Pepin K

References (5)

Title : A catalog of reference genomes from the human microbiome - Nelson_2010_Science_328_994
Author(s) : Nelson KE , Weinstock GM , Highlander SK , Worley KC , Creasy HH , Wortman JR , Rusch DB , Mitreva M , Sodergren E , Chinwalla AT , Feldgarden M , Gevers D , Haas BJ , Madupu R , Ward DV , Birren BW , Gibbs RA , Methe B , Petrosino JF , Strausberg RL , Sutton GG , White OR , Wilson RK , Durkin S , Giglio MG , Gujja S , Howarth C , Kodira CD , Kyrpides N , Mehta T , Muzny DM , Pearson M , Pepin K , Pati A , Qin X , Yandava C , Zeng Q , Zhang L , Berlin AM , Chen L , Hepburn TA , Johnson J , McCorrison J , Miller J , Minx P , Nusbaum C , Russ C , Sykes SM , Tomlinson CM , Young S , Warren WC , Badger J , Crabtree J , Markowitz VM , Orvis J , Cree A , Ferriera S , Fulton LL , Fulton RS , Gillis M , Hemphill LD , Joshi V , Kovar C , Torralba M , Wetterstrand KA , Abouellleil A , Wollam AM , Buhay CJ , Ding Y , Dugan S , Fitzgerald MG , Holder M , Hostetler J , Clifton SW , Allen-Vercoe E , Earl AM , Farmer CN , Liolios K , Surette MG , Xu Q , Pohl C , Wilczek-Boney K , Zhu D
Ref : Science , 328 :994 , 2010
Abstract : The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.
ESTHER : Nelson_2010_Science_328_994
PubMedSearch : Nelson_2010_Science_328_994
PubMedID: 20489017
Gene_locus related to this paper: strp2-q04l35 , strpn-AXE1 , strpn-pepx

Title : The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes - Skaletsky_2003_Nature_423_825
Author(s) : Skaletsky H , Kuroda-Kawaguchi T , Minx PJ , Cordum HS , Hillier L , Brown LG , Repping S , Pyntikova T , Ali J , Bieri T , Chinwalla A , Delehaunty A , Delehaunty K , Du H , Fewell G , Fulton L , Fulton R , Graves T , Hou SF , Latrielle P , Leonard S , Mardis E , Maupin R , McPherson J , Miner T , Nash W , Nguyen C , Ozersky P , Pepin K , Rock S , Rohlfing T , Scott K , Schultz B , Strong C , Tin-Wollam A , Yang SP , Waterston RH , Wilson RK , Rozen S , Page DC
Ref : Nature , 423 :825 , 2003
Abstract : The male-specific region of the Y chromosome, the MSY, differentiates the sexes and comprises 95% of the chromosome's length. Here, we report that the MSY is a mosaic of heterochromatic sequences and three classes of euchromatic sequences: X-transposed, X-degenerate and ampliconic. These classes contain all 156 known transcription units, which include 78 protein-coding genes that collectively encode 27 distinct proteins. The X-transposed sequences exhibit 99% identity to the X chromosome. The X-degenerate sequences are remnants of ancient autosomes from which the modern X and Y chromosomes evolved. The ampliconic class includes large regions (about 30% of the MSY euchromatin) where sequence pairs show greater than 99.9% identity, which is maintained by frequent gene conversion (non-reciprocal transfer). The most prominent features here are eight massive palindromes, at least six of which contain testis genes.
