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  • 1
    Publication Date: 2001-02-22
    Description: 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venter, J C -- Adams, M D -- Myers, E W -- Li, P W -- Mural, R J -- Sutton, G G -- Smith, H O -- Yandell, M -- Evans, C A -- Holt, R A -- Gocayne, J D -- Amanatides, P -- Ballew, R M -- Huson, D H -- Wortman, J R -- Zhang, Q -- Kodira, C D -- Zheng, X H -- Chen, L -- Skupski, M -- Subramanian, G -- Thomas, P D -- Zhang, J -- Gabor Miklos, G L -- Nelson, C -- Broder, S -- Clark, A G -- Nadeau, J -- McKusick, V A -- Zinder, N -- Levine, A J -- Roberts, R J -- Simon, M -- Slayman, C -- Hunkapiller, M -- Bolanos, R -- Delcher, A -- Dew, I -- Fasulo, D -- Flanigan, M -- Florea, L -- Halpern, A -- Hannenhalli, S -- Kravitz, S -- Levy, S -- Mobarry, C -- Reinert, K -- Remington, K -- Abu-Threideh, J -- Beasley, E -- Biddick, K -- Bonazzi, V -- Brandon, R -- Cargill, M -- Chandramouliswaran, I -- Charlab, R -- Chaturvedi, K -- Deng, Z -- Di Francesco, V -- Dunn, P -- Eilbeck, K -- Evangelista, C -- Gabrielian, A E -- Gan, W -- Ge, W -- Gong, F -- Gu, Z -- Guan, P -- Heiman, T J -- Higgins, M E -- Ji, R R -- Ke, Z -- Ketchum, K A -- Lai, Z -- Lei, Y -- Li, Z -- Li, J -- Liang, Y -- Lin, X -- Lu, F -- Merkulov, G V -- Milshina, N -- Moore, H M -- Naik, A K -- Narayan, V A -- Neelam, B -- Nusskern, D -- Rusch, D B -- Salzberg, S -- Shao, W -- Shue, B -- Sun, J -- Wang, Z -- Wang, A -- Wang, X -- Wang, J -- Wei, M -- Wides, R -- Xiao, C -- Yan, C -- Yao, A -- Ye, J -- Zhan, M -- Zhang, W -- Zhang, H -- Zhao, Q -- Zheng, L -- Zhong, F -- Zhong, W -- Zhu, S -- Zhao, S -- Gilbert, D -- Baumhueter, S -- Spier, G -- Carter, C -- Cravchik, A -- Woodage, T -- Ali, F -- An, H -- Awe, A -- Baldwin, D -- Baden, H -- Barnstead, M -- Barrow, I -- Beeson, K -- Busam, D -- Carver, A -- Center, A -- Cheng, M L -- Curry, L -- Danaher, S -- Davenport, L -- Desilets, R -- Dietz, S -- Dodson, K -- Doup, L -- Ferriera, S -- Garg, N -- Gluecksmann, A -- Hart, B -- Haynes, J -- Haynes, C -- Heiner, C -- Hladun, S -- Hostin, D -- Houck, J -- Howland, T -- Ibegwam, C -- Johnson, J -- Kalush, F -- Kline, L -- Koduru, S -- Love, A -- Mann, F -- May, D -- McCawley, S -- McIntosh, T -- McMullen, I -- Moy, M -- Moy, L -- Murphy, B -- Nelson, K -- Pfannkoch, C -- Pratts, E -- Puri, V -- Qureshi, H -- Reardon, M -- Rodriguez, R -- Rogers, Y H -- Romblad, D -- Ruhfel, B -- Scott, R -- Sitter, C -- Smallwood, M -- Stewart, E -- Strong, R -- Suh, E -- Thomas, R -- Tint, N N -- Tse, S -- Vech, C -- Wang, G -- Wetter, J -- Williams, S -- Williams, M -- Windsor, S -- Winn-Deen, E -- Wolfe, K -- Zaveri, J -- Zaveri, K -- Abril, J F -- Guigo, R -- Campbell, M J -- Sjolander, K V -- Karlak, B -- Kejariwal, A -- Mi, H -- Lazareva, B -- Hatton, T -- Narechania, A -- Diemer, K -- Muruganujan, A -- Guo, N -- Sato, S -- Bafna, V -- Istrail, S -- Lippert, R -- Schwartz, R -- Walenz, B -- Yooseph, S -- Allen, D -- Basu, A -- Baxendale, J -- Blick, L -- Caminha, M -- Carnes-Stine, J -- Caulk, P -- Chiang, Y H -- Coyne, M -- Dahlke, C -- Mays, A -- Dombroski, M -- Donnelly, M -- Ely, D -- Esparham, S -- Fosler, C -- Gire, H -- Glanowski, S -- Glasser, K -- Glodek, A -- Gorokhov, M -- Graham, K -- Gropman, B -- Harris, M -- Heil, J -- Henderson, S -- Hoover, J -- Jennings, D -- Jordan, C -- Jordan, J -- Kasha, J -- Kagan, L -- Kraft, C -- Levitsky, A -- Lewis, M -- Liu, X -- Lopez, J -- Ma, D -- Majoros, W -- McDaniel, J -- Murphy, S -- Newman, M -- Nguyen, T -- Nguyen, N -- Nodell, M -- Pan, S -- Peck, J -- Peterson, M -- Rowe, W -- Sanders, R -- Scott, J -- Simpson, M -- Smith, T -- Sprague, A -- Stockwell, T -- Turner, R -- Venter, E -- Wang, M -- Wen, M -- Wu, D -- Wu, M -- Xia, A -- Zandieh, A -- Zhu, X -- New York, N.Y. -- Science. 