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Steven Salzberg

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TOP 3
Michael C Schatz; Daniel D Sommer; Daniela Puiu; Steven L Salzberg; Arthur L Delcher; Giuseppe Narzisi; Adam M Phillippy; Mihai Pop
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.
Steven L Salzberg
NIH funding: It does support innovators.
Tanja Magoc; Derrick Wood; Steven L Salzberg
EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes.

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All Publications

2013: Michael C Schatz; Daniel D Sommer; Daniela Puiu; Steven L Salzberg; Arthur L Delcher; Giuseppe Narzisi; Adam M Phillippy; Mihai Pop
Hawkeye and AMOS: visualizing and assessing the quality of genome assemblies.
Briefings in bioinformatics 2013;14(2):213-24.
2013: Steven L Salzberg
NIH funding: It does support innovators.
Nature 2013;493(7430):26.
2013: Tanja Magoc; Derrick Wood; Steven L Salzberg
EDGE-pro: Estimated Degree of Gene Expression in Prokaryotic Genomes.
Evolutionary bioinformatics online 2013;9():127-36.
2012: Shawn Baker; George Church; Anika Joecker; Steven L Salzberg; Todd Smith; Michael Snyder; Jun Wang; John West; Elizabeth Worthey; Jeffrey G Reid
Genome interpretation and assembly-recent progress and next steps.
Nature biotechnology 2012;30(11):1081-3.
2012: Steven L Salzberg
A scientist and an advocate. An interview with Steven Salzberg by Kristie Nybo.
BioTechniques 2012;53(2):71.
2012: Steven L Salzberg
The perils of gene patents.
Clinical pharmacology and therapeutics 2012;91(6):969-71.
2012: Benjamin Langmead; Steven L Salzberg
Fast gapped-read alignment with Bowtie 2.
Nature methods 2012;9(4):357-9.
2012: Cole Trapnell; Loyal Goff; David R Kelley; Daehwan Kim; Geo Pertea; Harold Pimentel; John L Rinn; Adam Roberts; Steven L Salzberg; Lior Pachter
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks.
Nature protocols 2012;7(3):562-78.
2012: Steven L Salzberg; Michael C Schatz; Todd J Treangen; Aleksey Zimin; Arthur L Delcher; Sergey Koren; Tanja Magoc; Guillaume Marçais; Adam Phillippy; Mihai Pop; Daniela Puiu; Michael Roberts; James A. Yorke
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Genome research 2012;22(3):557-67.
2012: Derrick E Wood; Martin Steffen; Rajiswari Swaminathan; Brian P Anton; Yi-Chien Chang; Simon Kasif; Ami Levy-Moonshine; Henry Lin; Lais Osmani; Steven L Salzberg
Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.
Biology direct 2012;7():37.
2012: Aleksey V Zimin; David R Kelley; Guillaume Marçais; Michael Roberts; Steven L Salzberg; James A. Yorke
Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.
PloS one 2012;7(8):e42680.
2012: Todd J Treangen; Steven L Salzberg
Repetitive DNA and next-generation sequencing: computational challenges and solutions.
Nature reviews. Genetics 2012;13(1):36-46.
2012: David R Kelley; Mihai Pop; Arthur L Delcher; Bo Liu; Steven L Salzberg
Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.
Nucleic acids research 2012;40(1):e9.
2011: Tanja Magoč; Steven L Salzberg
FLASH: fast length adjustment of short reads to improve genome assemblies.
Bioinformatics (Oxford, England) 2011;27(21):2957-63.
2011: Adam J Bogdanove; Volker P Brendel; Arthur L Delcher; George Dimitrov; Karin S Dorman; J Maxwell Dow; Ayako Furutani; Sang-Wook Han; Hiromichi Ishihara; Gopaljee Jha; Ralf Koebnik; Jan E Leach; Sang-Won Lee; Hong Lu; Ramana Madupu; Damien F Meyer; Alok Pandey; Prabhu B Patil; Adam M Phillippy; Daniela Puiu; Pablo D Rabinowicz; Diana Radune; Misha Rajaram; Pamela C Ronald; Robert P Ryan; Michael C Schatz; Vikas Sharma; Martin Shumway; Daniel D Sommer; Ramesh V Sonti; Malinee Sriariyanun; Steven Sullivan; Boris Szurek; Cole Trapnell; Seiji Tsuge; Marie-Anne Van Sluys; Casiana M Vera-Cruz; Valérie Verdier; Frank F White; Samuel V Angiuoli; Gudlur Aparna; Faiza Benahmed; Steven L Salzberg
Two new complete genome sequences offer insight into host and tissue specificity of plant pathogenic Xanthomonas spp.
Journal of bacteriology 2011;193(19):5450-64.
2011: Arthur Brady; Steven L Salzberg
PhymmBL expanded: confidence scores, custom databases, parallelization and more.
Nature methods 2011;8(5):367.
2011: David Rasko; Patricia L Worsham; Terry G Abshire; Scott T Stanley; Jason D Bannan; Mark R Wilson; Richard J Langham; R Scott Decker; Lingxia Jiang; Timothy D Read; Adam M Phillippy; Steven L Salzberg; Mihai Pop; Matthew N Van Ert; Leo J Kenefic; Paul Keim; Claire M Fraser-Liggett; Jacques Ravel
Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation.
Proceedings of the National Academy of Sciences of the United States of America 2011;108(12):5027-32.
2011: Vladimir Shulaev; Daniel J Sargent; Ross N Crowhurst; Todd C Mockler; Otto Folkerts; Arthur L Delcher; Pankaj Jaiswal; Keithanne Mockaitis; Aaron Liston; Shrinivasrao P Mane; Paul Burns; Thomas M Davis; Janet P Slovin; Nahla Bassil; Roger Hellens; Clive Evans; Tim Harkins; Chinnappa Kodira; Brian Desany; Oswald R Crasta; Roderick V Jensen; Andrew C Allan; Todd P Michael; Joao Setubal; Jean-Marc Celton; D Jasper G Rees; Kelly P Williams; Sarah H Holt; Juan Jairo Ruiz Rojas; Mithu Chatterjee; Bo Liu; Herman Silva; Lee Meisel; Avital Adato; Sergei A Filichkin; Michela Troggio; Roberto Viola; Tia-Lynn Ashman; Hao Wang; Palitha Dharmawardhana; Justin Elser; Rajani Raja; Henry D Priest; Douglas W Bryant; Samuel E Fox; Scott A Givan; Larry J Wilhelm; Sushma Naithani; Alan Christoffels; David Y Salama; Jade Carter; Elena Lopez Girona; Anna Zdepski; Wenqin Wang; Randall A Kerstetter; Wilfried Schwab; Schuyler S Korban; Jahn Davik; Amparo Monfort; Beatrice Denoyes-Rothan; Pere Arus; Ron Mittler; Barry Flinn; Asaph Aharoni; Jeffrey L Bennetzen; Steven L Salzberg; Allan W Dickerman; Riccardo Velasco; Mark Borodovsky; Richard E Veilleux; Kevin M Folta
The genome of woodland strawberry (Fragaria vesca).
Nature genetics 2011;43(2):109-16.
2011: Samuel V Angiuoli; Steven L Salzberg
Mugsy: fast multiple alignment of closely related whole genomes.
Bioinformatics (Oxford, England) 2011;27(3):334-42.
2011: Daehwan Kim; Steven L Salzberg
TopHat-Fusion: an algorithm for discovery of novel fusion transcripts.
Genome biology 2011;12(8):R72.
2011: Liliana Florea; Theodore S Kalbfleisch; Alexander Souvorov; Steven L Salzberg
Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies.
PloS one 2011;6(6):e21400.
2011: Mihaela Pertea; Geo M Pertea; Steven L Salzberg
Detection of lineage-specific evolutionary changes among primate species.
BMC bioinformatics 2011;12():274.
2011: Samuel V Angiuoli; Steven L Salzberg; Julie C Hotopp; Hervé Tettelin
Improving pan-genome annotation using whole genome multiple alignment.
BMC bioinformatics 2011;12():272.
2011: Jacob Enk; Daniel Fisher; Christine E King; Ross D E MacPhee; Dennis O'Rourke; Regis Debruyne; Alison Devault; Steven L Salzberg; Todd Treangen; Hendrik Poinar
Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths.
Genome biology 2011;12(5):R51.
2011: David Lipman; Steven L Salzberg; Paul Flicek; Mark Gerstein; Rob Knight
Closure of the NCBI SRA and implications for the long-term future of genomics data storage.
Genome biology 2011;12(3):402.
2011: Richard J Roberts; Yi-Chien Chang; Zhenjun Hu; John Rachlin; Brian P Anton; Revonda M Pokrzywa; Han-Pil Choi; Lina L Faller; Jyotsna Guleria; Genevieve Housman; Niels Klitgord; Varun Mazumdar; Mark G McGettrick; Lais Osmani; Rajeswari Swaminathan; Kevin R Tao; Stan Letovsky; Dennis Vitkup; Daniel Segrè; Steven L Salzberg; Charles DeLisi; Martin Steffen; Simon Kasif
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes.
Nucleic acids research 2011;39(Database issue):D11-4.
2010: Todd R Miller; Arthur L Delcher; Steven L Salzberg; Elizabeth Saunders; John C Detter; Rolf U Halden
Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1.
Journal of bacteriology 2010;192(22):6101-2.
2010: Michael C Schatz; Arthur L Delcher; Steven L Salzberg
Assembly of large genomes using second-generation sequencing.
Genome research 2010;20(9):1165-73.
2010: Michael C Schatz; Benjamin Langmead; Steven L Salzberg
Cloud computing and the DNA data race.
Nature biotechnology 2010;28(7):691-3.
2010: Cole Trapnell; Brian A Williams; Geo Pertea; Ali Mortazavi; Gordon Kwan; Marijke J van Baren; Steven L Salzberg; Barbara J Wold; Lior Pachter
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Nature biotechnology 2010;28(5):511-5.
2010: Steven L Salzberg
Mind the gaps.
Nature methods 2010;7(2):105-6.
2010: Steven L Salzberg
Recent advances in RNA sequence analysis.
F1000 biology reports 2010;2():64.
2010: David R Kelley; Michael C Schatz; Steven L Salzberg
Quake: quality-aware detection and correction of sequencing errors.
Genome biology 2010;11(11):R116.
2010: David R Kelley; Steven L Salzberg
Clustering metagenomic sequences with interpolated Markov models.
BMC bioinformatics 2010;11():544.
2010: Steven L Salzberg; Mihaela Pertea
Do-it-yourself genetic testing.
Genome biology 2010;11(10):404.
2010: Xiangyu Deng; Adam M Phillippy; Zengxin Li; Steven L Salzberg; Wei Zhang
Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification.
BMC genomics 2010;11():500.
2010: Rami A Dalloul; Julie A Long; Aleksey V Zimin; Luqman Aslam; Kathryn Beal; Le Ann Blomberg; Pascal Bouffard; David W Burt; Oswald Crasta; Richard P M A Crooijmans; Kristal Cooper; Roger A Coulombe; Supriyo De; Mary E Delany; Jerry B Dodgson; Jennifer J Dong; Clive Evans; Karin M Frederickson; Paul Flicek; Liliana Florea; Otto Folkerts; Martien A M Groenen; Tim T Harkins; Javier Herrero; Steve Hoffmann; Hendrik-Jan Megens; Andrew Jiang; Pieter de Jong; Pete Kaiser; Heebal Kim; Kyu-Won Kim; Sungwon Kim; David Langenberger; Mi-Kyung Lee; Taeheon Lee; Shrinivasrao Mane; Guillaume Marcais; Manja Marz; Audrey P McElroy; Thero Modise; Mikhail Nefedov; Cédric Notredame; Ian R Paton; William Samuel Payne; Geo Pertea; Dennis Prickett; Daniela Puiu; Dan Qioa; Emanuele Raineri; Magali Ruffier; Steven L Salzberg; Michael C Schatz; Chantel Scheuring; Carl J Schmidt; Steven Schroeder; Stephen M J Searle; Edward J Smith; Jacqueline Smith; Tad S Sonstegard; Peter F Stadler; Hakim Tafer; Zhijian Jake Tu; Curtis P Van Tassell; Albert J Vilella; Kelly P Williams; James A. Yorke; Liqing Zhang; Hong-Bin Zhang; Xiaojun Zhang; Yang Zhang; Kent M Reed
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
PLoS biology 2010;8(9):.
