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GST Primary GST Primary Best Strategies for Health Care Quality Im... Best Strategies for Health Care Quality Improvement - Diabetes Quality Improvement Strategies for Antibio... Kathryn McDonald, Stanford-UCSF Evidence-b... Systematic review assessing the effect of ... Quality Improvement Strategies for Antibiotics Management Kathryn McDonald, Stanford-UCSF Evidence-based Practice Center, 117 Encina Commons, Stanford, CA 94305-6019, Kathy.mcdonald@stanford.edu Systematic review assessing the effect of quality improvement strategies on appropriate prescribing of antibiotics and appropriate choice of antibiotics. Adherence Adherence Assistive Devices Assistive Devices Childhood Burn Hanson MacMillan Childhood Burn Hanson MacMillan CLSA_9 CLSA_9 Cyberabuse Cyberabuse Cognitive Behavioural Therapy for Violent ... This review included randomized trials abo... Cognitive Behavioural Therapy for Violent Men who Batter Their Partners This review included randomized trials about the effects of cognitive behavioral therapy on domestic violence. The intervention included programs based on the Duluth Model. The violence had to be committed by a male toward his female partner. The violence also had to be physical. The primary outcomes were new arrests and convictions, and new reports of violence. CABG vs PCI CABG vs PCI Quality Improvement Strategies for Prevent... Quality Improvement Strategies for Preventing Nosocomial Infections (Created 17-Feb-06) Quality Improvement Strategies for Asthma ... Quality Improvement Strategies for Asthma Control Erectile Dysfunction (Created 30-Jan-06) Erectile Dysfunction (Created 30-Jan-06) Inequality - Smoking Cessation to Reduce S... This review was the first part of a projec... Inequality - Smoking Cessation to Reduce Socio-Economic Differences This review was the first part of a project about inequality. It included randomized trials about the effect of smoking cessation interventions on reducing socio-economic differences. The studies had to report data either on persons with low socio-economic groups status or, preferably, on both low and high socio-economic groups. Diet and Physical Activity to Reduce Socio... This review was the second part in a proje... Diet and Physical Activity to Reduce Socio-Economic Differences This review was the second part in a project about inequality. It included randomized trials about the effect of interventions on reducing socio-economic differences in diet and physical activity. The studies had to report data either on persons with low socio-economic groups status or, preferably, on both low and high socio-economic groups. Workfare The data in SRS are not identical to the d... Workfare The data in SRS are not identical to the data in the published report. We used SRS only for an updated search. The review included randomized trials about the effect of welfare-to-work programs. Participants were welfare recipients. There were basically two types of programs. The educational type tried to build knowledge and skills in order to help the welfare recipients acquire jobs that could support them economically. The "work first" approach was more aimed at getting the participants quickly into a job. Exercise interventions for the management ... The objective of this systematic review wa... Exercise interventions for the management of frailty The objective of this systematic review was to examine the effectiveness of current exercise interventions on the management of frailty. A comprehensive search of Medline, Embase, Psycinfo, Cinahl, Scopus, Ageline, Eric, and SportDiscus databases was conducted and produced 1808 citations. So far we have completed 2 levels of “title and abstract” screening and we ended up with 262 articles. We have just started the full text screening. Eligibility criteria included original studies whose participants were identified as frail or prefrail with specific criteria and in which structured physical activity was included as at least one component of the intervention. Create a free account, build a dictionary with saved terms to re-use later! Public Domestic Violence - Using Cognitive Behavior Therapy Smoking Cessation to Reduce Socio-Economic Differences Diet and Physical Activity to Reduce Socio-Economic