2001 Feb 16;291(5507):1304-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA. humangenome@celera.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11181995" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Chromosome Banding ; Chromosome Mapping ; Chromosomes, Artificial, Bacterial ; Computational Biology ; Consensus Sequence ; CpG Islands ; DNA, Intergenic ; Databases, Factual ; Evolution, Molecular ; Exons ; Female ; Gene Duplication ; Genes ; Genetic Variation ; *Genome, Human ; *Human Genome Project ; Humans ; Introns ; Male ; Phenotype ; Physical Chromosome Mapping ; Polymorphism, Single Nucleotide ; Proteins/genetics/physiology ; Pseudogenes ; Repetitive Sequences, Nucleic Acid ; Retroelements ; *Sequence Analysis, DNA/methods ; Species Specificity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2002-08-10
    Description: Primate-specific segmental duplications are considered important in human disease and evolution. The inability to distinguish between allelic and duplication sequence overlap has hampered their characterization as well as assembly and annotation of our genome. We developed a method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence. This test has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity. We mapped 169 large regions flanked by highly similar duplications. Twenty-four of these hot spots of genomic instability have been associated with genetic disease. Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bailey, Jeffrey A -- Gu, Zhiping -- Clark, Royden A -- Reinert, Knut -- Samonte, Rhea V -- Schwartz, Stuart -- Adams, Mark D -- Myers, Eugene W -- Li, Peter W -- Eichler, Evan E -- CA094816/CA/NCI NIH HHS/ -- GM58815/GM/NIGMS NIH HHS/ -- HG002318/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2002 Aug 9;297(5583):1003-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics, Center for Computational Genomics, and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH 44106, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12169732" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Base Sequence ; Biological Evolution ; Chromosomes, Human/genetics ; Computational Biology ; Databases, Nucleic Acid ; Exons ; Expressed Sequence Tags ; *Gene Duplication ; Gene Rearrangement ; *Genes, Duplicate ; Genetic Diseases, Inborn/genetics ; *Genome, Human ; Humans ; Models, Genetic ; Polymorphism, Single Nucleotide ; Proteome ; Recombination, Genetic ; Sequence Alignment
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2002-10-05
    Description: 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holt, Robert A -- Subramanian, G Mani -- Halpern, Aaron -- Sutton, Granger G -- Charlab, Rosane -- Nusskern, Deborah R -- Wincker, Patrick -- Clark, Andrew G -- Ribeiro, Jose M C -- Wides, Ron -- Salzberg, Steven L -- Loftus, Brendan -- Yandell, Mark -- Majoros, William H -- Rusch, Douglas B -- Lai, Zhongwu -- Kraft, Cheryl L -- Abril, Josep F -- Anthouard, Veronique -- Arensburger, Peter -- Atkinson, Peter W -- Baden, Holly -- de Berardinis, Veronique -- Baldwin, Danita -- Benes, Vladimir -- Biedler, Jim -- Blass, Claudia -- Bolanos, Randall -- Boscus, Didier -- Barnstead, Mary -- Cai, Shuang -- Center, Angela -- Chaturverdi, Kabir -- Christophides, George K -- Chrystal, Mathew A -- Clamp, Michele -- Cravchik, Anibal -- Curwen, Val -- Dana, Ali -- Delcher, Art -- Dew, Ian -- Evans, Cheryl A -- Flanigan, Michael -- Grundschober-Freimoser, Anne -- Friedli, Lisa -- Gu, Zhiping -- Guan, Ping -- Guigo, Roderic -- Hillenmeyer, Maureen E -- Hladun, Susanne L -- Hogan, James