, USA
    BMC Bioinformatics 13:264. 2012
    ..We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences...
  32. doi request reprint Supervised distance matrices
    Katherine S Pollard
    University of California, San Francisco, USA
    Stat Appl Genet Mol Biol 7:Article 33. 2008
    ..The proposed methods are widely applicable in genomics and other fields where high-dimensional data is collected on each subject...
  33. pmc SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2
    Matthew D Hirschey
    Gladstone Institute of Virology and Immunology, University of California, San Francisco, CA 94158, USA
    Aging (Albany NY) 3:635-42. 2011
    ..In this perspective, we take a first step by characterizing the evolutionary history of the sirtuins and these substrate families...
  34. doi request reprint Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypes
    Sandra L Taylor
    Biostatistics Graduate Group, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
    Genet Res (Camb) 92:39-53. 2010
    ..Our results show that the two-part CIM has greater power and a lower false positive rate than the other methods when a continuous phenotype is measured with many zero observations...
  35. pmc 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
    Wynn L Walker
    Department of Neurology and MIND Institute, University of California at Davis, Sacramento, California, USA
    BMC Genomics 9:494. 2008
    ..Existing methods can correct for batch effects only when samples from all biological groups are represented in every batch...
  36. pmc Novel genes exhibit distinct patterns of function acquisition and network integration
    John A Capra
    Gladstone Institutes, University of California, San Francisco, 1650 Owens St, San Francisco, CA 94158, USA
    Genome Biol 11:R127. 2010
    ..We developed a computational approach to investigate these issues by integrating genome-wide comparative phylogenetic analysis with functional and interaction data derived from small-scale and high-throughput experiments...
  37. pmc Toward Accurate and Quantitative Comparative Metagenomics
    Stephen Nayfach
    Integrative Program in Quantitative Biology, University of California, San Francisco, CA 94158, USA Gladstone Institutes, San Francisco, CA 94158, USA
    Cell 166:1103-16. 2016
    ..Only then can the potential of metagenomics for predictive ecological modeling, well-powered association studies, and effective microbiome medicine be fully realized. ..
  38. pmc An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography
    Stephen Nayfach
    Integrative Program in Quantitative Biology, University of California, San Francisco, San Francisco, California 94158, USA
    Genome Res 26:1612-1625. 2016
    ..Strain-level genetic variants present in metagenomes clearly reveal extensive structure and dynamics that are obscured when data are analyzed at a coarser taxonomic resolution...
  39. pmc Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin
    Sean Whalen
    Gladstone Institutes, San Francisco, California, USA
    Nat Genet 48:488-96. 2016
    ..We conclude that complex but consistent combinations of marks on the one-dimensional genome encode the three-dimensional structure of fine-scale regulatory interactions. ..
  40. pmc Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota
    A Sloan Devlin
    Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94143, USA
    Cell Host Microbe . 2016
    ..Our results demonstrate that it is possible to control host IS levels by targeting the microbiota and suggest a possible strategy for treating renal disease...
  41. ncbi request reprint Multiple testing. Part I. Single-step procedures for control of general type I error rates
    Sandrine Dudoit
    Division of Biostatistics, School of Public Health, University of California, Berkeley, USA
    Stat Appl Genet Mol Biol 3:Article13. 2004
    ..2004a). The proposed bootstrap multiple testing procedures are evaluated by a simulation study and applied to genomic data in the fourth article of the series (Pollard et al., 2004)...
  42. pmc Discovery of Reactive Microbiota-Derived Metabolites that Inhibit Host Proteases
    Chun Jun Guo
    Department of Bioengineering and Therapeutic Sciences and California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
    Cell . 2017
    ....
  43. pmc Accelerated Evolution of Enhancer Hotspots in the Mammal Ancestor
    Alisha K Holloway
    Gladstone Institute of Cardiovascular Disease, San Francisco, CA Department of Epidemiology and Biostatistics, University of California, San Francisco, CA
    Mol Biol Evol 33:1008-18. 2016
    ..This work underscores the idea that changes in developmental gene expression are important for mammalian evolution, and it pinpoints candidate genes for unique aspects of mammalian biology...
  44. pmc Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus
    Betty M Booker
    Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
    PLoS Genet 12:e1005738. 2016
    ..Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing. ..
  45. pmc Profile hidden Markov models for the detection of viruses within metagenomic sequence data
    Peter Skewes-Cox
    Biological and Medical Informatics Graduate Program, University of California San Francisco, San Francisco, California, United States of America Departments of Medicine, Biochemistry and Biophysics, and Microbiology, University of California San Francisco, San Francisco, California, United States of America Howard Hughes Medical Institute, Bethesda, Maryland, United States of America
    PLoS ONE 9:e105067. 2014
    ..We also provide the software necessary to build custom profile HMMs or update the vFams as more viruses are discovered (http://derisilab.ucsf.edu/software/vFam). ..
  46. pmc Gene regulatory networks in lactation: identification of global principles using bioinformatics
    Danielle G Lemay
    Department of Food Science and Technology, University of California, One Shields Ave, Davis, CA 95616, USA
    BMC Syst Biol 1:56. 2007
    ..The molecular events underlying mammary development during pregnancy, lactation, and involution are incompletely understood...
  47. pmc The UCSC Archaeal Genome Browser
    Kevin L Schneider
    Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 34:D407-10. 2006
    ..We encourage submission of new experimental and bioinformatic analysis from contributors. The purpose of this tool is to aid biological discovery and facilitate greater collaboration within the archaeal research community...
  48. pmc Identifying genetic networks underlying myometrial transition to labor
    Nathan Salomonis
    Gladstone Institute of Cardiovascular Disease, 1650 Owens Street, San Francisco, CA 94158, USA
    Genome Biol 6:R12. 2005
    ..Although several marker genes have been identified, little is known about the underlying global gene expression patterns and pathways that orchestrate these striking changes...