2010: Mihaela Pertea; Steven L Salzberg
Between a chicken and a grape: estimating the number of human genes.
Genome biology 2010;11(5):206.
2010: David R Kelley; Steven L Salzberg
Detection and correction of false segmental duplications caused by genome mis-assembly.
Genome biology 2010;11(3):R28.
2009: Arthur Brady; Steven L Salzberg
Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models.
Nature methods 2009;6(9):673-6.
2009: Matthew Berriman; Brian J Haas; Philip T LoVerde; R Alan Wilson; Gary P Dillon; Gustavo C Cerqueira; Susan T Mashiyama; Bissan Al-Lazikani; Luiza F Andrade; Peter Ashton; Martin A Aslett; Daniella C Bartholomeu; Gaelle Blandin; Conor R Caffrey; Avril Coghlan; Richard Coulson; Tim A Day; Art Delcher; Ricardo DeMarco; Appolinaire Djikeng; Tina Eyre; John A Gamble; Elodie Ghedin; Yong Gu; Christiane Hertz-Fowler; Hirohisha Hirai; Yuriko Hirai; Robin Houston; Alasdair Ivens; David A Johnston; Daniela Lacerda; Camila D Macedo; Paul McVeigh; Zemin Ning; Guilherme Oliveira; John P Overington; Julian Parkhill; Mihaela Pertea; Raymond J Pierce; Anna V Protasio; Michael A Quail; Marie-Adèle Rajandream; Jane Rogers; Mohammed Sajid; Steven L Salzberg; Mario Stanke; Adrian R Tivey; Owen R White; David L Williams; Jennifer Wortman; Wenjie Wu; Mostafa Zamanian; Adhemar Zerlotini; Claire M Fraser-Liggett; Barclay G Barrell; Najib M El-Sayed
The genome of the blood fluke Schistosoma mansoni.
Nature 2009;460(7253):352-8.
2009: Adam Phillippy; Kunmi Ayanbule; Nathan J Edwards; Steven L Salzberg
Insignia: a DNA signature search web server for diagnostic assay development.
Nucleic acids research 2009;37(Web Server issue):W229-34.
2009: Cole Trapnell; Steven L Salzberg
How to map billions of short reads onto genomes.
Nature biotechnology 2009;27(5):455-7.
2009: Cole Trapnell; Lior Pachter; Steven L Salzberg
TopHat: discovering splice junctions with RNA-Seq.
Bioinformatics (Oxford, England) 2009;25(9):1105-11.
2009: Steven L Salzberg; Daniela Puiu; Daniel D Sommer; Vishvanath Nene; Norman H Lee
Genome sequence of the Wolbachia endosymbiont of Culex quinquefasciatus JHB.
Journal of bacteriology 2009;191(5):1725.
2009: Benjamin Langmead; Michael C Schatz; Jimmy Lin; Mihai Pop; Steven L Salzberg
Searching for SNPs with cloud computing.
Genome biology 2009;10(11):R134.
2009: Adam Phillippy; Xiangyu Deng; Wei Zhang; Steven L Salzberg
Efficient oligonucleotide probe selection for pan-genomic tiling arrays.
BMC bioinformatics 2009;10():293.
2009: Carl Kingsford; Niranjan Nagarajan; Steven L Salzberg
2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates.
PloS one 2009;4(7):e6402.
2009: Aleksey V Zimin; Arthur L Delcher; Liliana Florea; David R Kelley; Michael C Schatz; Daniela Puiu; Finnian Hanrahan; Geo Pertea; Curtis P Van Tassell; Tad S Sonstegard; Guillaume Marçais; Michael Roberts; Poorani Subramanian; James A. Yorke; Steven L Salzberg
A whole-genome assembly of the domestic cow, Bos taurus.
Genome biology 2009;10(4):R42.
2009: Benjamin Langmead; Cole Trapnell; Mihai Pop; Steven L Salzberg
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome biology 2009;10(3):R25.
2009: Jacques Ravel; Lingxia Jiang; Scott T Stanley; Mark R Wilson; R Scott Decker; Timothy D Read; Patricia Worsham; Paul Keim; Steven L Salzberg; Claire M Fraser-Liggett; David Rasko
The complete genome sequence of Bacillus anthracis Ames "Ancestor".
Journal of bacteriology 2009;191(1):445-6.
2009: Mihaela Pertea; Kunmi Ayanbule; Megan Smedinghoff; Steven L Salzberg
OperonDB: a comprehensive database of predicted operons in microbial genomes.
Nucleic acids research 2009;37(Database issue):D479-82.
2008: Jane M Carlton; John H Adams; Joana Carneiro Da Silva; Shelby L Bidwell; Hernan Lorenzi; Elisabet Caler; Jonathan Crabtree; Samuel V Angiuoli; Emilio F Merino; Paolo Amedeo; Qin Cheng; Richard M R Coulson; Brendan S Crabb; Hernando A Del Portillo; Kobby Essien; Tamara V Feldblyum; Carmen Fernandez-Becerra; Paul R Gilson; Amy H Gueye; Xiang Guo; Simon Kang'a; Taco W A Kooij; Michael Korsinczky; Esmeralda V-S Meyer; Vishvanath Nene; Ian Paulsen; Owen R White; Stuart A Ralph; Qinghu Ren; Tobias J Sargeant; Steven L Salzberg; Christian J Stoeckert; Steven A Sullivan; Marcio M Yamamoto; Stephen L Hoffman; Jennifer Wortman; Malcolm J Gardner; Mary R Galinski; John W Barnwell; Claire M Fraser-Liggett
Comparative genomics of the neglected human malaria parasite Plasmodium vivax.
Nature 2008;455(7214):757-63.
2008: Carl Kingsford; Steven L Salzberg
What are decision trees?
Nature biotechnology 2008;26(9):1011-3.
2008: Steven L Salzberg
The contents of the syringe.
Nature 2008;454(7201):160-1.
2008: Ray Ming; Shaobin Hou; Yun Feng; Qingyi Yu; Alexandre Dionne-Laporte; Jimmy Saw; Pavel Senin; Wei Wang; Benjamin V Ly; Kanako L T Lewis; Steven L Salzberg; Lu Feng; Meghan R Jones; Rachel L Skelton; Jan E Murray; Cuixia Chen; Wubin Qian; Junguo Shen; Peng Du; Moriah Eustice; Eric Tong; Haibao Tang; Eric Lyons; Robert E Paull; Todd P Michael; Kerr Wall; Danny W Rice; Henrik Albert; Ming-Li Wang; Yun J Zhu; Michael Schatz; Niranjan Nagarajan; Ricelle A Acob; Peizhu Guan; Andrea Blas; Ching Man Wai; Christine M Ackerman; Yan Ren; Chao Liu; Jianmei Wang; Jianping Wang; Jong-Kuk Na; Eugene V Shakirov; Brian Haas; Jyothi Thimmapuram; David Nelson; Xiyin Wang; John E Bowers; Andrea R Gschwend; Arthur L Delcher; Ratnesh Singh; Jon Y Suzuki; Savarni Tripathi; Kabi Neupane; Hairong Wei; Beth Irikura; Maya Paidi; Ning Jiang; Wenli Zhang; Gernot Presting; Aaron Windsor; Rafael Navajas-Pérez; Manuel J Torres; F. Alex Feltus; Brad Porter; Yingjun Li; A Max Burroughs; Ming-Cheng Luo; Lei Liu; David A Christopher; Steve Mount; Paul H Moore; Tak Sugimura; Jiming Jiang; Mary A Schuler; Vikki Friedman; Thomas Mitchell-Olds; Dorothy E Shippen; Claude W dePamphilis; Jeffrey D Palmer; Michael Freeling; Andrew H Paterson; Dennis Gonsalves; Lei Wang; Maqsudul Alam
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).
Nature 2008;452(7190):991-6.
2008: Mihai Pop; Steven L Salzberg
Bioinformatics challenges of new sequencing technology.
Trends in genetics : TIG 2008;24(3):142-9.
2008: Hong Lu; Prabhu Patil; Marie-Anne Van Sluys; Frank F White; Robert P Ryan; J Maxwell Dow; Pablo D Rabinowicz; Steven L Salzberg; Jan E Leach; Ramesh Sonti; Volker Brendel; Adam J Bogdanove
Acquisition and evolution of plant pathogenesis-associated gene clusters and candidate determinants of tissue-specificity in xanthomonas.
PloS one 2008;3(11):e3828.
2008: Daniela Puiu; Steven L Salzberg
Re-assembly of the genome of Francisella tularensis subsp. holarctica OSU18.
PloS one 2008;3(10):e3427.
2008: Steven L Salzberg; Daniel D Sommer; Daniela Puiu; Vincent T Lee
Gene-boosted assembly of a novel bacterial genome from very short reads.
PLoS computational biology 2008;4(9):e1000186.
2008: Steven L Salzberg; Daniel D Sommer; Michael C Schatz; Adam M Phillippy; Pablo D Rabinowicz; Seiji Tsuge; Ayako Furutani; Hirokazu Ochiai; Arthur L Delcher; David Kelley; Ramana Madupu; Daniela Puiu; Diana Radune; Martin Shumway; Cole Trapnell; Gudlur Aparna; Gopaljee Jha; Alok Pandey; Prabhu Patil; Hiromichi Ishihara; Damien F Meyer; Boris Szurek; Valerie Verdier; Ralf Koebnik; J Maxwell Dow; Robert P Ryan; Hisae Hirata; Shinji Tsuyumu; Sang Won Lee; Young-Su Seo; Malinee Sriariyanum; Pamela C Ronald; Ramesh V Sonti; Marie-Anne Van Sluys; Jan E Leach; Frank F White; Adam J Bogdanove
Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A.
BMC genomics 2008;9():204.
2008: Brian J Haas; Steven L Salzberg; Wei Zhu; Mihaela Pertea; Jonathan E Allen; Joshua Orvis; Owen R White; C Robin Buell; Jennifer Wortman
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
Genome biology 2008;9(1):R7.