R -- Hong, Young S -- Hoover, Jeffrey -- Jaillon, Olivier -- Ke, Zhaoxi -- Kodira, Chinnappa -- Kokoza, Elena -- Koutsos, Anastasios -- Letunic, Ivica -- Levitsky, Alex -- Liang, Yong -- Lin, Jhy-Jhu -- Lobo, Neil F -- Lopez, John R -- Malek, Joel A -- McIntosh, Tina C -- Meister, Stephan -- Miller, Jason -- Mobarry, Clark -- Mongin, Emmanuel -- Murphy, Sean D -- O'Brochta, David A -- Pfannkoch, Cynthia -- Qi, Rong -- Regier, Megan A -- Remington, Karin -- Shao, Hongguang -- Sharakhova, Maria V -- Sitter, Cynthia D -- Shetty, Jyoti -- Smith, Thomas J -- Strong, Renee -- Sun, Jingtao -- Thomasova, Dana -- Ton, Lucas Q -- Topalis, Pantelis -- Tu, Zhijian -- Unger, Maria F -- Walenz, Brian -- Wang, Aihui -- Wang, Jian -- Wang, Mei -- Wang, Xuelan -- Woodford, Kerry J -- Wortman, Jennifer R -- Wu, Martin -- Yao, Alison -- Zdobnov, Evgeny M -- Zhang, Hongyu -- Zhao, Qi -- Zhao, Shaying -- Zhu, Shiaoping C -- Zhimulev, Igor -- Coluzzi, Mario -- della Torre, Alessandra -- Roth, Charles W -- Louis, Christos -- Kalush, Francis -- Mural, Richard J -- Myers, Eugene W -- Adams, Mark D -- Smith, Hamilton O -- Broder, Samuel -- Gardner, Malcolm J -- Fraser, Claire M -- Birney, Ewan -- Bork, Peer -- Brey, Paul T -- Venter, J Craig -- Weissenbach, Jean -- Kafatos, Fotis C -- Collins, Frank H -- Hoffman, Stephen L -- R01AI44273/AI/NIAID NIH HHS/ -- U01AI48846/AI/NIAID NIH HHS/ -- U01AI50687/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2002 Oct 4;298(5591):129-49.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA. robert.holt@celera.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12364791" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anopheles/classification/*genetics/parasitology/physiology ; Biological Evolution ; Blood ; Chromosome Inversion ; Chromosomes, Artificial, Bacterial ; Computational Biology ; DNA Transposable Elements ; Digestion ; Drosophila melanogaster/genetics ; Enzymes/chemistry/genetics/metabolism ; Expressed Sequence Tags ; Feeding Behavior ; Gene Expression Regulation ; *Genes, Insect ; Genetic Variation ; *Genome ; Haplotypes ; Humans ; Insect Proteins/chemistry/genetics/physiology ; Insect Vectors/genetics/parasitology/physiology ; Malaria, Falciparum/transmission ; Molecular Sequence Data ; Mosquito Control ; Physical Chromosome Mapping ; Plasmodium falciparum/growth & development ; Polymorphism, Single Nucleotide ; Proteome ; *Sequence Analysis, DNA ; Species Specificity ; Transcription Factors/chemistry/genetics/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2000-03-25
    Description: 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Adams, M D -- Celniker, S E -- Holt, R A -- Evans, C A -- Gocayne, J D -- Amanatides, P G -- Scherer, S E -- Li, P W -- Hoskins, R A -- Galle, R F -- George, R A -- Lewis, S E -- Richards, S -- Ashburner, M -- Henderson, S N -- Sutton, G G -- Wortman, J R -- Yandell, M D -- Zhang, Q -- Chen, L X -- Brandon, R C -- Rogers, Y H -- Blazej, R G -- Champe, M -- Pfeiffer, B D -- Wan, K H -- Doyle, C -- Baxter, E G -- Helt, G -- Nelson, C R -- Gabor, G L -- Abril, J F -- Agbayani, A -- An, H J -- Andrews-Pfannkoch, C -- Baldwin, D -- Ballew, R M -- Basu, A -- Baxendale, J -- Bayraktaroglu, L -- Beasley, E M -- Beeson, K Y -- Benos, P V -- Berman, B P -- Bhandari, D -- Bolshakov, S -- Borkova, D -- Botchan, M R -- Bouck, J -- Brokstein, P -- Brottier, P -- Burtis, K C -- Busam, D A -- Butler, H -- Cadieu, E -- Center, A -- Chandra, I -- Cherry, J M -- Cawley, S -- Dahlke, C -- Davenport, L B -- Davies, P -- de Pablos, B -- Delcher, A -- Deng, Z -- Mays, A D -- Dew, I -- Dietz, S M -- Dodson, K -- Doup, L E -- Downes, M -- Dugan-Rocha, S -- Dunkov, B C -- Dunn, P -- Durbin, K J -- Evangelista, C C -- Ferraz, C -- Ferriera, S -- Fleischmann, W -- Fosler, C -- Gabrielian, A E -- Garg, N S -- Gelbart, W M -- Glasser, K -- Glodek, A -- Gong, F -- Gorrell, J H -- Gu, Z -- Guan, P -- Harris, M -- Harris, N L -- Harvey, D -- Heiman, T J -- Hernandez, J R -- Houck, J -- Hostin, D -- Houston, K A -- Howland, T J -- Wei, M H -- Ibegwam, C -- Jalali, M -- Kalush, F -- Karpen, G H -- Ke, Z -- Kennison, J A -- Ketchum, K A -- Kimmel, B E -- Kodira, C D -- Kraft, C -- Kravitz, S -- Kulp, D -- Lai, Z -- Lasko, P -- Lei, Y -- Levitsky, A A -- Li, J -- Li, Z -- Liang, Y -- Lin, X -- Liu, X -- Mattei, B -- McIntosh, T C -- McLeod, M P -- McPherson, D -- Merkulov, G -- Milshina, N V -- Mobarry, C -- Morris, J -- Moshrefi, A -- Mount, S M -- Moy, M -- Murphy, B -- Murphy, L -- Muzny, D M -- Nelson, D L -- Nelson, D R -- Nelson, K A -- Nixon, K -- Nusskern, D R -- Pacleb, J M -- Palazzolo, M -- Pittman, G S -- Pan, S -- Pollard, J -- Puri, V -- Reese, M G -- Reinert, K -- Remington, K -- Saunders, R D -- Scheeler, F -- Shen, H -- Shue, B C -- Siden-Kiamos, I -- Simpson, M -- Skupski, M P -- Smith, T -- Spier, E -- Spradling, A C -- Stapleton, M -- Strong, R -- Sun, E -- Svirskas, R -- Tector, C -- Turner, R -- Venter, E -- Wang, A H -- Wang, X -- Wang, Z Y -- Wassarman, D A -- Weinstock, G M -- Weissenbach, J -- Williams, S M -- WoodageT -- Worley, K C -- Wu, D -- Yang, S -- Yao, Q A -- Ye, J -- Yeh, R F -- Zaveri, J S -- Zhan, M -- Zhang, G -- Zhao, Q -- Zheng, L -- Zheng, X H -- Zhong, F N -- Zhong, W -- Zhou, X -- Zhu, S -- Zhu, X -- Smith, H O -- Gibbs, R A -- Myers, E W -- Rubin, G M -- Venter, J C -- P50-HG00750/HG/NHGRI NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2000 Mar 24;287(5461):2185-95.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10731132" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biological Transport/genetics ; Chromatin/genetics ; Cloning, Molecular ; Computational Biology ; Contig Mapping ; Cytochrome P-450 Enzyme System/genetics ; DNA Repair/genetics ; DNA Replication/genetics ; Drosophila melanogaster/*genetics/metabolism ; Euchromatin ; Gene Library ; Genes, Insect ; *Genome ; Heterochromatin/genetics ; Insect Proteins/chemistry/genetics/physiology ; Nuclear Proteins/genetics ; Protein Biosynthesis ; *Sequence Analysis, DNA ; Transcription, Genetic
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2002-06-01
    Description: The high degree of similarity between the mouse and human genomes is demonstrated through analysis of the sequence of mouse chromosome 16 (Mmu 16), which was obtained as part of a whole-genome shotgun assembly of the mouse genome. The mouse genome is about 10% smaller than the human genome, owing to a lower repetitive DNA content. Comparison of the structure and protein-coding potential of Mmu 16 with that of the homologous segments of the human genome identifies regions of conserved synteny with human chromosomes (Hsa) 3, 8, 12, 16, 21, and 22. Gene content and order are highly conserved between Mmu 16 and the syntenic blocks of the human genome. Of the 731 predicted genes on Mmu 16, 509 align with orthologs on the corresponding portions of the human genome, 44 are likely paralogous to these genes, and 164 genes have homologs elsewhere in the human genome; there are 14 genes for which we could find no human counterpart.