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Celera Corporation

About: Celera Corporation is a based out in . It is known for research contribution in the topics: Single-nucleotide polymorphism & Genome. The organization has 899 authors who have published 554 publications receiving 87644 citations. The organization is also known as: Celera Genomics.


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Journal ArticleDOI
J. Craig Venter1, Mark Raymond Adams1, Eugene W. Myers1, Peter W. Li1  +269 moreInstitutions (12)
16 Feb 2001-Science
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Abstract: A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

12,098 citations

Journal ArticleDOI
24 Mar 2000-Science
TL;DR: The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.
Abstract: The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

6,180 citations

Journal ArticleDOI
TL;DR: The PANTHER/X ontology is used to give a high-level representation of gene function across the human and mouse genomes, and the family HMMs are used to rank missense single nucleotide polymorphisms (SNPs) according to their likelihood of affecting protein function.
Abstract: In the genomic era, one of the fundamental goals is to characterize the function of proteins on a large scale. We describe a method, PANTHER, for relating protein sequence relationships to function relationships in a robust and accurate way. PANTHER is composed of two main components: the PANTHER library (PANTHER/LIB) and the PANTHER index (PANTHER/X). PANTHER/LIB is a collection of "books," each representing a protein family as a multiple sequence alignment, a Hidden Markov Model (HMM), and a family tree. Functional divergence within the family is represented by dividing the tree into subtrees based on shared function, and by subtree HMMs. PANTHER/X is an abbreviated ontology for summarizing and navigating molecular functions and biological processes associated with the families and subfamilies. We apply PANTHER to three areas of active research. First, we report the size and sequence diversity of the families and subfamilies, characterizing the relationship between sequence divergence and functional divergence across a wide range of protein families. Second, we use the PANTHER/X ontology to give a high-level representation of gene function across the human and mouse genomes. Third, we use the family HMMs to rank missense single nucleotide polymorphisms (SNPs), on a database-wide scale, according to their likelihood of affecting protein function.

2,857 citations

Journal ArticleDOI
Robert A. Holt1, G. Mani Subramanian1, Aaron L. Halpern1, Granger G. Sutton1, Rosane Charlab1, Deborah R. Nusskern1, Patrick Wincker2, Andrew G. Clark3, José M. C. Ribeiro4, Ron Wides5, Steven L. Salzberg6, Brendan J. Loftus6, Mark Yandell1, William H. Majoros6, William H. Majoros1, Douglas B. Rusch1, Zhongwu Lai1, Cheryl L. Kraft1, Josep F. Abril, Véronique Anthouard2, Peter Arensburger7, Peter W. Atkinson7, Holly Baden1, Véronique de Berardinis2, Danita Baldwin1, Vladimir Benes, Jim Biedler8, Claudia Blass, Randall Bolanos1, Didier Boscus2, Mary Barnstead1, Shuang Cai1, Kabir Chatuverdi1, George K. Christophides, Mathew A. Chrystal9, Michele Clamp10, Anibal Cravchik1, Val Curwen10, Ali N Dana9, Arthur L. Delcher1, Ian M. Dew1, Cheryl A. Evans1, Michael Flanigan1, Anne Grundschober-Freimoser11, Lisa Friedli7, Zhiping Gu1, Ping Guan1, Roderic Guigó, Maureen E. Hillenmeyer9, Susanne L. Hladun1, James R. Hogan9, Young S. Hong9, Jeffrey Hoover1, Olivier Jaillon2, Zhaoxi Ke9, Zhaoxi Ke1, Chinnappa D. Kodira1, Kokoza Eb, Anastasios C. Koutsos12, Ivica Letunic, Alex Levitsky1, Yong Liang1, Jhy-Jhu Lin1, Jhy-Jhu Lin6, Neil F. Lobo9, John Lopez1, Joel A. Malek6, Tina C. McIntosh1, Stephan Meister, Jason R. Miller1, Clark M. Mobarry1, Emmanuel Mongin13, Sean D. Murphy1, David A. O'Brochta11, Cynthia Pfannkoch1, Rong Qi1, Megan A. Regier1, Karin A. Remington1, Hongguang Shao8, Maria V. Sharakhova9, Cynthia Sitter1, Jyoti Shetty6, Thomas J. Smith1, Renee Strong1, Jingtao Sun1, Dana Thomasova, Lucas Q. Ton9, Pantelis Topalis12, Zhijian Tu8, Maria F. Unger9, Brian P. Walenz1, Aihui Wang1, Jian Wang1, Mei Wang1, X. Wang9, Kerry J. Woodford1, Jennifer R. Wortman6, Jennifer R. Wortman1, Martin Wu6, Alison Yao1, Evgeny M. Zdobnov, Hongyu Zhang1, Qi Zhao1, Shaying Zhao6, Shiaoping C. Zhu1, Igor F. Zhimulev, Mario Coluzzi14, Alessandra della Torre14, Charles Roth15, Christos Louis12, Francis Kalush1, Richard J. Mural1, Eugene W. Myers1, Mark Raymond Adams1, Hamilton O. Smith1, Samuel Broder1, Malcolm J. Gardner6, Claire M. Fraser6, Ewan Birney13, Peer Bork, Paul T. Brey15, J. Craig Venter6, J. Craig Venter1, Jean Weissenbach2, Fotis C. Kafatos, Frank H. Collins9, Stephen L. Hoffman1 
04 Oct 2002-Science
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

Journal ArticleDOI
01 Apr 2004-Nature
TL;DR: This first comprehensive analysis of the genome sequence of the Brown Norway (BN) rat strain is reported, which is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution.
Abstract: The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.

1,964 citations


Authors

Showing all 899 results

NameH-indexPapersCitations
Steven L. Salzberg147407231756
Mark Raymond Adams1471187135038
Thomas J. Smith1401775113919
Andrew G. Clark140823123333
Scott L. Friedman12648862931
Stephen L. Hoffman10445838597
J. Craig Venter9721496263
Robert A. Holt92245116496
Jun Li9033961485
David Ross8651827604
Matthew Bogyo8133622696
Jinghui Zhang80294119324
John P. Kane7630220148
Jennifer R. Wortman7611571435
Daniel H. Huson6920045675
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
20212
20202
20192
20181
20172
20161