Author
Bruce W. Birren
Other affiliations: Massachusetts Institute of Technology, California Institute of Technology, Bio-Rad Laboratories
Bio: Bruce W. Birren is an academic researcher from Broad Institute. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 103, co-authored 205 publications receiving 113491 citations. Previous affiliations of Bruce W. Birren include Massachusetts Institute of Technology & California Institute of Technology.
Topics: Genome, Gene, Genomics, Population, Human genome
Papers published on a yearly basis
Papers
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Broad Institute1, Tehran University of Medical Sciences2, George Washington University3, European Bioinformatics Institute4, Sapienza University of Rome5, Temple University6, Tomsk State University7, University of Notre Dame8, Centre national de la recherche scientifique9, French Institute of Health and Medical Research10, Imperial College London11, James Cook University12, Massachusetts Institute of Technology13, Simon Fraser University14, University of California, Davis15, Institut de recherche pour le développement16, Kansas State University17, Foundation for Research & Technology – Hellas18, University of Perugia19, Virginia Tech20, University of Nevada, Las Vegas21, Baylor College of Medicine22, Boston College23, Harvard University24, University of Manchester25, University of California, San Francisco26, University of Cyprus27, National Health Laboratory Service28, University of Crete29, Kenya Medical Research Institute30, University of Arizona31, University of Pennsylvania32, Indian Council of Medical Research33, New Mexico State University34, Liverpool School of Tropical Medicine35, Vanderbilt University Medical Center36, Vanderbilt University37, University of Geneva38, Swiss Institute of Bioinformatics39, Texas A&M University40, Chiang Mai University41, Rio de Janeiro State University42, Oswaldo Cruz Foundation43, Indiana University44, University of Santiago de Compostela45, Wellcome Trust Sanger Institute46, Liverpool John Moores University47, University of Georgia48, Harvey Mudd College49, University of California, Irvine50, University of Groningen51, Centers for Disease Control and Prevention52, Biogen Idec53
TL;DR: The authors investigated the genomic basis of vectorial capacity and explore new avenues for vector control, sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila.
Abstract: Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100 million years of evolution Comparative analyses show faster rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, relative to Drosophila Some determinants of vectorial capacity, such as chemosensory genes, do not show elevated turnover but instead diversify through protein-sequence changes This dynamism of anopheline genes and genomes may contribute to their flexible capacity to take advantage of new ecological niches, including adapting to humans as primary hosts
476 citations
University of Massachusetts Medical School1, Massachusetts Institute of Technology2, Hebrew University of Jerusalem3, Harvard University4, National Institute of Genetics5, National Institutes of Health6, University of Edinburgh7, State University of New York System8, Oregon State University9, Cold Spring Harbor Laboratory10, University of Cambridge11, University of Nottingham12, Karolinska Institutet13, Södertörn University14, University of Warwick15, Howard Hughes Medical Institute16, University of Kansas17, Stowers Institute for Medical Research18
TL;DR: Differences in gene content and regulation explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source and provide tools for investigation across the Schizosaccharomyces clade.
Abstract: The fission yeast clade--comprising Schizosaccharomyces pombe, S. octosporus, S. cryophilus, and S. japonicus--occupies the basal branch of Ascomycete fungi and is an important model of eukaryote biology. A comparative annotation of these genomes identified a near extinction of transposons and the associated innovation of transposon-free centromeres. Expression analysis established that meiotic genes are subject to antisense transcription during vegetative growth, which suggests a mechanism for their tight regulation. In addition, trans-acting regulators control new genes within the context of expanded functional modules for meiosis and stress response. Differences in gene content and regulation also explain why, unlike the budding yeast of Saccharomycotina, fission yeasts cannot use ethanol as a primary carbon source. These analyses elucidate the genome structure and gene regulation of fission yeast and provide tools for investigation across the Schizosaccharomyces clade.
474 citations
TL;DR: A model is proposed in which RORα interacts with the thyroid hormone signalling pathway to induce Purkinje-cell maturation, in which staggerer mice were found to carry a deletion within the ROR α gene that prevents translation of the ligand-binding homology domain.
Abstract: Homozygous staggerer (sg) mice show a characteristic severe cerebellar ataxia due to a cell-autonomous defect in the development of Purkinje cells. These cells show immature morphology, synaptic arrangement, biochemical properties and gene expression, and are reduced in numbers. In addition, sg heterozygotes show accelerated dendritic atrophy and cell loss, suggesting that sg has a role in mature Purkinje cells. Effects of this mutation on cerebellar development have been studied for 25 years, but its molecular basis has remained unknown. We have genetically mapped staggerer to an interval of 160 kilobases on mouse chromosome 9 which was found to contain the gene encoding RORalpha, a member of the nuclear hormone-receptor superfamily. Staggerer mice were found to carry a deletion within the RORalpha gene that prevents translation of the ligand-binding homology domain. We propose a model based on these results, in which RORalpha interacts with the thyroid hormone signalling pathway to induce Purkinje-cell maturation.