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mural, Richard J -- Adams, Mark D -- Myers, Eugene W -- Smith, Hamilton O -- Miklos, George L Gabor -- Wides, Ron -- Halpern, Aaron -- Li, Peter W -- Sutton, Granger G -- Nadeau, Joe -- Salzberg, Steven L -- Holt, Robert A -- Kodira, Chinnappa D -- Lu, Fu -- Chen, Lin -- Deng, Zuoming -- Evangelista, Carlos C -- Gan, Weiniu -- Heiman, Thomas J -- Li, Jiayin -- Li, Zhenya -- Merkulov, Gennady V -- Milshina, Natalia V -- Naik, Ashwinikumar K -- Qi, Rong -- Shue, Bixiong Chris -- Wang, Aihui -- Wang, Jian -- Wang, Xin -- Yan, Xianghe -- Ye, Jane -- Yooseph, Shibu -- Zhao, Qi -- Zheng, Liansheng -- Zhu, Shiaoping C -- Biddick, Kendra -- Bolanos, Randall -- Delcher, Arthur L -- Dew, Ian M -- Fasulo, Daniel -- Flanigan, Michael J -- Huson, Daniel H -- Kravitz, Saul A -- Miller, Jason R -- Mobarry, Clark M -- Reinert, Knut -- Remington, Karin A -- Zhang, Qing -- Zheng, Xiangqun H -- Nusskern, Deborah R -- Lai, Zhongwu -- Lei, Yiding -- Zhong, Wenyan -- Yao, Alison -- Guan, Ping -- Ji, Rui-Ru -- Gu, Zhiping -- Wang, Zhen-Yuan -- Zhong, Fei -- Xiao, Chunlin -- Chiang, Chia-Chien -- Yandell, Mark -- Wortman, Jennifer R -- Amanatides, Peter G -- Hladun, Suzanne L -- Pratts, Eric C -- Johnson, Jeffery E -- Dodson, Kristina L -- Woodford, Kerry J -- Evans, Cheryl A -- Gropman, Barry -- Rusch, Douglas B -- Venter, Eli -- Wang, Mei -- Smith, Thomas J -- Houck, Jarrett T -- Tompkins, Donald E -- Haynes, Charles -- Jacob, Debbie -- Chin, Soo H -- Allen, David R -- Dahlke, Carl E -- Sanders, Robert -- Li, Kelvin -- Liu, Xiangjun -- Levitsky, Alexander A -- Majoros, William H -- Chen, Quan -- Xia, Ashley C -- Lopez, John R -- Donnelly, Michael T -- Newman, Matthew H -- Glodek, Anna -- Kraft, Cheryl L -- Nodell, Marc -- Ali, Feroze -- An, Hui-Jin -- Baldwin-Pitts, Danita -- Beeson, Karen Y -- Cai, Shuang -- Carnes, Mark -- Carver, Amy -- Caulk, Parris M -- Center, Angela -- Chen, Yen-Hui -- Cheng, Ming-Lai -- Coyne, My D -- Crowder, Michelle -- Danaher, Steven -- Davenport, Lionel B -- Desilets, Raymond -- Dietz, Susanne M -- Doup, Lisa -- Dullaghan, Patrick -- Ferriera, Steven -- Fosler, Carl R -- Gire, Harold C -- Gluecksmann, Andres -- Gocayne, Jeannine D -- Gray, Jonathan -- Hart, Brit -- Haynes, Jason -- Hoover, Jeffery -- Howland, Tim -- Ibegwam, Chinyere -- Jalali, Mena -- Johns, David -- Kline, Leslie -- Ma, Daniel S -- MacCawley, Steven -- Magoon, Anand -- Mann, Felecia -- May, David -- McIntosh, Tina C -- Mehta, Somil -- Moy, Linda -- Moy, Mee C -- Murphy, Brian J -- Murphy, Sean D -- Nelson, Keith A -- Nuri, Zubeda -- Parker, Kimberly A -- Prudhomme, Alexandre C -- Puri, Vinita N -- Qureshi, Hina -- Raley, John C -- Reardon, Matthew S -- Regier, Megan A -- Rogers, Yu-Hui C -- Romblad, Deanna L -- Schutz, Jakob -- Scott, John L -- Scott, Richard -- Sitter, Cynthia D -- Smallwood, Michella -- Sprague, Arlan C -- Stewart, Erin -- Strong, Renee V -- Suh, Ellen -- Sylvester, Karena -- Thomas, Reginald -- Tint, Ni Ni -- Tsonis, Christopher -- Wang, Gary -- Wang, George -- Williams, Monica S -- Williams, Sherita M -- Windsor, Sandra M -- Wolfe, Keriellen -- Wu, Mitchell M -- Zaveri, Jayshree -- Chaturvedi, Kabir -- Gabrielian, Andrei E -- Ke, Zhaoxi -- Sun, Jingtao -- Subramanian, Gangadharan -- Venter, J Craig -- Pfannkoch, Cynthia M -- Barnstead, Mary -- Stephenson, Lisa D -- New York, N.Y. -- Science. 2002 May 31;296(5573):1661-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Celera Genomics, 45 West Gude Drive, Rockville, MD 20850, USA. richard.mural@celera.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12040188" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Chromosomes/*genetics ; Chromosomes, Human/genetics ; Computational Biology ; Conserved Sequence ; Databases, Nucleic Acid ; Evolution, Molecular ; Genes ; Genetic Markers ; *Genome ; *Genome, Human ; Genomics ; Humans ; Mice ; Mice, Inbred A/genetics ; Mice, Inbred DBA/genetics ; Mice, Inbred Strains/*genetics ; Molecular Sequence Data ; Physical Chromosome Mapping ; Proteins/chemistry/genetics ; Sequence Alignment ; *Sequence Analysis, DNA ; Species Specificity ; *Synteny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2000-03-24
