TY - Generic T1 - Draft Genome Sequences from a Novel Clade of Bacillus cereus sensu lato Strains Isolated from the International Space Station Y1 - 2017 A1 - Kasthuri Venkateswaran A1 - Aleksandra Checinska-Sielaff A1 - Joy Klubnik A1 - Todd Treangen A1 - M.J. Rosovitz A1 - Nicholas H. Bergman JA - Genome Announcements VL - 1 ER - TY - JOUR T1 - The fruRBA operon is necessary for Group A Streptococcal growth in fructose and for resistance to neutrophil killing during growth in whole human blood. JF - Infect Immun Y1 - 2016 A1 - Valdes, Kayla M A1 - Sundar, Ganesh S A1 - Vega, Luis A A1 - Belew, Ashton T A1 - Islam, Emrul A1 - Binet, Rachel A1 - El-Sayed, Najib M A1 - Le Breton, Yoann A1 - McIver, Kevin S AB -

Bacterial pathogens rely on the availability of nutrients for survival in the host environment. The phosphoenolpyruvate-phosphotransferase system (PTS) is a global regulatory network connecting sugar uptake with signal transduction. Since the fructose PTS has been shown to impact virulence in several Streptococci, including the human pathogen S. pyogenes (the group A Streptococcus, GAS), we characterized its role in carbon metabolism and pathogenesis in the M1T1 strain 5448. Growth in fructose as a sole carbon source resulted in 103 genes affected transcriptionally, where the fru locus (fruRBA) was the most induced. RT-PCR showed that fruRBA formed an operon, which was repressed by FruR in the absence of fructose, in addition to being under carbon catabolic repression. Growth assays and carbon utilization profiles revealed that although the entire fru operon was required for growth in fructose, FruA was the main transporter for fructose and was also involved in the utilization of three additional PTS sugars: cellobiose, mannitol, and N-acetyl-D-galactosamine. Inactivation of sloR, a fruA homolog that was also up regulated in presence of fructose, failed to reveal a role as a secondary fructose transporter. Whereas the ability of both ΔfruR and ΔfruB mutants to survive in the presence of whole human blood or neutrophils was impaired, the phenotype was not reproduced in murine whole blood, nor were those mutants attenuated in a mouse intraperitoneal infection. Since the ΔfruA mutant exhibited no phenotype in the human or mouse assays, we propose that FruR and FruB are important for GAS survival in a human-specific environment.

M3 - 10.1128/IAI.01296-15 ER - TY - JOUR T1 - Identification guide to the heterobranch sea slugs (Mollusca: Gastropoda) from Bocas del Toro, Panama JF - Marine Biodiversity Records Y1 - 2016 A1 - Goodheart, Jessica A1 - Ellingson, Ryan A. A1 - Vital, Xochitl G. A1 - ão Filho, Hilton C. A1 - McCarthy, Jennifer B. A1 - Medrano, Sabrina M. A1 - Bhave, Vishal J. A1 - ía-Méndez, Kimberly A1 - énez, Lina M. A1 - ópez, Gina A1 - Hoover, Craig A. A1 - Awbrey, Jaymes D. A1 - De Jesus, Jessika M. A1 - Gowacki, William A1 - Krug, Patrick J. A1 - és, Ángel VL - 96737453830254034557880541418411912544728739317415779780725696418782226404216145163412560451520488424050829677 UR - http://mbr.biomedcentral.com/articles/10.1186/s41200-016-0048-zhttp://link.springer.com/content/pdf/10.1186/s41200-016-0048-z CP - 12343–4 J1 - Mar Biodivers Rec M3 - 10.1186/s41200-016-0048-z ER - TY - JOUR T1 - The fruRBA Operon Is Necessary for Group A Streptococcal Growth in Fructose and for Resistance to Neutrophil Killing during Growth in Whole Human Blood JF - Infection and Immunity Y1 - 2016 A1 - Valdes, Kayla M. A1 - Sundar, Ganesh S. A1 - Vega, Luis A. A1 - Belew, Ashton T. A1 - Islam, Emrul A1 - Binet, Rachel A1 - El-Sayed, Najib M. A1 - Le Breton, Yoann A1 - McIver, Kevin S. ED - Camilli, A. VL - 84 UR - http://iai.asm.org/lookup/doi/10.1128/IAI.01296-15 CP - 4 J1 - Infect. Immun. M3 - 10.1128/IAI.01296-15 ER - TY - JOUR T1 - Therapeutic relevance of the protein phosphatase 2A in cancer JF - Oncotarget.com Y1 - 2016 A1 - Cunningham, Chelsea E. A1 - Li, Shuangshuang A1 - Vizeacoumar, Frederick S. A1 - Bhanumathy, Kalpana Kalyanasundaram A1 - Lee, Joo Sang A1 - Parameswaran, Sreejit A1 - Furber, Levi A1 - Abuhussein, Omar A1 - Paul, James M. A1 - McDonald, Megan A1 - Templeton, Shaina D. A1 - Shukla, Hersh A1 - El Zawily, Amr M. A1 - Boyd, Frederick A1 - Alli, Nezeka A1 - Mousseau, Darrell D. A1 - Geyer, Ron A1 - Bonham, Keith A1 - Anderson, Deborah H. A1 - Yan, Jiong A1 - Yu-Lee, Li-Yuan A1 - Weaver, Beth A. A1 - Uppalapati, Maruti A1 - Ruppin, Eytan A1 - Sablina, Anna A1 - Freywald, Andrew A1 - Vizeacoumar, Franco J. UR - https://www.oncotarget.com/article/11399 J1 - Oncotarget M3 - 10.18632/oncotarget.11399 ER - TY - JOUR T1 - Essential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes. JF - Sci Rep Y1 - 2015 A1 - Le Breton, Yoann A1 - Belew, Ashton T A1 - Valdes, Kayla M A1 - Islam, Emrul A1 - Curry, Patrick A1 - Tettelin, Hervé A1 - Shirtliff, Mark E A1 - El-Sayed, Najib M A1 - McIver, Kevin S AB -

Streptococcus pyogenes (Group A Streptococcus, GAS) remains a major public health burden worldwide, infecting over 750 million people leading to over 500,000 deaths annually. GAS pathogenesis is complex, involving genetically distinct GAS strains and multiple infection sites. To overcome fastidious genetic manipulations and accelerate pathogenesis investigations in GAS, we developed a mariner-based system (Krmit) for en masse monitoring of complex mutant pools by transposon sequencing (Tn-seq). Highly saturated transposant libraries (Krmit insertions in ca. every 25 nucleotides) were generated in two distinct GAS clinical isolates, a serotype M1T1 invasive strain 5448 and a nephritogenic serotype M49 strain NZ131, and analyzed using a Bayesian statistical model to predict GAS essential genes, identifying sets of 227 and 241 of those genes in 5448 and NZ131, respectively. A large proportion of GAS essential genes corresponded to key cellular processes and metabolic pathways, and 177 were found conserved within the GAS core genome established from 20 available GAS genomes. Selected essential genes were validated using conditional-expression mutants. Finally, comparison to previous essentiality analyses in S. sanguinis and S. pneumoniae revealed significant overlaps, providing valuable insights for the development of new antimicrobials to treat infections by GAS and other pathogenic streptococci.

VL - 5 M3 - 10.1038/srep09838 ER - TY - JOUR T1 - A molecular phylogeny for the oldest (nonditrysian) lineages of extant Lepidoptera, with implications for classification, comparative morphology and life-history evolution JF - Systematic Entomology Y1 - 2015 A1 - Regier, Jerome C A1 - Mitter, Charles A1 - KRISTENSEN, NIELS P. A1 - Davis, Donald R. A1 - VAN NIEUKERKEN, ERIK J. A1 - ROTA, JADRANKA A1 - Simonsen, Thomas J. A1 - Mitter, Kim T. A1 - Kawahara, Akito Y. A1 - Yen, Shen-Horn A1 - Michael P. Cummings A1 - Zwick, Andreas M3 - 10.1111/syen.12129 ER - TY - JOUR T1 - Systematics and biogeography of Pleurobranchus  Cuvier, 1804, sea slugs (Heterobranchia: Nudipleura: Pleurobranchidae) JF - Zoological Journal of the Linnean Society Y1 - 2015 A1 - Goodheart, Jessica A1 - Camacho-García, Yolanda A1 - Padula, Vinicius A1 - Schrödl, Michael A1 - Cervera, Juan L. A1 - Gosliner, Terrence M. A1 - Valdés, Ángel AB - Species of Pleurobranchus (Mollusca: Gastropoda: Heterobranchia: Nudipleura: Pleurobranchidae) are commonly found worldwide, but there is a substantial amount of confusion regarding the ranges and identification of individual species. Difficulties in phylogenetic reconstruction and identification of pleurobranchids using morphological traits has resulted in complex classification schemes, with several species having disjunct ranges across physical and biogeographical barriers (including the tropical Indo-Pacific, the eastern Pacific, and the Atlantic). A sizeable number of species of Pleurobranchus has been described; however, many of these species are morphologically and biogeographically similar to others, and probably constitute synonyms. This paper provides a phylogenetic framework of classification for Pleurobranchus based on the mitochondrial genes cytochrome c oxidase I (COI) and 16S rDNA and the nuclear gene histone 3 (H3) using Bayesian and maximum likelihood approaches. Molecular phylogenies obtained recovered most of the well-established species of Pleurobranchus and some morphological characters were found to have taxonomic value for delimiting species in this group. Automatic barcode gap discovery (ABGD) analyses substantiated the distinctiveness of units/species recovered in the phylogenetic analyses, with some exceptions. Morphological descriptions for the 14 species recovered in the molecular phylogeny and discussions on the biogeography and colour variation are included. UR - http://doi.wiley.com/10.1111/zoj.12237 J1 - Zool J Linn Soc M3 - 10.1111/zoj.12237 ER - TY - JOUR T1 - A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration. JF - Mol Syst Biol Y1 - 2014 A1 - Yizhak, Keren A1 - Le Dévédec, Sylvia E A1 - Rogkoti, Vasiliki Maria A1 - Baenke, Franziska A1 - de Boer, Vincent C A1 - Frezza, Christian A1 - Schulze, Almut A1 - van de Water, Bob A1 - Ruppin, Eytan AB -

Over the last decade, the field of cancer metabolism has mainly focused on studying the role of tumorigenic metabolic rewiring in supporting cancer proliferation. Here, we perform the first genome‐scale computational study of the metabolic underpinnings of cancer migration. We build genome‐scale metabolic models of the NCI‐60 cell lines that capture the Warburg effect (aerobic glycolysis) typically occurring in cancer cells. The extent of the Warburg effect in each of these cell line models is quantified by the ratio of glycolytic to oxidative ATP flux (AFR), which is found to be highly positively associated with cancer cell migration. We hence predicted that targeting genes that mitigate the Warburg effect by reducing the AFR may specifically inhibit cancer migration. By testing the anti‐migratory effects of silencing such 17 top predicted genes in four breast and lung cancer cell lines, we find that up to 13 of these novel predictions significantly attenuate cell migration either in all or one cell line only, while having almost no effect on cell proliferation. Furthermore, in accordance with the predictions, a significant reduction is observed in the ratio between experimentally measured ECAR and OCR levels following these perturbations. Inhibiting anti‐migratory targets is a promising future avenue in treating cancer since it may decrease cytotoxic‐related side effects that plague current anti‐proliferative treatments. Furthermore, it may reduce cytotoxic‐related clonal selection of more aggressive cancer cells and the likelihood of emerging resistance.

VL - 10 M3 - 10.15252/msb.20145746 ER - TY - JOUR T1 - CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation JF - Nucleic Acids ResNucleic Acids ResNucleic Acids Res Y1 - 2014 A1 - Plasschaert, R. N. A1 - Vigneau, S. A1 - Tempera, I. A1 - Gupta, R. A1 - Maksimoska, J. A1 - Everett, L. A1 - Davuluri, R. A1 - Mamorstein, R. A1 - Lieberman, P. M. A1 - Schultz, D. A1 - Sridhar Hannenhalli A1 - Bartolomei, M. S. KW - *Gene Expression Regulation KW - *Regulatory Elements, Transcriptional KW - Animals KW - Binding Sites KW - Cell Differentiation/*genetics KW - Cells, Cultured KW - Embryonic Stem Cells/cytology/*metabolism KW - Mice KW - Nucleotide Motifs KW - Protein Binding KW - Repressor Proteins/*metabolism AB - CTCF (CCCTC-binding factor) is a highly conserved multifunctional DNA-binding protein with thousands of binding sites genome-wide. Our previous work suggested that differences in CTCF's binding site sequence may affect the regulation of CTCF recruitment and its function. To investigate this possibility, we characterized changes in genome-wide CTCF binding and gene expression during differentiation of mouse embryonic stem cells. After separating CTCF sites into three classes (LowOc, MedOc and HighOc) based on similarity to the consensus motif, we found that developmentally regulated CTCF binding occurs preferentially at LowOc sites, which have lower similarity to the consensus. By measuring the affinity of CTCF for selected sites, we show that sites lost during differentiation are enriched in motifs associated with weaker CTCF binding in vitro. Specifically, enrichment for T at the 18(th) position of the CTCF binding site is associated with regulated binding in the LowOc class and can predictably reduce CTCF affinity for binding sites. Finally, by comparing changes in CTCF binding with changes in gene expression during differentiation, we show that LowOc and HighOc sites are associated with distinct regulatory functions. Our results suggest that the regulatory control of CTCF is dependent in part on specific motifs within its binding site. VL - 42 SN - 1362-4962 (Electronic)
0305-1048 (Linking) N1 - Plasschaert, Robert N
Vigneau, Sebastien
Tempera, Italo
Gupta, Ravi
Maksimoska, Jasna
Everett, Logan
Davuluri, Ramana
Mamorstein, Ronen
Lieberman, Paul M
Schultz, David
Hannenhalli, Sridhar
Bartolomei, Marisa S
eng
K99AI099153/AI/NIAID NIH HHS/
P30 CA10815/CA/NCI NIH HHS/
R01 CA140652/CA/NCI NIH HHS/
R01-GM052880/GM/NIGMS NIH HHS/
R01CA140652/CA/NCI NIH HHS/
R01GM085226/GM/NIGMS NIH HHS/
R01HD042026/HD/NICHD NIH HHS/
T32GM008216/GM/NIGMS NIH HHS/
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
England
2013/10/15 06:00
Nucleic Acids Res. 2014 Jan;42(2):774-89. doi: 10.1093/nar/gkt910. Epub 2013 Oct 10. U2 - 3902912 J1 - Nucleic acids researchNucleic acids research ER - TY - JOUR T1 - Phenotype-based cell-specific metabolic modeling reveals metabolic liabilities of cancer. JF - Elife Y1 - 2014 A1 - Yizhak, Keren A1 - Gaude, Edoardo A1 - Le Dévédec, Sylvia A1 - Waldman, Yedael Y A1 - Stein, Gideon Y A1 - van de Water, Bob A1 - Frezza, Christian A1 - Ruppin, Eytan KW - algorithms KW - Antineoplastic Agents KW - Biomarkers, Tumor KW - Carboxy-Lyases KW - Cell Line, Tumor KW - Cell Proliferation KW - Citric Acid Cycle KW - Fatty Acids KW - Gene Knockdown Techniques KW - Genome, Human KW - HUMANS KW - Lymphocytes KW - Models, Biological KW - Neoplasms KW - Oxidation-Reduction KW - PHENOTYPE KW - Precision Medicine AB -

Utilizing molecular data to derive functional physiological models tailored for specific cancer cells can facilitate the use of individually tailored therapies. To this end we present an approach termed PRIME for generating cell-specific genome-scale metabolic models (GSMMs) based on molecular and phenotypic data. We build >280 models of normal and cancer cell-lines that successfully predict metabolic phenotypes in an individual manner. We utilize this set of cell-specific models to predict drug targets that selectively inhibit cancerous but not normal cell proliferation. The top predicted target, MLYCD, is experimentally validated and the metabolic effects of MLYCD depletion investigated. Furthermore, we tested cell-specific predicted responses to the inhibition of metabolic enzymes, and successfully inferred the prognosis of cancer patients based on their PRIME-derived individual GSMMs. These results lay a computational basis and a counterpart experimental proof of concept for future personalized metabolic modeling applications, enhancing the search for novel selective anticancer therapies.