ESTHER : Skaletsky_2003_Nature_423_825
PubMedSearch : Skaletsky_2003_Nature_423_825
PubMedID: 12815422
Gene_locus related to this paper: human-NLGN4Y

Title : Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana - Tabata_2000_Nature_408_823
Author(s) : Tabata S , Kaneko T , Nakamura Y , Kotani H , Kato T , Asamizu E , Miyajima N , Sasamoto S , Kimura T , Hosouchi T , Kawashima K , Kohara M , Matsumoto M , Matsuno A , Muraki A , Nakayama S , Nakazaki N , Naruo K , Okumura S , Shinpo S , Takeuchi C , Wada T , Watanabe A , Yamada M , Yasuda M , Sato S , de la Bastide M , Huang E , Spiegel L , Gnoj L , O'Shaughnessy A , Preston R , Habermann K , Murray J , Johnson D , Rohlfing T , Nelson J , Stoneking T , Pepin K , Spieth J , Sekhon M , Armstrong J , Becker M , Belter E , Cordum H , Cordes M , Courtney L , Courtney W , Dante M , Du H , Edwards J , Fryman J , Haakensen B , Lamar E , Latreille P , Leonard S , Meyer R , Mulvaney E , Ozersky P , Riley A , Strowmatt C , Wagner-McPherson C , Wollam A , Yoakum M , Bell M , Dedhia N , Parnell L , Shah R , Rodriguez M , See LH , Vil D , Baker J , Kirchoff K , Toth K , King L , Bahret A , Miller B , Marra M , Martienssen R , McCombie WR , Wilson RK , Murphy G , Bancroft I , Volckaert G , Wambutt R , Dusterhoft A , Stiekema W , Pohl T , Entian KD , Terryn N , Hartley N , Bent E , Johnson S , Langham SA , McCullagh B , Robben J , Grymonprez B , Zimmermann W , Ramsperger U , Wedler H , Balke K , Wedler E , Peters S , van Staveren M , Dirkse W , Mooijman P , Lankhorst RK , Weitzenegger T , Bothe G , Rose M , Hauf J , Berneiser S , Hempel S , Feldpausch M , Lamberth S , Villarroel R , Gielen J , Ardiles W , Bents O , Lemcke K , Kolesov G , Mayer K , Rudd S , Schoof H , Schueller C , Zaccaria P , Mewes HW , Bevan M , Fransz P
Ref : Nature , 408 :823 , 2000
Abstract : The genome of the model plant Arabidopsis thaliana has been sequenced by an international collaboration, The Arabidopsis Genome Initiative. Here we report the complete sequence of chromosome 5. This chromosome is 26 megabases long; it is the second largest Arabidopsis chromosome and represents 21% of the sequenced regions of the genome. The sequence of chromosomes 2 and 4 have been reported previously and that of chromosomes 1 and 3, together with an analysis of the complete genome sequence, are reported in this issue. Analysis of the sequence of chromosome 5 yields further insights into centromere structure and the sequence determinants of heterochromatin condensation. The 5,874 genes encoded on chromosome 5 reveal several new functions in plants, and the patterns of gene organization provide insights into the mechanisms and extent of genome evolution in plants.
ESTHER : Tabata_2000_Nature_408_823
PubMedSearch : Tabata_2000_Nature_408_823
PubMedID: 11130714
Gene_locus related to this paper: arath-At5g11650 , arath-At5g16120 , arath-at5g18630 , arath-AT5G20520 , arath-At5g21950 , arath-AT5G27320 , arath-CXE15 , arath-F1N13.220 , arath-F14F8.240 , arath-q3e9e4 , arath-q8lae9 , arath-Q8LFB7 , arath-q9ffg7 , arath-q9fij5 , arath-Q9LVU7 , arath-q66gm8 , arath-SCPL34 , arath-B9DFR3 , arath-a0a1p8bcz0