2007: andrew clark; Michael B Eisen; Douglas R Smith; Casey M Bergman; Brian Oliver; Therese A Markow; Thomas C Kaufman; Manolis Kellis; William Gelbart; Venky N Iyer; Daniel A Pollard; Timothy B Sackton; Amanda M Larracuente; Nadia D Singh; Jose P Abad; Dawn N Abt; Boris Adryan; Montserrat Aguade; Hiroshi Akashi; Wyatt W Anderson; Charles F Aquadro; David H Ardell; Roman Arguello; Carlo G Artieri; Daniel A Barbash; Daniel Barker; Paolo Barsanti; Phil Batterham; Serafim Batzoglou; Dave Begun; Arjun Bhutkar; Enrico Blanco; Stephanie A Bosak; Robert K Bradley; Adrianne D Brand; Michael R Brent; Angela N Brooks; Randall H Brown; Roger K Butlin; Corrado Caggese; Brian R. Calvi; A Bernardo de Carvalho; Anat Caspi; Sergio Castrezana; Susan E Celniker; Jean L Chang; Charles Chapple; Sourav Chatterji; Asif Chinwalla; Alberto Civetta; Sandra W Clifton; Josep M Comeron; James C Costello; Jerry A Coyne; Jennifer Daub; Robert G David; Arthur L Delcher; Kim Delehaunty; Chuong B Do; Heather Ebling; Kevin Edwards; Thomas Eickbush; Jay Evans; Alan Filipski; Sven Findeiss; Eva Freyhult; Lucinda Fulton; Robert Fulton; Ana C L Garcia; Anastasia Gardiner; David A Garfield; Barry E Garvin; Greg Gibson; Donald G Gilbert; Sante Gnerre; Jennifer Godfrey; Robert Good; Valer Gotea; Brenton Gravely; Anthony J Greenberg; Sam Griffiths-Jones; Samuel Gross; Roderic Guigo; Erik A Gustafson; Wilfried Haerty; Matthew W Hahn; Daniel L Halligan; Aaron L Halpern; Gillian M Halter; Mira V Han; Andreas Heger; LaDeana Hillier; Angie S Hinrichs; Ian Holmes; Roger A Hoskins; Melissa J Hubisz; Dan Hultmark; Melanie A Huntley; David B Jaffe; Santosh Jagadeeshan; William R Jeck; Justin Johnson; Corbin D Jones; William C Jordan; Gary Karpen; Eiko Kataoka; Peter D Keightley; Pouya Kheradpour; Ewen F Kirkness; Leonardo B Koerich; Karsten Kristiansen; Dave Kudrna; Rob J Kulathinal; Sudhir Kumar; Roberta Kwok; Eric Lander; Charles H Langley; Richard Lapoint; Brian P Lazzaro; So-Jeong Lee; Lisa Levesque; Ruiqiang Li; Chiao-Feng Lin; Michael F Lin; Kerstin Lindblad-Toh; Ana Llopart; Manyuan Long; Lloyd Low; Elena Lozovsky; Jian Lu; Meizhong Luo; Carlos A Machado; Wojciech Makalowski; Mar Marzo; Muneo Matsuda; Luciano Matzkin; Bryant McAllister; Carolyn S McBride; Brendan McKernan; Kevin McKernan; Maria Mendez-Lago; Patrick Minx; Michael U Mollenhauer; Kristi Montooth; Steve Mount; Xu Mu; Eugene Myers; Barbara Negre; Stuart Newfeld; Rasmus Nielsen; Mohamed A F Noor; Patrick O'Grady; Lior Pachter; Montserrat Papaceit; Matthew J Parisi; Michael Parisi; Leopold Parts; Jakob S Pedersen; Graziano Pesole; Adam M Phillippy; Chris P Ponting; Mihai Pop; Damiano Porcelli; Jeffrey R Powell; Sonja J Prohaska; Kim Pruitt; Marta Puig; Hadi Quesneville; Kristipati Ravi Ram; David Rand; Matthew D Rasmussen; Laura K Reed; Robert Reenan; Amy Reily; Karin A Remington; Tania T Rieger; Michael G Ritchie; Charles Robin; Yu-Hui Rogers; Claudia Rohde; Julio Rozas; Marc J Rubenfield; Alfredo Ruiz; Susan Russo; Steven L Salzberg; Alejandro Sanchez-Gracia; David J Saranga; Hajime Sato; Stephen W Schaeffer; Michael C Schatz; Todd Schlenke; Russell Schwartz; Carmen Segarra; Rama S Singh; Laura K Sirot; Marina Sirota; Nicholas B Sisneros; Chris D Smith; Temple F Smith; John Spieth; Deborah E Stage; Alexander Stark; Wolfgang Stephan; Robert L Strausberg; Sebastian Strempel; David Sturgill; Granger Sutton; Granger G Sutton; Wei Tao; Sarah Teichmann; Yoshiko N Tobari; Yoshihiko Tomimura; Jason M Tsolas; Vera L S Valente; Eli Venter; J Craig Venter; Saverio Vicario; Filipe G Vieira; Albert J Vilella; Alfredo Villasante; Brian Walenz; Jun Wang; Marvin Wasserman; Thomas Watts; Derek Wilson; Richard K Wilson; Rod A Wing; Mariana F Wolfner; Alex Wong; Gane Ka-Shu Wong; Chung-I Wu; Gabriel Wu; Daisuke Yamamoto; Hsiao-Pei Yang; Shiaw-Pyng Yang; James A. Yorke; Kiyohito Yoshida; Evgeny Zdobnov; Peili Zhang; Yu Zhang; Aleksey V Zimin; Jennifer Baldwin; Amr Abdouelleil; Jamal Abdulkadir; Adal Abebe; Brikti Abera; Justin Abreu; St Christophe Acer; Lynne Aftuck; Allen Alexander; Peter An; Erica Anderson; Scott Anderson; Harindra Arachi; Marc Azer; Pasang Bachantsang; Andrew Barry; Tashi Bayul; Aaron Berlin; Daniel Bessette; Toby Bloom; Jason Blye; Leonid Boguslavskiy; Claude Bonnet; Boris Boukhgalter; Imane Bourzgui; Adam Brown; Patrick Cahill; Sheridon Channer; Yama Cheshatsang; Lisa Chuda; Mieke Citroen; Alville Collymore; Patrick Cooke; Maura Costello; Katie D'Aco; Riza Daza; Georgius De Haan; Stuart DeGray; Christina DeMaso; Norbu Dhargay; Kimberly Dooley; Erin Dooley; Missole Doricent; Passang Dorje; Kunsang Dorjee; Alan Dupes; Richard Elong; Jill Falk; Abderrahim Farina; Susan Faro; Diallo Ferguson; Sheila Fisher; Chelsea D Foley; Alicia Franke; Dennis Friedrich; Loryn Gadbois; Gary Gearin; Christina R Gearin; Georgia Giannoukos; Tina Goode; Joseph Graham; Edward Grandbois; Sharleen Grewal; Kunsang Gyaltsen; Nabil Hafez; Birhane Hagos; Jennifer Hall; Charlotte Henson; Andrew Hollinger; Tracey Honan; Monika D Huard; Leanne Hughes; Brian Hurhula; M Erii Husby; Asha Kamat; Ben Kanga; Seva Kashin; Dmitry Khazanovich; Peter Kisner; Krista Lance; Marcia Lara; William Lee; Niall Lennon; Frances Letendre; Rosie LeVine; Alex Lipovsky; Xiaohong Liu; Jinlei Liu; Shangtao Liu; Tashi Lokyitsang; Yeshi Lokyitsang; Rakela Lubonja; Annie Lui; Pen MacDonald; Vasilia Magnisalis; Kebede Maru; Charles Matthews; William McCusker; Susan McDonough; Teena Mehta; James Meldrim; Louis Meneus; Oana Mihai; Atanas Mihalev; Tanya Mihova; Rachel Mittelman; Valentine Mlenga; Anna Montmayeur; Leonidas Mulrain; Adam Navidi; Jerome Naylor; Tamrat Negash; Thu Nguyen; Nga Nguyen; Robert Nicol; Choe Norbu; Nyima Norbu; Nathaniel Novod; Barry O'Neill; Sahal Osman; Eva Markiewicz; Otero L Oyono; Christopher Patti; Pema Phunkhang; Fritz Pierre; Margaret Priest; Sujaa Raghuraman; Filip Rege; Rebecca Reyes; Cecil Rise; Peter Rogov; Keenan Ross; Elizabeth Ryan; Sampath Settipalli; Terry Shea; Ngawang Sherpa; Lu Shi; Diana Shih; Todd Sparrow; Jessica Spaulding; John Stalker; Nicole Stange-Thomann; Sharon Stavropoulos; Catherine Stone; Christopher Strader; Senait Tesfaye; Talene Thomson; Yama Thoulutsang; Dawa Thoulutsang; Kerri Topham; Ira Topping; Tsamla Tsamla; Helen Vassiliev; Andy Vo; Tsering Wangchuk; Tsering Wangdi; Michael Weiand; Jane Wilkinson; Adam Wilson; Shailendra Yadav; Geneva Young; Qing Yu; Lisa Zembek; Danni Zhong; Andrew Zimmer; Zac Zwirko; David B Jaffe; Pablo Alvarez; Will Brockman; Jonathan Butler; CheeWhye Chin; Sante Gnerre; Manfred Grabherr; Michael Kleber; Evan Mauceli; Iain MacCallum
Evolution of genes and genomes on the Drosophila phylogeny.
Nature 2007;450(7167):203-18.
2007: Elodie Ghedin; Shiliang Wang; David Spiro; Elisabet Caler; Qi Zhao; Jonathan Crabtree; Jonathan E Allen; Arthur L Delcher; David B Guiliano; Diego Miranda-Saavedra; Samuel V Angiuoli; Todd Creasy; Paolo Amedeo; Brian Haas; Najib M El-Sayed; Jennifer Wortman; Tamara Feldblyum; Luke Tallon; Michael Schatz; Martin Shumway; Hean Koo; Steven L Salzberg; Seth Schobel; Mihaela Pertea; Mihai Pop; Owen R White; Geoffrey J Barton; Clotilde K S Carlow; Michael J Crawford; Jennifer Daub; Matthew W Dimmic; Chris F Estes; Jeremy M Foster; Mehul Ganatra; William F Gregory; Nicholas M Johnson; Jinming Jin; Richard Komuniecki; Ian F Korf; Sanjay Kumar; Sandra Laney; Benwen Li; Wen Li; Tim H Lindblom; Sara Lustigman; Dong Ma; Claude V Maina; David M A Martin; James P McCarter; Larry McReynolds; Makedonka Mitreva; Thomas B Nutman; John Parkinson; José M Peregrín-Alvarez; Catherine Poole; Qinghu Ren; Lori Saunders; Ann E Sluder; Katherine Smith; Mario Stanke; Thomas R Unnasch; Jenna Ware; Aguan D Wei; Gary Weil; Deryck J Williams; Yinhua Zhang; Steven A Williams; Claire M Fraser-Liggett; Barton Slatko; Mark L Blaxter; Alan L Scott
Draft genome of the filarial nematode parasite Brugia malayi.
Science (New York, N.Y.) 2007;317(5845):1756-60.
2007: Carleton L Kingsford; Arthur L Delcher; Steven L Salzberg
A unified model explaining the offsets of overlapping and near-overlapping prokaryotic genes.
Molecular biology and evolution 2007;24(9):2091-8.
2007: Vishvanath Nene; Jennifer Wortman; Daniel Lawson; Brian Haas; Chinnappa Kodira; Zhijian Jake Tu; Brendan Loftus; Zhiyong Xi; Karyn Megy; Manfred Grabherr; Quinghu Ren; Evgeny M Zdobnov; Neil F Lobo; Kathryn S Campbell; Susan E Brown; Maria F Bonaldo; Jingsong Zhu; Steven P Sinkins; David G Hogenkamp; Paolo Amedeo; Peter Arensburger; Peter W Atkinson; Shelby Bidwell; Jim Biedler; Ewan Birney; Robert V Bruggner; Javier Costas; Monique R Coy; Jonathan Crabtree; Matt Crawford; Becky Debruyn; David Decaprio; Karin Eiglmeier; Eric Eisenstadt; Hamza El-Dorry; William M Gelbart; Suely L Gomes; Martin Hammond; Linda I Hannick; James R Hogan; Michael H Holmes; David Jaffe; J Spencer Johnston; Ryan C Kennedy; Hean Koo; Saul Kravitz; Evgenia Kriventseva; David Kulp; Kurt Labutti; Eduardo Lee; Song Li; Diane D Lovin; Chunhong Mao; Evan Mauceli; Carlos F M Menck; Jason R Miller; Philip Montgomery; Akio Mori; Ana L Nascimento; Horacio F Naveira; Chad Nusbaum; Sinéad O'leary; Joshua Orvis; Mihaela Pertea; Hadi Quesneville; Kyanne R Reidenbach; Yu-Hui Rogers; Charles W Roth; Jennifer R Schneider; Michael Schatz; Martin Shumway; Mario Stanke; Eric O Stinson; Jose M C Tubio; Janice P Vanzee; Sergio Verjovski-Almeida; Doreen Werner; Owen R White; Stefan Wyder; Qiandong Zeng; Qi Zhao; Yongmei Zhao; Catherine A Hill; Alexander S Raikhel; Marcelo B Soares; Dennis L Knudson; Norman H Lee; James Galagan; Steven L Salzberg; Ian Paulsen; George Dimopoulos; Frank H Collins; Bruce Birren; Claire M Fraser-Liggett; David Severson
Genome sequence of Aedes aegypti, a major arbovirus vector.
Science (New York, N.Y.) 2007;316(5832):1718-23.
2007: Steven L Salzberg; Carleton L Kingsford; Giovanni Cattoli; David Spiro; Daniel Janies; Mona Mehrez Aly; Ian H Brown; Emmanuel Couacy-Hymann; Gian Mario De Mia; Do Huu Dung; Annalisa Guercio; Tony Joannis; Ali Safar Maken Ali; Azizullah Osmani; Iolanda Padalino; Magdi D Saad; Vladimir Savić; Naomi A Sengamalay; Samuel Yingst; Jennifer Zaborsky; Olga Zorman-Rojs; Elodie Ghedin; Ilaria Capua
Genome analysis linking recent European and African influenza (H5N1) viruses.
Emerging infectious diseases 2007;13(5):713-8.
2007: Adam Phillippy; Jacquline A Mason; Kunmi Ayanbule; Daniel D Sommer; Elisa Taviani; Anwar Huq; Rita R Colwell; Ivor T Knight; Steven L Salzberg
Comprehensive DNA signature discovery and validation.
PLoS computational biology 2007;3(5):e98.
2007: Arthur L Delcher; Kirsten A Bratke; Edwin C Powers; Steven L Salzberg
Identifying bacterial genes and endosymbiont DNA with Glimmer.
Bioinformatics (Oxford, England) 2007;23(6):673-9.