Differences Workfare Exercise Interventions for the Management of Frailty Search     Simple Advanced Refine (2 coded questions)  Any of these:   Exact Phrase: All of these: None of these: Author: Periodical: Projects: No restrictions   Libraries: Public   Select SRS Projects Show Saved Terms Select Library Show articles that do not have abstracts  Type of Article Clinical Trial Editorial Letter Meta-Analysis Practice Guideline Randomized Controlled Trial Review Addresses Bibliography Biography Case Reports Classical Article Clinical Conference Clinical Trial, Phase I Clinical Trial, Phase II Clinical Trial, Phase III Clinical Trial, Phase IV Comment Comparative Study Consensus Development Conference Consensus Development Conference, NIH Controlled Clinical Trial Corrected and Republished Article Dictionary Directory Duplicate Publication English Abstract Evaluation Studies Festschrift Government Publications Guideline Historical Article Interview In Vitro Journal Article Lectures Legal Cases Legislation Multicenter Study News Newspaper Article Overall Patient Education Handout Periodical Index Published Erratum Retracted Publication Research Support, N.I.H., Extramural Research Support, N.I.H., Intramural Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. 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Retraction of Publication Scientific Integrity Review Support of Research Technical Report Twin Study Validation Studies Not a Primary Study or Review Unknown Primary Study Case Series Case Control Cohort Study Observational Study Qualitative Research CBA or ITS Registry Double Blind Controlled before after study Quasi-randomized trial Simple before after study Cluster-RCT Non-Randomized Study Report Book Book chapter Dissertation Conference procedings Secondary Research Not RCT Humans or Animals Humans Animals Results(1-13 of 13) Sort By: Publication Date Relevance Took: 1.422 seconds to search 17,750,454  Action: Copy Results to new Clipboard Build Search Link Page 1 of 1 1 (13 articles found) Improving Phrap-based assembly of the rat using "reliable" overlaps. 2008 Michael Roberts,Aleksey V Zimin,Wayne Hayes,Brian R Hunt,Cevat Ustun,James R White,Paul Havlak,James Yorke The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of "reliable" overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have crea... ( view more )ted a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our "reliable-overlap" algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles Evolutionary and biomedical insights from the rhesus macaque genome. Apr 13, 2007 Rhesus Macaque Genome Sequencing and Analysis Consortium ,Richard A Gibbs,Jeffrey Rogers,Michael G Katze,Roger Bumgarner,George M Weinstock,Elaine R Mardis,Karin A Remington,Robert L Strausberg,J Craig Venter,Richard K Wilson,Mark A Batzer,Carlos D Bustamante,Evan E Eichler,Matthew W Hahn,Ross C Hardison,Kateryna D Makova,Webb Miller,Aleksandar Milosavljevic,Robert E Palermo,Adam Siepel,James M Sikela,Tony Attaway,Stephanie Bell,Kelly E Bernard,Christian J Buhay,Mimi N Chandrabose,Marvin Dao,Clay Davis,Kimberly D Delehaunty,Yan Ding,Huyen H Dinh,Shannon Dugan-Rocha,Lucinda A Fulton,Ramatu Ayiesha Gabisi,Toni T Garner,Jennifer Godfrey,Alicia C Hawes,Judith Hernandez,Sandra Hines,Michael Holder,Jennifer Hume,Shalini N Jhangiani,Vandita Joshi,Ziad Mohid Khan,Ewen F Kirkness,Andrew Cree,R Gerald Fowler,Sandra Lee,Lora R Lewis,Zhangwan Li,Yih-Shin Liu,Stephanie M Moore,Donna Muzny,Lynne V Nazareth,Dinh Ngoc Ngo,Geoffrey O Okwuonu,Grace Pai,David Parker,Heidie A Paul,Cynthia Pfannkoch,Craig S Pohl,Yu-Hui Rogers,San Juana Ruiz,Aniko Sabo,Jireh Santibanez,Brian W Schneider,Scott M Smith,Erica Sodergren,Amanda F Svatek,Teresa R Utterback,Selina Vattathil,Wesley Warren,Courtney Sherell White,Asif T Chinwalla,Yucheng Feng,Aaron L Halpern,Ladeana W Hillier,Xiaoqiu Huang,Pat Minx,Joanne O Nelson,Kymberlie H Pepin,Xiang Qin,Granger G Sutton,Eli Venter,Brian P Walenz,John W Wallis,Kim C Worley,Shiaw-Pyng Yang,Steven M Jones,Marco A Marra,Mariano Rocchi,Jacqueline E Schein,Robert Baertsch,Laura Clarke,Miklós Csürös,Jarret Glasscock,R Alan Harris,Paul Havlak,Andrew R Jackson,Huaiyang Jiang,Yue Liu,David N Messina,Yufeng Shen,Henry Xing-Zhi Song,Todd Wylie,Lan Zhang,Ewan Birney,Kyudong Han,Miriam K Konkel,Jungnam