Title : Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana - Mayer_1999_Nature_402_769
Author(s) : Mayer K , Schuller C , Wambutt R , Murphy G , Volckaert G , Pohl T , Dusterhoft A , Stiekema W , Entian KD , Terryn N , Harris B , Ansorge W , Brandt P , Grivell L , Rieger M , Weichselgartner M , de Simone V , Obermaier B , Mache R , Muller M , Kreis M , Delseny M , Puigdomenech P , Watson M , Schmidtheini T , Reichert B , Portatelle D , Perez-Alonso M , Boutry M , Bancroft I , Vos P , Hoheisel J , Zimmermann W , Wedler H , Ridley P , Langham SA , McCullagh B , Bilham L , Robben J , Van der Schueren J , Grymonprez B , Chuang YJ , Vandenbussche F , Braeken M , Weltjens I , Voet M , Bastiaens I , Aert R , Defoor E , Weitzenegger T , Bothe G , Ramsperger U , Hilbert H , Braun M , Holzer E , Brandt A , Peters S , van Staveren M , Dirske W , Mooijman P , Klein Lankhorst R , Rose M , Hauf J , Kotter P , Berneiser S , Hempel S , Feldpausch M , Lamberth S , Van den Daele H , De Keyser A , Buysshaert C , Gielen J , Villarroel R , De Clercq R , van Montagu M , Rogers J , Cronin A , Quail M , Bray-Allen S , Clark L , Doggett J , Hall S , Kay M , Lennard N , McLay K , Mayes R , Pettett A , Rajandream MA , Lyne M , Benes V , Rechmann S , Borkova D , Blocker H , Scharfe M , Grimm M , Lohnert TH , Dose S , de Haan M , Maarse A , Schafer M , Muller-Auer S , Gabel C , Fuchs M , Fartmann B , Granderath K , Dauner D , Herzl A , Neumann S , Argiriou A , Vitale D , Liguori R , Piravandi E , Massenet O , Quigley F , Clabauld G , Mundlein A , Felber R , Schnabl S , Hiller R , Schmidt W , Lecharny A , Aubourg S , Chefdor F , Cooke R , Berger C , Montfort A , Casacuberta E , Gibbons T , Weber N , Vandenbol M , Bargues M , Terol J , Torres A , Perez-Perez A , Purnelle B , Bent E , Johnson S , Tacon D , Jesse T , Heijnen L , Schwarz S , Scholler P , Heber S , Francs P , Bielke C , Frishman D , Haase D , Lemcke K , Mewes HW , Stocker S , Zaccaria P , Bevan M , Wilson RK , de la Bastide M , Habermann K , Parnell L , Dedhia N , Gnoj L , Schutz K , Huang E , Spiegel L , Sehkon M , Murray J , Sheet P , Cordes M , Abu-Threideh J , Stoneking T , Kalicki J , Graves T , Harmon G , Edwards J , Latreille P , Courtney L , Cloud J , Abbott A , Scott K , Johnson D , Minx P , Bentley D , Fulton B , Miller N , Greco T , Kemp K , Kramer J , Fulton L , Mardis E , Dante M , Pepin K , Hillier L , Nelson J , Spieth J , Ryan E , Andrews S , Geisel C , Layman D , Du H , Ali J , Berghoff A , Jones K , Drone K , Cotton M , Joshu C , Antonoiu B , Zidanic M , Strong C , Sun H , Lamar B , Yordan C , Ma P , Zhong J , Preston R , Vil D , Shekher M , Matero A , Shah R , Swaby IK , O'Shaughnessy A , Rodriguez M , Hoffmann J , Till S , Granat S , Shohdy N , Hasegawa A , Hameed A , Lodhi M , Johnson A , Chen E , Marra M , Martienssen R , McCombie WR
Ref : Nature , 402 :769 , 1999
Abstract : The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.
