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-valueCONCLUSIONS: 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.
A1 - Lindblad-Toh, Kerstin
A1 - Llopart, Ana
A1 - Long, Manyuan
A1 - Low, Lloyd
A1 - Lozovsky, Elena
A1 - Lu, Jian
A1 - Luo, Meizhong
A1 - Machado, Carlos A.
A1 - Makalowski, Wojciech
A1 - Marzo, Mar
A1 - Matsuda, Muneo
A1 - Matzkin, Luciano
A1 - McAllister, Bryant
A1 - McBride, Carolyn S.
A1 - McKernan, Brendan
A1 - McKernan, Kevin
A1 - Mendez-Lago, Maria
A1 - Minx, Patrick
A1 - Mollenhauer, Michael U.
A1 - Montooth, Kristi
A1 - Stephen M. Mount
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 - M. Pop
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 - Schatz, Michael C.
A1 - Schlenke, Todd
A1 - Schwartz, Russell
A1 - Segarra, Carmen
A1 - Singh, Rama S.
A1 - Sirot, Laura
A1 - Sirota, Marina
A1 - Sisneros, Nicholas B.
A1 - Smith, Chris D.
A1 - Smith, Temple F.
A1 - Spieth, John
A1 - Stage, Deborah E.
A1 - Stark, Alexander
A1 - Stephan, Wolfgang
A1 - Strausberg, Robert L.
A1 - Strempel, Sebastian
A1 - Sturgill, David
A1 - Sutton, Granger
A1 - Sutton, Granger G.
A1 - Tao, Wei
A1 - Teichmann, Sarah
A1 - Tobari, Yoshiko N.
A1 - Tomimura, Yoshihiko
A1 - Tsolas, Jason M.
A1 - Valente, Vera L. S.
A1 - Venter, Eli
A1 - Venter, J. Craig
A1 - Vicario, Saverio
A1 - Vieira, Filipe G.
A1 - Vilella, Albert J.
A1 - Villasante, Alfredo
A1 - Walenz, Brian
A1 - Wang, Jun
A1 - Wasserman, Marvin
A1 - Watts, Thomas
A1 - Wilson, Derek
A1 - Wilson, Richard K.
A1 - Wing, Rod A.
A1 - Wolfner, Mariana F.
A1 - Wong, Alex
A1 - Wong, Gane Ka-Shu
A1 - Wu, Chung- I.
A1 - Wu, Gabriel
A1 - Yamamoto, Daisuke
A1 - Yang, Hsiao-Pei
A1 - Yang, Shiaw-Pyng
A1 - Yorke, James A.
A1 - Yoshida, Kiyohito
A1 - 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 - Haan, Georgius De
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
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 - 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
A1 - Lindblad-Toh, Kerstin
A1 - Llopart, Ana
A1 - Long, Manyuan
A1 - Low, Lloyd
A1 - Lozovsky, Elena
A1 - Lu, Jian
A1 - Luo, Meizhong
A1 - Machado, Carlos A
A1 - Makalowski, Wojciech
A1 - Marzo, Mar
A1 - Matsuda, Muneo
A1 - Matzkin, Luciano
A1 - McAllister, Bryant
A1 - McBride, Carolyn S
A1 - McKernan, Brendan
A1 - McKernan, Kevin
A1 - Mendez-Lago, Maria
A1 - 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 - Schatz, Michael C
A1 - Schlenke, Todd
A1 - Schwartz, Russell
A1 - Segarra, Carmen
A1 - Singh, Rama S
A1 - Sirot, Laura
A1 - Sirota, Marina
A1 - Sisneros, Nicholas B
A1 - Smith, Chris D
A1 - Smith, Temple F
A1 - Spieth, John
A1 - Stage, Deborah E
A1 - Stark, Alexander
A1 - Stephan, Wolfgang
A1 - Strausberg, Robert L
A1 - Strempel, Sebastian
A1 - Sturgill, David
A1 - Sutton, Granger
A1 - Sutton, Granger G
A1 - Tao, Wei
A1 - Teichmann, Sarah
A1 - Tobari, Yoshiko N
A1 - Tomimura, Yoshihiko
A1 - Tsolas, Jason M
A1 - Valente, Vera L S
A1 - Venter, Eli
A1 - Venter, J Craig
A1 - Vicario, Saverio
A1 - Vieira, Filipe G
A1 - Vilella, Albert J
A1 - Villasante, Alfredo
A1 - Walenz, Brian
A1 - Wang, Jun
A1 - Wasserman, Marvin
A1 - Watts, Thomas
A1 - Wilson, Derek
A1 - Wilson, Richard K
A1 - Wing, Rod A
A1 - Wolfner, Mariana F
A1 - Wong, Alex
A1 - Wong, Gane Ka-Shu
A1 - Wu, Chung-I
A1 - Wu, Gabriel
A1 - Yamamoto, Daisuke
A1 - Yang, Hsiao-Pei
A1 - Yang, Shiaw-Pyng
A1 - Yorke, James A
A1 - Yoshida, Kiyohito
A1 - 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 -