Institution
TigerLogic
About: TigerLogic is a based out in . It is known for research contribution in the topics: Genome & Gene. The organization has 170 authors who have published 122 publications receiving 27103 citations.
Topics: Genome, Gene, Genomics, Comparative genomics, Whole genome sequencing
Papers
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TL;DR: An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence of the genome from the bacterium Haemophilus influenzae Rd.
Abstract: An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.
5,944 citations
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European Bioinformatics Institute1, TigerLogic2, Stanford University3, University of California, Berkeley4, University of Pennsylvania5, Harvard University6, Imperial College London7, Rockefeller University8, Katholieke Universiteit Leuven9, Utrecht University10, University of Colorado Denver11, Max Planck Society12
TL;DR: The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
Abstract: Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum Information About a Microarray Experiment (MIAME), that describes the minimum information required to ensure that microarray data can be easily interpreted and that results derived from its analysis can be independently verified. The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools. With respect to MIAME, we concentrate on defining the content and structure of the necessary information rather than the technical format for capturing it.
4,030 citations
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Celera Corporation1, Centre national de la recherche scientifique2, Cornell University3, National Institutes of Health4, Bar-Ilan University5, TigerLogic6, University of California, Riverside7, Virginia Tech8, University of Notre Dame9, Wellcome Trust Sanger Institute10, University of Maryland Biotechnology Institute11, University of Crete12, European Bioinformatics Institute13, Sapienza University of Rome14, Pasteur Institute15
TL;DR: Analysis of the PEST strain of A. gambiae revealed strong evidence for about 14,000 protein-encoding transcripts, and prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted.
Abstract: Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.
2,033 citations
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Wellcome Trust Sanger Institute1, London Research Institute2, Katholieke Universiteit Leuven3, Max Planck Society4, GATC Biotech5, Université catholique de Louvain6, Centre national de la recherche scientifique7, University of Exeter8, Institut national agronomique Paris Grignon9, University of Málaga10, Pablo de Olavide University11, University of Salamanca12, University of Sussex13, Salk Institute for Biological Studies14, Stanford University15, Cold Spring Harbor Laboratory16, TigerLogic17, Rosalind Franklin University of Medicine and Science18, Russian Academy of Sciences19, Technical University of Denmark20
TL;DR: The genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote, is sequenced and highly conserved genes important for eukARYotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing are identified.
Abstract: We have sequenced and annotated the genome of fission yeast (Schizosaccharomyces pombe), which contains the smallest number of protein-coding genes yet recorded for a eukaryote: 4,824. The centromeres are between 35 and 110 kilobases (kb) and contain related repeats including a highly conserved 1.8-kb element. Regions upstream of genes are longer than in budding yeast (Saccharomyces cerevisiae), possibly reflecting more-extended control regions. Some 43% of the genes contain introns, of which there are 4,730. Fifty genes have significant similarity with human disease genes; half of these are cancer related. We identify highly conserved genes important for eukaryotic cell organization including those required for the cytoskeleton, compartmentation, cell-cycle control, proteolysis, protein phosphorylation and RNA splicing. These genes may have originated with the appearance of eukaryotic life. Few similarly conserved genes that are important for multicellular organization were identified, suggesting that the transition from prokaryotes to eukaryotes required more new genes than did the transition from unicellular to multicellular organization.
1,686 citations
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TL;DR: The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.
Abstract: The spliced alignment of expressed sequence data to genomic sequence has proven a key tool in the comprehensive annotation of genes in eukaryotic genomes. A novel algorithm was developed to assemble clusters of overlapping transcript alignments (ESTs and full-length cDNAs) into maximal alignment assemblies, thereby comprehensively incorporating all available transcript data and capturing subtle splicing variations. Complete and partial gene structures identified by this method were used to improve The Institute for Genomic Research Arabidopsis genome annotation (TIGR release v.4.0). The alignment assemblies permitted the automated modeling of several novel genes and >1000 alternative splicing variations as well as updates (including UTR annotations) to nearly half of the ~27 000 annotated protein coding genes. The algorithm of the Program to Assemble Spliced Alignments (PASA) tool is described, as well as the results of automated updates to Arabidopsis gene annotations.
1,441 citations
Authors
Showing all 170 results
Name | H-index | Papers | Citations |
---|---|---|---|
Steven L. Salzberg | 147 | 407 | 231756 |
Mark Raymond Adams | 147 | 1187 | 135038 |
Ian T. Paulsen | 112 | 354 | 69460 |
Claire M. Fraser | 108 | 352 | 76292 |
John Quackenbush | 99 | 427 | 67029 |
J. Craig Venter | 97 | 214 | 96263 |
Jacques Ravel | 86 | 323 | 45793 |
Owen White | 78 | 105 | 84710 |
C. Robin Buell | 78 | 224 | 25061 |
Jennifer R. Wortman | 76 | 115 | 71435 |
Brian J. Haas | 75 | 133 | 75680 |
Hans-Peter Klenk | 67 | 564 | 31086 |
William C. Nierman | 65 | 154 | 23950 |
Carol J. Bult | 65 | 178 | 41336 |
Neil Hall | 65 | 199 | 25490 |