2007: Jane M Carlton; Robert Hirt; Joana Carneiro Da Silva; Arthur L Delcher; Michael Schatz; Qi Zhao; Jennifer Wortman; Shelby L Bidwell; U Cecilia M Alsmark; Sébastien Besteiro; thomas sicheritz-ponten; Christophe Noel; Joel B Dacks; Peter G Foster; Cedric Simillion; Yves Van de Peer; Diego Miranda-Saavedra; Geoffrey J Barton; Gareth D Westrop; Sylke Müller; Daniele Dessi; Pier Luigi Fiori; Qinghu Ren; Ian Paulsen; Hanbang Zhang; Felix D Bastida-Corcuera; Augusto Simoes-Barbosa; Mark T Brown; Richard D Hayes; Mandira Mukherjee; Cheryl Y Okumura; Rachel Schneider; Alias J Smith; Stepanka Vanacova; Maria Villalvazo; Brian J Haas; Mihaela Pertea; Tamara V Feldblyum; Terry R Utterback; Chung-Li Shu; Kazutoyo Osoegawa; Pieter J de Jong; Ivan Hrdy; Lenka Horvathova; Zuzana Zubacova; Pavel Dolezal; Shehre-Banoo Malik; John M Logsdon; Katrin Henze; Arti Gupta; Ching C Wang; Rebecca L Dunne; Jacqueline A Upcroft; Peter Upcroft; Owen R White; Steven L Salzberg; Petrus Tang; Cheng-Hsun Chiu; Ying-Shiung Lee; T Martin Embley; Graham H Coombs; Jeremy C Mottram; Jan Tachezy; Claire M Fraser-Liggett; Patricia J Johnson
Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis.
Science (New York, N.Y.) 2007;315(5809):207-12.
2007: Mihaela Pertea; Steve Mount; Steven L Salzberg
A computational survey of candidate exonic splicing enhancer motifs in the model plant Arabidopsis thaliana.
BMC bioinformatics 2007;8():159.
2007: Michael C Schatz; Adam Phillippy; Ben Shneiderman; Steven L Salzberg
Hawkeye: an interactive visual analytics tool for genome assemblies.
Genome biology 2007;8(3):R34.
2007: Daniel D Sommer; Arthur L Delcher; Steven L Salzberg; Mihai Pop
Minimus: a fast, lightweight genome assembler.
BMC bioinformatics 2007;8():64.
2007: Carleton L Kingsford; Kunmi Ayanbule; Steven L Salzberg
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake.
Genome biology 2007;8(2):R22.
2007: Steven L Salzberg
Genome re-annotation: a wiki solution?
Genome biology 2007;8(1):102.
2006: Jonathan Eisen; Robert S Coyne; Martin Wu; Dongying Wu; Mathangi Thiagarajan; Jennifer Wortman; Jonathan H Badger; Qinghu Ren; Paolo Amedeo; Kristie M Jones; Luke J Tallon; Arthur L Delcher; Steven L Salzberg; Joana Carneiro Da Silva; Brian J Haas; William H Majoros; Maryam Farzad; Jane M Carlton; Roger K Smith; Jyoti Garg; Ronald E Pearlman; Kathleen M Karrer; Lei Sun; Gerard Manning; Nels C Elde; Aaron P Turkewitz; David J Asai; David E Wilkes; Yufeng Wang; Hong Cai; Kathleen Collins; B Andrew Stewart; Suzanne R Lee; Katarzyna Wilamowska; Zasha Weinberg; Walter L Ruzzo; Dorota Wloga; Jacek Gaertig; Joseph Frankel; Che-Chia Tsao; Martin A Gorovsky; Patrick J Keeling; Ross F Waller; patron nicola; J Michael Cherry; Nicholas A Stover; Cynthia J Krieger; Christina del Toro; Hilary F Ryder; Sondra C Williamson; Rebecca A Barbeau; Eileen P Hamilton; Eduardo Orias
Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.
PLoS biology 2006;4(9):e286.
2006: John Quackenbush; Steven L Salzberg
It is time to end the patenting of software.
Bioinformatics (Oxford, England) 2006;22(12):1416-7.
2006: Steven L Salzberg; Elodie Ghedin; David Spiro
Shared data are key to beating threat from flu.
Nature 2006;440(7084):605.
2006: Renae L Malek; Hong-ying Wang; Anne E Kwitek; Andrew S Greene; Nirmal K Bhagabati; Gretta Borchardt; Lisa Cahill; Tracey Currier; Bryan Frank; Xianping Fu; Michael Hasinoff; Eleanor Howe; Noah E Letwin; Truong V Luu; Alexander Saeed; Hedieh Sajadi; Steven L Salzberg; Razvan Sultana; Mathangi Thiagarajan; Jennifer Tsai; Kathleen Veratti; Joseph White; John Quackenbush; Howard J Jacob; Norman H Lee
Physiogenomic resources for rat models of heart, lung and blood disorders.
Nature genetics 2006;38(2):234-9.
2006: Jonathan E Allen; Steven L Salzberg
A phylogenetic generalized hidden Markov model for predicting alternatively spliced exons.
Algorithms for molecular biology : AMB 2006;1():14.
2006: Jonathan E Allen; William H Majoros; Mihaela Pertea; Steven L Salzberg
JIGSAW, GeneZilla, and GlimmerHMM: puzzling out the features of human genes in the ENCODE regions.
Genome biology 2006;7 Suppl 1():S9.1-13.
2005: William C Nierman; Arnab Pain; Michael J Anderson; Jennifer Wortman; Heenam Stanley Kim; Javier Arroyo; Matthew Berriman; Keietsu Abe; David B Archer; Clara Bermejo; Joan Bennett; Paul Bowyer; Dan Chen; Matthew Collins; Richard Coulsen; Robert Davies; Paul S Dyer; Mark Farman; Natalie Fedorova Abrams; Natalie Fedorova; Tamara V Feldblyum; Reinhard Fischer; Nigel Fosker; Audrey Fraser; Jose L García; Maria J García; Arlette Goble; Gustavo H Goldman; Katsuya Gomi; Sam Griffith-Jones; Rhian Gwilliam; Brian Haas; Hubertus Haas; David Harris; H Horiuchi; Jiaqi Huang; Sean Humphray; Javier Jiménez; Nancy Keller; Hoda Khouri; Katsuhiko Kitamoto; Tetsuo Kobayashi; Sven Konzack; Resham Kulkarni; Toshitaka Kumagai; Anne Lafon; Anne Lafton; Jean-Paul Latgé; Weixi Li; Angela Lord; Charles Lu; William H Majoros; Gregory S May; Bruce L Miller; Yasmin Mohamoud; Maria Molina; Michel Monod; Isabelle Mouyna; Stephanie Mulligan; Lee Murphy; Susan O'Neil; Ian Paulsen; Miguel A Peñalva; Mihaela Pertea; Claire Price; Bethan L Pritchard; Michael A Quail; Ester Rabbinowitsch; Neil Rawlins; Marie-Adele Rajandream; Utz Reichard; Hubert Renauld; Geoff Robson; Santiago Rodriguez de Córdoba; Jose M Rodríguez-Peña; Catherine M Ronning; Simon Rutter; Steven L Salzberg; Miguel Sanchez; Juan C Sánchez-Ferrero; David Saunders; kathy seeger; Rob Squares; Steven Squares; Michio Takeuchi; Fredj Tekaia; Geoffrey Turner; Carlos Vazquez de Aldana; Janice Weidman; Owen R White; John Woodward; Jae-Hyuk Yu; Claire M Fraser-Liggett; James E Galagan; Kiyoshi Asai; Masayuki Machida; Neil Hall; Bart Barrell; David W Denning
Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus.
Nature 2005;438(7071):1151-6.
2005: Steven L Salzberg; James A. Yorke
Beware of mis-assembled genomes.
Bioinformatics (Oxford, England) 2005;21(24):4320-1.
2005: Elodie Ghedin; Naomi A Sengamalay; Martin Shumway; Jennifer Zaborsky; Tamara Feldblyum; Vik Subbu; David Spiro; Jeff Sitz; Hean Koo; Pavel Bolotov; Dmitry Dernovoy; Tatiana Tatusova; Yiming Bao; Kirsten St George; Jill Taylor; David Lipman; Claire M Fraser-Liggett; Jeffery Taubenberger; Steven L Salzberg
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution.
Nature 2005;437(7062):1162-6.
2005: Jonathan E Allen; Steven L Salzberg
JIGSAW: integration of multiple sources of evidence for gene prediction.
Bioinformatics (Oxford, England) 2005;21(18):3596-603.
2005: piero carninci; T Kasukawa; S Katayama; J Gough; M C Frith; N Maeda; R Oyama; T Ravasi; B Lenhard; C Wells; R Kodzius; K Shimokawa; Vladimir Bajic; S E Brenner; S Batalov; Alistair Forrest; M Zavolan; M J Davis; L G Wilming; V Aidinis; J E Allen; A Ambesi-Impiombato; R Apweiler; R N Aturaliya; Timothy Lawrence Bailey; M Bansal; L Baxter; K W Beisel; Tom Bersano; H Bono; Alistair Chalk; K P Chiu; V Choudhary; A Christoffels; D R Clutterbuck; M L Crowe; E Dalla; B P Dalrymple; B de Bono; G Della Gatta; D di Bernardo; T Down; P Engstrom; M Fagiolini; G Faulkner; C F Fletcher; T Fukushima; M Furuno; S Futaki; manuela gariboldi; P Georgii-Hemming; Thomas Gingeras; Takashi Gojobori; R E Green; S Gustincich; M Harbers; Y Hayashi; T K Hensch; N Hirokawa; D Hill; L Huminiecki; M Iacono; Kazuho Ikeo; A Iwama; T Ishikawa; M Jakt; Alexander Kanapin; M Katoh; Y Kawasawa; J Kelso; H Kitamura; H Kitano; george kollias; S P T Krishnan; A Kruger; S K Kummerfeld; I V Kurochkin; L F Lareau; D Lazarevic; Leonard Lipovich; J Liu; S Liuni; S McWilliam; M Madan Babu; M Madera; LUIGI MARCHIONNI; H Matsuda; S Matsuzawa; H Miki; F Mignone; S Miyake; K Morris; S Mottagui-Tabar; N Mulder; N Nakano; H Nakauchi; P Ng; R Nilsson; S Nishiguchi; S Nishikawa; F Nori; O Ohara; Yasushi Okazaki; V Orlando; K C Pang; W J Pavan; G Pavesi; G Pesole; Nikolai Petrovsky; S Piazza; J Reed; J F Reid; B Z Ring; M Ringwald; B Rost; Y Ruan; Steven L Salzberg; A Sandelin; C Schneider; Christian Schönbach; K Sekiguchi; Colin Semple; S Seno; L Sessa; Y Sheng; Y Shibata; H Shimada; K Shimada; D Silva; B Sinclair; S Sperling; Elia Stupka; K Sugiura; R Sultana; Y Takenaka; K Taki; K Tammoja; S L Tan; S Tang; Martin Taylor; J Tegner; S A Teichmann; H R Ueda; E van Nimwegen; R Verardo; C L Wei; K Yagi; H Yamanishi; E Zabarovsky; S Zhu; A Zimmer; Winston Hide; Carol Bult; S M Grimmond; Rohan Teasdale; Edison Liu; V Brusic; John Quackenbush; Claes Wahlestedt; J S Mattick; D A Hume; C Kai; D Sasaki; Y Tomaru; S Fukuda; M Kanamori-Katayama; M Suzuki; J Aoki; T Arakawa; J Iida; K Imamura; Masayoshi Itoh; T Kato; Hideya Kawaji; N Kawagashira; T Kawashima; M Kojima; S Kondo; H Konno; K Nakano; N Ninomiya; T Nishio; M Okada; C Plessy; K Shibata; T Shiraki; S Suzuki; M Tagami; Kazunori Waki; A Watahiki; Y Okamura-Oho; H Suzuki; J Kawai; Y Hayashizaki
The transcriptional landscape of the mammalian genome.
Science (New York, N.Y.) 2005;309(5740):1559-63.