464 citations
University of California, Riverside1, University of Geneva2, Swiss Institute of Bioinformatics3, University of Notre Dame4, J. Craig Venter Institute5, University of Santiago de Compostela6, Iowa State University7, Colorado State University8, Harvard University9, Indiana University10, University of Barcelona11, Broad Institute12, University of Texas at Arlington13, University of Maryland, Baltimore14, Max Planck Society15, Liverpool School of Tropical Medicine16, Swedish University of Agricultural Sciences17, Hoffmann-La Roche18, Virginia Tech19, University of Wisconsin-Madison20, Kansas State University21, Auburn University22, University of A Coruña23, International Livestock Research Institute24, University of Maryland, College Park25, National Institutes of Health26, University of Illinois at Urbana–Champaign27, University of Göttingen28, Imperial College London29, University of Texas Medical Branch30, Johns Hopkins University31, University of California, Davis32, George Washington University33, Boston College34
TL;DR: The genomic sequence of C. quinquefasciatus is described, which reveals distinctions related to vector capacities and habitat preferences, and confirmed that inoculation with unfamiliar bacteria prompted strong immune responses in Culex.
Abstract: Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.
452 citations
University of Nevada, Reno1, Purdue University2, Monsanto3, Old Dominion University4, North Carolina State University5, University College London6, Oklahoma State University–Stillwater7, Spanish National Research Council8, National Institutes of Health9, Wellcome Trust10, University of Cambridge11, J. Craig Venter Institute12, Leidos13, Broad Institute14, University of Notre Dame15, University of Nevada, Las Vegas16, University of Barcelona17, Carlos III Health Institute18, University of Massachusetts Medical School19, University of Connecticut20, University of Oxford21, University of Lausanne22, Virginia Tech23, West Virginia University24, Indiana University25, University of Maryland, Baltimore26, Kansas State University27, Texas A&M University28, University of Minnesota29, National University of Singapore30, University of Manchester31, University of California, San Francisco32, Iowa State University33, Colorado State University34, Pennsylvania State University35, University of California, Riverside36, Max Planck Society37, ANSES38, University of Santiago de Compostela39, Pompeu Fabra University40, California State Polytechnic University, Pomona41, University of Queensland42, University of the Sunshine Coast43, Swiss Institute of Bioinformatics44, University of Geneva45, University of Copenhagen46, University of Tennessee Health Science Center47, University of Vigo48, Wellcome Trust Sanger Institute49, University of Illinois at Urbana–Champaign50, Quinnipiac University51, International Livestock Research Institute52
TL;DR: Insights from genome analyses into parasitic processes unique to ticks, including host ‘questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival are reported.
Abstract: Ticks transmit more pathogens to humans and animals than any other arthropod. We describe the 2.1 Gbp nuclear genome of the tick, Ixodes scapularis (Say), which vectors pathogens that cause Lyme disease, human granulocytic anaplasmosis, babesiosis and other diseases. The large genome reflects accumulation of repetitive DNA, new lineages of retro-transposons, and gene architecture patterns resembling ancient metazoans rather than pancrustaceans. Annotation of scaffolds representing ∼57% of the genome, reveals 20,486 protein-coding genes and expansions of gene families associated with tick-host interactions. We report insights from genome analyses into parasitic processes unique to ticks, including host 'questing', prolonged feeding, cuticle synthesis, blood meal concentration, novel methods of haemoglobin digestion, haem detoxification, vitellogenesis and prolonged off-host survival. We identify proteins associated with the agent of human granulocytic anaplasmosis, an emerging disease, and the encephalitis-causing Langat virus, and a population structure correlated to life-history traits and transmission of the Lyme disease agent.
406 citations
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TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Abstract: The human genome holds an extraordinary trove of information about human development, physiology, medicine and evolution. Here we report the results of an international collaboration to produce and make freely available a draft sequence of the human genome. We also present an initial analysis of the data, describing some of the insights that can be gleaned from the sequence.
22,269 citations
TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
Abstract: Next-generation DNA sequencing (NGS) projects, such as the 1000 Genomes Project, are already revolutionizing our understanding of genetic variation among individuals. However, the massive data sets generated by NGS—the 1000 Genome pilot alone includes nearly five terabases—make writing feature-rich, efficient, and robust analysis tools difficult for even computationally sophisticated individuals. Indeed, many professionals are limited in the scope and the ease with which they can answer scientific questions by the complexity of accessing and manipulating the data produced by these machines. Here, we discuss our Genome Analysis Toolkit (GATK), a structured programming framework designed to ease the development of efficient and robust analysis tools for next-generation DNA sequencers using the functional programming philosophy of MapReduce. The GATK provides a small but rich set of data access patterns that encompass the majority of analysis tool needs. Separating specific analysis calculations from common data management infrastructure enables us to optimize the GATK framework for correctness, stability, and CPU and memory efficiency and to enable distributed and shared memory parallelization. We highlight the capabilities of the GATK by describing the implementation and application of robust, scale-tolerant tools like coverage calculators and single nucleotide polymorphism (SNP) calling. We conclude that the GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
20,557 citations
28 Jul 2005
TL;DR: PfPMP1）与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。
18,940 citations
TL;DR: SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies.
Abstract: The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V−SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online (http://bioinf.spbau.ru/spades). It is distributed as open source software.
16,859 citations
TL;DR: The Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available, providing a unified solution for transcriptome reconstruction in any sample.
Abstract: Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.
15,665 citations