ESTHER : Mayer_1999_Nature_402_769
PubMedSearch : Mayer_1999_Nature_402_769
PubMedID: 10617198
Gene_locus related to this paper: arath-AT4G00500 , arath-AT4G16690 , arath-AT4G17480 , arath-AT4G24380 , arath-AT4g30610 , arath-o65513 , arath-o65713 , arath-LPAAT , arath-f4jt64

Title : The DNA sequence of human chromosome 22 - Dunham_1999_Nature_402_489
Author(s) : Dunham I , Hunt AR , Collins JE , Bruskiewich R , Beare DM , Clamp M , Smink LJ , Ainscough R , Almeida JP , Babbage AK , Bagguley C , Bailey J , Barlow KF , Bates KN , Beasley OP , Bird CP , Blakey SE , Bridgeman AM , Buck D , Burgess J , Burrill WD , Burton J , Carder C , Carter NP , Chen Y , Clark G , Clegg SM , Cobley VE , Cole CG , Collier RE , Connor R , Conroy D , Corby NR , Coville GJ , Cox AV , Davis J , Dawson E , Dhami PD , Dockree C , Dodsworth SJ , Durbin RM , Ellington AG , Evans KL , Fey JM , Fleming K , French L , Garner AA , Gilbert JGR , Goward ME , Grafham DV , Griffiths MND , Hall C , Hall RE , Hall-Tamlyn G , Heathcott RW , Ho S , Holmes S , Hunt SE , Jones MC , Kershaw J , Kimberley AM , King A , Laird GK , Langford CF , Leversha MA , Lloyd C , Lloyd DM , Martyn ID , Mashreghi-Mohammadi M , Matthews LH , Mccann OT , Mcclay J , Mclaren S , McMurray AA , Milne SA , Mortimore BJ , Odell CN , Pavitt R , Pearce AV , Pearson D , Phillimore BJCT , Phillips SH , Plumb RW , Ramsay H , Ramsey Y , Rogers L , Ross MT , Scott CE , Sehra HK , Skuce CD , Smalley S , Smith ML , Soderlund C , Spragon L , Steward CA , Sulston JE , Swann RM , Vaudin M , Wall M , Wallis JM , Whiteley MN , Willey DL , Williams L , Williams SA , Williamson H , Wilmer TE , Wilming L , Wright CL , Hubbard T , Bentley DR , Beck S , Rogers J , Shimizu N , Minoshima S , Kawasaki K , Sasaki T , Asakawa S , Kudoh J , Shintani A , Shibuya K , Yoshizaki Y , Aoki N , Mitsuyama S , Roe BA , Chen F , Chu L , Crabtree J , Deschamps S , Do A , Do T , Dorman A , Fang F , Fu Y , Hu P , Hua A , Kenton S , Lai H , Lao HI , Lewis J , Lewis S , Lin S-P , Loh P , Malaj E , Nguyen T , Pan H , Phan S , Qi S , Qian Y , Ray L , Ren Q , Shaull S , Sloan D , Song L , Wang Q , Wang Y , Wang Z , White J , Willingham D , Wu H , Yao Z , Zhan M , Zhang G , Chissoe S , Murray J , Miller N , Minx P , Fulton R , Johnson D , Bemis G , Bentley D , Bradshaw H , Bourne S , Cordes M , Du Z , Fulton L , Goela D , Graves T , Hawkins J , Hinds K , Kemp K , Latreille P , Layman D , Ozersky P , Rohlfing T , Scheet P , Walker C , Wamsley A , Wohldmann P , Pepin K , Nelson J , Korf I , Bedell JA , Hillier L , Mardis E , Waterston R , Wilson R , Emanuel BS , Shaikh T , Kurahashi H , Saitta S , Budarf ML , McDermid HE , Johnson A , Wong ACC , Morrow BE , Edelmann L , Kim UJ , Shizuya H , Simon MI , Dumanski JP , Peyrard M , Kedra D , Seroussi E , Fransson I , Tapia I , Bruder CE , O'Brien KP
Ref : Nature , 402 :489 , 1999
Abstract : Knowledge of the complete genomic DNA sequence of an organism allows a systematic approach to defining its genetic components. The genomic sequence provides access to the complete structures of all genes, including those without known function, their control elements, and, by inference, the proteins they encode, as well as all other biologically important sequences. Furthermore, the sequence is a rich and permanent source of information for the design of further biological studies of the organism and for the study of evolution through cross-species sequence comparison. The power of this approach has been amply demonstrated by the determination of the sequences of a number of microbial and model organisms. The next step is to obtain the complete sequence of the entire human genome. Here we report the sequence of the euchromatic part of human chromosome 22. The sequence obtained consists of 12 contiguous segments spanning 33.4 megabases, contains at least 545 genes and 134 pseudogenes, and provides the first view of the complex chromosomal landscapes that will be found in the rest of the genome.
ESTHER : Dunham_1999_Nature_402_489
PubMedSearch : Dunham_1999_Nature_402_489
PubMedID: 10591208
Gene_locus related to this paper: human-CES5A , human-SERHL2