2005: C Robin Buell; Qiaoping Yuan; Shu Ouyang; Jia Liu; Wei Zhu; Aihui Wang; Rama Maiti; Brian Haas; Jennifer Wortman; Mihaela Pertea; Kristine M Jones; Mary Kim; Larry Overton; Tamara Tsitrin; Douglas Fadrosh; Jayati Bera; Bruce Weaver; Shaohua Jin; Shivani Johri; Matt Reardon; Kristen Webb; Jessica Hill; Kelly Moffat; Luke Tallon; Susan Van Aken; Matthew Lewis; Teresa Utterback; Tamara Feldblyum; Victoria L Zismann; Stacey Iobst; Joseph Hsiao; Aymeric R de Vazeille; Steven L Salzberg; Owen R White; Claire M Fraser-Liggett; Yeisoo Yu; HeyRan Kim; Teri Rambo; Jennifer Currie; Kristi Collura; Shelly Kernodle-Thompson; Fusheng Wei; Kudrna Kudrna; Jetty Siva S Ammiraju; Meizhong Luo; Jose Luis Goicoechea; Rod A Wing; David Henry; Ryan Oates; Michael Palmer; Gina Pries; Christopher Saski; Jessica Simmons; Carol Soderlund; William Nelson; Melissa de la Bastide; Lori Spiegel; Lidia Nascimento; Emily Huang; Raymond Preston; Theresa Zutavern; Lance Palmer; Andrew O'Shaughnessy; Sujit Dike; W Richard McCombie; Pat Minx; Holly Cordum; Richard Wilson; Weiwei Jin; Hye-Ran Lee; Jiming Jiang; Scott Jackson
Sequence, annotation, and analysis of synteny between rice chromosome 3 and diverged grass species.
Genome research 2005;15(9):1284-91.
2005: Edward C Holmes; Elodie Ghedin; Naomi Miller; Jill Taylor; Yiming Bao; Kirsten St George; Bryan T Grenfell; Steven L Salzberg; Claire M Fraser-Liggett; David Lipman; Jeffery Taubenberger
Whole-genome analysis of human influenza A virus reveals multiple persistent lineages and reassortment among recent H3N2 viruses.
PLoS biology 2005;3(9):e300.
2005: Matthew Berriman; Elodie Ghedin; Christiane Hertz-Fowler; Gaëlle Blandin; Hubert Renauld; Daniella C Bartholomeu; Nicola J Lennard; Elisabet Caler; Nancy E Hamlin; Brian Haas; Ulrike Böhme; Linda Hannick; Martin A Aslett; Joshua Shallom; Lucio Marcello; Lihua Hou; Bill Wickstead; U Cecilia M Alsmark; Claire Arrowsmith; Rebecca J Atkin; Andrew J Barron; Frederic Bringaud; Karen Brooks; Mark Carrington; Inna Cherevach; Tracey-Jane Chillingworth; Carol Churcher; Louise N Clark; Craig H Corton; Ann Cronin; Rob M Davies; Jonathon Doggett; Appolinaire Djikeng; Tamara Feldblyum; Mark Field; Audrey Fraser; Ian Goodhead; Zahra Hance; David Harper; Barbara R Harris; Heidi Hauser; Jessica Hostetler; Alasdair Ivens; Kay Jagels; David Johnson; Justin Johnson; Kristine Jones; Arnaud Kerhornou; Hean Koo; Natasha Larke; Scott M Landfear; Christopher Larkin; Vanessa Leech; Alexandra Line; Angela Lord; Annette Macleod; Paul J Mooney; Sharon Moule; David M A Martin; Gareth W Morgan; Karen Mungall; Halina Norbertczak; Doug Ormond; Grace Pai; Chris S Peacock; Jeremy Peterson; Michael A Quail; Ester Rabbinowitsch; Marie-Adele Rajandream; Chris Reitter; Steven L Salzberg; Mandy Sanders; Seth Schobel; Sarah Sharp; Mark Simmonds; Anjana J Simpson; Luke Tallon; C Michael R Turner; Andrew Tait; Adrian R Tivey; Susan Van Aken; Danielle Walker; David Wanless; Shiliang Wang; Brian White; Owen R White; Sally Whitehead; John Woodward; Jennifer Wortman; Mark D Adams; T Martin Embley; Keith Gull; Elisabetta Ullu; J David Barry; Alan H Fairlamb; Fred Opperdoes; Barclay G Barrell; John E Donelson; Neil Hall; Claire M Fraser-Liggett; Sara E Melville; Najib M El-Sayed
The genome of the African trypanosome Trypanosoma brucei.
Science (New York, N.Y.) 2005;309(5733):416-22.
2005: Najib M El-Sayed; Peter J Myler; Daniella C Bartholomeu; Daniel Nilsson; Gautam Aggarwal; Anh-Nhi Tran; Elodie Ghedin; Elizabeth A Worthey; Arthur L Delcher; Gaëlle Blandin; Scott Westenberger; Elisabet Caler; Gustavo Cerqueira; Carole Branche; Brian Haas; Atashi Anupama; Erik Arner; Lena Aslund; Philip Attipoe; Esteban Bontempi; Frédéric Bringaud; Peter Burton; Eithon Cadag; David A Campbell; Mark Carrington; Jonathan Crabtree; Hamid Darban; Jose Franco da Silveira; Pieter de Jong; Kimberly Edwards; Paul T Englund; Gholam Fazelina; Tamara Feldblyum; Marcela Ferella; Alberto Carlos Frasch; Keith Gull; David Horn; Lihua Hou; Yiting Huang; Ellen Kindlund; Michele Klingbeil; Sindy Kluge; Hean Koo; Daniela Lacerda; Mariano J Levin; Hernan Lorenzi; Tin Louie; Carlos Renato Machado; Richard McCulloch; Alan McKenna; Yumi Mizuno; Jeremy C Mottram; Siri Nelson; Stephen Ochaya; Kazutoyo Osoegawa; Grace Pai; Marilyn Parsons; Martin Pentony; Ulf Pettersson; Mihai Pop; Jose Ramirez; Joel Rinta; Laura Robertson; Steven L Salzberg; Daniel O Sanchez; Amber Seyler; Reuben Sharma; Jyoti Shetty; Anjana J Simpson; Ellen Sisk; Martti T Tammi; Rick L Tarleton; Santuza Teixeira; Susan Van Aken; Christy Vogt; Pauline N Ward; Bill Wickstead; Jennifer Wortman; Owen R White; Claire M Fraser-Liggett; Kenneth D Stuart; Björn Andersson
The genome sequence of Trypanosoma cruzi, etiologic agent of Chagas disease.
Science (New York, N.Y.) 2005;309(5733):409-15.
2005: Najib M El-Sayed; Peter J Myler; Gaëlle Blandin; Matthew Berriman; Jonathan Crabtree; Gautam Aggarwal; Elisabet Caler; Hubert Renauld; Elizabeth A Worthey; Christiane Hertz-Fowler; Elodie Ghedin; Christopher Peacock; Daniella C Bartholomeu; Brian J Haas; Anh-Nhi Tran; Jennifer Wortman; U Cecilia M Alsmark; Samuel Angiuoli; Atashi Anupama; Jonathan Badger; Frederic Bringaud; Eithon Cadag; Jane M Carlton; Gustavo Cerqueira; Todd Creasy; Arthur L Delcher; Appolinaire Djikeng; T Martin Embley; Christopher Hauser; Alasdair Ivens; Sarah K Kummerfeld; Jose Pereira-Leal; Daniel Nilsson; Jeremy Peterson; Steven L Salzberg; Joshua Shallom; Joana Carneiro Da Silva; Jaideep Sundaram; Scott Westenberger; Owen R White; Sara E Melville; John E Donelson; Björn Andersson; Kenneth D Stuart; Neil Hall
Comparative genomics of trypanosomatid parasitic protozoa.
Science (New York, N.Y.) 2005;309(5733):404-9.
2005: Malcolm J Gardner; Richard Bishop; Trushar Shah; Etienne de Villiers; Jane M Carlton; Neil Hall; Qinghu Ren; Ian Paulsen; Arnab Pain; Matthew Berriman; Robert J M Wilson; Shigeharu Sato; Stuart A Ralph; David J Mann; Zikai Xiong; Shamira J Shallom; Janice Weidman; Lingxia Jiang; Jeffery Lynn; Bruce Weaver; Azadeh Shoaibi; Alexander R Domingo; Delia Wasawo; Jonathan Crabtree; Jennifer Wortman; Brian Haas; Samuel V Angiuoli; Todd H Creasy; Charles Lu; Bernard Suh; Joana Carneiro Da Silva; Teresa R Utterback; Tamara V Feldblyum; Mihaela Pertea; Jonathan Allen; William C Nierman; Evans L N Taracha; Steven L Salzberg; Owen R White; Henry A Fitzhugh; Subhash Morzaria; J Craig Venter; Claire M Fraser-Liggett; Vishvanath Nene
Genome sequence of Theileria parva, a bovine pathogen that transforms lymphocytes.
Science (New York, N.Y.) 2005;309(5731):134-7.
2005: William H Majoros; Mihaela Pertea; Steven L Salzberg
Efficient implementation of a generalized pair hidden Markov model for comparative gene finding.
Bioinformatics (Oxford, England) 2005;21(9):1782-8.
2005: Brendan J Loftus; Eula Fung; Paola Roncaglia; Don Rowley; Paolo Amedeo; Dan Bruno; Jessica Vamathevan; Molly Miranda; Iain J Anderson; James A Fraser; Jonathan E Allen; Ian E Bosdet; Michael R Brent; Readman Chiu; Tamara L Doering; Maureen J Donlin; Cletus A D'Souza; Deborah S Fox; Viktoriya Grinberg; Jianmin Fu; Marilyn Fukushima; Brian J Haas; James C Huang; Guilhem Janbon; Steven J M Jones; Hean L Koo; Martin I Krzywinski; June K Kwon-Chung; Klaus B Lengeler; Rama Maiti; Marco A Marra; Robert E Marra; Carrie A Mathewson; Thomas G Mitchell; Mihaela Pertea; Florenta R Riggs; Steven L Salzberg; Jacqueline E Schein; Alla Shvartsbeyn; Heesun Shin; Martin Shumway; Charles A Specht; Bernard B Suh; Aaron Tenney; Terry R Utterback; Brian L Wickes; Jennifer Wortman; Natasja H Wye; James W Kronstad; Jennifer lodge; Joseph Heitman; Ronald W Davis; Claire M Fraser-Liggett; Richard W Hyman
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.
Science (New York, N.Y.) 2005;307(5713):1321-4.
2005: Steven L Salzberg; Julie C Hotopp; Arthur L Delcher; Mihai Pop; Douglas R Smith; Michael B Eisen; William C Nelson
Correction: Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.
Genome biology 2005;6(7):402.
2005: Steven L Salzberg; Julie C Hotopp; Arthur L Delcher; Mihai Pop; Douglas R Smith; Michael B Eisen; William C Nelson
Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.
Genome biology 2005;6(3):R23.
2005: William H Majoros; Mihaela Pertea; Arthur L Delcher; Steven L Salzberg
Efficient decoding algorithms for generalized hidden Markov model gene finders.
BMC bioinformatics 2005;6():16.
2004: Brian J Haas; Arthur L Delcher; Jennifer Wortman; Steven L Salzberg
DAGchainer: a tool for mining segmental genome duplications and synteny.
Bioinformatics (Oxford, England) 2004;20(18):3643-6.
2004: William H Majoros; Mihaela Pertea; Steven L Salzberg
TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.
Bioinformatics (Oxford, England) 2004;20(16):2878-9.
2004: Naomi Ward; Øivind Larsen; James Sakwa; Live Bruseth; Hoda Khouri; A Scott Durkin; George Dimitrov; Lingxia Jiang; David Scanlan; Katherine H Kang; Matt Lewis; Karen E Nelson; Barbara Methé; Martin Wu; John F Heidelberg; Ian Paulsen; Derrick Fouts; Jacques Ravel; Hervé Tettelin; Qinghu Ren; Tim Read; Robert T DeBoy; Rekha Seshadri; Steven L Salzberg; Harald B Jensen; Nils Kåre Birkeland; William C Nelson; Robert J Dodson; Svenn H Grindhaug; Ingeborg Holt; Ingvar Eidhammer; Inge Jonasen; Susan Vanaken; Terry Utterback; Tamara V Feldblyum; Claire M Fraser-Liggett; Johan R Lillehaug; Jonathan Eisen
Genomic insights into methanotrophy: the complete genome sequence of Methylococcus capsulatus (Bath).
PLoS biology 2004;2(10):e303.
2004: Mihai Pop; Adam Phillippy; Arthur L Delcher; Steven L Salzberg
Comparative genome assembly.
Briefings in bioinformatics 2004;5(3):237-48.
2004: Steven L Salzberg; Deanna Church; Michael DiCuccio; Eugene Yaschenko; James Ostell
The genome Assembly Archive: a new public resource.