VL - 3 M3 - 10.7554/eLife.03641 ER - TY - JOUR T1 - Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding JF - BMC Genomics Y1 - 2013 A1 - He, Ximiao A1 - Chatterjee, Raghunath A1 - John, Sam A1 - Bravo, Hector A1 - Sathyanarayana, B K A1 - Biddie, Simon C A1 - FitzGerald, Peter C A1 - Stamatoyannopoulos, John A A1 - Hager, Gordon L A1 - Vinson, Charles VL - 14 UR - http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-428 CP - 1 J1 - BMC GenomicsBMC Genomics M3 - 10.1186/1471-2164-14-428 ER - TY - JOUR T1 - Genome sequencing of four strains of Rickettsia prowazekii, the causative agent of epidemic typhus, including one flying squirrel isolate JF - Genome announcementsGenome announcements Y1 - 2013 A1 - Bishop-Lilly, Kimberly A. A1 - Ge, Hong A1 - Butani, Amy A1 - Osborne, Brian A1 - Verratti, Kathleen A1 - Mokashi, Vishwesh A1 - Nagarajan, Niranjan A1 - M. Pop A1 - Read, Timothy D. A1 - Richards, Allen L. PB - American Society for Microbiology VL - 1 SN - 2169-8287 ER - TY - JOUR T1 - Re-evaluation of the Doriopsilla areolata Bergh, 1880 (Mollusca: Opisthobranchia) subspecies complex in the eastern Atlantic Ocean and its relationship to South African Doriopsilla miniata (Alder & Hancock, 1864) based on molecular data JF - Marine Biodiversity Y1 - 2013 A1 - Goodheart, Jessica A1 - Valdés, Ángel VL - 43 UR - http://link.springer.com/10.1007/s12526-012-0136-1http://link.springer.com/content/pdf/10.1007/s12526-012-0136-1 CP - 2 J1 - Mar Biodiv M3 - 10.1007/s12526-012-0136-1 ER - TY - JOUR T1 - Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage. JF - ISME J Y1 - 2012 A1 - Dupont, Chris L A1 - Rusch, Douglas B A1 - Yooseph, Shibu A1 - Lombardo, Mary-Jane A1 - Richter, R Alexander A1 - Valas, Ruben A1 - Novotny, Mark A1 - Yee-Greenbaum, Joyclyn A1 - Selengut, Jeremy D A1 - Haft, Dan H A1 - Halpern, Aaron L A1 - Lasken, Roger S A1 - Nealson, Kenneth A1 - Friedman, Robert A1 - Venter, J Craig KW - Computational Biology KW - Gammaproteobacteria KW - Genome, Bacterial KW - Genomic Library KW - metagenomics KW - Oceans and Seas KW - Phylogeny KW - plankton KW - Rhodopsin KW - Rhodopsins, Microbial KW - RNA, Ribosomal, 16S KW - Seawater AB -

Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition.

VL - 6 CP - 6 M3 - 10.1038/ismej.2011.189 ER - TY - JOUR T1 - Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage JF - The ISME journalThe ISME journal Y1 - 2012 A1 - Dupont, Chris L. A1 - Rusch, Douglas B. A1 - Yooseph, Shibu A1 - Lombardo, Mary-Jane A1 - Richter, R. Alexander A1 - Valas, Ruben A1 - Novotny, Mark A1 - Yee-Greenbaum, Joyclyn A1 - J. Selengut A1 - Haft, Dan H. A1 - Halpern, Aaron L. A1 - Lasken, Roger S. A1 - Nealson, Kenneth A1 - Friedman, Robert A1 - Venter, J. Craig KW - Computational Biology KW - Gammaproteobacteria KW - Genome, Bacterial KW - Genomic Library KW - metagenomics KW - Oceans and Seas KW - Phylogeny KW - plankton KW - Rhodopsin KW - RNA, Ribosomal, 16S KW - Seawater AB - Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition. VL - 6 N1 - http://www.ncbi.nlm.nih.gov/pubmed/22170421?dopt=Abstract ER - TY - JOUR T1 - Identification of Coli Surface Antigen 23, a Novel Adhesin of Enterotoxigenic Escherichia coli JF - Infection and immunityInfection and immunity Y1 - 2012 A1 - Del Canto, F. A1 - Botkin, D. J. A1 - Valenzuela, P. A1 - Popov, V. A1 - Ruiz-Perez, F. A1 - Nataro, J. P. A1 - Levine, M. M. A1 - Stine, O. C. A1 - M. Pop A1 - Torres, A. G. A1 - others, PB - American Society for Microbiology VL - 80 ER - TY - JOUR T1 - MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space JF - Systematic Biology Y1 - 2012 A1 - F. Ronquist A1 - Teslenko, M. A1 - van der Mark, P. A1 - Ayres, D. L. A1 - Darling, A. A1 - Hohna, S. A1 - B. Larget A1 - Liu, L. A1 - Suchard, M. A. A1 - J. P. Huelsenbeck VL - 61 M3 - 10.1093/sysbio/sys029 ER - TY - JOUR T1 - Speeding Up Particle Trajectory Simulations under Moving Force Fields using GPUs JF - Journal of Computing and Information Science in EngineeringJournal of Computing and Information Science in Engineering Y1 - 2012 A1 - Patro, R. A1 - Dickerson, J. P. A1 - Bista, S. A1 - Gupta, S. K. A1 - Varshney, Amitabh AB - In this paper, we introduce a GPU-based framework forsimulating particle trajectories under both static and dynamic force fields. By exploiting the highly parallel nature of the problem and making efficient use of the available hardware, our simulator exhibits a significant speedup over its CPU- based analog. We apply our framework to a specific experi- mental simulation: the computation of trapping probabilities associated with micron-sized silica beads in optical trapping workbenches. When evaluating large numbers of trajectories (4096), we see approximately a 356 times speedup of the GPU-based simulator over its CPU-based counterpart. ER - TY - JOUR T1 - Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity JF - PLoS neglected tropical diseasesPLoS neglected tropical diseases Y1 - 2012 A1 - Ricaldi, Jessica N. A1 - Fouts, Derrick E. A1 - J. Selengut A1 - Harkins, Derek M. A1 - Patra, Kailash P. A1 - Moreno, Angelo A1 - Lehmann, Jason S. A1 - Purushe, Janaki A1 - Sanka, Ravi A1 - Torres, Michael A1 - Webster, Nicholas J. A1 - Vinetz, Joseph M. A1 - Matthias, Michael A. KW - DNA, Bacterial KW - Evolution, Molecular KW - Gene Transfer, Horizontal KW - Genome, Bacterial KW - Genomic islands KW - HUMANS KW - Leptospira KW - Molecular Sequence Data KW - Multigene Family KW - Prophages KW - Sequence Analysis, DNA KW - Virulence factors AB - The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T) and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics. VL - 6 N1 - http://www.ncbi.nlm.nih.gov/pubmed/23145189?dopt=Abstract ER - TY - JOUR T1 - Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. JF - PLoS Negl Trop Dis Y1 - 2012 A1 - Ricaldi, Jessica N A1 - Fouts, Derrick E A1 - Selengut, Jeremy D A1 - Harkins, Derek M A1 - Patra, Kailash P A1 - Moreno, Angelo A1 - Lehmann, Jason S A1 - Purushe, Janaki A1 - Sanka, Ravi A1 - Torres, Michael A1 - Webster, Nicholas J A1 - Vinetz, Joseph M A1 - Matthias, Michael A KW - DNA, Bacterial KW - Evolution, Molecular KW - Gene Transfer, Horizontal KW - Genome, Bacterial KW - Genomic islands KW - HUMANS KW - Leptospira KW - Molecular Sequence Data KW - Multigene Family KW - Prophages KW - Sequence Analysis, DNA KW - Virulence factors AB -

The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835) provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae) that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T) and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT). Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for its infectiousness and its unique antigenic characteristics.

VL - 6 CP - 10 M3 - 10.1371/journal.pntd.0001853 ER - TY - JOUR T1 - Genome-Wide Survey of Natural Selection on Functional, Structural, and Network Properties of Polymorphic Sites in Saccharomyces Paradoxus JF - Molecular Biology and EvolutionMol Biol EvolMolecular Biology and EvolutionMol Biol Evol Y1 - 2011 A1 - Vishnoi, Anchal A1 - Sethupathy, Praveen A1 - Simola, Daniel A1 - Plotkin, Joshua B. A1 - Sridhar Hannenhalli KW - derived allele frequency KW - Evolution KW - natural selection KW - yeast AB - Background. To characterize the genetic basis of phenotypic evolution, numerous studies have identified individual genes that have likely evolved under natural selection. However, phenotypic changes may represent the cumulative effect of similar evolutionary forces acting on functionally related groups of genes. Phylogenetic analyses of divergent yeast species have identified functional groups of genes that have evolved at significantly different rates, suggestive of differential selection on the functional properties. However, due to environmental heterogeneity over long evolutionary timescales, selection operating within a single lineage may be dramatically different, and it is not detectable via interspecific comparisons alone. Moreover, interspecific studies typically quantify selection on protein-coding regions using the Dn/Ds ratio, which cannot be extended easily to study selection on noncoding regions or synonymous sites. The population genetic-based analysis of selection operating within a single lineage ameliorates these limitations. Findings. We investigated selection on several properties associated with genes, promoters, or polymorphic sites, by analyzing the derived allele frequency spectrum of single nucleotide polymorphisms (SNPs) in 28 strains of Saccharomyces paradoxus. We found evidence for significant differential selection between many functionally relevant categories of SNPs, underscoring the utility of function-centric approaches for discovering signatures of natural selection. When comparable, our findings are largely consistent with previous studies based on interspecific comparisons, with one notable exception: our study finds that mutations from an ancient amino acid to a relatively new amino acid are selectively disfavored, whereas interspecific comparisons have found selection against ancient amino acids. Several of our findings have not been addressed through prior interspecific studies: we find that synonymous mutations from preferred to unpreferred codons are selected against and that synonymous SNPs in the linker regions of proteins are relatively less constrained than those within protein domains. Conclusions. We present the first global survey of selection acting on various functional properties in S. paradoxus. We found that selection pressures previously detected over long evolutionary timescales have also shaped the evolution of S. paradoxus. Importantly, we also make novel discoveries untenable via conventional interspecific analyses. VL - 28 SN - 0737-4038, 1537-1719 ER - TY - JOUR T1 - Long-term effects of ocean warming on the prokaryotic community: evidence from the vibrios JF - The ISME JournalThe ISME journal Y1 - 2011 A1 - Vezzulli, Luigi A1 - Brettar, Ingrid A1 - Pezzati, Elisabetta A1 - Reid, Philip C. A1 - Rita R. Colwell A1 - Höfle, Manfred G. A1 - Pruzzo, Carla KW - ecophysiology KW - ecosystems KW - environmental biotechnology KW - geomicrobiology KW - ISME J KW - microbe interactions KW - microbial communities KW - microbial ecology KW - microbial engineering KW - microbial epidemiology KW - microbial genomics KW - microorganisms AB - The long-term effects of ocean warming on prokaryotic communities are unknown because of lack of historical data. We overcame this gap by applying a retrospective molecular analysis to the bacterial community on formalin-fixed samples from the historical Continuous Plankton Recorder archive, which is one of the longest and most geographically extensive collections of marine biological samples in the world. We showed that during the last half century, ubiquitous marine bacteria of the Vibrio genus, including Vibrio cholerae, increased in dominance within the plankton-associated bacterial community of the North Sea, where an unprecedented increase in bathing infections related to these bacteria was recently reported. Among environmental variables, increased sea surface temperature explained 45% of the variance in Vibrio data, supporting the view that ocean warming is favouring the spread of vibrios and may be the cause of the globally increasing trend in their associated diseases. VL - 6 SN - 1751-7362 ER - TY - Generic T1 - MDMap: A system for data-driven layout and exploration of molecular dynamics simulations T2 - Biological Data Visualization (BioVis), 2011 IEEE Symposium on Y1 - 2011 A1 - Patro, R. A1 - Ip, Cheuk Yiu A1 - Bista, S. A1 - Cho, S. S. A1 - Thirumalai, D. A1 - Varshney, Amitabh KW - Biology KW - biomolecular KW - computing KW - data KW - digital KW - driven KW - DYNAMICS KW - exploration KW - folding KW - graph KW - landscapes KW - Layout KW - MDMap KW - method KW - molecular KW - processes KW - simulation KW - Simulations KW - space KW - state KW - Stochastic KW - THEORY KW - time-varying KW - Trajectory KW - transition AB - Contemporary molecular dynamics simulations result in a glut of simulation data, making analysis and discovery a difficult and burdensome task. We present MDMap, a system designed to summarize long-running molecular dynamics (MD) simulations. We represent a molecular dynamics simulation as a state transition graph over a set of intermediate (stable and semi-stable) states. The transitions amongst the states together with their frequencies represent the flow of a biomolecule through the trajectory space. MDMap automatically determines potential intermediate conformations and the transitions amongst them by analyzing the conformational space explored by the MD simulation. MDMap is an automated system to visualize MD simulations as state-transition diagrams, and can replace the current tedious manual layouts of biomolecular folding landscapes with an automated tool. The layout of the representative states and the corresponding transitions among them is presented to the user as a visual synopsis of the long-running MD simulation. We compare and contrast multiple presentations of the state transition diagrams, such as conformational embedding, and spectral, hierarchical, and force-directed graph layouts. We believe this system could provide a road-map for the visualization of other stochastic time-varying simulations in a variety of different domains. JA - Biological Data Visualization (BioVis), 2011 IEEE Symposium on ER - TY - JOUR T1 - A robust and rotationally invariant local surface descriptor with applications to non-local mesh processing JF - Graphical ModelsGraphical Models Y1 - 2011 A1 - Maximo, A. A1 - Patro, R. A1 - Varshney, Amitabh A1 - Farias, R. KW - Local descriptors KW - Non-local mesh processing KW - shape analysis KW - Similarity processing AB - In recent years, we have witnessed a striking increase in research concerning how to describe a meshed surface. These descriptors are commonly used to encode mesh properties or guide mesh processing, not to augment existing computations by replication. In this work, we first define a robust surface descriptor based on a local height field representation, and present a transformation via the extraction of Zernike moments. Unlike previous work, our local surface descriptor is innately rotationally invariant. Second, equipped with this novel descriptor, we present SAMPLE – similarity augmented mesh processing using local exemplars – a method which uses feature neighbourhoods to propagate mesh processing done in one part of the mesh, the local exemplar, to many others. Finally, we show that SAMPLE can be used in a number of applications, such as detail transfer and parameterization. VL - 73 SN - 1524-0703 ER - TY - JOUR T1 - Social Snapshot: A System for Temporally Coupled Social Photography JF - Computer Graphics and Applications, IEEEComputer Graphics and Applications, IEEE Y1 - 2011 A1 - Patro, R. A1 - Ip, Cheuk Yiu A1 - Bista, S. A1 - Varshney, Amitabh KW - 3D KW - ACQUISITION KW - computing KW - coupled KW - data KW - Photography KW - reconstruction KW - sciences KW - snapshot KW - social KW - spatiotemporal KW - temporally AB - Social Snapshot actively acquires and reconstructs temporally dynamic data. The system enables spatiotemporal 3D photography using commodity devices, assisted by their auxiliary sensors and network functionality. It engages users, making them active rather than passive participants in data acquisition. VL - 31 SN - 0272-1716 ER - TY - JOUR T1 - The Alveolate Perkinsus marinus: biological insights from EST gene discovery. JF - BMC Genomics Y1 - 2010 A1 - Joseph, Sandeep J A1 - Fernández-Robledo, José A A1 - Gardner, Malcolm J A1 - El-Sayed, Najib M A1 - Kuo, Chih-Horng A1 - Schott, Eric J A1 - Wang, Haiming A1 - Kissinger, Jessica C A1 - Vasta, Gerardo R KW - Alveolata KW - Animals KW - Expressed Sequence Tags KW - Ostreidae KW - Phylogeny AB -