Lee,Arian F A Smit,Brygg Ullmer,Hui Wang,Jinchuan Xing,Richard Burhans,Ze Cheng,John E Karro,Jian Ma,Brian Raney,Xinwei She,Michael J Cox,Jeffery P Demuth,Laura J Dumas,Sang-Gook Han,Janet Hopkins,Anis Karimpour-Fard,Young H Kim,Jonathan R Pollack,Tomas Vinar,Charles Addo-Quaye,Jeremiah Degenhardt,Alexandra Denby,Melissa J Hubisz,Amit Indap,Carolin Kosiol,Bruce T Lahn,Heather A Lawson,Alison Marklein,Rasmus Nielsen,Eric J Vallender,Andrew G Clark,Betsy Ferguson,Ryan D Hernandez,Kashif Hirani,Hildegard Kehrer-Sawatzki,Jessica Kolb,Shobha Patil,Ling-Ling Pu,Yanru Ren,David Glenn Smith,David A Wheeler,Ian Schenck,Edward V Ball,Rui Chen,David N Cooper,Belinda Giardine,Fan Hsu,W James Kent,Arthur Lesk,David L Nelson,William E O'brien,Kay Prüfer,Peter D Stenson,James C Wallace,Hui Ke,Xiao-Ming Liu,Peng Wang,Andy Peng Xiang,Fan Yang,Galt P Barber,David Haussler,Donna Karolchik,Andy D Kern,Robert M Kuhn,Kayla E Smith,Ann S Zwieg The rhesus macaque (Macaca mulatta) is an abundant primate species that diverged from the ancestors of Homo sapiens about 25 million years ago. Because they are genetically and physiologically similar to humans, rhesus monkeys are the most widely used nonhuman primate in basic and applied biomedica... ( view more )l research. We determined the genome sequence of an Indian-origin Macaca mulatta female and compared the data with chimpanzees and humans to reveal the structure of ancestral primate genomes and to identify evidence for positive selection and lineage-specific expansions and contractions of gene families. A comparison of sequences from individual animals was used to investigate their underlying genetic diversity. The complete description of the macaque genome blueprint enhances the utility of this animal model for biomedical research and improves our understanding of the basic biology of the species. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments. Aug 29, 2006 William Salerno,Paul Havlak,Jonathan Miller A power-law distribution of the length of perfectly conserved sequence from mouse/human whole-genome intersection and alignment is exhibited. Spatial correlations of these elements within the mouse genome are studied. It is argued that these power-law distributions and correlations are comprised in... ( view more ) part by functional noncoding sequence and ought to be accounted for in estimating the statistical significance of apparent sequence conservation. These inter-genomic correlations of conservation are placed in the context of previously observed intra-genomic correlations, and their possible origins and consequences are discussed. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles The DNA sequence, annotation and analysis of human chromosome 3. Apr 27, 2006 Donna M Muzny,Steven E Scherer,Rajinder Kaul,Jing Wang,Jun Yu,Ralf Sudbrak,Christian J Buhay,Rui Chen,Andrew Cree,Yan Ding,Shannon Dugan-Rocha,Rachel Gill,Preethi Gunaratne,R Alan Harris,Alicia C Hawes,Judith Hernandez,Anne V Hodgson,Jennifer Hume,Andrew Jackson,Ziad Mohid Khan,Christie Kovar-Smith,Lora R Lewis,Ryan J Lozado,Michael L Metzker,Aleksandar Milosavljevic,George R Miner,Margaret B Morgan,Lynne V Nazareth,Graham Scott,Erica Sodergren,Xing-Zhi Song,David Steffen,Sharon Wei,David A Wheeler,Mathew W Wright,Kim C Worley,Ye Yuan,Zhengdong Zhang,Charles Q Adams,M Ali Ansari-Lari,Mulu Ayele,Mary J Brown,Guan Chen,Zhijian Chen,James Clendenning,Kerstin P Clerc-Blankenburg,Runsheng Chen,Zhu Chen,Clay Davis,Oliver Delgado,Huyen H Dinh,Wei Dong,Heather Draper,Stephen Ernst,Gang Fu,Manuel L Gonzalez-Garay,Dawn K Garcia,Will Gillett,Jun Gu,Bailin Hao,Eric Haugen,Paul Havlak,Xin He,Steffen Hennig,Songnian Hu,Wei Huang,Laronda R Jackson,Leni S Jacob,Susan H Kelly,Michael Kube,Ruth Levy,Zhangwan Li,Bin Liu,Jing Liu,Wen Liu,Jing Lu,Manjula Maheshwari,Bao-Viet Nguyen,Geoffrey O Okwuonu,Anthony Palmeiri,Shiran Pasternak,Lesette M Perez,Karen A Phelps,Farah J H Plopper,Boqin Qiang,Christopher Raymond,Ruben Rodriguez,Channakhone Saenphimmachak,Jireh Santibanez,Hua Shen,Yan Shen,Sandhya Subramanian,Paul E Tabor,Daniel Verduzco,Lenee Waldron,Jian Wang,Jun Wang,Qiaoyan Wang,Gabrielle A Williams,Gane K-S Wong,Zhijian Yao,JingKun Zhang,Xiuqing Zhang,Guoping Zhao,Jianling Zhou,Yang Zhou,David Nelson,Hans Lehrach,Richard Reinhardt,Susan L Naylor,Huanming