PLoS biology 2004;2(9):E285.
2004: Elodie Ghedin; Frédéric Bringaud; Jeremy Peterson; Peter J Myler; Matthew Berriman; Alasdair Ivens; Björn Andersson; Esteban Bontempi; Jonathan Eisen; Samuel V Angiuoli; David Wanless; Anna Von Arx; Lee Murphy; Nicola Lennard; Steven L Salzberg; Mark D Adams; Owen R White; Neil Hall; Kenneth Stuart; Claire M Fraser-Liggett; Najib M El-Sayed
Gene synteny and evolution of genome architecture in trypanosomatids.
Molecular and biochemical parasitology 2004;134(2):183-91.
2004: Arnab Pain; John Woodward; Michael A Quail; Michael J Anderson; Richard Clark; Matthew Collins; Nigel Fosker; Audrey Fraser; David Harris; Natasha Larke; Lee Murphy; Sean Humphray; Susan O'Neil; Mihaela Pertea; Claire Price; Ester Rabbinowitsch; Marie-Adele Rajandream; Steven L Salzberg; David Saunders; kathy seeger; Sarah Sharp; Tim Warren; David W Denning; Bart Barrell; Neil Hall
Insight into the genome of Aspergillus fumigatus: analysis of a 922 kb region encompassing the nitrate assimilation gene cluster.
Fungal genetics and biology : FG & B 2004;41(4):443-53.
2004: William H Majoros; Steven L Salzberg
An empirical analysis of training protocols for probabilistic gene finders.
BMC bioinformatics 2004;5():206.
2004: Benjamin P Berman; Barret D Pfeiffer; Todd R Laverty; Steven L Salzberg; Gerald M Rubin; Michael B Eisen; Susan E Celniker
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura.
Genome biology 2004;5(9):R61.
2004: Stefan Kurtz; Adam Phillippy; Arthur L Delcher; Michael Smoot; Martin Shumway; Corina Antonescu; Steven L Salzberg
Versatile and open software for comparing large genomes.
Genome biology 2004;5(2):R12.
2004: Pawel Gajer; Michael Schatz; Steven L Salzberg
Automated correction of genome sequence errors.
Nucleic acids research 2004;32(2):562-9.
2004: Mihai Pop; Daniel S Kosack; Steven L Salzberg
Hierarchical scaffolding with Bambus.
Genome research 2004;14(1):149-59.
2004: Jonathan E Allen; Mihaela Pertea; Steven L Salzberg
Computational gene prediction using multiple sources of evidence.
Genome research 2004;14(1):142-8.
2003: Brian J Haas; Arthur L Delcher; Steve Mount; Jennifer Wortman; Roger K Smith; Linda I Hannick; Rama Maiti; Catherine M Ronning; Douglas B Rusch; Christopher D Town; Steven L Salzberg; Owen R White
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies.
Nucleic acids research 2003;31(19):5654-66.
2003: Najib M A El-Sayed; Elodie Ghedin; Jinming Song; Annette MacLeod; Frederic Bringaud; Christopher Larkin; David Wanless; Jeremy Peterson; Lihua Hou; Sonya Taylor; Alison Tweedie; Nicolas Biteau; Hanif Khalak; Xiaoying Lin; Tanya Mason; Linda Hannick; Elisabet Caler; Gaëlle Blandin; Daniella Bartholomeu; Anjana J Simpson; Samir Kaul; Hong Zhao; Grace Pai; Susan Van Aken; Teresa Utterback; Brian Haas; Hean L Koo; Lowell Umayam; Bernard Suh; Caroline Gerrard; Vanessa Leech; Rong Qi; Shiguo Zhou; David Schwartz; Tamara Feldblyum; Steven L Salzberg; Andrew Tait; C Michael R Turner; Elisabetta Ullu; Owen R White; Sara Melville; Mark D Adams; Claire M Fraser-Liggett; John E Donelson
The sequence and analysis of Trypanosoma brucei chromosome II.
Nucleic acids research 2003;31(16):4856-63.
2003: William H Majoros; Mihaela Pertea; Corina Antonescu; Steven L Salzberg
GlimmerM, Exonomy and Unveil: three ab initio eukaryotic genefinders.
Nucleic acids research 2003;31(13):3601-4.
2003: Natalia Volfovsky; Brian J Haas; Steven L Salzberg
Computational discovery of internal micro-exons.
Genome research 2003;13(6A):1216-21.
2003: Steven L Salzberg
Genomics: Yeast rises again.
Nature 2003;423(6937):233-4.
2003: Timothy D Read; Scott N Peterson; Nicolas Tourasse; Les W Baillie; Ian Paulsen; Karen E Nelson; Hervé Tettelin; Derrick E Fouts; Jonathan Eisen; Steven R Gill; Erik K Holtzapple; Ole Andreas Okstad; Erlendur Helgason; Jennifer Rilstone; Martin Wu; James F Kolonay; Maureen J Beanan; Robert J Dodson; Lauren M Brinkac; Michelle G Giglio; Robert T DeBoy; Ramana Madpu; Sean C Daugherty; A Scott Durkin; Daniel H Haft; William C Nelson; Jeremy D Peterson; Mihai Pop; Hoda M Khouri; Diana Radune; Jonathan L Benton; Yasmin Mahamoud; Lingxia Jiang; Ioana R Hance; Janice F Weidman; Kristi J Berry; Roger D Plaut; Alex M Wolf; Kisha L Watkins; William C Nierman; Alyson Hazen; Robin Cline; Caroline Redmond; Joanne E Thwaite; Owen R White; Steven L Salzberg; Brendan Thomason; Arthur M Friedlander; Theresa Koehler; Philip C Hanna; Anne-Brit Kolstø; Claire M Fraser-Liggett
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria.
Nature 2003;423(6935):81-6.
2003: Steven L Salzberg; Ewan Birney; Sean Eddy; Owen R White
Unrestricted free access works and must continue.
Nature 2003;422(6934):801.
2003: Timothy D Read; Garry S A Myers; Robert brunham; William C Nelson; Ian Paulsen; John F Heidelberg; Erik Holtzapple; Hoda Khouri; N B Federova; H A Carty; Lowell Umayam; Daniel H Haft; J Peterson; Maureen J Beanan; Owen R White; Steven L Salzberg; Ruching Hsia; Grant McClarty; Roger Rank; Patrik M Bavoil; Claire M Fraser-Liggett
Genome sequence of Chlamydophila caviae (Chlamydia psittaci GPIC): examining the role of niche-specific genes in the evolution of the Chlamydiaceae.
Nucleic acids research 2003;31(8):2134-47.
2003: Maria D Ermolaeva; Martin Wu; Jonathan Eisen; Steven L Salzberg
The age of the Arabidopsis thaliana genome duplication.
Plant molecular biology 2003;51(6):859-66.
2003: Ronald Atlas; Philip Campbell; Nicholas R Cozzarelli; Greg Curfman; Lynn Enquist; Gerald Fink; Annette Flanagin; Jacqueline Fletcher; Elizabeth George; Gordon Hammes; David Heyman; Thomas Inglesby; Samuel Kaplan; Donald Kennedy; Judith Krug; Rachel Levinson; Emilie Marcus; Henry Metzger; Stephen S Morse; Alison O'Brien; Andrew Onderdonk; George Poste; Beatrice Renault; Robert Rich; ARIELLA ROSENGARD; Steven L Salzberg; Mary Scanlan; Thomas Shenk; Herbert Tabor; Harold Varmus; Eckard Wimmer; Keith Yamamoto
Statement on the consideration of biodefence and biosecurity.
Nature 2003;421(6925):771.
2003: Arthur L Delcher; Steven L Salzberg; Adam Phillippy
Using MUMmer to identify similar regions in large sequence sets.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2003;Chapter 10():Unit 10.3.
2002: Claire M Fraser-Liggett; Jonathan Eisen; Karen E Nelson; Ian Paulsen; Steven L Salzberg
The value of complete microbial genome sequencing (you get what you pay for).
Journal of bacteriology 2002;184(23):6403-5; discusion 6405.
2002: Mihaela Pertea; Steven L Salzberg
Using GlimmerM to find genes in eukaryotic genomes.
Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.] 2002;Chapter 4():Unit 4.4.
2002: Evgeny M Zdobnov; Christian von Mering; Ivica Letunic; David Torrents; Mikita Suyama; Richard R Copley; George Christophides; Dana Thomasova; Robert A Holt; G. SUBRAMANIAN; Hans-Michael Mueller; George Dimopoulos; John H Law; Michael A Wells; Ewan Birney; Rosane Charlab; Aaron L Halpern; Elena Kokoza; Cheryl L Kraft; Zhongwu Lai; Suzanna Lewis; Christos Louis; Carolina Barillas-Mury; Deborah Nusskern; Gerald M Rubin; Steven L Salzberg; Granger G Sutton; Pantelis Topalis; Ron Wides; Patrick Wincker; Mark Yandell; Frank H Collins; Jose Ribeiro; William M Gelbart; Fotis C Kafatos; Peer Bork
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster.
Science (New York, N.Y.) 2002;298(5591):149-59.
2002: Robert A Holt; G. SUBRAMANIAN; Aaron Halpern; Granger G Sutton; Rosane Charlab; Deborah R Nusskern; Patrick Wincker; andrew clark; José M C Ribeiro; Ron Wides; Steven L Salzberg; Brendan Loftus; Mark Yandell; William H Majoros; Douglas B Rusch; Zhongwu Lai; Cheryl L Kraft; Josep F Abril; Veronique Anthouard; Peter Arensburger; Peter W Atkinson; Holly Baden; Veronique de Berardinis; Danita Baldwin; Vladimir Benes; Jim Biedler; Claudia Blass; Randall Bolanos; Didier Boscus; Mary Barnstead; Shuang Cai; Angela Center; Kabir Chaturverdi; George Christophides; Mathew A Chrystal; Michele Clamp; Anibal Cravchik; Val Curwen; Ali Dana; Art Delcher; Ian Dew; Cheryl A Evans; Michael Flanigan; Anne Grundschober-Freimoser; Lisa Friedli; Zhiping Gu; Ping Guan; Roderic Guigo; Maureen E Hillenmeyer; Susanne L Hladun; James R Hogan; Young S Hong; Jeffrey Hoover; Olivier Jaillon; Zhaoxi Ke; Chinnappa Kodira; Elena Kokoza; Anastasios Koutsos; Ivica Letunic; Alex Levitsky; Yong Liang; Jhy-Jhu Lin; Neil F Lobo; John R Lopez; Joel A Malek; Tina C McIntosh; Stephan Meister; Jason Miller; Clark Mobarry; Emmanuel Mongin; Sean D Murphy; David A O'Brochta; Cynthia Pfannkoch; Rong Qi; Megan A Regier; Karin Remington; Hongguang Shao; Maria V Sharakhova; Cynthia D Sitter; Jyoti Shetty; Thomas J Smith; Renee Strong; Jingtao Sun; Dana Thomasova; Lucas Q Ton; Pantelis Topalis; Zhijian Tu; Maria F Unger; Brian Walenz; Aihui Wang; Jian Wang; Mei Wang; Xuelan Wang; Kerry J Woodford; Jennifer Wortman; Martin Wu; Alison Yao; Evgeny M Zdobnov; Hongyu Zhang; Qi Zhao; Shaying Zhao; Shiaoping C Zhu; Igor Zhimulev; Mario Coluzzi; Alessandra della Torre; Charles W Roth; Christos Louis; Francis Kalush; Richard J Mural; Eugene W Myers; Mark D Adams; Hamilton O Smith; Samuel Broder; Malcolm J Gardner; Claire M Fraser-Liggett; Ewan Birney; Peer Bork; Paul T Brey; J Craig Venter; Jean Weissenbach; Fotis C Kafatos; Frank H Collins; Stephen L Hoffman
The genome sequence of the malaria mosquito Anopheles gambiae.
Science (New York, N.Y.) 2002;298(5591):129-49.
2002: Malcolm J Gardner; Shamira J Shallom; Jane M Carlton; Steven L Salzberg; Vishvanath Nene; Azadeh Shoaibi; Anne Ciecko; Jeffery Lynn; Michael Rizzo; Bruce Weaver; Behnam Jarrahi; Michael Brenner; Babak Parvizi; Luke Tallon; Azita Moazzez; David Granger; Claire Fujii; Cheryl Hansen; James Pederson; Tamara Feldblyum; Jeremy Peterson; Bernard Suh; Sam Angiuoli; Mihaela Pertea; Jonathan Allen; Jeremy Selengut; Owen R White; Leda M Cummings; Hamilton O Smith; Mark D Adams; J Craig Venter; Daniel J Carucci; Stephen L Hoffman; Claire M Fraser-Liggett
Sequence of Plasmodium falciparum chromosomes 2, 10, 11 and 14.