BACKGROUND: Perkinsus marinus, a protozoan parasite of the eastern oyster Crassostrea virginica, has devastated natural and farmed oyster populations along the Atlantic and Gulf coasts of the United States. It is classified as a member of the Perkinsozoa, a recently established phylum considered close to the ancestor of ciliates, dinoflagellates, and apicomplexans, and a key taxon for understanding unique adaptations (e.g. parasitism) within the Alveolata. Despite intense parasite pressure, no disease-resistant oysters have been identified and no effective therapies have been developed to date.

RESULTS: To gain insight into the biological basis of the parasite's virulence and pathogenesis mechanisms, and to identify genes encoding potential targets for intervention, we generated>31,000 5' expressed sequence tags (ESTs) derived from four trophozoite libraries generated from two P. marinus strains. Trimming and clustering of the sequence tags yielded 7,863 unique sequences, some of which carry a spliced leader. Similarity searches revealed that 55% of these had hits in protein sequence databases, of which 1,729 had their best hit with proteins from the chromalveolates (E-value

CONCLUSIONS: Our transcriptome analysis of P. marinus, the first for any member of the Perkinsozoa, contributes new insight into its biology and taxonomic position. It provides a very informative, albeit preliminary, glimpse into the expression of genes encoding functionally relevant proteins as potential targets for chemotherapy, and evidence for the presence of a relict plastid. Further, although P. marinus sequences display significant similarity to those from both apicomplexans and dinoflagellates, the presence of trans-spliced transcripts confirms the previously established affinities with the latter. The EST analysis reported herein, together with the recently completed sequence of the P. marinus genome and the development of transfection methodology, should result in improved intervention strategies against dermo disease.

VL - 11 M3 - 10.1186/1471-2164-11-228 ER - TY - JOUR T1 - Environmental reservoirs of Vibrio cholerae and their role in cholera JF - Environmental Microbiology ReportsEnvironmental Microbiology Reports Y1 - 2010 A1 - Vezzulli, Luigi A1 - Pruzzo, Carla A1 - Huq, Anwar A1 - Rita R. Colwell AB - In the aquatic environment, Vibrio cholerae has been reported to be associated with a variety of living organisms, including animals with an exoskeleton of chitin, aquatic plants, protozoa, bivalves, waterbirds, as well as abiotic substrates (e.g. sediments). Most of these are well-known or putative environmental reservoirs for the bacterium, defined as places where the pathogen lives over time, with the potential to be released and to cause human infection. Environmental reservoirs also serve as V. cholerae disseminators and vectors. They can be responsible for the start of an epidemic, may be critical to cholera endemicity, and affect the evolution of pathogen virulence. To date, in addition to the generally recognized role of zooplankton as the largest environmental reservoir for V. cholerae, other environmental reservoirs play some role in cholera epidemiology by favouring persistence of the pathogen during inter-epidemic periods. Little is known about the ecological factors affecting V. cholerae survival in association with aquatic substrates. Studies aimed at these aspects, i.e. understanding how environmental reservoirs interact, are affected by climate, and contribute to disease epidemiology, will be useful for understanding global implications of V. cholerae and the disease cholera. VL - 2 SN - 1758-2229 ER - TY - JOUR T1 - Saliency Guided Summarization of Molecular Dynamics Simulations JF - Scientific Visualization: Advanced ConceptsScientific Visualization: Advanced Concepts Y1 - 2010 A1 - Patro, R. A1 - Ip, C. Y. A1 - Varshney, Amitabh A1 - Hagen, H. AB - We present a novel method to measure saliency in molecular dynamics simulation data. This saliency measure is based on a multiscale center-surround mechanism, which is fast and efficient to compute. We explore the use of the saliency function to guide the selection of representative and anomalous timesteps for summarization of simulations. To this end, we also introduce a multiscale keyframe selection procedure which automatically provides keyframes representing the simulation at varying levels of coarseness. We compare our saliency guided keyframe approach against other methods, and show that it consistently selects superior keyframes as measured by their predictive power in reconstructing the simulation. VL - 1 ER - TY - JOUR T1 - Young Proteins Experience More Variable Selection Pressures Than Old Proteins JF - Genome ResearchGenome Res.Genome ResearchGenome Res. Y1 - 2010 A1 - Vishnoi, Anchal A1 - Kryazhimskiy, Sergey A1 - Bazykin, Georgii A. A1 - Sridhar Hannenhalli A1 - Plotkin, Joshua B. AB - It is well known that young proteins tend to experience weaker purifying selection and evolve more quickly than old proteins. Here, we show that, in addition, young proteins tend to experience more variable selection pressures over time than old proteins. We demonstrate this pattern in three independent taxonomic groups: yeast, Drosophila, and mammals. The increased variability of selection pressures on young proteins is highly significant even after controlling for the fact that young proteins are typically shorter and experience weaker purifying selection than old proteins. The majority of our results are consistent with the hypothesis that the function of a young gene tends to change over time more readily than that of an old gene. At the same time, our results may be caused in part by young genes that serve constant functions over time, but nevertheless appear to evolve under changing selection pressures due to depletion of adaptive mutations. In either case, our results imply that the evolution of a protein-coding sequence is partly determined by its age and origin, and not only by the phenotypic properties of the encoded protein. We discuss, via specific examples, the consequences of these findings for understanding of the sources of evolutionary novelty. VL - 20 SN - 1088-9051, 1549-5469 ER - TY - JOUR T1 - Automated classification of bird and amphibian calls using machine learning: A comparison of methods JF - Ecological Informatics Y1 - 2009 A1 - Acevedo, Miguel A. A1 - Corrada-Bravo, Carlos J. A1 - Corrada-Bravo, Hector A1 - Villanueva-Rivera, Luis J. A1 - Aide, T. Mitchell VL - 4 UR - http://linkinghub.elsevier.com/retrieve/pii/S1574954109000351http://api.elsevier.com/content/article/PII:S1574954109000351?httpAccept=text/xmlhttp://api.elsevier.com/content/article/PII:S1574954109000351?httpAccept=text/plain CP - 4 J1 - Ecological Informatics M3 - 10.1016/j.ecoinf.2009.06.005 ER - TY - JOUR T1 - CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features JF - Genome BiologyGenome Biology Y1 - 2009 A1 - Essien, Kobby A1 - Vigneau, Sebastien A1 - Apreleva, Sofia A1 - Singh, Larry N. A1 - Bartolomei, Marisa S. A1 - Sridhar Hannenhalli AB - CTCF (CCCTC-binding factor) is an evolutionarily conserved zinc finger protein involved in diverse functions ranging from negative regulation of MYC, to chromatin insulation of the beta-globin gene cluster, to imprinting of the Igf2 locus. The 11 zinc fingers of CTCF are known to differentially contribute to the CTCF-DNA interaction at different binding sites. It is possible that the differences in CTCF-DNA conformation at different binding sites underlie CTCF's functional diversity. If so, the CTCF binding sites may belong to distinct classes, each compatible with a specific functional role. VL - 10 SN - 1465-6906 ER - TY - JOUR T1 - InterPro: the integrative protein signature database. JF - Nucleic Acids Res Y1 - 2009 A1 - Hunter, Sarah A1 - Apweiler, Rolf A1 - Attwood, Teresa K A1 - Bairoch, Amos A1 - Bateman, Alex A1 - Binns, David A1 - Bork, Peer A1 - Das, Ujjwal A1 - Daugherty, Louise A1 - Duquenne, Lauranne A1 - Finn, Robert D A1 - Gough, Julian A1 - Haft, Daniel A1 - Hulo, Nicolas A1 - Kahn, Daniel A1 - Kelly, Elizabeth A1 - Laugraud, Aurélie A1 - Letunic, Ivica A1 - Lonsdale, David A1 - Lopez, Rodrigo A1 - Madera, Martin A1 - Maslen, John A1 - McAnulla, Craig A1 - McDowall, Jennifer A1 - Mistry, Jaina A1 - Mitchell, Alex A1 - Mulder, Nicola A1 - Natale, Darren A1 - Orengo, Christine A1 - Quinn, Antony F A1 - Selengut, Jeremy D A1 - Sigrist, Christian J A A1 - Thimma, Manjula A1 - Thomas, Paul D A1 - Valentin, Franck A1 - Wilson, Derek A1 - Wu, Cathy H A1 - Yeats, Corin KW - Databases, Protein KW - Proteins KW - Sequence Analysis, Protein KW - Systems Integration AB -

The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total approximately 58,000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/).