Yang,Maynard Olson,George Weinstock,Richard A Gibbs After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chrom... ( view more )osomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest unbroken stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also includes a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles The finished DNA sequence of human chromosome 12. Mar 16, 2006 Steven E Scherer,Donna M Muzny,Christian J Buhay,Rui Chen,Andrew Cree,Yan Ding,Shannon Dugan-Rocha,Rachel Gill,Preethi Gunaratne,R Alan Harris,Alicia C Hawes,Judith Hernandez,Anne V Hodgson,Jennifer Hume,Andrew Jackson,Ziad Mohid Khan,Christie Kovar-Smith,Lora R Lewis,Ryan J Lozado,Michael L Metzker,Aleksandar Milosavljevic,George R Miner,Kate T Montgomery,Margaret B Morgan,Lynne V Nazareth,Graham Scott,Erica Sodergren,Xing-Zhi Song,David Steffen,Ruth C Lovering,David A Wheeler,Kim C Worley,Yi Yuan,Zhengdong Zhang,Charles Q Adams,M Ali Ansari-Lari,Mulu Ayele,Mary J Brown,Guan Chen,Zhijian Chen,Kerstin P Clerc-Blankenburg,Clay Davis,Oliver Delgado,Huyen H Dinh,Heather Draper,Manuel L Gonzalez-Garay,Paul Havlak,Laronda R Jackson,Leni S Jacob,Susan H Kelly,Li Li,Zhangwan Li,Jing Liu,Wen Liu,Jing Lu,Manjula Maheshwari,Bao-Viet Nguyen,Geoffrey O Okwuonu,Shiran Pasternak,Lesette M Perez,Farah J H Plopper,Jireh Santibanez,Hua Shen,Paul E Tabor,Daniel Verduzco,Lenee Waldron,Qiaoyan Wang,Gabrielle A Williams,Jingkun Zhang,Jianling Zhou,Carlana C Allen,Anita G Amin,Vivian Anyalebechi,Michael Bailey,Joseph A Barbaria,Kesha E Bimage,Nathaniel P Bryant,Paula E Burch,Carrie E Burkett,Kevin L Burrell,Eliana Calderon,Veronica Cardenas,Kelvin Carter,Kristal Casias,Iracema Cavazos,Sandra R Cavazos,Heather Ceasar,Joseph Chacko,Sheryl N Chan,Dean Chavez,Constantine Christopoulos,Joseph Chu,Raynard Cockrell,Caroline D Cox,Michelle Dang,Stephanie R Dathorne,Robert David,Candi Mon'Et Davis,Latarsha Davy-Carroll,Denise R Deshazo,Jeremy E Donlin,Lisa D'Souza,Kristy A Eaves,Amy Egan,Alexandra J Emery-Cohen,Michael Escotto,Nicole Flagg,Lisa D Forbes,Abdul M Gabisi,Melissa Garza,Cerissa Hamilton,Nicholas Henderson,Omar Hernandez,Sandra Hines,Marilyn E Hogues,Mei Huang,DeVincent G Idlebird,Rudy Johnson,Angela Jolivet,Sally Jones,Ryan Kagan,Laquisha M King,Belita Leal,Heather Lebow,Sandra Lee,Jaclyn M LeVan,Lakeshia C Lewis,Pamela London,Lorna M Lorensuhewa,Hermela Loulseged,Demetria A Lovett,Alice Lucier,Raymond L Lucier,Jie Ma,Renita C Madu,Patricia Mapua,Ashley D Martindale,Evangelina Martinez,Elizabeth Massey,Samantha Mawhiney,Michael G Meador,Sylvia Mendez,Christian Mercado,Iracema C Mercado,Christina E Merritt,Zachary L Miner,Emmanuel Minja,Teresa Mitchell,Farida Mohabbat,Khatera Mohabbat,Baize Montgomery,Niki Moore,Sidney Morris,Mala Munidasa,Robin N Ngo,Ngoc B Nguyen,Elizabeth Nickerson,Ogechi O Nwaokelemeh,Stanley Nwokenkwo,Melissa Obregon,Maryann Oguh,Njideka Oragunye,Rodolfo J Oviedo,Bridgette J Parish,David N Parker,Julia Parrish,Kenya L Parks,Heidie A Paul,Brett A Payton,Agapito Perez,William Perrin,Adam Pickens,Eltrick L Primus,Ling-Ling Pu,Maria Puazo,Miyo M Quiles,Juana B Quiroz,Dina Rabata,Kacy Reeves,San Juana Ruiz,Hongmei Shao,Ida Sisson,Titilola Sonaike,Richard P Sorelle,Angelica E Sutton,Amanda F Svatek,Leah Anne Svetz,Kavitha S Tamerisa,Tineace R Taylor,Brian Teague,Nicole Thomas,Rachel D Thorn,Zulma Y Trejos,Brenda K Trevino,Ogechi N Ukegbu,Jeremy B Urban,Lydia I Vasquez,Virginia A Vera,Donna M Villasana,Ling Wang,Stephanie Ward-Moore,James T Warren,Xuehong Wei,Flower White,Angela L Williamson,Regina Wleczyk,Hailey S Wooden,Steven H Wooden,Jennifer Yen,Lillienne Yoon,Vivienne Yoon,Sara E Zorrilla,David Nelson,Raju Kucherlapati,George Weinstock,Richard A Gibbs,Baylor College of Medicine Human Genome Sequencing Center Sequence Production Team Human chromosome 12 contains more than 1,400 coding genes and 487 loci that have been directly implicated in human disease. The q arm of chromosome 12 contains one of the largest blocks of linkage disequilibrium found in the human genome. Here we present the finished sequence of human chromosome 12... ( view more ), which has been finished to high quality and spans approximately 132 megabases, representing approximately 4.5% of the human genome. Alignment of the human chromosome 12 sequence across vertebrates reveals the origin of individual segments in chicken, and a unique history of rearrangement through rodent and primate lineages. The rate of base substitutions in recent evolutionary history shows an overall slowing in hominids compared with primates and rodents. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles MicroRNA enrichment among short 'ultraconserved' sequences in insects. 2006 T Tran,P Havlak,J Miller MicroRNAs are short (approximately 22 nt) regulatory RNA molecules that play key roles in metazoan development and have been implicated in human disease. First discovered in Caenorhabditis elegans, over 2500 microRNAs have been isolated in metazoans and plants; it has been estimated that there may ... ( view more )be more than a thousand microRNA genes in the human genome alone. Motivated by the experimental observation of strong conservation of the microRNA let-7 among nearly all metazoans, we developed a novel methodology to characterize the class of such strongly conserved sequences: we identified a non-redundant set of all sequences 20 to 29 bases in length that are shared among three insects: fly, bee and mosquito. Among the few hundred sequences greater than 20 bases in length are close to 40% of the 78 confirmed fly microRNAs, along with other non-coding RNAs and coding sequence. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles The DNA sequence of the human X chromosome. Mar 17, 2005 Mark T Ross,Darren V Grafham,Alison J Coffey,Steven Scherer,Kirsten McLay,Donna Muzny,Matthias Platzer,Gareth R Howell,Christine Burrows,Christine P Bird,Adam Frankish,Frances L Lovell,Kevin L Howe,Jennifer L Ashurst,Robert S Fulton,Ralf Sudbrak,Gaiping Wen,Matthew C Jones,Matthew E Hurles,T Daniel Andrews,Carol E Scott,Stephen Searle,Juliane Ramser,Adam Whittaker,Rebecca Deadman,Nigel P Carter,Sarah E Hunt,Rui Chen,Andrew Cree,Preethi Gunaratne,Paul Havlak,Anne Hodgson,Michael L Metzker,Stephen Richards,Graham Scott,David Steffen,Erica Sodergren,David A Wheeler,Kim C Worley,Rachael Ainscough,Kerrie D Ambrose,M Ali Ansari-Lari,Swaroop Aradhya,Robert I S Ashwell,Anne K Babbage,Claire L Bagguley,Andrea Ballabio,Ruby Banerjee,Gary E Barker,Karen F Barlow,Ian P Barrett,Karen N Bates,David M Beare,Helen Beasley,Oliver Beasley,Alfred Beck,Graeme Bethel,Karin Blechschmidt,Nicola Brady,Sarah Bray-Allen,Anne M Bridgeman,Andrew J Brown,Mary J Brown,David Bonnin,Elspeth A Bruford,Christian Buhay,Paula Burch,Deborah Burford,Joanne Burgess,Wayne Burrill,John Burton,Jackie M Bye,Carol Carder,Laura Carrel,Joseph Chako,Joanne C Chapman,Dean Chavez,Ellson Chen,Guan Chen,Yuan Chen,Zhijian Chen,Craig Chinault,Alfredo Ciccodicola,Sue Y Clark,Graham Clarke,Chris M Clee,Sheila Clegg,Kerstin Clerc-Blankenburg,Karen Clifford,Vicky Cobley,Charlotte G Cole,Jen S Conquer,Nicole Corby,Richard E Connor,Robert David,Joy Davies,Clay Davis,John Davis,Oliver Delgado,Denise Deshazo,Pawandeep Dhami,Yan Ding,Huyen Dinh,Steve Dodsworth,Heather Draper,Shannon Dugan-Rocha,Andrew Dunham,Matthew Dunn,K James Durbin,Ireena Dutta,Tamsin Eades,Matthew Ellwood,Alexandra Emery-Cohen,Helen Errington,Kathryn L Evans,Louisa Faulkner,Fiona Francis,John Frankland,Audrey E Fraser,Petra Galgoczy,James Gilbert,Rachel Gill,Gernot Glöckner,Simon G Gregory,Susan Gribble,Coline Griffiths,Russell Grocock,Yanghong Gu,Rhian Gwilliam,Cerissa Hamilton,Elizabeth A Hart,Alicia Hawes,Paul D Heath,Katja Heitmann,Steffen Hennig,Judith Hernandez,Bernd Hinzmann,Sarah Ho,Michael Hoffs,Phillip J Howden,Elizabeth J Huckle,Jennifer Hume,Paul J Hunt,Adrienne R Hunt,Judith Isherwood,Leni Jacob,David Johnson,Sally Jones,Pieter J de Jong,Shirin S Joseph,Stephen Keenan,Susan Kelly,Joanne K Kershaw,Ziad Khan,Petra Kioschis,Sven Klages,Andrew J Knights,Anna Kosiura,Christie Kovar-Smith,Gavin K Laird,Cordelia Langford,Stephanie Lawlor,Margaret Leversha,Lora Lewis,Wen Liu,Christine Lloyd,David M Lloyd,Hermela Loulseged,Jane E Loveland,Jamieson D Lovell,Ryan Lozado,Jing Lu,Rachael Lyne,Jie Ma,Manjula Maheshwari,Lucy H Matthews,Jennifer McDowall,Stuart McLaren,Amanda McMurray,Patrick Meidl,Thomas Meitinger,Sarah Milne,George Miner,Shailesh L Mistry,Margaret Morgan,Sidney Morris,Ines Müller,James C Mullikin,Ngoc Nguyen,Gabriele Nordsiek,Gerald Nyakatura,Christopher N O'Dell,Geoffery Okwuonu,Sophie Palmer,Richard Pandian,David Parker,Julia