Nature 2002;419(6906):531-4.
2002: Jane M Carlton; Samuel V Angiuoli; Bernard B Suh; Taco W Kooij; Mihaela Pertea; Joana Carneiro Da Silva; Maria D Ermolaeva; Jonathan E Allen; Jeremy D Selengut; Hean L Koo; Jeremy D Peterson; Mihai Pop; Daniel S Kosack; Martin F Shumway; Shelby L Bidwell; Shamira J Shallom; Susan E van Aken; Steven B Riedmuller; Tamara V Feldblyum; Jennifer K Cho; John Quackenbush; Martha Sedegah; Azadeh Shoaibi; Leda M Cummings; Laurence Florens; John R Yates; J Dale Raine; Robert E Sinden; Michael A Harris; Deirdre A Cunningham; Peter R Preiser; Lawrence W Bergman; Akhil B Vaidya; Leo H van Lin; Chris J Janse; Andrew P Waters; Hamilton O Smith; Owen R White; Steven L Salzberg; J Craig Venter; Claire M Fraser-Liggett; Stephen L Hoffman; Malcolm J Gardner; Daniel J Carucci
Genome sequence and comparative analysis of the model rodent malaria parasite Plasmodium yoelii yoelii.
Nature 2002;419(6906):512-9.
2002: Malcolm J Gardner; Neil Hall; Eula Fung; Owen R White; Matthew Berriman; Richard W Hyman; Jane M Carlton; Arnab Pain; Karen E Nelson; Sharen Bowman; Ian Paulsen; Keith James; Jonathan Eisen; Kim Rutherford; Steven L Salzberg; Alister Craig; Sue Kyes; Man-Suen Chan; Vishvanath Nene; Shamira J Shallom; Bernard Suh; Jeremy Peterson; Sam Angiuoli; Mihaela Pertea; Jonathan Allen; Jeremy Selengut; Daniel Haft; Michael W Mather; Akhil B Vaidya; David M A Martin; Alan H Fairlamb; Martin J Fraunholz; David S Roos; Stuart A Ralph; Geoffrey I McFadden; Leda M Cummings; G. SUBRAMANIAN; Chris Mungall; J Craig Venter; Daniel J Carucci; Stephen L Hoffman; Chris Newbold; Ronald W Davis; Claire M Fraser-Liggett; Bart Barrell
Genome sequence of the human malaria parasite Plasmodium falciparum.
Nature 2002;419(6906):498-511.
2002: Ian Paulsen; Rekha Seshadri; Karen E Nelson; Jonathan Eisen; John F Heidelberg; Timothy D Read; Robert J Dodson; Lowell Umayam; Lauren M Brinkac; Maureen J Beanan; Sean C Daugherty; Robert T Deboy; A Scott Durkin; James F Kolonay; Ramana Madupu; William C Nelson; Bola Ayodeji; Margaret Kraul; Jyoti Shetty; Joel Malek; Susan E Van Aken; Steven Riedmuller; Hervé Tettelin; Steven R Gill; Owen R White; Steven L Salzberg; David L Hoover; Luther E Lindler; Shirley M Halling; Stephen M Boyle; Claire M Fraser-Liggett
The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbionts.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(20):13148-53.
2002: Robert D Fleischmann; David Alland; Jonathan Eisen; L Carpenter; Owen R White; J Peterson; Robert T Deboy; Robert J Dodson; Michelle G Giglio; Daniel H Haft; EK Hickey; James F Kolonay; William C Nelson; Lowell Umayam; Maria D Ermolaeva; Steven L Salzberg; Arthur L Delcher; Teresa Utterback; Janice Weidman; Hoda Khouri; J Gill; A Mikula; William R Bishai; W R Jacobs Jr; J Craig Venter; Claire M Fraser-Liggett
Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains.
Journal of bacteriology 2002;184(19):5479-90.
2002: Timothy D Read; Steven L Salzberg; Mihai Pop; Martin Shumway; Lowell Umayam; Lingxia Jiang; Erik Holtzapple; Joseph D Busch; Kimothy Smith; James M Schupp; Daniel Solomon; Paul Keim; Claire M Fraser-Liggett
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.
Science (New York, N.Y.) 2002;296(5575):2028-33.
2002: Arthur L Delcher; Adam Phillippy; Jane Carlton; Steven L Salzberg
Fast algorithms for large-scale genome alignment and comparison.
Nucleic acids research 2002;30(11):2478-83.
2002: Richard J Mural; Mark D Adams; Eugene W Myers; Hamilton O Smith; George L Gabor Miklos; Ron Wides; Aaron Halpern; Peter W Li; Granger G Sutton; Joe Nadeau; Steven L Salzberg; Robert A Holt; Chinnappa D Kodira; Fu Lu; Lin Chen; Zuoming Deng; Carlos C Evangelista; Weiniu Gan; Thomas J Heiman; Jiayin Li; Zhenya Li; Gennady V Merkulov; Natalia V Milshina; Ashwinikumar K Naik; Rong Qi; Bixiong Chris Shue; Aihui Wang; Jian Wang; Xin Wang; Xianghe Yan; Jane Ye; Shibu Yooseph; Qi Zhao; Liansheng Zheng; Shiaoping C Zhu; Kendra Biddick; Randall Bolanos; Arthur L Delcher; Ian M Dew; Daniel Fasulo; Michael J Flanigan; Daniel H Huson; Saul A Kravitz; Jason R Miller; Clark M Mobarry; Knut Reinert; Karin A Remington; Qing Zhang; Xiangqun H Zheng; Deborah R Nusskern; Zhongwu Lai; Yiding Lei; Wenyan Zhong; Alison Yao; Ping Guan; Rui-Ru Ji; Zhiping Gu; Zhen-Yuan Wang; Fei Zhong; Chunlin Xiao; Chia-Chien Chiang; Mark Yandell; Jennifer Wortman; Peter G Amanatides; Suzanne L Hladun; Eric C Pratts; Jeffery E Johnson; Kristina L Dodson; Kerry J Woodford; Cheryl A Evans; Barry Gropman; Douglas B Rusch; Eli Venter; Mei Wang; Thomas J Smith; Jarrett T Houck; Donald E Tompkins; Charles Haynes; Debbie Jacob; Soo H Chin; David R Allen; Carl E Dahlke; Robert Sanders; Kelvin Li; Xiangjun Liu; Alexander A Levitsky; William H Majoros; Quan Chen; Ashley C Xia; John R Lopez; Michael T Donnelly; Matthew H Newman; Anna Glodek; Cheryl L Kraft; Marc Nodell; Feroze Ali; Hui-Jin An; Danita Baldwin-Pitts; Karen Y Beeson; Shuang Cai; Mark Carnes; Amy Carver; Parris M Caulk; Angela Center; Yen-Hui Chen; Ming-Lai Cheng; My D Coyne; Michelle Crowder; Steven Danaher; Lionel B Davenport; Raymond Desilets; Susanne M Dietz; Lisa Doup; Patrick Dullaghan; Steven Ferriera; Carl R Fosler; Harold C Gire; Andres Gluecksmann; Jeannine D Gocayne; Jonathan Gray; Brit Hart; Jason Haynes; Jeffery Hoover; Tim Howland; Chinyere Ibegwam; Mena Jalali; David Johns; Leslie Kline; Daniel S Ma; Steven MacCawley; Anand Magoon; Felecia Mann; David May; Tina C McIntosh; Somil Mehta; Linda Moy; Mee C Moy; Brian J Murphy; Sean D Murphy; Keith A Nelson; Zubeda Nuri; Kimberly A Parker; Alexandre C Prudhomme; Vinita N Puri; Hina Qureshi; John C Raley; Matthew S Reardon; Megan A Regier; Yu-Hui C Rogers; Deanna L Romblad; Jakob Schutz; John L Scott; Richard Scott; Cynthia D Sitter; Michella Smallwood; Arlan C Sprague; Erin Stewart; Renee V Strong; Ellen Suh; Karena Sylvester; Reginald Thomas; Ni Ni Tint; Christopher Tsonis; Gary Wang; George Wang; Monica S Williams; Sherita M Williams; Sandra M Windsor; Keriellen Wolfe; Mitchell M Wu; Jayshree Zaveri; Kabir Chaturvedi; Andrei E Gabrielian; Zhaoxi Ke; Jingtao Sun; G. SUBRAMANIAN; J Craig Venter; Cynthia M Pfannkoch; Mary Barnstead; Lisa D Stephenson
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome.
Science (New York, N.Y.) 2002;296(5573):1661-71.
2002: Eske Willerslev; Tobias Mourier; Anders J Hansen; Bent Christensen; Ian Barnes; Steven L Salzberg
Contamination in the draft of the human genome masquerades as lateral gene transfer.
DNA sequence : the journal of DNA sequencing and mapping 2002;13(2):75-6.
2002: Brian J Haas; Natalia Volfovsky; Christopher D Town; Maxim Troukhan; Nickolai N Alexandrov; Kenneth A Feldmann; Richard B Flavell; Owen R White; Steven L Salzberg
Full-length messenger RNA sequences greatly improve genome annotation.
Genome biology 2002;3(6):RESEARCH0029.
2002: Mihaela Pertea; Steven L Salzberg
Computational gene finding in plants.
Plant molecular biology 2002;48(1-2):39-48.
2001: B E Suzek; Maria D Ermolaeva; M Schreiber; Steven L Salzberg
A probabilistic method for identifying start codons in bacterial genomes.
Bioinformatics (Oxford, England) 2001;17(12):1123-30.
2001: Sean P Kennedy; Wailap Victor Ng; Steven L Salzberg; Leroy Hood; Shiladitya DasSarma
Understanding the adaptation of Halobacterium species NRC-1 to its extreme environment through computational analysis of its genome sequence.
Genome research 2001;11(10):1641-50.
2001: Steven L Salzberg; Jonathan Eisen
Lateral gene transfer or viral colonization?
Science (New York, N.Y.) 2001;293(5532):1048.
2001: Hervé Tettelin; K E Nelson; Ian Paulsen; Jonathan Eisen; T D Read; S Peterson; J Heidelberg; R T DeBoy; D H Haft; R J Dodson; A S Durkin; Michelle G Giglio; J F Kolonay; W C Nelson; J D Peterson; L A Umayam; Owen R White; Steven L Salzberg; M R Lewis; D Radune; E Holtzapple; H Khouri; A M Wolf; T R Utterback; C L Hansen; L A McDonald; T V Feldblyum; S Angiuoli; T Dickinson; E K Hickey; I E Holt; B J Loftus; F Yang; Hamilton O Smith; J C Venter; B A Dougherty; Donald A Morrison; Susan Kay Hollingshead; Claire M Fraser-Liggett
Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.
Science (New York, N.Y.) 2001;293(5529):498-506.
2001: Steven L Salzberg; Owen R White; J Peterson; Jonathan Eisen
Microbial genes in the human genome: lateral transfer or gene loss?
Science (New York, N.Y.) 2001;292(5523):1903-6.
2001: Michael Bevan; K Mayer; Owen R White; Jonathan Eisen; Daphne Preuss; T Bureau; Steven L Salzberg; H W Mewes
Sequence and analysis of the Arabidopsis genome.
Current opinion in plant biology 2001;4(2):105-10.
2001: W C Nierman; T V Feldblyum; M T Laub; Ian Paulsen; K E Nelson; Jonathan Eisen; J F Heidelberg; M R Alley; N Ohta; Janine R Maddock; I Potocka; W C Nelson; A Newton; C Stephens; N D Phadke; Bert Ely; R T DeBoy; R J Dodson; A S Durkin; Michelle G Giglio; D H Haft; J F Kolonay; J Smit; M B Craven; H Khouri; J Shetty; K Berry; T Utterback; K Tran; A Wolf; J Vamathevan; M Ermolaeva; Owen R White; Steven L Salzberg; J C Venter; L Shapiro; Claire M Fraser-Liggett; Jonathan Eisen
Complete genome sequence of Caulobacter crescentus.
Proceedings of the National Academy of Sciences of the United States of America 2001;98(7):4136-41.