VL - 37 CP - Database issue M3 - 10.1093/nar/gkn785 ER - TY - JOUR T1 - InterPro: the integrative protein signature database JF - Nucleic acids researchNucleic Acids Research Y1 - 2009 A1 - Hunter, Sarah A1 - Apweiler, Rolf A1 - Attwood, Teresa K. A1 - Bairoch, Amos A1 - Bateman, Alex A1 - Binns, David A1 - Bork, Peer A1 - Das, Ujjwal A1 - Daugherty, Louise A1 - Duquenne, Lauranne A1 - Finn, Robert D. A1 - Gough, Julian A1 - Haft, Daniel A1 - Hulo, Nicolas A1 - Kahn, Daniel A1 - Kelly, Elizabeth A1 - Laugraud, Aurélie A1 - Letunic, Ivica A1 - Lonsdale, David A1 - Lopez, Rodrigo A1 - Madera, Martin A1 - Maslen, John A1 - McAnulla, Craig A1 - McDowall, Jennifer A1 - Mistry, Jaina A1 - Mitchell, Alex A1 - Mulder, Nicola A1 - Natale, Darren A1 - Orengo, Christine A1 - Quinn, Antony F. A1 - J. Selengut A1 - Sigrist, Christian J. A. A1 - Thimma, Manjula A1 - Thomas, Paul D. A1 - Valentin, Franck A1 - Wilson, Derek A1 - Wu, Cathy H. A1 - Yeats, Corin KW - Databases, Protein KW - Proteins KW - Sequence Analysis, Protein KW - Systems Integration AB - The InterPro database (http://www.ebi.ac.uk/interpro/) integrates together predictive models or 'signatures' representing protein domains, families and functional sites from multiple, diverse source databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Integration is performed manually and approximately half of the total approximately 58,000 signatures available in the source databases belong to an InterPro entry. Recently, we have started to also display the remaining un-integrated signatures via our web interface. Other developments include the provision of non-signature data, such as structural data, in new XML files on our FTP site, as well as the inclusion of matchless UniProtKB proteins in the existing match XML files. The web interface has been extended and now links out to the ADAN predicted protein-protein interaction database and the SPICE and Dasty viewers. The latest public release (v18.0) covers 79.8% of UniProtKB (v14.1) and consists of 16 549 entries. InterPro data may be accessed either via the web address above, via web services, by downloading files by anonymous FTP or by using the InterProScan search software (http://www.ebi.ac.uk/Tools/InterProScan/). VL - 37 N1 - http://www.ncbi.nlm.nih.gov/pubmed/18940856?dopt=Abstract ER - TY - JOUR T1 - Modeling and visualization of human activities for multicamera networks JF - EURASIP Journal on Image and Video ProcessingEURASIP Journal on Image and Video Processing Y1 - 2009 A1 - Sankaranarayanan, A. C. A1 - Patro, R. A1 - Turaga, P. A1 - Varshney, Amitabh A1 - Chellappa, Rama VL - 2009 ER - TY - JOUR T1 - PTM-Switchboard—a database of posttranslational modifications of transcription factors, the mediating enzymes and target genes JF - Nucleic acids researchNucleic Acids Research Y1 - 2009 A1 - Everett, L. A1 - Vo, A. A1 - Sridhar Hannenhalli PB - Oxford Univ Press VL - 37 ER - TY - CHAP T1 - Salient Frame Detection for Molecular Dynamics Simulations T2 - Scientific VisualizationScientific Visualization Y1 - 2009 A1 - Kim, Youngmin A1 - Patro, Robert A1 - Ip, Cheuk Yiu A1 - O'Leary, Dianne P. A1 - Anishkin, Andriy A1 - Sukharev, Sergei A1 - Varshney, Amitabh ED - Ebert, D. S. ED - Gr, ED - x6f, ED - x, ED - ller, E. ED - Hagen, H. ED - Kaufman, A. JA - Scientific VisualizationScientific Visualization PB - Dagstuhl Seminar Proceedings 09251 ER - TY - JOUR T1 - Dual role colonization factors connecting Vibrio cholerae's lifestyles in human and aquatic environments open new perspectives for combating infectious diseases JF - Current Opinion in BiotechnologyCurrent Opinion in Biotechnology Y1 - 2008 A1 - Vezzulli, Luigi A1 - Guzmán, Carlos A. A1 - Rita R. Colwell A1 - Pruzzo, Carla AB - Vibrio cholerae exhibits two distinctive lifestyles, one inside the milieu of the human intestine and the other in the aquatic environment. Recently, the existence of V. cholerae ligands involved in colonization of both human intestine and environmental chitin surfaces via the same binding specificity has been shown. Such molecules, here named ‘dual role colonization factors (DRCFs)’, are example of a tight connection between the two V. cholerae's lifestyles. It is suggested that DRCFs and, more generally, bacterial factors and pathways having roles in pathogenesis and in the out of the human body life may be promising targets for development of novel prophylactic or therapeutic interventions that may also affect V. cholerae fitness in its environmental reservoirs. VL - 19 SN - 0958-1669 ER - TY - JOUR T1 - Global impact of Vibrio cholerae interactions with chitin JF - Environmental MicrobiologyEnvironmental Microbiology Y1 - 2008 A1 - Pruzzo, Carla A1 - Vezzulli, Luigi A1 - Rita R. Colwell AB - The interaction of Vibrio cholerae with chitin exemplifies for microbial ecology a successful bacteria–substrate interaction with complex and significant influence on the lifestyle of the bacterium. Chitin is one of the most abundant polymers on earth and possibly the most abundant in the aquatic environment, where its association with V. cholerae has provided the microorganism with a number of advantages, including food availability, adaptation to environmental nutrient gradients, tolerance to stress and protection from predators. Emergent properties of V. cholerae–chitin interactions occur at multiple hierarchical levels in the environment and include cell metabolic and physiological responses e.g. chemotaxis, cell multiplication, induction of competence, biofilm formation, commensal and symbiotic relationship with higher organisms, cycling of nutrients, and pathogenicity for humans and aquatic animals. As factors mediating virulence of V. cholerae for humans and aquatic animals derive from mechanisms of adaptation to its environment, at different levels of hierarchical scale, V. cholerae interactions with chitin represent a useful model for examination of the role of primary habitat selection in the development of traits that have been identified as virulence factors in human disease. VL - 10 SN - 1462-2920 ER - TY - JOUR T1 - The minimum information about a genome sequence (MIGS) specification JF - Nature biotechnologyNature biotechnology Y1 - 2008 A1 - Field, Dawn A1 - Garrity, George A1 - Gray, Tanya A1 - Morrison, Norman A1 - J. Selengut A1 - Sterk, Peter A1 - Tatusova, Tatiana A1 - Thomson, Nicholas A1 - Allen, Michael J. A1 - Angiuoli, Samuel V. A1 - Ashburner, Michael A1 - Axelrod, Nelson A1 - Baldauf, Sandra A1 - Ballard, Stuart A1 - Boore, Jeffrey A1 - Cochrane, Guy A1 - Cole, James A1 - Dawyndt, Peter A1 - De Vos, Paul A1 - DePamphilis, Claude A1 - Edwards, Robert A1 - Faruque, Nadeem A1 - Feldman, Robert A1 - Gilbert, Jack A1 - Gilna, Paul A1 - Glöckner, Frank Oliver A1 - Goldstein, Philip A1 - Guralnick, Robert A1 - Haft, Dan A1 - Hancock, David A1 - Hermjakob, Henning A1 - Hertz-Fowler, Christiane A1 - Hugenholtz, Phil A1 - Joint, Ian A1 - Kagan, Leonid A1 - Kane, Matthew A1 - Kennedy, Jessie A1 - Kowalchuk, George A1 - Kottmann, Renzo A1 - Kolker, Eugene A1 - Kravitz, Saul A1 - Kyrpides, Nikos A1 - Leebens-Mack, Jim A1 - Lewis, Suzanna E. A1 - Li, Kelvin A1 - Lister, Allyson L. A1 - Lord, Phillip A1 - Maltsev, Natalia A1 - Markowitz, Victor A1 - Martiny, Jennifer A1 - Methe, Barbara A1 - Mizrachi, Ilene A1 - Moxon, Richard A1 - Nelson, Karen A1 - Parkhill, Julian A1 - Proctor, Lita A1 - White, Owen A1 - Sansone, Susanna-Assunta A1 - Spiers, Andrew A1 - Stevens, Robert A1 - Swift, Paul A1 - Taylor, Chris A1 - Tateno, Yoshio A1 - Tett, Adrian A1 - Turner, Sarah A1 - Ussery, David A1 - Vaughan, Bob A1 - Ward, Naomi A1 - Whetzel, Trish A1 - San Gil, Ingio A1 - Wilson, Gareth A1 - Wipat, Anil KW - Chromosome mapping KW - Databases, Factual KW - information dissemination KW - Information Storage and Retrieval KW - Information Theory KW - Internationality AB - With the quantity of genomic data increasing at an exponential rate, it is imperative that these data be captured electronically, in a standard format. Standardization activities must proceed within the auspices of open-access and international working bodies. To tackle the issues surrounding the development of better descriptions of genomic investigations, we have formed the Genomic Standards Consortium (GSC). Here, we introduce the minimum information about a genome sequence (MIGS) specification with the intent of promoting participation in its development and discussing the resources that will be required to develop improved mechanisms of metadata capture and exchange. As part of its wider goals, the GSC also supports improving the 'transparency' of the information contained in existing genomic databases. VL - 26 N1 - http://www.ncbi.nlm.nih.gov/pubmed/18464787?dopt=Abstract ER - TY - JOUR T1 - COMPUTATIONAL BIOLOGY JF - Nucleic acids researchNucleic Acids Research Y1 - 2007 A1 - Leparc, G. G. A1 - Mitra, R. D. A1 - Vardhanabhuti, S. A1 - Wang, J. A1 - Sridhar Hannenhalli A1 - Smit, S. A1 - Widmann, J. A1 - Knight, R. A1 - Wu, S. A1 - Zhang, Y. A1 - others, PB - Information Retrieval Ltd VL - 35 ER - TY - JOUR T1 - Evolution of genes and genomes on the Drosophila phylogeny JF - NatureNature Y1 - 2007 A1 - Clark, Andrew G. A1 - Eisen, Michael B. A1 - Smith, Douglas R. A1 - Bergman, Casey M. A1 - Oliver, Brian A1 - Markow, Therese A. A1 - Kaufman, Thomas C. A1 - Kellis, Manolis A1 - Gelbart, William A1 - Iyer, Venky N. A1 - Pollard, Daniel A. A1 - Sackton, Timothy B. A1 - Larracuente, Amanda M. A1 - Singh, Nadia D. A1 - Abad, Jose P. A1 - Abt, Dawn N. A1 - Adryan, Boris A1 - Aguade, Montserrat A1 - Akashi, Hiroshi A1 - Anderson, Wyatt W. A1 - Aquadro, Charles F. A1 - Ardell, David H. A1 - Arguello, Roman A1 - Artieri, Carlo G. A1 - Barbash, Daniel A. A1 - Barker, Daniel A1 - Barsanti, Paolo A1 - Batterham, Phil A1 - Batzoglou, Serafim A1 - Begun, Dave A1 - Bhutkar, Arjun A1 - Blanco, Enrico A1 - Bosak, Stephanie A. A1 - Bradley, Robert K. A1 - Brand, Adrianne D. A1 - Brent, Michael R. A1 - Brooks, Angela N. A1 - Brown, Randall H. A1 - Butlin, Roger K. A1 - Caggese, Corrado A1 - Calvi, Brian R. A1 - Carvalho, A. Bernardo de A1 - Caspi, Anat A1 - Castrezana, Sergio A1 - Celniker, Susan E. A1 - Chang, Jean L. A1 - Chapple, Charles A1 - Chatterji, Sourav A1 - Chinwalla, Asif A1 - Civetta, Alberto A1 - Clifton, Sandra W. A1 - Comeron, Josep M. A1 - Costello, James C. A1 - Coyne, Jerry A. A1 - Daub, Jennifer A1 - David, Robert G. A1 - Delcher, Arthur L. A1 - Delehaunty, Kim A1 - Do, Chuong B. A1 - Ebling, Heather A1 - Edwards, Kevin A1 - Eickbush, Thomas A1 - Evans, Jay D. A1 - Filipski, Alan A1 - Findei, A1 - Sven A1 - Freyhult, Eva A1 - Fulton, Lucinda A1 - Fulton, Robert A1 - Garcia, Ana C. L. A1 - Gardiner, Anastasia A1 - Garfield, David A. A1 - Garvin, Barry E. A1 - Gibson, Greg A1 - Gilbert, Don A1 - Gnerre, Sante A1 - Godfrey, Jennifer A1 - Good, Robert A1 - Gotea, Valer A1 - Gravely, Brenton A1 - Greenberg, Anthony J. A1 - Griffiths-Jones, Sam A1 - Gross, Samuel A1 - Guigo, Roderic A1 - Gustafson, Erik A. A1 - Haerty, Wilfried A1 - Hahn, Matthew W. A1 - Halligan, Daniel L. A1 - Halpern, Aaron L. A1 - Halter, Gillian M. A1 - Han, Mira V. A1 - Heger, Andreas A1 - Hillier, LaDeana A1 - Hinrichs, Angie S. A1 - Holmes, Ian A1 - Hoskins, Roger A. A1 - Hubisz, Melissa J. A1 - Hultmark, Dan A1 - Huntley, Melanie A. A1 - Jaffe, David B. A1 - Jagadeeshan, Santosh A1 - Jeck, William R. A1 - Johnson, Justin A1 - Jones, Corbin D. A1 - Jordan, William C. A1 - Karpen, Gary H. A1 - Kataoka, Eiko A1 - Keightley, Peter D. A1 - Kheradpour, Pouya A1 - Kirkness, Ewen F. A1 - Koerich, Leonardo B. A1 - Kristiansen, Karsten A1 - Kudrna, Dave A1 - Kulathinal, Rob J. A1 - Kumar, Sudhir A1 - Kwok, Roberta A1 - Lander, Eric A1 - Langley, Charles H. A1 - Lapoint, Richard A1 - Lazzaro, Brian P. A1 - Lee, So-Jeong A1 - Levesque, Lisa A1 - Li, Ruiqiang A1 - Lin, Chiao-Feng A1 - Lin, Michael F. 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A1 - Patti, Christopher A1 - Phunkhang, Pema A1 - Pierre, Fritz A1 - Priest, Margaret A1 - Raghuraman, Sujaa A1 - Rege, Filip A1 - Reyes, Rebecca A1 - Rise, Cecil A1 - Rogov, Peter A1 - Ross, Keenan A1 - Ryan, Elizabeth A1 - Settipalli, Sampath A1 - Shea, Terry A1 - Sherpa, Ngawang A1 - Shi, Lu A1 - Shih, Diana A1 - Sparrow, Todd A1 - Spaulding, Jessica A1 - Stalker, John A1 - Stange-Thomann, Nicole A1 - Stavropoulos, Sharon A1 - Stone, Catherine A1 - Strader, Christopher A1 - Tesfaye, Senait A1 - Thomson, Talene A1 - Thoulutsang, Yama A1 - Thoulutsang, Dawa A1 - Topham, Kerri A1 - Topping, Ira A1 - Tsamla, Tsamla A1 - Vassiliev, Helen A1 - Vo, Andy A1 - Wangchuk, Tsering A1 - Wangdi, Tsering A1 - Weiand, Michael A1 - Wilkinson, Jane A1 - Wilson, Adam A1 - Yadav, Shailendra A1 - Young, Geneva A1 - Yu, Qing A1 - Zembek, Lisa A1 - Zhong, Danni A1 - Zimmer, Andrew A1 - Zwirko, Zac A1 - Jaffe, David B. A1 - Alvarez, Pablo A1 - Brockman, Will A1 - Butler, Jonathan A1 - Chin, CheeWhye A1 - Gnerre, Sante A1 - Grabherr, Manfred A1 - Kleber, Michael A1 - Mauceli, Evan A1 - MacCallum, Iain AB - Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species. VL - 450 SN - 0028-0836 N1 - [szlig] ER - TY - JOUR T1 - Evolution of genes and genomes on the Drosophila phylogeny. JF - Nature Y1 - 2007 A1 - Clark, Andrew G A1 - Eisen, Michael B A1 - Smith, Douglas R A1 - Bergman, Casey M A1 - Oliver, Brian A1 - Markow, Therese A A1 - Kaufman, Thomas C A1 - Kellis, Manolis A1 - Gelbart, William A1 - Iyer, Venky N A1 - Pollard, Daniel A A1 - Sackton, Timothy B A1 - Larracuente, Amanda M A1 - Singh, Nadia D A1 - Abad, Jose P A1 - Abt, Dawn N A1 - Adryan, Boris A1 - Aguade, Montserrat A1 - Akashi, Hiroshi A1 - Anderson, Wyatt W A1 - Aquadro, Charles F A1 - Ardell, David H A1 - Arguello, Roman A1 - Artieri, Carlo G A1 - Barbash, Daniel A A1 - Barker, Daniel A1 - Barsanti, Paolo A1 - Batterham, Phil A1 - Batzoglou, Serafim A1 - Begun, Dave A1 - Bhutkar, Arjun A1 - Blanco, Enrico A1 - Bosak, Stephanie A A1 - Bradley, Robert K A1 - Brand, Adrianne D A1 - Brent, Michael R A1 - Brooks, Angela N A1 - Brown, Randall H A1 - Butlin, Roger K A1 - Caggese, Corrado A1 - Calvi, Brian R A1 - Bernardo de Carvalho, A A1 - Caspi, Anat A1 - Castrezana, Sergio A1 - Celniker, Susan E A1 - Chang, Jean L A1 - Chapple, Charles A1 - Chatterji, Sourav A1 - Chinwalla, Asif A1 - Civetta, Alberto A1 - Clifton, Sandra W A1 - Comeron, Josep M A1 - Costello, James C A1 - Coyne, Jerry A A1 - Daub, Jennifer A1 - David, Robert G A1 - Delcher, Arthur L A1 - Delehaunty, Kim A1 - Do, Chuong B A1 - Ebling, Heather A1 - Edwards, Kevin A1 - Eickbush, Thomas A1 - Evans, Jay D A1 - Filipski, Alan A1 - Findeiss, Sven A1 - Freyhult, Eva A1 - Fulton, Lucinda A1 - Fulton, Robert A1 - Garcia, Ana C L A1 - Gardiner, Anastasia A1 - Garfield, David A A1 - Garvin, Barry E A1 - Gibson, Greg A1 - Gilbert, Don A1 - Gnerre, Sante A1 - Godfrey, Jennifer A1 - Good, Robert A1 - Gotea, Valer A1 - Gravely, Brenton A1 - Greenberg, Anthony J A1 - Griffiths-Jones, Sam A1 - Gross, Samuel A1 - Guigo, Roderic A1 - Gustafson, Erik A A1 - Haerty, Wilfried A1 - Hahn, Matthew W A1 - Halligan, Daniel L A1 - Halpern, Aaron L A1 - Halter, Gillian M A1 - Han, Mira V A1 - Heger, Andreas A1 - Hillier, LaDeana A1 - Hinrichs, Angie S A1 - 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Minx, Patrick A1 - Mollenhauer, Michael U A1 - Montooth, Kristi A1 - Mount, Stephen M A1 - Mu, Xu A1 - Myers, Eugene A1 - Negre, Barbara A1 - Newfeld, Stuart A1 - Nielsen, Rasmus A1 - Noor, Mohamed A F A1 - O'Grady, Patrick A1 - Pachter, Lior A1 - Papaceit, Montserrat A1 - Parisi, Matthew J A1 - Parisi, Michael A1 - Parts, Leopold A1 - Pedersen, Jakob S A1 - Pesole, Graziano A1 - Phillippy, Adam M A1 - Ponting, Chris P A1 - Pop, Mihai A1 - Porcelli, Damiano A1 - Powell, Jeffrey R A1 - Prohaska, Sonja A1 - Pruitt, Kim A1 - Puig, Marta A1 - Quesneville, Hadi A1 - Ram, Kristipati Ravi A1 - Rand, David A1 - Rasmussen, Matthew D A1 - Reed, Laura K A1 - Reenan, Robert A1 - Reily, Amy A1 - Remington, Karin A A1 - Rieger, Tania T A1 - Ritchie, Michael G A1 - Robin, Charles A1 - Rogers, Yu-Hui A1 - Rohde, Claudia A1 - Rozas, Julio A1 - Rubenfield, Marc J A1 - Ruiz, Alfredo A1 - Russo, Susan A1 - Salzberg, Steven L A1 - Sanchez-Gracia, Alejandro A1 - Saranga, David J A1 - Sato, Hajime A1 - Schaeffer, Stephen W A1 - 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Zdobnov, Evgeny A1 - Zhang, Peili A1 - Zhang, Yu A1 - Zimin, Aleksey V A1 - Baldwin, Jennifer A1 - Abdouelleil, Amr A1 - Abdulkadir, Jamal A1 - Abebe, Adal A1 - Abera, Brikti A1 - Abreu, Justin A1 - Acer, St Christophe A1 - Aftuck, Lynne A1 - Alexander, Allen A1 - An, Peter A1 - Anderson, Erica A1 - Anderson, Scott A1 - Arachi, Harindra A1 - Azer, Marc A1 - Bachantsang, Pasang A1 - Barry, Andrew A1 - Bayul, Tashi A1 - Berlin, Aaron A1 - Bessette, Daniel A1 - Bloom, Toby A1 - Blye, Jason A1 - Boguslavskiy, Leonid A1 - Bonnet, Claude A1 - Boukhgalter, Boris A1 - Bourzgui, Imane A1 - Brown, Adam A1 - Cahill, Patrick A1 - Channer, Sheridon A1 - Cheshatsang, Yama A1 - Chuda, Lisa A1 - Citroen, Mieke A1 - Collymore, Alville A1 - Cooke, Patrick A1 - Costello, Maura A1 - D'Aco, Katie A1 - Daza, Riza A1 - De Haan, Georgius A1 - DeGray, Stuart A1 - DeMaso, Christina A1 - Dhargay, Norbu A1 - Dooley, Kimberly A1 - Dooley, Erin A1 - Doricent, Missole A1 - Dorje, Passang A1 - Dorjee, Kunsang A1 - Dupes, Alan A1 - Elong, Richard A1 - Falk, Jill A1 - Farina, Abderrahim A1 - Faro, Susan A1 - Ferguson, Diallo A1 - Fisher, Sheila A1 - Foley, Chelsea D A1 - Franke, Alicia A1 - Friedrich, Dennis A1 - Gadbois, Loryn A1 - Gearin, Gary A1 - Gearin, Christina R A1 - Giannoukos, Georgia A1 - Goode, Tina A1 - Graham, Joseph A1 - Grandbois, Edward A1 - Grewal, Sharleen A1 - Gyaltsen, Kunsang A1 - Hafez, Nabil A1 - Hagos, Birhane A1 - Hall, Jennifer A1 - Henson, Charlotte A1 - Hollinger, Andrew A1 - Honan, Tracey A1 - Huard, Monika D A1 - Hughes, Leanne A1 - Hurhula, Brian A1 - Husby, M Erii A1 - Kamat, Asha A1 - Kanga, Ben A1 - Kashin, Seva A1 - Khazanovich, Dmitry A1 - Kisner, Peter A1 - Lance, Krista A1 - Lara, Marcia A1 - Lee, William A1 - Lennon, Niall A1 - Letendre, Frances A1 - LeVine, Rosie A1 - Lipovsky, Alex A1 - Liu, Xiaohong A1 - Liu, Jinlei A1 - Liu, Shangtao A1 - Lokyitsang, Tashi A1 - Lokyitsang, Yeshi A1 - Lubonja, Rakela A1 - Lui, Annie A1 - MacDonald, Pen A1 - Magnisalis, Vasilia A1 - Maru, Kebede A1 - Matthews, Charles A1 - McCusker, William A1 - McDonough, Susan A1 - Mehta, Teena A1 - Meldrim, James A1 - Meneus, Louis A1 - Mihai, Oana A1 - Mihalev, Atanas A1 - Mihova, Tanya A1 - Mittelman, Rachel A1 - Mlenga, Valentine A1 - Montmayeur, Anna A1 - Mulrain, Leonidas A1 - Navidi, Adam A1 - Naylor, Jerome A1 - Negash, Tamrat A1 - Nguyen, Thu A1 - Nguyen, Nga A1 - Nicol, Robert A1 - Norbu, Choe A1 - Norbu, Nyima A1 - Novod, Nathaniel A1 - O'Neill, Barry A1 - Osman, Sahal A1 - Markiewicz, Eva A1 - Oyono, Otero L A1 - Patti, Christopher A1 - Phunkhang, Pema A1 - Pierre, Fritz A1 - Priest, Margaret A1 - Raghuraman, Sujaa A1 - Rege, Filip A1 - Reyes, Rebecca A1 - Rise, Cecil A1 - Rogov, Peter A1 - Ross, Keenan A1 - Ryan, Elizabeth A1 - Settipalli, Sampath A1 - Shea, Terry A1 - Sherpa, Ngawang A1 - Shi, Lu A1 - Shih, Diana A1 - Sparrow, Todd A1 - Spaulding, Jessica A1 - Stalker, John A1 - Stange-Thomann, Nicole A1 - Stavropoulos, Sharon A1 - Stone, Catherine A1 - Strader, Christopher A1 - Tesfaye, Senait A1 - Thomson, Talene A1 - Thoulutsang, Yama A1 - Thoulutsang, Dawa A1 - Topham, Kerri A1 - Topping, Ira A1 - Tsamla, Tsamla A1 - Vassiliev, Helen A1 - Vo, Andy A1 - Wangchuk, Tsering A1 - Wangdi, Tsering A1 - Weiand, Michael A1 - Wilkinson, Jane A1 - Wilson, Adam A1 - Yadav, Shailendra A1 - Young, Geneva A1 - Yu, Qing A1 - Zembek, Lisa A1 - Zhong, Danni A1 - Zimmer, Andrew A1 - Zwirko, Zac A1 - Jaffe, David B A1 - Alvarez, Pablo A1 - Brockman, Will A1 - Butler, Jonathan A1 - Chin, CheeWhye A1 - Gnerre, Sante A1 - Grabherr, Manfred A1 - Kleber, Michael A1 - Mauceli, Evan A1 - MacCallum, Iain KW - Animals KW - Codon KW - DNA Transposable Elements KW - Drosophila KW - Drosophila Proteins KW - Evolution, Molecular KW - Gene Order KW - Genes, Insect KW - Genome, Insect KW - Genome, Mitochondrial KW - Genomics KW - Immunity KW - Multigene Family KW - Phylogeny KW - Reproduction KW - RNA, Untranslated KW - sequence alignment KW - Sequence Analysis, DNA KW - Synteny AB -