Parrish,Shiran Pasternak,Dina Patel,Alex V Pearce,Danita M Pearson,Sarah E Pelan,Lesette Perez,Keith M Porter,Yvonne Ramsey,Kathrin Reichwald,Susan Rhodes,Kerry A Ridler,David Schlessinger,Mary G Schueler,Harminder K Sehra,Charles Shaw-Smith,Hua Shen,Elizabeth M Sheridan,Ratna Shownkeen,Carl D Skuce,Michelle L Smith,Elizabeth C Sotheran,Helen E Steingruber,Charles A Steward,Roy Storey,R Mark Swann,David Swarbreck,Paul E Tabor,Stefan Taudien,Tineace Taylor,Brian Teague,Karen Thomas,Andrea Thorpe,Kirsten Timms,Alan Tracey,Steve Trevanion,Anthony C Tromans,Michele d'Urso,Daniel Verduzco,Donna Villasana,Lenee Waldron,Melanie Wall,Qiaoyan Wang,James Warren,Georgina L Warry,Xuehong Wei,Anthony West,Siobhan L Whitehead,Mathew N Whiteley,Jane E Wilkinson,David L Willey,Gabrielle Williams,Leanne Williams,Angela Williamson,Helen Williamson,Laurens Wilming,Rebecca L Woodmansey,Paul W Wray,Jennifer Yen,Jingkun Zhang,Jianling Zhou,Huda Zoghbi,Sara Zorilla,David Buck,Richard Reinhardt,Annemarie Poustka,André Rosenthal,Hans Lehrach,Alfons Meindl,Patrick J Minx,Ladeana W Hillier,Huntington F Willard,Richard K Wilson,Robert H Waterston,Catherine M Rice,Mark Vaudin,Alan Coulson,David L Nelson,George Weinstock,John E Sulston,Richard Durbin,Tim Hubbard,Richard A Gibbs,Stephan Beck,Jane Rogers,David R Bentley The human X chromosome has a unique biology that was shaped by its evolution as the sex chromosome shared by males and females. We have determined 99.3% of the euchromatic sequence of the X chromosome. Our analysis illustrates the autosomal origin of the mammalian sex chromosomes, the stepwise proc... ( view more )ess that led to the progressive loss of recombination between X and Y, and the extent of subsequent degradation of the Y chromosome. LINE1 repeat elements cover one-third of the X chromosome, with a distribution that is consistent with their proposed role as way stations in the process of X-chromosome inactivation. We found 1,098 genes in the sequence, of which 99 encode proteins expressed in testis and in various tumour types. A disproportionately high number of mendelian diseases are documented for the X chromosome. Of this number, 168 have been explained by mutations in 113 X-linked genes, which in many cases were characterized with the aid of the DNA sequence. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Jan 2005 Stephen Richards,Yue Liu,Brian R Bettencourt,Pavel Hradecky,Stan Letovsky,Rasmus Nielsen,Kevin Thornton,Melissa J Hubisz,Rui Chen,Richard P Meisel,Olivier Couronne,Sujun Hua,Mark A Smith,Peili Zhang,Jing Liu,Harmen J Bussemaker,Marinus F van Batenburg,Sally L Howells,Steven E Scherer,Erica Sodergren,Beverly B Matthews,Madeline A Crosby,Andrew J Schroeder,Daniel Ortiz-Barrientos,Catharine M Rives,Michael L Metzker,Donna M Muzny,Graham Scott,David Steffen,David A Wheeler,Kim C Worley,Paul Havlak,K James Durbin,Amy Egan,Rachel Gill,Jennifer Hume,Margaret B Morgan,George Miner,Cerissa Hamilton,Yanmei Huang,Lenée Waldron,Daniel Verduzco,Kerstin P Clerc-Blankenburg,Inna Dubchak,Mohamed A F Noor,Wyatt Anderson,Kevin P White,Andrew G Clark,Stephen W Schaeffer,William Gelbart,George M Weinstock,Richard A Gibbs We have sequenced the genome of a second Drosophila species, Drosophila pseudoobscura, and compared this to the genome sequence of Drosophila melanogaster, a primary model organism. Throughout evolution the vast majority of Drosophila genes have remained on the same chromosome arm, but within each ... ( view more )arm gene order has been extensively reshuffled, leading to a minimum of 921 syntenic blocks shared between the species. A repetitive sequence is found in the D. pseudoobscura genome at many junctions between adjacent syntenic blocks. Analysis of this novel repetitive element family suggests that recombination between offset elements may have given rise to many paracentric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage. Based on sequence similarity and synteny, 10,516 putative orthologs have been identified as a core gene set conserved over 25-55 million years (Myr) since the pseudoobscura/melanogaster divergence. Genes expressed in the testes had higher amino acid sequence divergence than the genome-wide average, consistent with the rapid evolution of sex-specific proteins. Cis-regulatory sequences are more conserved than random and nearby sequences between the species--but the difference is slight, suggesting that the evolution of cis-regulatory elements is flexible. Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles Genomic segmental polymorphisms in inbred mouse strains. Sep 2004 Jiangzhen Li,Tao Jiang,Jian-Hua Mao,Allan Balmain,Leif Peterson,Charles Harris,Pulivarthi H Rao,Paul Havlak,Richard Gibbs,Wei-Wen Cai By analyzing genomic copy-number differences using high-resolution mouse whole-genome BAC arrays, we uncover substantial differences in regional DNA content between inbred strains of mice. The identification of these apparently common segmental polymorphisms suggests that these differences can cont... ( view more )ribute to genetic variability and pathologic susceptibility. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Apr 1, 2004 Richard A Gibbs,George M Weinstock,Michael L Metzker,Donna M Muzny,Erica J Sodergren,Steven Scherer,Graham Scott,David Steffen,Kim C Worley,Paula E Burch,Geoffrey Okwuonu,Sandra Hines,Lora Lewis,Christine DeRamo,Oliver Delgado,Shannon Dugan-Rocha,George Miner,Margaret Morgan,Alicia Hawes,Rachel Gill, Celera,Robert A Holt,Mark D Adams,Peter G Amanatides,Holly Baden-Tillson,Mary Barnstead,Soo Chin,Cheryl A Evans,Steve Ferriera,Carl Fosler,Anna Glodek,Zhiping Gu,Don Jennings,Cheryl L Kraft,Trixie Nguyen,Cynthia M Pfannkoch,Cynthia Sitter,Granger G Sutton,J Craig Venter,Trevor Woodage,Douglas Smith,Hong-Mei Lee,Erik Gustafson,Patrick Cahill,Arnold Kana,Lynn Doucette-Stamm,Keith Weinstock,Kim Fechtel,Robert B Weiss,Diane M Dunn,Eric D Green,Robert W Blakesley,Gerard G Bouffard,Pieter J De Jong,Kazutoyo Osoegawa,Baoli Zhu,Marco Marra,Jacqueline Schein,Ian Bosdet,Chris Fjell,Steven Jones,Martin Krzywinski,Carrie Mathewson,Asim Siddiqui,Natasja Wye,John McPherson,Shaying Zhao,Claire M Fraser,Jyoti Shetty,Sofiya Shatsman,Keita Geer,Yixin Chen,Sofyia Abramzon,William C Nierman,Paul H Havlak,Rui Chen,K James Durbin,Amy Egan,Yanru Ren,Xing-Zhi Song,Bingshan Li,Yue Liu,Xiang Qin,Simon Cawley,Kim C Worley,A J Cooney,Lisa M D'Souza,Kirt Martin,Jia Qian Wu,Manuel L Gonzalez-Garay,Andrew R Jackson,Kenneth J Kalafus,Michael P McLeod,Aleksandar Milosavljevic,Davinder Virk,Andrei Volkov,David A Wheeler,Zhengdong Zhang,Jeffrey A Bailey,Evan E Eichler,Eray Tuzun,Ewan Birney,Emmanuel Mongin,Abel Ureta-Vidal,Cara Woodwark,Evgeny Zdobnov,Peer Bork,Mikita Suyama,David Torrents,Marina Alexandersson,Barbara J Trask,Janet M Young,Hui Huang,Huajun Wang,Heming Xing,Sue Daniels,Darryl Gietzen,Jeanette Schmidt,Kristian Stevens,Ursula Vitt,Jim Wingrove,Francisco Camara,M Mar Albà,Josep F Abril,Roderic Guigo,Arian Smit,Inna Dubchak,Edward M Rubin,Olivier Couronne,Alexander Poliakov,Norbert Hübner,Detlev Ganten,Claudia Goesele,Oliver Hummel,Thomas Kreitler,Young-Ae Lee,Jan Monti,Herbert Schulz,Heike Zimdahl,Heinz Himmelbauer,Hans Lehrach,Howard J Jacob,Susan Bromberg,Jo Gullings-Handley,Michael I Jensen-Seaman,Anne E Kwitek,Jozef Lazar,Dean Pasko,Peter J Tonellato,Simon Twigger,Chris P Ponting,Jose M Duarte,Stephen Rice,Leo Goodstadt,Scott A Beatson,Richard D Emes,Eitan E Winter,Caleb Webber,Petra Brandt,Gerald Nyakatura,Margaret Adetobi,Francesca Chiaromonte,Laura Elnitski,Pallavi Eswara,Ross C Hardison,Minmei Hou,Diana Kolbe,Kateryna Makova,Webb Miller,Anton Nekrutenko,Cathy Riemer,Scott Schwartz,James Taylor,Shan Yang,Yi Zhang,Klaus Lindpaintner,T Dan Andrews,Mario Caccamo,Michele Clamp,Laura Clarke,Valerie Curwen,Richard Durbin,Eduardo Eyras,Stephen M Searle,Gregory M Cooper,Serafim Batzoglou,Michael Brudno,Arend Sidow,Eric A Stone,J Craig Venter,Bret A Payseur,Guillaume Bourque,Carlos López-Otín,Xose S Puente,Kushal Chakrabarti,Sourav Chatterji,Colin Dewey,Lior Pachter,Nicolas Bray,Von Bing Yap,Anat Caspi,Glenn Tesler,Pavel A Pevzner,David Haussler,Krishna M Roskin,Robert Baertsch,Hiram Clawson,Terrence S Furey,Angie S Hinrichs,Donna Karolchik,William J Kent,Kate R Rosenbloom,Heather Trumbower,Matt Weirauch,David N Cooper,Peter D Stenson,Bin Ma,Michael Brent,Manimozhiyan Arumugam,David Shteynberg,Richard R Copley,Martin S Taylor,Harold Riethman,Uma Mudunuri,Jane Peterson,Mark Guyer,Adam Felsenfeld,Susan Old,Stephen Mockrin,Francis Collins,Rat Genome Sequencing Project Consortium The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over ... ( view more )90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles The Atlas genome assembly system. Apr 2004 Paul Havlak,Rui Chen,K James Durbin,Amy Egan,Yanru Ren,Xing-Zhi Song,George M Weinstock,Richard A Gibbs Atlas is a suite of programs developed for assembly of genomes by a "combined approach" that uses DNA sequence reads from both BACs and whole-genome shotgun (WGS) libraries. The BAC clones afford advantages of localized assembly with reduced computational load, and provide a robust method for deali... ( view more )ng with repeated sequences. Inclusion of WGS sequences facilitates use of different clone insert sizes and reduces data production costs. A core function of Atlas software is recruitment of WGS sequences into appropriate BACs based on sequence overlaps. Because construction of consensus sequences is from local assembly of these reads, only small (<0.1%) units of the genome are assembled at a time. Once assembled, each BAC is used to derive a genomic layout. This "sequence-based" growth of the genome map has greater precision than with non-sequence-based methods. Use of BACs allows correction of artifacts due to repeats at each stage of the process. This is aided by ancillary data such as BAC fingerprint, other genomic maps, and syntenic relations with other genomes. Atlas was used to assemble a draft DNA sequence of the rat genome; its major components including overlapper and split-scaffold are also being used in pure WGS projects. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles Challenges associated with creating a pharmaceutical stockpile to respond to a terrorist event. Aug 2002 R Havlak,S E Gorman,S A Adams The Centers for Disease Control and Prevention (CDC) was called into action to develop a National Pharmaceutical Stockpile (NPS). The NPS was created to respond to terrorism events involving blast, chemical and biological agents. There are many challenges associated with creating, managing and usin... ( view more )g such an asset. This paper provides a helpful background for clinicians and those planning to develop pharmaceutical and/or medical materiel stockpiles for national use. It also describes major challenges and offers suggestions for meeting those challenges. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles Loader Lite: a new software tool for the ABI PRISM 3700 DNA sequencer. Jun 2002 G B I Scott,D L Steffen,D Edgar,J T Warren,C L Kovár,S E Scherer,P H Havlak,R A Gibbs Here we describe the development of a novel software tool entitled Loader Lite that generates plate records or sample sheetsfor the ABI PRISMs 3700 DNA sequencer. The major advantage of this program is that it enables the ongoing operation of sequencing instruments without reference to external net... ( view more )work(s). The autonomous operation of sequencing instruments is critical if sample throughput is to be maintained during periods of network outage. Loader Lite employs a deliberate strategy of inputting anonymous tray barcodes at run time. After sequencing, the barcodes are reconciled with relevant project details by reference to a database. This software takes advantage of barcode scanning technology by creating plate records directly on the local computer, serving an individual sequencer, immediately before importing and linking. This real-time synthesis of the plate records at the point of loading all but eliminates loading errors. Loader Lite is user-friendly, fully configurable, and permits the running of partial or full 384-well sample trays, using any standard combinations of run modules, dye sets, mobility files, analysis modules, etc. The 96-well format is not supported; however, this capability will appear in subsequent versions that are currently under development. This application is designed as an added value, adjunct program to the regular ABI PRISM 3700 Data Collection software. We have successfully used Loader Lite over the past six months to load approximately 7 million sequencing reactions and believe its utility and functionality will prove to be attractive to the wider sequencing community. ( view less ) View Full Abstract View Article Details View Coded Data Related Articles Page 1 of 1 1 (13 articles found)

      
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