Genomes and Genes
Katherine S Pollard
Affiliation: University of California
- 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...
- 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....
- 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...
- 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...
- 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...
- 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....
- 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...
- 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...
- 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...
- 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. ..
- 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...
- 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....
- 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?..
- 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...
- 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...
- 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...
- Global marine bacterial diversity peaks at high latitudes in winterJoshua Ladau
The Gladstone Institutes, University of California, San Francisco, CA, 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. ..
- 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...
- 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...
- 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...
- 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...
- Chromatin remodelling complex dosage modulates transcription factor function in heart developmentJun K Takeuchi
Gladstone Institute of Cardiovascular Disease, San Francisco, California 94158, USA
Nat Commun 2:187. 2011....