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.

VL - 450 CP - 7167 M3 - 10.1038/nature06341 ER - TY - JOUR T1 - Genome-wide expression profiling and bioinformatics analysis of diurnally regulated genes in the mouse prefrontal cortex JF - Genome BiolGenome Biol Y1 - 2007 A1 - Yang, S. A1 - Wang, K. A1 - Valladares, O. A1 - Sridhar Hannenhalli A1 - Bucan, M. A1 - others, VL - 8 ER - TY - JOUR T1 - High-throughput sequence alignment using Graphics Processing Units JF - BMC BioinformaticsBMC Bioinformatics Y1 - 2007 A1 - Schatz, Michael C. A1 - Trapnell, Cole A1 - Delcher, Arthur L. A1 - Varshney, Amitabh VL - 8 SN - 1471-2105 ER - TY - JOUR T1 - New developments in the InterPro database. JF - Nucleic Acids Res Y1 - 2007 A1 - Mulder, Nicola J A1 - Apweiler, Rolf A1 - Attwood, Teresa K A1 - Bairoch, Amos A1 - Bateman, Alex A1 - Binns, David A1 - Bork, Peer A1 - Buillard, Virginie A1 - Cerutti, Lorenzo A1 - Copley, Richard A1 - Courcelle, Emmanuel A1 - Das, Ujjwal A1 - Daugherty, Louise A1 - Dibley, Mark A1 - Finn, Robert A1 - Fleischmann, Wolfgang A1 - Gough, Julian A1 - Haft, Daniel A1 - Hulo, Nicolas A1 - Hunter, Sarah A1 - Kahn, Daniel A1 - Kanapin, Alexander A1 - Kejariwal, Anish A1 - Labarga, Alberto A1 - Langendijk-Genevaux, Petra S A1 - Lonsdale, David A1 - Lopez, Rodrigo A1 - Letunic, Ivica A1 - Madera, Martin A1 - Maslen, John A1 - McAnulla, Craig A1 - McDowall, Jennifer A1 - Mistry, Jaina A1 - Mitchell, Alex A1 - Nikolskaya, Anastasia N A1 - Orchard, Sandra A1 - Orengo, Christine A1 - Petryszak, Robert A1 - Selengut, Jeremy D A1 - Sigrist, Christian J A A1 - Thomas, Paul D A1 - Valentin, Franck A1 - Wilson, Derek A1 - Wu, Cathy H A1 - Yeats, Corin KW - Databases, Protein KW - Internet KW - Protein Structure, Tertiary KW - Proteins KW - Sequence Analysis, Protein KW - Systems Integration KW - User-Computer Interface AB -

InterPro is an integrated resource for protein families, domains and functional sites, which integrates the following protein signature databases: PROSITE, PRINTS, ProDom, Pfam, SMART, TIGRFAMs, PIRSF, SUPERFAMILY, Gene3D and PANTHER. The latter two new member databases have been integrated since the last publication in this journal. There have been several new developments in InterPro, including an additional reading field, new database links, extensions to the web interface and additional match XML files. InterPro has always provided matches to UniProtKB proteins on the website and in the match XML file on the FTP site. Additional matches to proteins in UniParc (UniProt archive) are now available for download in the new match XML files only. The latest InterPro release (13.0) contains more than 13 000 entries, covering over 78% of all proteins in UniProtKB. The database is available for text- and sequence-based searches via a webserver (http://www.ebi.ac.uk/interpro), and for download by anonymous FTP (ftp://ftp.ebi.ac.uk/pub/databases/interpro). The InterProScan search tool is now also available via a web service at http://www.ebi.ac.uk/Tools/webservices/WSInterProScan.html.

VL - 35 CP - Database issue M3 - 10.1093/nar/gkl841 ER - TY - JOUR T1 - Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation JF - Nucleic Acids ResearchNucleic Acids Research Y1 - 2007 A1 - Vardhanabhuti, Saran A1 - Wang, Junwen A1 - Sridhar Hannenhalli AB - Computational discovery of cis-regulatory elements remains challenging. To cope with the high false positives, evolutionary conservation is routinely used. However, conservation is only one of the attributes of cis-regulatory elements and is neither necessary nor sufficient. Here, we assess two additional attributes—positional and inter-motif distance specificity—that are critical for interactions between transcription factors. We first show that for a greater than expected fraction of known motifs, the genes that contain the motifs in their promoters in a position-specific or distance-specific manner are related, both in function and/or in expression pattern. We then use the position and distance specificity to discover novel motifs. Our work highlights the importance of distance and position specificity, in addition to the evolutionary conservation, in discovering cis-regulatory motifs. VL - 35 ER - TY - JOUR T1 - Variola virus topoisomerase: DNA cleavage specificity and distribution of sites in Poxvirus genomes JF - VirologyVirology Y1 - 2007 A1 - Minkah, Nana A1 - Hwang, Young A1 - Perry, Kay A1 - Van Duyne, Gregory D. A1 - Hendrickson, Robert A1 - Lefkowitz, Elliot J. A1 - Sridhar Hannenhalli A1 - Bushman, Frederic D. KW - Annotation of topoisomerase sites KW - Sequence specific recognition KW - Topoisomerase IB KW - Variola virus AB - Topoisomerase enzymes regulate superhelical tension in DNA resulting from transcription, replication, repair, and other molecular transactions. Poxviruses encode an unusual type IB topoisomerase that acts only at conserved DNA sequences containing the core pentanucleotide 5'-(T/C)CCTT-3'. In X-ray structures of the variola virus topoisomerase bound to DNA, protein-DNA contacts were found to extend beyond the core pentanucleotide, indicating that the full recognition site has not yet been fully defined in functional studies. Here we report quantitation of DNA cleavage rates for an optimized 13 bp site and for all possible single base substitutions (40 total sites), with the goals of understanding the molecular mechanism of recognition and mapping topoisomerase sites in poxvirus genome sequences. The data allow a precise definition of enzyme-DNA interactions and the energetic contributions of each. We then used the resulting "action matrix" to show that favorable topoisomerase sites are distributed all along the length of poxvirus DNA sequences, consistent with a requirement for local release of superhelical tension in constrained topological domains. In orthopox genomes, an additional central cluster of sites was also evident. A negative correlation of predicted topoisomerase sites was seen relative to early terminators, but no correlation was seen with early or late promoters. These data define the full variola virus topoisomerase recognition site and provide a new window on topoisomerase function in vivo. VL - 365 SN - 0042-6822 ER - TY - JOUR T1 - Patterns of sequence conservation in presynaptic neural genes JF - Genome BiolGenome Biol Y1 - 2006 A1 - Hadley, D. A1 - Murphy, T. A1 - Valladares, O. A1 - Sridhar Hannenhalli A1 - Ungar, L. A1 - Kim, J. A1 - Bucan, M. A1 - others, VL - 7 ER - TY - JOUR T1 - Genome-Wide Analysis of Chromosomal Features Repressing Human Immunodeficiency Virus Transcription JF - Journal of VirologyJ. Virol.Journal of VirologyJ. Virol. Y1 - 2005 A1 - Lewinski, M. K. A1 - Bisgrove, D. A1 - Shinn, P. A1 - Chen, H. A1 - Hoffmann, C. A1 - Sridhar Hannenhalli A1 - Verdin, E. A1 - Berry, C. C. A1 - Ecker, J. R. A1 - Bushman, F. D. AB - We have investigated regulatory sequences in noncoding human DNA that are associated with repression of an integrated human immunodeficiency virus type 1 (HIV-1) promoter. HIV-1 integration results in the formation of precise and homogeneous junctions between viral and host DNA, but integration takes place at many locations. Thus, the variation in HIV-1 gene expression at different integration sites reports the activity of regulatory sequences at nearby chromosomal positions. Negative regulation of HIV transcription is of particular interest because of its association with maintaining HIV in a latent state in cells from infected patients. To identify chromosomal regulators of HIV transcription, we infected Jurkat T cells with an HIV-based vector transducing green fluorescent protein (GFP) and separated cells into populations containing well-expressed (GFP-positive) or poorly expressed (GFP-negative) proviruses. We then determined the chromosomal locations of the two classes by sequencing 971 junctions between viral and cellular DNA. Possible effects of endogenous cellular transcription were characterized by transcriptional profiling. Low-level GFP expression correlated with integration in (i) gene deserts, (ii) centromeric heterochromatin, and (iii) very highly expressed cellular genes. These data provide a genome-wide picture of chromosomal features that repress transcription and suggest models for transcriptional latency in cells from HIV-infected patients. VL - 79 SN - 0022-538X, 1098-5514 ER - TY - JOUR T1 - Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes JF - Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America Y1 - 2004 A1 - Seshadri, Rekha A1 - Myers, Garry S. A. A1 - Tettelin, Hervé A1 - Eisen, Jonathan A. A1 - Heidelberg, John F. A1 - Dodson, Robert J. A1 - Davidsen, Tanja M. A1 - DeBoy, Robert T. A1 - Fouts, Derrick E. A1 - Haft, Dan H. A1 - J. Selengut A1 - Ren, Qinghu A1 - Brinkac, Lauren M. A1 - Madupu, Ramana A1 - Kolonay, Jamie A1 - Durkin, A. Scott A1 - Daugherty, Sean C. A1 - Shetty, Jyoti A1 - Shvartsbeyn, Alla A1 - Gebregeorgis, Elizabeth A1 - Geer, Keita A1 - Tsegaye, Getahun A1 - Malek, Joel A1 - Ayodeji, Bola A1 - Shatsman, Sofiya A1 - McLeod, Michael P. A1 - Smajs, David A1 - Howell, Jerrilyn K. A1 - Pal, Sangita A1 - Amin, Anita A1 - Vashisth, Pankaj A1 - McNeill, Thomas Z. A1 - Xiang, Qin A1 - Sodergren, Erica A1 - Baca, Ernesto A1 - Weinstock, George M. A1 - Norris, Steven J. A1 - Fraser, Claire M. A1 - Paulsen, Ian T. KW - ATP-Binding Cassette Transporters KW - Bacterial Proteins KW - Base Sequence KW - Borrelia burgdorferi KW - Genes, Bacterial KW - Genome, Bacterial KW - Leptospira interrogans KW - Models, Genetic KW - Molecular Sequence Data KW - Mouth KW - Sequence Homology, Amino Acid KW - Treponema KW - Treponema pallidum AB - We present the complete 2,843,201-bp genome sequence of Treponema denticola (ATCC 35405) an oral spirochete associated with periodontal disease. Analysis of the T. denticola genome reveals factors mediating coaggregation, cell signaling, stress protection, and other competitive and cooperative measures, consistent with its pathogenic nature and lifestyle within the mixed-species environment of subgingival dental plaque. Comparisons with previously sequenced spirochete genomes revealed specific factors contributing to differences and similarities in spirochete physiology as well as pathogenic potential. The T. denticola genome is considerably larger in size than the genome of the related syphilis-causing spirochete Treponema pallidum. The differences in gene content appear to be attributable to a combination of three phenomena: genome reduction, lineage-specific expansions, and horizontal gene transfer. Genes lost due to reductive evolution appear to be largely involved in metabolism and transport, whereas some of the genes that have arisen due to lineage-specific expansions are implicated in various pathogenic interactions, and genes acquired via horizontal gene transfer are largely phage-related or of unknown function. VL - 101 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15064399?dopt=Abstract ER - TY - JOUR T1 - Gene synteny and evolution of genome architecture in trypanosomatids. JF - Mol Biochem Parasitol Y1 - 2004 A1 - Ghedin, Elodie A1 - Bringaud, Frederic A1 - Peterson, Jeremy A1 - Myler, Peter A1 - Berriman, Matthew A1 - Ivens, Alasdair A1 - Andersson, Björn A1 - Bontempi, Esteban A1 - Eisen, Jonathan A1 - Angiuoli, Sam A1 - Wanless, David A1 - Von Arx, Anna A1 - Murphy, Lee A1 - Lennard, Nicola A1 - Salzberg, Steven A1 - Adams, Mark D A1 - White, Owen A1 - Hall, Neil A1 - Stuart, Kenneth A1 - Fraser, Claire M A1 - el-Sayed, Najib M A KW - Animals KW - Computational Biology KW - Evolution, Molecular KW - Gene Order KW - Genome, Protozoan KW - Genomics KW - Leishmania major KW - Multigene Family KW - Recombination, Genetic KW - Retroelements KW - Selection, Genetic KW - Synteny KW - Trypanosoma brucei brucei KW - Trypanosoma cruzi KW - Trypanosomatina AB -

