Katherine S Pollard
Affiliation: University of California
- A genome-wide approach to identifying novel-imprinted genesKatherine 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...
- Transcriptional control in embryonic Drosophila midline guidance assessed through a whole genome approachTiago 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...
- Forces shaping the fastest evolving regions in the human genomeKatherine 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...
- G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genesDanielle G Lemay
Genome Center, University of California Davis, 451 Health Science Dr, Davis, CA, 95616, United States of America
BMC Bioinformatics 13:253. 2012....
- Detection of nonneutral substitution rates on mammalian phylogeniesKatherine 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...
- Noncoding sequences near duplicated genes evolve rapidlyDennis 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...
- An RNA gene expressed during cortical development evolved rapidly in humansKatherine 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...
- ProteinHistorian: tools for the comparative analysis of eukaryote protein originJohn 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/...
- The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genomeDennis Kostka
Gladstone Institute of Cardiovascular Disease, University of California, San Francisco, USA
Mol Biol Evol 29:1047-57. 2012....
- The bovine lactation genome: insights into the evolution of mammalian milkDanielle 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...
- Ongoing GC-biased evolution is widespread in the human genome and enriched near recombination hot spotsSol 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...
- GC-biased evolution near human accelerated regionsSol Katzman
Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
PLoS Genet 6:e1000960. 2010....
- Substitution patterns are GC-biased in divergent sequences across the metazoansJohn A Capra
Gladstone Institutes, University of California, San Francisco, USA
Genome Biol Evol 3:516-27. 2011....
- From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptomeDanielle 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. ..
- Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversionTimothy 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...
- Accelerated sequence divergence of conserved genomic elements in Drosophila melanogasterAlisha 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...
- Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysisSamantha 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...
- A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomesJohn 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. ..
- Global marine bacterial diversity peaks at high latitudes in winterJoshua 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. ..
- Transcriptional map of respiratory versatility in the hyperthermophilic crenarchaeon Pyrobaculum aerophilumAaron 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...
- Evaluation of two methods to estimate and monitor bird populationsSandra 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...
- PhylOTU: a high-throughput procedure quantifies microbial community diversity and resolves novel taxa from metagenomic dataThomas 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?..
- Statistical inference for simultaneous clustering of gene expression dataKatherine 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...
- A taxonomic signature of obesity in the microbiome? Getting to the guts of the matterMariel 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. ..
- Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resourceThomas 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...
- 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 patientsWynn 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...
- Supervised distance matricesKatherine 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...
- Composite interval mapping to identify quantitative trait loci for point-mass mixture phenotypesSandra 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...
- SIRT1 and SIRT3 deacetylate homologous substrates: AceCS1,2 and HMGCS1,2Matthew 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...
- Novel genes exhibit distinct patterns of function acquisition and network integrationJohn 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...
- Many human accelerated regions are developmental enhancersJohn A Capra
Gladstone Institutes, University of California, San Francisco, CA 94158, USA
Philos Trans R Soc Lond B Biol Sci 368:20130025. 2013....
- Gene regulatory networks in lactation: identification of global principles using bioinformaticsDanielle 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...
- The UCSC Archaeal Genome BrowserKevin 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...
- Identifying genetic networks underlying myometrial transition to laborNathan 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...