    Description: We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly's sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Myers, E W -- Sutton, G G -- Delcher, A L -- Dew, I M -- Fasulo, D P -- Flanigan, M J -- Kravitz, S A -- Mobarry, C M -- Reinert, K H -- Remington, K A -- Anson, E L -- Bolanos, R A -- Chou, H H -- Jordan, C M -- Halpern, A L -- Lonardi, S -- Beasley, E M -- Brandon, R C -- Chen, L -- Dunn, P J -- Lai, Z -- Liang, Y -- Nusskern, D R -- Zhan, M -- Zhang, Q -- Zheng, X -- Rubin, G M -- Adams, M D -- Venter, J C -- New York, N.Y. -- Science. 2000 Mar 24;287(5461):2196-204.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Celera Genomics, Inc., 45 West Gude Drive, Rockville, MD 20850, USA. Gene.Myers@celera.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10731133" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Animals ; Chromatin/genetics ; *Computational Biology ; Contig Mapping ; Drosophila melanogaster/*genetics ; Euchromatin ; Genes, Insect ; *Genome ; Heterochromatin/genetics ; Molecular Sequence Data ; Physical Chromosome Mapping ; Repetitive Sequences, Nucleic Acid ; *Sequence Analysis, DNA ; Sequence Tagged Sites
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2013-01-31
    Description: Motivation: Optical flow is a key method used for quantitative motion estimation of biological structures in light microscopy. It has also been used as a key module in segmentation and tracking systems and is considered a mature technology in the field of computer vision. However, most of the research focused on 2D natural images, which are small in size and rich in edges and texture information. In contrast, 3D time-lapse recordings of biological specimens comprise up to several terabytes of image data and often exhibit complex object dynamics as well as blurring due to the point-spread-function of the microscope. Thus, new approaches to optical flow are required to improve performance for such data. Results: We solve optical flow in large 3D time-lapse microscopy datasets by defining a Markov random field (MRF) over super-voxels in the foreground and applying motion smoothness constraints between super-voxels instead of voxel-wise. This model is tailored to the specific characteristics of light microscopy datasets: super-voxels help registration in textureless areas, the MRF over super-voxels efficiently propagates motion information between neighboring cells and the background subtraction and super-voxels reduce the dimensionality of the problem by an order of magnitude. We validate our approach on large 3D time-lapse datasets of Drosophila and zebrafish development by analyzing cell motion patterns. We show that our approach is, on average, 10 x faster than commonly used optical flow implementations in the Insight Tool-Kit (ITK) and reduces the average flow end point error by 50% in regions with complex dynamic processes, such as cell divisions. Availability: Source code freely available in the Software section at http://janelia.org/lab/keller-lab . Contact: amatf@janelia.hhmi.org or kellerp@janelia.hhmi.org Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 8
    Publication Date: 2005-06-01
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 9
    Publication Date: 2010-06-06
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 10
    Publication Date: 2006-07-15
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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