The trypanosomatid protozoa Trypanosoma brucei, Trypanosoma cruzi and Leishmania major are related human pathogens that cause markedly distinct diseases. Using information from genome sequencing projects currently underway, we have compared the sequences of large chromosomal fragments from each species. Despite high levels of divergence at the sequence level, these three species exhibit a striking conservation of gene order, suggesting that selection has maintained gene order among the trypanosomatids over hundreds of millions of years of evolution. The few sites of genome rearrangement between these species are marked by the presence of retrotransposon-like elements, suggesting that retrotransposons may have played an important role in shaping trypanosomatid genome organization. A degenerate retroelement was identified in L. major by examining the regions near breakage points of the synteny. This is the first such element found in L. major suggesting that retroelements were found in the common ancestor of all three species.

VL - 134 CP - 2 M3 - 10.1016/j.molbiopara.2003.11.012 ER - TY - JOUR T1 - The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough JF - Nature biotechnologyNature biotechnology Y1 - 2004 A1 - Heidelberg, John F. A1 - Seshadri, Rekha A1 - Haveman, Shelley A. A1 - Hemme, Christopher L. A1 - Paulsen, Ian T. A1 - Kolonay, James F. A1 - Eisen, Jonathan A. A1 - Ward, Naomi A1 - Methe, Barbara A1 - Brinkac, Lauren M. A1 - Daugherty, Sean C. A1 - DeBoy, Robert T. A1 - Dodson, Robert J. A1 - Durkin, A. Scott A1 - Madupu, Ramana A1 - Nelson, William C. A1 - Sullivan, Steven A. A1 - Fouts, Derrick A1 - Haft, Daniel H. A1 - J. Selengut A1 - Peterson, Jeremy D. A1 - Davidsen, Tanja M. A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Radune, Diana A1 - Dimitrov, George A1 - Hance, Mark A1 - Tran, Kevin A1 - Khouri, Hoda A1 - Gill, John A1 - Utterback, Terry R. A1 - Feldblyum, Tamara V. A1 - Wall, Judy D. A1 - Voordouw, Gerrit A1 - Fraser, Claire M. KW - Desulfovibrio vulgaris KW - Energy Metabolism KW - Genome, Bacterial KW - Molecular Sequence Data AB - Desulfovibrio vulgaris Hildenborough is a model organism for studying the energy metabolism of sulfate-reducing bacteria (SRB) and for understanding the economic impacts of SRB, including biocorrosion of metal infrastructure and bioremediation of toxic metal ions. The 3,570,858 base pair (bp) genome sequence reveals a network of novel c-type cytochromes, connecting multiple periplasmic hydrogenases and formate dehydrogenases, as a key feature of its energy metabolism. The relative arrangement of genes encoding enzymes for energy transduction, together with inferred cellular location of the enzymes, provides a basis for proposing an expansion to the 'hydrogen-cycling' model for increasing energy efficiency in this bacterium. Plasmid-encoded functions include modification of cell surface components, nitrogen fixation and a type-III protein secretion system. This genome sequence represents a substantial step toward the elucidation of pathways for reduction (and bioremediation) of pollutants such as uranium and chromium and offers a new starting point for defining this organism's complex anaerobic respiration. VL - 22 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15077118?dopt=Abstract ER - TY - BOOK T1 - Lecture Notes in Computer ScienceComputer Vision - ECCV 2004An MCMC-Based Particle Filter for Tracking Multiple Interacting Targets Y1 - 2004 A1 - Khan, Zia A1 - Balch, Tucker A1 - Dellaert, Frank ED - Kanade, Takeo ED - Kittler, Josef ED - Kleinberg, Jon M. ED - Mattern, Friedemann ED - Mitchell, John C. ED - Nierstrasz, Oscar ED - Pandu Rangan, C. ED - Steffen, Bernhard ED - Sudan, Madhu ED - Terzopoulos, Demetri ED - Tygar, Dough ED - Vardi, Moshe Y. ED - Weikum, Gerhard ED - Pajdla, ás ED - Matas, ří PB - Springer Berlin Heidelberg CY - Berlin, Heidelberg VL - 3024 SN - 978-3-540-21981-1 UR - http://www.springerlink.com/index/10.1007/b97873http://www.springerlink.com/index/pdf/10.1007/b97873http://link.springer.com/10.1007/978-3-540-24673-2_23http://www.springerlink.com/index/pdf/10.1007/978-3-540-24673-2_23 M3 - 10.1007/b9787310.1007/978-3-540-24673-2_23 ER - TY - JOUR T1 - Viable but Nonculturable Vibrio Cholerae O1 in the Aquatic Environment of Argentina JF - Applied and Environmental MicrobiologyAppl. Environ. Microbiol.Applied and Environmental MicrobiologyAppl. Environ. Microbiol. Y1 - 2004 A1 - Binsztein, Norma A1 - Costagliola, Marcela C. A1 - Pichel, Mariana A1 - Jurquiza, Verónica A1 - Ramírez, Fernando C. A1 - Akselman, Rut A1 - Vacchino, Marta A1 - Huq, Anwarul A1 - Rita R. Colwell AB - In Argentina, as in other countries of Latin America, cholera has occurred in an epidemic pattern. Vibrio cholerae O1 is native to the aquatic environment, and it occurs in both culturable and viable but nonculturable (VNC) forms, the latter during interepidemic periods. This is the first report of the presence of VNC V. cholerae O1 in the estuarine and marine waters of the Río de la Plata and the Argentine shelf of the Atlantic Ocean, respectively. Employing immunofluorescence and PCR methods, we were able to detect reservoirs of V. cholerae O1 carrying the virulence-associated genes ctxA and tcpA. The VNC forms of V. cholerae O1 were identified in samples of water, phytoplankton, and zooplankton; the latter organisms were mainly the copepods Acartia tonsa, Diaptomus sp., Paracalanus crassirostris, and Paracalanus parvus. We found that under favorable conditions, the VNC form of V. cholerae can revert to the pathogenic, transmissible state. We concluded that V. cholerae O1 is a resident of Argentinean waters, as has been shown to be the case in other geographic regions of the world. VL - 70 SN - 0099-2240, 1098-5336 ER - TY - JOUR T1 - Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species JF - Nucleic acids researchNucleic Acids Research Y1 - 2004 A1 - Nelson, Karen E. A1 - Fouts, Derrick E. A1 - Mongodin, Emmanuel F. A1 - Ravel, Jacques A1 - DeBoy, Robert T. A1 - Kolonay, James F. A1 - Rasko, David A. A1 - Angiuoli, Samuel V. A1 - Gill, Steven R. A1 - Paulsen, Ian T. A1 - Peterson, Jeremy A1 - White, Owen A1 - Nelson, William C. A1 - Nierman, William A1 - Beanan, Maureen J. A1 - Brinkac, Lauren M. A1 - Daugherty, Sean C. A1 - Dodson, Robert J. A1 - Durkin, A. Scott A1 - Madupu, Ramana A1 - Haft, Daniel H. A1 - J. Selengut A1 - Van Aken, Susan A1 - Khouri, Hoda A1 - Fedorova, Nadia A1 - Forberger, Heather A1 - Tran, Bao A1 - Kathariou, Sophia A1 - Wonderling, Laura D. A1 - Uhlich, Gaylen A. A1 - Bayles, Darrell O. A1 - Luchansky, John B. A1 - Fraser, Claire M. KW - Base Composition KW - Chromosomes, Bacterial KW - DNA Transposable Elements KW - Food Microbiology KW - Genes, Bacterial KW - Genome, Bacterial KW - Genomics KW - Listeria monocytogenes KW - Meat KW - Open Reading Frames KW - Physical Chromosome Mapping KW - Polymorphism, Single Nucleotide KW - Prophages KW - Serotyping KW - Species Specificity KW - Synteny KW - virulence AB - The genomes of three strains of Listeria monocytogenes that have been associated with food-borne illness in the USA were subjected to whole genome comparative analysis. A total of 51, 97 and 69 strain-specific genes were identified in L.monocytogenes strains F2365 (serotype 4b, cheese isolate), F6854 (serotype 1/2a, frankfurter isolate) and H7858 (serotype 4b, meat isolate), respectively. Eighty-three genes were restricted to serotype 1/2a and 51 to serotype 4b strains. These strain- and serotype-specific genes probably contribute to observed differences in pathogenicity, and the ability of the organisms to survive and grow in their respective environmental niches. The serotype 1/2a-specific genes include an operon that encodes the rhamnose biosynthetic pathway that is associated with teichoic acid biosynthesis, as well as operons for five glycosyl transferases and an adenine-specific DNA methyltransferase. A total of 8603 and 105 050 high quality single nucleotide polymorphisms (SNPs) were found on the draft genome sequences of strain H7858 and strain F6854, respectively, when compared with strain F2365. Whole genome comparative analyses revealed that the L.monocytogenes genomes are essentially syntenic, with the majority of genomic differences consisting of phage insertions, transposable elements and SNPs. VL - 32 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15115801?dopt=Abstract ER - TY - JOUR T1 - The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000 JF - Proceedings of the National Academy of Sciences of the United States of AmericaProceedings of the National Academy of Sciences of the United States of America Y1 - 2003 A1 - Buell, C. Robin A1 - Joardar, Vinita A1 - Lindeberg, Magdalen A1 - J. Selengut A1 - Paulsen, Ian T. A1 - Gwinn, Michelle L. A1 - Dodson, Robert J. A1 - DeBoy, Robert T. A1 - Durkin, A. Scott A1 - Kolonay, James F. A1 - Madupu, Ramana A1 - Daugherty, Sean A1 - Brinkac, Lauren A1 - Beanan, Maureen J. A1 - Haft, Daniel H. A1 - Nelson, William C. A1 - Davidsen, Tanja A1 - Zafar, Nikhat A1 - Zhou, Liwei A1 - Liu, Jia A1 - Yuan, Qiaoping A1 - Khouri, Hoda A1 - Fedorova, Nadia A1 - Tran, Bao A1 - Russell, Daniel A1 - Berry, Kristi A1 - Utterback, Teresa A1 - Aken, Susan E. van A1 - Feldblyum, Tamara V. A1 - D'Ascenzo, Mark A1 - Deng, Wen-Ling A1 - Ramos, Adela R. A1 - Alfano, James R. A1 - Cartinhour, Samuel A1 - Chatterjee, Arun K. A1 - Delaney, Terrence P. A1 - Lazarowitz, Sondra G. A1 - Martin, Gregory B. A1 - Schneider, David J. A1 - Tang, Xiaoyan A1 - Bender, Carol L. A1 - White, Owen A1 - Fraser, Claire M. A1 - Collmer, Alan KW - Arabidopsis KW - Base Sequence KW - Biological Transport KW - Genome, Bacterial KW - Lycopersicon esculentum KW - Molecular Sequence Data KW - Plant Growth Regulators KW - Plasmids KW - Pseudomonas KW - Reactive Oxygen Species KW - Siderophores KW - virulence AB - We report the complete genome sequence of the model bacterial pathogen Pseudomonas syringae pathovar tomato DC3000 (DC3000), which is pathogenic on tomato and Arabidopsis thaliana. The DC3000 genome (6.5 megabases) contains a circular chromosome and two plasmids, which collectively encode 5,763 ORFs. We identified 298 established and putative virulence genes, including several clusters of genes encoding 31 confirmed and 19 predicted type III secretion system effector proteins. Many of the virulence genes were members of paralogous families and also were proximal to mobile elements, which collectively comprise 7% of the DC3000 genome. The bacterium possesses a large repertoire of transporters for the acquisition of nutrients, particularly sugars, as well as genes implicated in attachment to plant surfaces. Over 12% of the genes are dedicated to regulation, which may reflect the need for rapid adaptation to the diverse environments encountered during epiphytic growth and pathogenesis. Comparative analyses confirmed a high degree of similarity with two sequenced pseudomonads, Pseudomonas putida and Pseudomonas aeruginosa, yet revealed 1,159 genes unique to DC3000, of which 811 lack a known function. VL - 100 N1 - http://www.ncbi.nlm.nih.gov/pubmed/12928499?dopt=Abstract ER - TY - JOUR T1 - Genome of Geobacter sulfurreducens: metal reduction in subsurface environments JF - Science (New York, N.Y.)Science (New York, N.Y.) Y1 - 2003 A1 - Methé, B. A. A1 - Nelson, K. E. A1 - Eisen, J. A. A1 - Paulsen, I. T. A1 - Nelson, W. A1 - Heidelberg, J. F. A1 - Wu, D. A1 - Wu, M. A1 - Ward, N. A1 - Beanan, M. J. A1 - Dodson, R. J. A1 - Madupu, R. A1 - Brinkac, L. M. A1 - Daugherty, S. C. A1 - DeBoy, R. T. A1 - Durkin, A. S. A1 - Gwinn, M. A1 - Kolonay, J. F. A1 - Sullivan, S. A. A1 - Haft, D. H. A1 - J. Selengut A1 - Davidsen, T. M. A1 - Zafar, N. A1 - White, O. A1 - Tran, B. A1 - Romero, C. A1 - Forberger, H. A. A1 - Weidman, J. A1 - Khouri, H. A1 - Feldblyum, T. V. A1 - Utterback, T. R. A1 - Van Aken, S. E. A1 - Lovley, D. R. A1 - Fraser, C. M. KW - Acetates KW - Acetyl Coenzyme A KW - Aerobiosis KW - Anaerobiosis KW - Bacterial Proteins KW - Carbon KW - Chemotaxis KW - Chromosomes, Bacterial KW - Cytochromes c KW - Electron Transport KW - Energy Metabolism KW - Genes, Bacterial KW - Genes, Regulator KW - Genome, Bacterial KW - Geobacter KW - Hydrogen KW - Metals KW - Movement KW - Open Reading Frames KW - Oxidation-Reduction KW - Phylogeny AB - The complete genome sequence of Geobacter sulfurreducens, a delta-proteobacterium, reveals unsuspected capabilities, including evidence of aerobic metabolism, one-carbon and complex carbon metabolism, motility, and chemotactic behavior. These characteristics, coupled with the possession of many two-component sensors and many c-type cytochromes, reveal an ability to create alternative, redundant, electron transport networks and offer insights into the process of metal ion reduction in subsurface environments. As well as playing roles in the global cycling of metals and carbon, this organism clearly has the potential for use in bioremediation of radioactive metals and in the generation of electricity. VL - 302 N1 - http://www.ncbi.nlm.nih.gov/pubmed/14671304?dopt=Abstract ER - TY - JOUR T1 - The sequence and analysis of Trypanosoma brucei chromosome II. JF - Nucleic Acids Res Y1 - 2003 A1 - el-Sayed, Najib M A A1 - Ghedin, Elodie A1 - Song, Jinming A1 - MacLeod, Annette A1 - Bringaud, Frederic A1 - Larkin, Christopher A1 - Wanless, David A1 - Peterson, Jeremy A1 - Hou, Lihua A1 - Taylor, Sonya A1 - Tweedie, Alison A1 - Biteau, Nicolas A1 - Khalak, Hanif G A1 - Lin, Xiaoying A1 - Mason, Tanya A1 - Hannick, Linda A1 - Caler, Elisabet A1 - Blandin, Gaëlle A1 - Bartholomeu, Daniella A1 - Simpson, Anjana J A1 - Kaul, Samir A1 - Zhao, Hong A1 - Pai, Grace A1 - Van Aken, Susan A1 - Utterback, Teresa A1 - Haas, Brian A1 - Koo, Hean L A1 - Umayam, Lowell A1 - Suh, Bernard A1 - Gerrard, Caroline A1 - Leech, Vanessa A1 - Qi, Rong A1 - Zhou, Shiguo A1 - Schwartz, David A1 - Feldblyum, Tamara A1 - Salzberg, Steven A1 - Tait, Andrew A1 - Turner, C Michael R A1 - Ullu, Elisabetta A1 - White, Owen A1 - Melville, Sara A1 - Adams, Mark D A1 - Fraser, Claire M A1 - Donelson, John E KW - Animals KW - Antigens, Protozoan KW - Chromosome mapping KW - Chromosomes KW - DNA, Protozoan KW - Gene Duplication KW - Genes, Protozoan KW - Molecular Sequence Data KW - Pseudogenes KW - Recombination, Genetic KW - Sequence Analysis, DNA KW - Trypanosoma brucei brucei AB -

We report here the sequence of chromosome II from Trypanosoma brucei, the causative agent of African sleeping sickness. The 1.2-Mb pairs encode about 470 predicted genes organised in 17 directional clusters on either strand, the largest cluster of which has 92 genes lined up over a 284-kb region. An analysis of the GC skew reveals strand compositional asymmetries that coincide with the distribution of protein-coding genes, suggesting these asymmetries may be the result of transcription-coupled repair on coding versus non-coding strand. A 5-cM genetic map of the chromosome reveals recombinational 'hot' and 'cold' regions, the latter of which is predicted to include the putative centromere. One end of the chromosome consists of a 250-kb region almost exclusively composed of RHS (pseudo)genes that belong to a newly characterised multigene family containing a hot spot of insertion for retroelements. Interspersed with the RHS genes are a few copies of truncated RNA polymerase pseudogenes as well as expression site associated (pseudo)genes (ESAGs) 3 and 4, and 76 bp repeats. These features are reminiscent of a vestigial variant surface glycoprotein (VSG) gene expression site. The other end of the chromosome contains a 30-kb array of VSG genes, the majority of which are pseudogenes, suggesting that this region may be a site for modular de novo construction of VSG gene diversity during transposition/gene conversion events.

VL - 31 CP - 16 ER - TY - CHAP T1 - Combinatorial Algorithms for Design of DNA Arrays T2 - Chip TechnologyChip Technology Y1 - 2002 A1 - Sridhar Hannenhalli A1 - Hubbell, Earl A1 - Lipshutz, Robert A1 - Pevzner, Pavel ED - Hoheisel, Jörg ED - Brazma, A. ED - Büssow, K. ED - Cantor, C. ED - Christians, F. ED - Chui, G. ED - Diaz, R. ED - Drmanac, R. ED - Drmanac, S. ED - Eickhoff, H. ED - Fellenberg, K. ED - Sridhar Hannenhalli ED - Hoheisel, J. ED - Hou, A. ED - Hubbell, E. ED - Jin, H. ED - Jin, P. ED - Jurinke, C. ED - Konthur, Z. ED - Köster, H. ED - Kwon, S. ED - Lacy, S. ED - Lehrach, H. ED - Lipshutz, R. ED - Little, D. ED - Lueking, A. ED - McGall, G. ED - Moeur, B. ED - Nordhoff, E. ED - Nyarsik, L. ED - Pevzner, P. ED - Robinson, A. ED - Sarkans, U. ED - Shafto, J. ED - Sohail, M. ED - Southern, E. ED - Swanson, D. ED - Ukrainczyk, T. ED - van den Boom, D. ED - Vilo, J. ED - Vingron, M. ED - Walter, G. ED - Xu, C. AB - Optimal design of DNA arrays requires the development of algorithms with two-fold goals: reducing the effects caused by unintended illumination ( border length minimization problem ) and reducing the complexity of masks ( mask decomposition problem ). We describe algorithms that reduce the number of rectangles in mask decomposition by 20–30% as compared to a standard array design under the assumption that the arrangement of oligonucleotides on the array is fixed. This algorithm produces provably optimal solution for all studied real instances of array design. We also address the difficult problem of finding an arrangement which minimizes the border length and come up with a new idea of threading that significantly reduces the border length as compared to standard designs. JA - Chip TechnologyChip Technology T3 - Advances in Biochemical Engineering/Biotechnology PB - Springer Berlin / Heidelberg VL - 77 SN - 978-3-540-43215-9 ER - TY - JOUR T1 - Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii JF - NatureNature Y1 - 2002 A1 - Carlton, Jane M. A1 - Angiuoli, Samuel V. A1 - Suh, Bernard B. A1 - Kooij, Taco W. A1 - Pertea, Mihaela A1 - Silva, Joana C. A1 - Ermolaeva, Maria D. A1 - Allen, Jonathan E. A1 - J. Selengut A1 - Koo, Hean L. A1 - Peterson, Jeremy D. A1 - M. Pop A1 - Kosack, Daniel S. A1 - Shumway, Martin F. A1 - Bidwell, Shelby L. A1 - Shallom, Shamira J. A1 - Aken, Susan E. van A1 - Riedmuller, Steven B. A1 - Feldblyum, Tamara V. A1 - Cho, Jennifer K. A1 - Quackenbush, John A1 - Sedegah, Martha A1 - Shoaibi, Azadeh A1 - Cummings, Leda M. A1 - Florens, Laurence A1 - Yates, John R. A1 - Raine, J. Dale A1 - Sinden, Robert E. A1 - Harris, Michael A. A1 - Cunningham, Deirdre A. A1 - Preiser, Peter R. A1 - Bergman, Lawrence W. A1 - Vaidya, Akhil B. A1 - Lin, Leo H. van A1 - Janse, Chris J. A1 - Waters, Andrew P. A1 - Smith, Hamilton O. A1 - White, Owen R. A1 - Salzberg, Steven L. A1 - Venter, J. Craig A1 - Fraser, Claire M. A1 - Hoffman, Stephen L. A1 - Gardner, Malcolm J. A1 - Carucci, Daniel J. AB - Species of malaria parasite that infect rodents have long been used as models for malaria disease research. Here we report the whole-genome shotgun sequence of one species, Plasmodium yoelii yoelii, and comparative studies with the genome of the human malaria parasite Plasmodium falciparum clone 3D7. A synteny map of 2,212 P. y. yoelii contiguous DNA sequences (contigs) aligned to 14 P. falciparum chromosomes reveals marked conservation of gene synteny within the body of each chromosome. Of about 5,300 P. falciparum genes, more than 3,300 P. y. yoelii orthologues of predominantly metabolic function were identified. Over 800 copies of a variant antigen gene located in subtelomeric regions were found. This is the first genome sequence of a model eukaryotic parasite, and it provides insight into the use of such systems in the modelling of Plasmodium biology and disease. VL - 419 SN - 0028-0836 ER - TY - JOUR T1 - Genome sequence of the human malaria parasite Plasmodium falciparum JF - NatureNature Y1 - 2002 A1 - Gardner, Malcolm J. A1 - Hall, Neil A1 - Fung, Eula A1 - White, Owen A1 - Berriman, Matthew A1 - Hyman, Richard W. A1 - Carlton, Jane M. A1 - Pain, Arnab A1 - Nelson, Karen E. A1 - Bowman, Sharen A1 - Paulsen, Ian T. A1 - James, Keith A1 - Eisen, Jonathan A. A1 - Rutherford, Kim A1 - Salzberg, Steven L. A1 - Craig, Alister A1 - Kyes, Sue A1 - Chan, Man-Suen A1 - Nene, Vishvanath A1 - Shallom, Shamira J. A1 - Suh, Bernard A1 - Peterson, Jeremy A1 - Angiuoli, Sam A1 - Pertea, Mihaela A1 - Allen, Jonathan A1 - J. Selengut A1 - Haft, Daniel A1 - Mather, Michael W. A1 - Vaidya, Akhil B. A1 - Martin, David M. A. A1 - Fairlamb, Alan H. A1 - Fraunholz, Martin J. A1 - Roos, David S. A1 - Ralph, Stuart A. A1 - McFadden, Geoffrey I. A1 - Cummings, Leda M. A1 - Subramanian, G. Mani A1 - Mungall, Chris A1 - Venter, J. Craig A1 - Carucci, Daniel J. A1 - Hoffman, Stephen L. A1 - Newbold, Chris A1 - Davis, Ronald W. A1 - Fraser, Claire M. A1 - Barrell, Bart KW - Animals KW - Chromosome Structures KW - DNA Repair KW - DNA Replication KW - DNA, Protozoan KW - Evolution, Molecular KW - Genome, Protozoan KW - HUMANS KW - Malaria Vaccines KW - Malaria, Falciparum KW - Membrane Transport Proteins KW - Molecular Sequence Data KW - Plasmodium falciparum KW - Plastids KW - Proteome KW - Protozoan Proteins KW - Recombination, Genetic KW - Sequence Analysis, DNA AB - The parasite Plasmodium falciparum is responsible for hundreds of millions of cases of malaria, and kills more than one million African children annually. Here we report an analysis of the genome sequence of P. falciparum clone 3D7. The 23-megabase nuclear genome consists of 14 chromosomes, encodes about 5,300 genes, and is the most (A + T)-rich genome sequenced to date. Genes involved in antigenic variation are concentrated in the subtelomeric regions of the chromosomes. Compared to the genomes of free-living eukaryotic microbes, the genome of this intracellular parasite encodes fewer enzymes and transporters, but a large proportion of genes are devoted to immune evasion and host-parasite interactions. Many nuclear-encoded proteins are targeted to the apicoplast, an organelle involved in fatty-acid and isoprenoid metabolism. The genome sequence provides the foundation for future studies of this organism, and is being exploited in the search for new drugs and vaccines to fight malaria. VL - 419 N1 - http://www.ncbi.nlm.nih.gov/pubmed/12368864?dopt=Abstract ER - TY - JOUR T1 - Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14 JF - NatureNature Y1 - 2002 A1 - Gardner, Malcolm J. A1 - Shallom, Shamira J. A1 - Carlton, Jane M. A1 - Salzberg, Steven L. A1 - Nene, Vishvanath A1 - Shoaibi, Azadeh A1 - Ciecko, Anne A1 - Lynn, Jeffery A1 - Rizzo, Michael A1 - Weaver, Bruce A1 - Jarrahi, Behnam A1 - Brenner, Michael A1 - Parvizi, Babak A1 - Tallon, Luke A1 - Moazzez, Azita A1 - Granger, David A1 - Fujii, Claire A1 - Hansen, Cheryl A1 - Pederson, James A1 - Feldblyum, Tamara A1 - Peterson, Jeremy A1 - Suh, Bernard A1 - Angiuoli, Sam A1 - Pertea, Mihaela A1 - Allen, Jonathan A1 - J. Selengut A1 - White, Owen A1 - Cummings, Leda M. A1 - Smith, Hamilton O. A1 - Adams, Mark D. A1 - Venter, J. Craig A1 - Carucci, Daniel J. A1 - Hoffman, Stephen L. A1 - Fraser, Claire M. KW - Animals KW - Chromosomes KW - DNA, Protozoan KW - Genome, Protozoan KW - Plasmodium falciparum KW - Proteome KW - Protozoan Proteins KW - Sequence Analysis, DNA AB - The mosquito-borne malaria parasite Plasmodium falciparum kills an estimated 0.7-2.7 million people every year, primarily children in sub-Saharan Africa. Without effective interventions, a variety of factors-including the spread of parasites resistant to antimalarial drugs and the increasing insecticide resistance of mosquitoes-may cause the number of malaria cases to double over the next two decades. To stimulate basic research and facilitate the development of new drugs and vaccines, the genome of Plasmodium falciparum clone 3D7 has been sequenced using a chromosome-by-chromosome shotgun strategy. We report here the nucleotide sequences of chromosomes 10, 11 and 14, and a re-analysis of the chromosome 2 sequence. These chromosomes represent about 35% of the 23-megabase P. falciparum genome. VL - 419 N1 - http://www.ncbi.nlm.nih.gov/pubmed/12368868?dopt=Abstract ER - TY - Generic T1 - Sequencing the human genome T2 - Proceedings of the sixth annual international conference on Computational biology Y1 - 2002 A1 - Venter, J. C. JA - Proceedings of the sixth annual international conference on Computational biology PB - ACM ER - TY - CONF T1 - Automatically tracking and analyzing the behavior of live insect colonies T2 - the fifth international conferenceProceedings of the fifth international conference on Autonomous agents - AGENTS '01 Y1 - 2001 A1 - Balch, Tucker A1 - Khan, Zia A1 - Veloso, Manuela JA - the fifth international conferenceProceedings of the fifth international conference on Autonomous agents - AGENTS '01 PB - ACM Press CY - Montreal, Quebec, CanadaNew York, New York, USA SN - 158113326X UR - http://portal.acm.org/citation.cfm?doid=375735http://portal.acm.org/citation.cfm?doid=375735.376434 M3 - 10.1145/37573510.1145/375735.376434 ER - TY - JOUR T1 - The genome sequence of Drosophila melanogaster. JF - Science Y1 - 2000 A1 - Adams, M D A1 - Celniker, S E A1 - Holt, R A A1 - Evans, C A A1 - Gocayne, J D A1 - Amanatides, P G A1 - Scherer, S E A1 - Li, P W A1 - Hoskins, R A A1 - Galle, R F A1 - George, R A A1 - Lewis, S E A1 - Richards, S A1 - Ashburner, M A1 - Henderson, S N A1 - Sutton, G G A1 - Wortman, J R A1 - Yandell, M D A1 - Zhang, Q A1 - Chen, L X A1 - Brandon, R C A1 - Rogers, Y H A1 - Blazej, R G A1 - Champe, M A1 - Pfeiffer, B D A1 - Wan, K H A1 - Doyle, C A1 - Baxter, E G A1 - Helt, G A1 - Nelson, C R A1 - Gabor, G L A1 - Abril, J F A1 - Agbayani, A A1 - An, H J A1 - Andrews-Pfannkoch, C A1 - Baldwin, D A1 - Ballew, R M A1 - Basu, A A1 - Baxendale, J A1 - Bayraktaroglu, L A1 - Beasley, E M A1 - Beeson, K Y A1 - Benos, P V A1 - Berman, B P A1 - Bhandari, D A1 - Bolshakov, S A1 - Borkova, D A1 - Botchan, M R A1 - Bouck, J A1 - Brokstein, P A1 - Brottier, P A1 - Burtis, K C A1 - Busam, D A A1 - Butler, H A1 - Cadieu, E A1 - Center, A A1 - Chandra, I A1 - Cherry, J M A1 - Cawley, S A1 - Dahlke, C A1 - Davenport, L B A1 - Davies, P A1 - de Pablos, B A1 - Delcher, A A1 - Deng, Z A1 - Mays, A D A1 - Dew, I A1 - Dietz, S M A1 - Dodson, K A1 - Doup, L E A1 - Downes, M A1 - Dugan-Rocha, S A1 - Dunkov, B C A1 - Dunn, P A1 - Durbin, K J A1 - Evangelista, C C A1 - Ferraz, C A1 - Ferriera, S A1 - Fleischmann, W A1 - Fosler, C A1 - Gabrielian, A E A1 - Garg, N S A1 - Gelbart, W M A1 - Glasser, K A1 - Glodek, A A1 - Gong, F A1 - Gorrell, J H A1 - Gu, Z A1 - Guan, P A1 - Harris, M A1 - Harris, N L A1 - Harvey, D A1 - Heiman, T J A1 - Hernandez, J R A1 - Houck, J A1 - Hostin, D A1 - Houston, K A A1 - Howland, T J A1 - Wei, M H A1 - Ibegwam, C A1 - Jalali, M A1 - Kalush, F A1 - Karpen, G H A1 - Ke, Z A1 - Kennison, J A A1 - Ketchum, K A A1 - Kimmel, B E A1 - Kodira, C D A1 - Kraft, C A1 - Kravitz, S A1 - Kulp, D A1 - Lai, Z A1 - Lasko, P A1 - Lei, Y A1 - Levitsky, A A A1 - Li, J A1 - Li, Z A1 - Liang, Y A1 - Lin, X A1 - Liu, X A1 - Mattei, B A1 - McIntosh, T C A1 - McLeod, M P A1 - McPherson, D A1 - Merkulov, G A1 - Milshina, N V A1 - Mobarry, C A1 - Morris, J A1 - Moshrefi, A A1 - Mount, S M A1 - Moy, M A1 - Murphy, B A1 - Murphy, L A1 - Muzny, D M A1 - Nelson, D L A1 - Nelson, D R A1 - Nelson, K A A1 - Nixon, K A1 - Nusskern, D R A1 - Pacleb, J M A1 - Palazzolo, M A1 - Pittman, G S A1 - Pan, S A1 - Pollard, J A1 - Puri, V A1 - Reese, M G A1 - Reinert, K A1 - Remington, K A1 - Saunders, R D A1 - Scheeler, F A1 - Shen, H A1 - Shue, B C A1 - Sidén-Kiamos, I A1 - Simpson, M A1 - Skupski, M P A1 - Smith, T A1 - Spier, E A1 - Spradling, A C A1 - Stapleton, M A1 - Strong, R A1 - Sun, E A1 - Svirskas, R A1 - Tector, C A1 - Turner, R A1 - Venter, E A1 - Wang, A H A1 - Wang, X A1 - Wang, Z Y A1 - Wassarman, D A A1 - Weinstock, G M A1 - Weissenbach, J A1 - Williams, S M A1 - Worley, K C A1 - Wu, D A1 - Yang, S A1 - Yao, Q A A1 - Ye, J A1 - Yeh, R F A1 - Zaveri, J S A1 - Zhan, M A1 - Zhang, G A1 - Zhao, Q A1 - Zheng, L A1 - Zheng, X H A1 - Zhong, F N A1 - Zhong, W A1 - Zhou, X A1 - Zhu, S A1 - Zhu, X A1 - Smith, H O A1 - Gibbs, R A A1 - Myers, E W A1 - Rubin, G M A1 - Venter, J C KW - Animals KW - Biological Transport KW - Chromatin KW - Cloning, Molecular KW - Computational Biology KW - Contig Mapping KW - Cytochrome P-450 Enzyme System KW - DNA Repair KW - DNA Replication KW - Drosophila melanogaster KW - Euchromatin KW - Gene Library KW - Genes, Insect KW - Genome KW - Heterochromatin KW - Insect Proteins KW - Nuclear Proteins KW - Protein Biosynthesis KW - Sequence Analysis, DNA KW - Transcription, Genetic AB -

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.

VL - 287 CP - 5461 ER - TY - JOUR T1 - Ligand-Receptor Pairing Via Tree Comparison JF - Journal of Computational BiologyJournal of Computational Biology Y1 - 2000 A1 - Bafna, Vineet A1 - Sridhar Hannenhalli A1 - Rice, Ken A1 - Vawter, Lisa AB - This paper introduces a novel class of tree comparison problems strongly motivated by an important and cost intensive step in drug discovery pipeline viz., mapping cell bound receptors to the ligands they bind to and vice versa. Tree comparison studies motivated by problems such as virus-host tree comparison, gene-species tree comparison and consensus tree problem have been reported. None of these studies are applicable in our context because in all these problems, there is a well-defined mapping of the nodes the trees are built on across the set of trees being compared. A new class of tree comparison problems arises in cases where finding the correspondence among the nodes of the trees being compared is itself the problem. The problem arises while trying to find the interclass correspondence between the members of a pair of coevolving classes, e.g., cell bound receptors and their ligands. Given the evolution of the two classes, the combinatorial problem is to find a mapping among the leaves of the two trees that optimizes a given cost function. In this work we formulate various combinatorial optimization problems motivated by the aforementioned biological problem for the first time. We present hardness results, give an efficient algorithm for a restriction of the problem and demonstrate its applicability. VL - 7 SN - 1066-5277, 1557-8666 ER - TY - JOUR T1 - Genetic nomenclature for Trypanosoma and Leishmania. JF - Mol Biochem Parasitol Y1 - 1998 A1 - Clayton, C A1 - Adams, M A1 - Almeida, R A1 - Baltz, T A1 - Barrett, M A1 - Bastien, P A1 - Belli, S A1 - Beverley, S A1 - Biteau, N A1 - Blackwell, J A1 - Blaineau, C A1 - Boshart, M A1 - Bringaud, F A1 - Cross, G A1 - Cruz, A A1 - Degrave, W A1 - Donelson, J A1 - El-Sayed, N A1 - Fu, G A1 - Ersfeld, K A1 - Gibson, W A1 - Gull, K A1 - Ivens, A A1 - Kelly, J A1 - Vanhamme, L KW - Animals KW - Leishmania KW - Terminology as Topic KW - Trypanosoma VL - 97 CP - 1-2 ER - TY - CHAP T1 - Towards a computational theory of genome rearrangements T2 - Computer Science TodayComputer Science Today Y1 - 1995 A1 - Sridhar Hannenhalli A1 - Pevzner, Pavel ED - van Leeuwen, Jan AB - Analysis of genome rearrangements in molecular biology started in the late 1930's, when Dobzhansky and Sturtevant published a milestone paper presenting a rearrangement scenario with 17 inversions for the species of Drosophila. However, until recently there were no computer science results allowing a biologist to analyze genome rearrangements. The paper describes combinatorial problems motivated by genome rearrangements, surveys recently developed algorithms for genomic sequence comparison and presents applications of these algorithms to analyze rearrangements in herpes viruses, plant organelles, and mammalian chromosomes. JA - Computer Science TodayComputer Science Today T3 - Lecture Notes in Computer Science PB - Springer Berlin / Heidelberg VL - 1000 SN - 978-3-540-60105-0 ER - TY - JOUR T1 - copia-like retrotransposons are ubiquitous among plants JF - Proc Natl Acad Sci USAProc Natl Acad Sci USA Y1 - 1992 A1 - Voytas, D. F. A1 - Michael P. Cummings A1 - Koniczny, A. A1 - Ausubel, F. M. A1 - Rodermel, S. R. AB - Transposable genetic elements are assumed to be a feature of all eukaryotic genomes. Their identification, however, has largely been haphazard, limited principally to organisms subjected to molecular or genetic scrutiny. We assessed the phylogenetic distribution of copia-like retrotransposons, a class of transposable element that proliferates by reverse transcription, using a polymerase chain reaction assay designed to detect copia-like element reverse transcriptase sequences. copia-like retrotransposons were identified in 64 plant species as well as the photosynthetic protist Volvox carteri. The plant species included representatives from 9 of 10 plant divisions, including bryophytes, lycopods, ferns, gymnosperms, and angiosperms. DNA sequence analysis of 29 cloned PCR products and of a maize retrotransposon cDNA confirmed the identity of these sequences as copia-like reverse transcriptase sequences, thereby demonstrating that this class of retrotransposons is a ubiquitous component of plant genomes. VL - 89 ER - TY - JOUR T1 - A superfamily of ıt Arabidopsis thaliana retrotransposons JF - GeneticsGenetics Y1 - 1991 A1 - Konieczny, A. A1 - Voytas, D. F. A1 - Michael P. Cummings A1 - Ausubel, F. M. AB - We describe a superfamily of Arabidopsis thaliana retrotransposable elements that consists of at least ten related families designated Ta1-Ta10. The Ta1 family has been described previously. Two genomic clones representing the Ta2 and Ta3 elements were isolated from an A. thaliana (race Landsberg erecta) lambda library using sequences derived from the reverse transcriptase region of Ta1 as hybridization probes. Nucleotide sequence analysis showed that the Ta1, Ta2 and Ta3 families share greater than 75% amino acid identity in pairwise comparisons of their reverse transcriptase and RNase H genes. In addition to Ta1, Ta2 and Ta3, we identified seven other related retrotransposon families in Landsberg erecta, Ta4-Ta10, using degenerate primers and the polymerase chain reaction to amplify a highly conserved region of retrotransposon-encoded reverse transcriptase. One to two copies of elements Ta2-Ta10 are present in the genomes of the A. thaliana races Landsberg erecta and Columbia indicating that the superfamily comprises at least 0.1% of the A. thaliana genome. The nucleotide sequences of the reverse transcriptase regions of the ten element families place them in the category of copia-like retrotransposons and phylogenetic analysis of the amino acid sequences suggests that horizontal transfer may have played a role in their evolution. VL - 127 ER - TY - JOUR T1 - The structure, distribution and evolution of the ıt Ta1 retrotransposable element family of ıt Arabidopsis thaliana JF - GeneticsGenetics Y1 - 1990 A1 - Voytas, D. F. A1 - Konieczny, A. A1 - Michael P. Cummings A1 - Ausubel, F. M. AB - The Ta1 elements are a low copy number, copia-like retrotransposable element family of Arabidopsis thaliana. Six Ta1 insertions comprise all of the Ta1 element copies found in three geographically diverse A. thaliana races. These six elements occupy three distinct target sites: Ta1-1 is located on chromosome 5 and is common to all three races (Col-0, Kas-1 and La-0). Ta1-2 is present in two races on chromosome 4 (Kas-1 and La-0), and Ta1-3, also located on chromosome 4, is present only in one race (La-0). The six Ta1 insertions share greater than 96% nucleotide identity, yet are likely to be incapable of further transposition due to deletions or nucleotide changes that alter either the coding capacity of the elements or conserved protein domains required for retrotransposition. Nucleotide sequence comparisons of these elements and the distribution of Ta1 among 12 additional A. thaliana geographical races suggest that Ta1-1 predated the global dispersal of A. thaliana. As the species spread throughout the world, two additional transposition events occurred which gave rise first to Ta1-2 and finally to Ta1-3. VL - 126 ER -