2001: Qiaoping Yuan; John Quackenbush; Razvan Sultana; Mihaela Pertea; Steven L Salzberg; C Robin Buell
Rice bioinformatics. analysis of rice sequence data and leveraging the data to other plant species.
Plant physiology 2001;125(3):1166-74.
2001: Maria D Ermolaeva; Owen R White; Steven L Salzberg
Prediction of operons in microbial genomes.
Nucleic acids research 2001;29(5):1216-21.
2001: Mihaela Pertea; X Lin; Steven L Salzberg
GeneSplicer: a new computational method for splice site prediction.
Nucleic acids research 2001;29(5):1185-90.
2001: J C Venter; M D Adams; E W Myers; P W Li; R J Mural; G G Sutton; Hamilton O Smith; M Yandell; C A Evans; R A Holt; J D Gocayne; P Amanatides; R M Ballew; D H Huson; Jennifer Wortman; Q Zhang; C D Kodira; X H Zheng; L Chen; M Skupski; G. SUBRAMANIAN; P D Thomas; J Zhang; G L Gabor Miklos; C Nelson; S Broder; andrew clark; J Nadeau; Victor A McKusick; N Zinder; Arnold J Levine; Richard J Roberts; M Simon; C Slayman; M Hunkapiller; R Bolanos; A Delcher; I Dew; D Fasulo; M Flanigan; L Florea; A Halpern; S Hannenhalli; S Kravitz; S Levy; C Mobarry; K Reinert; K Remington; J Abu-Threideh; E Beasley; K Biddick; V Bonazzi; R Brandon; M Cargill; I Chandramouliswaran; R Charlab; K Chaturvedi; Z Deng; V Di Francesco; P Dunn; K Eilbeck; C Evangelista; A E Gabrielian; W Gan; W Ge; F Gong; Z Gu; P Guan; T J Heiman; M E Higgins; R R Ji; Z Ke; K A Ketchum; Z Lai; Y Lei; Z Li; J Li; Y Liang; X Lin; F Lu; G V Merkulov; N Milshina; H M Moore; A K Naik; V A Narayan; B Neelam; D Nusskern; D B Rusch; Steven L Salzberg; W Shao; B Shue; J Sun; Z Wang; A Wang; X Wang; J Wang; M Wei; R Wides; C Xiao; C Yan; A Yao; J Ye; M Zhan; W Zhang; H Zhang; Q Zhao; L Zheng; F Zhong; W Zhong; S Zhu; Shaying Zhao; D Gilbert; S Baumhueter; G Spier; C Carter; A Cravchik; T Woodage; F Ali; H An; A Awe; D Baldwin; H Baden; M Barnstead; I Barrow; K Beeson; D Busam; A Carver; A Center; M L Cheng; L Curry; S Danaher; L Davenport; R Desilets; S Dietz; K Dodson; L Doup; S Ferriera; N Garg; A Gluecksmann; B Hart; J Haynes; C Haynes; C Heiner; S Hladun; Damon Hostin; J Houck; T Howland; C Ibegwam; J Johnson; F Kalush; L Kline; S Koduru; A Love; F Mann; D May; S McCawley; T McIntosh; I McMullen; M Moy; L Moy; B Murphy; K Nelson; C Pfannkoch; E Pratts; V Puri; H Qureshi; M Reardon; R Rodriguez; Y H Rogers; D Romblad; B Ruhfel; R Scott; C Sitter; M Smallwood; E Stewart; R Strong; Edward Suh; R Thomas; N N Tint; S Tse; C Vech; Gaofeng Wang; J Wetter; S Williams; M Williams; S Windsor; E Winn-Deen; K Wolfe; J Zaveri; K Zaveri; Josep F Abril; R Guigó; M J Campbell; K V Sjolander; B Karlak; A Kejariwal; H Mi; B Lazareva; T Hatton; A Narechania; K Diemer; A Muruganujan; N Guo; S Sato; V Bafna; S Istrail; R Lippert; R Schwartz; B Walenz; S Yooseph; D Allen; A Basu; J Baxendale; L Blick; M Caminha; J Carnes-Stine; P Caulk; Y H Chiang; M Coyne; C Dahlke; A Mays; M Dombroski; M Donnelly; D Ely; S Esparham; C Fosler; H Gire; S Glanowski; K Glasser; A Glodek; M Gorokhov; K Graham; B Gropman; M Harris; J Heil; S Henderson; J Hoover; D Jennings; C Jordan; J Jordan; J Kasha; L Kagan; C Kraft; A Levitsky; M Lewis; X Liu; J Lopez; D Ma; W Majoros; J McDaniel; S Murphy; M Newman; T Nguyen; N Nguyen; M Nodell; S Pan; J Peck; M Peterson; W Rowe; R Sanders; J Scott; M Simpson; T Smith; A Sprague; T Stockwell; R Turner; E Venter; M Wang; M Wen; D Wu; M Wu; A Xia; A Zandieh; X Zhu
The sequence of the human genome.
Science (New York, N.Y.) 2001;291(5507):1304-51.
2001: Natalia Volfovsky; Brian J Haas; Steven L Salzberg
A clustering method for repeat analysis in DNA sequences.
Genome biology 2001;2(8):RESEARCH0027.
2000: M Salanoubat; K Lemcke; M Rieger; W Ansorge; M Unseld; B Fartmann; G Valle; H Blöcker; Manuel Perez-Alonso; B Obermaier; M Delseny; M Boutry; L A Grivell; R Mache; P Puigdomènech; V De Simone; N Choisne; F Artiguenave; C Robert; P Brottier; P Wincker; L Cattolico; J Weissenbach; W Saurin; F Quétier; M Schäfer; S Müller-Auer; C Gabel; M Fuchs; V Benes; E Wurmbach; H Drzonek; H Erfle; N Jordan; S Bangert; R Wiedelmann; H Kranz; H Voss; R Holland; P Brandt; G Nyakatura; A Vezzi; M D'Angelo; A Pallavicini; S Toppo; B Simionati; A Conrad; K Hornischer; G Kauer; T H Löhnert; G Nordsiek; J Reichelt; M Scharfe; O Schön; M Bargues; J Terol; Joan CLIMENT; P Navarro; C Collado; A Perez-Perez; B Ottenwälder; D Duchemin; R Cooke; M Laudie; C Berger-Llauro; B Purnelle; D Masuy; M de Haan; A C Maarse; J P Alcaraz; A Cottet; E Casacuberta; A Monfort; A Argiriou; M flores; R Liguori; D Vitale; G Mannhaupt; D Haase; H Schoof; S Rudd; P Zaccaria; H W Mewes; K F Mayer; S Kaul; C D Town; H L Koo; L J Tallon; J Jenkins; T Rooney; M Rizzo; A Walts; T Utterback; C Y Fujii; T P Shea; T H Creasy; B Haas; R Maiti; D Wu; J Peterson; S Van Aken; G Pai; J Militscher; P Sellers; J E Gill; T V Feldblyum; D Preuss; X Lin; W C Nierman; Steven L Salzberg; Owen R White; J C Venter; Claire M Fraser-Liggett; T Kaneko; Y Nakamura; S Sato; T Kato; E Asamizu; S Sasamoto; T Kimura; K Idesawa; K Kawashima; Y Kishida; C Kiyokawa; M Kohara; M Matsumoto; A Matsuno; A Muraki; S Nakayama; N Nakazaki; S Shinpo; C Takeuchi; T Wada; A Watanabe; M Yamada; M Yasuda; S Tabata
Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana.
Nature 2000;408(6814):820-2.
2000: A Theologis; J R Ecker; C J Palm; N A Federspiel; S Kaul; Owen R White; J Alonso; H Altafi; R Araujo; C L Bowman; S Y Brooks; E Buehler; A Chan; Q Chao; H Chen; R F Cheuk; C W Chin; M K Chung; L Conn; A B Conway; A R Conway; T H Creasy; K Dewar; P Dunn; P Etgu; T V Feldblyum; J Feng; B Fong; C Y Fujii; J E Gill; A D Goldsmith; B Haas; N F Hansen; B Hughes; L Huizar; J L Hunter; J Jenkins; C Johnson-Hopson; S Khan; E Khaykin; C J Kim; H L Koo; I Kremenetskaia; D B Kurtz; A Kwan; B Lam; S Langin-Hooper; A Lee; J M Lee; C A Lenz; J H Li; Y Li; X Lin; S X Liu; Z A Liu; J S Luros; R Maiti; A Marziali; J Militscher; M Miranda; M Nguyen; W C Nierman; B I Osborne; G Pai; J Peterson; P K Pham; M Rizzo; T Rooney; D Rowley; H Sakano; Steven L Salzberg; J R Schwartz; P Shinn; A M Southwick; H Sun; L J Tallon; G Tambunga; M J Toriumi; C D Town; T Utterback; S Van Aken; M Vaysberg; V S Vysotskaia; M Walker; D Wu; G Yu; Claire M Fraser-Liggett; J C Venter; R W Davis
Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.
Nature 2000;408(6814):816-20.
2000: Frank Liang; Ingeborg Holt; Geo Pertea; Svetlana Karamycheva; Steven L Salzberg; John Quackenbush
An optimized protocol for analysis of EST sequences.
Nucleic acids research 2000;28(18):3657-65.
2000: Claire M Fraser-Liggett; Jonathan Eisen; Steven L Salzberg
Microbial genome sequencing.
Nature 2000;406(6797):799-803.
2000: Maria D Ermolaeva; Hanif Khalak; Owen R White; Hamilton O Smith; Steven L Salzberg
Prediction of transcription terminators in bacterial genomes.
Journal of molecular biology 2000;301(1):27-33.
2000: J F Heidelberg; Jonathan Eisen; W C Nelson; R A Clayton; Michelle G Giglio; R J Dodson; D H Haft; E K Hickey; J D Peterson; L Umayam; S R Gill; K E Nelson; T D Read; Hervé Tettelin; D Richardson; M D Ermolaeva; J Vamathevan; S Bass; H Qin; I Dragoi; P Sellers; L McDonald; T Utterback; R D Fleishmann; W C Nierman; Owen R White; Steven L Salzberg; Hamilton O Smith; Rita R Colwell; J J Mekalanos; J C Venter; Claire M Fraser-Liggett
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
Nature 2000;406(6795):477-83.
2000: Frank Liang; Ingeborg Holt; Geo Pertea; Svetlana Karamycheva; Steven L Salzberg; John Quackenbush
Gene index analysis of the human genome estimates approximately 120,000 genes.
Nature genetics 2000;25(2):239-40.
2000: Timothy D Read; Robert brunham; C Shen; Steven R Gill; John F Heidelberg; Owen R White; EK Hickey; J Peterson; Teresa Utterback; K Berry; S Bass; K Linher; Janice Weidman; Hoda Khouri; B Craven; C Bowman; Robert J Dodson; Michelle G Giglio; W Nelson; Robert T Deboy; James F Kolonay; Grant McClarty; Steven L Salzberg; Jonathan Eisen; Claire M Fraser-Liggett
Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.
Nucleic acids research 2000;28(6):1397-406.
2000: Hervé Tettelin; N J Saunders; J Heidelberg; A C Jeffries; K E Nelson; Jonathan Eisen; K A Ketchum; D W Hood; J F Peden; R J Dodson; W C Nelson; Michelle G Giglio; R DeBoy; J D Peterson; E K Hickey; D H Haft; Steven L Salzberg; Owen R White; R D Fleischmann; B A Dougherty; T Mason; A Ciecko; D S Parksey; E Blair; H Cittone; E B Clark; M D Cotton; T R Utterback; H Khouri; H Qin; J Vamathevan; J Gill; V Scarlato; V Masignani; M Pizza; G Grandi; L Sun; Hamilton O Smith; Claire M Fraser-Liggett; E R Moxon; R Rappuoli; J C Venter
Complete genome sequence of Neisseria meningitidis serogroup B strain MC58.
Science (New York, N.Y.) 2000;287(5459):1809-15.
2000: Mihaela Pertea; Steven L Salzberg; Malcolm J Gardner
Finding genes in Plasmodium falciparum.
Nature 2000;404(6773):34; discussion 34-5.
2000: Jonathan Eisen; John F Heidelberg; Owen R White; Steven L Salzberg
Evidence for symmetric chromosomal inversions around the replication origin in bacteria.
Genome biology 2000;1(6):RESEARCH0011.
1999: X Lin; S Kaul; S Rounsley; T P Shea; M I Benito; C D Town; C Y Fujii; T Mason; C L Bowman; M Barnstead; T V Feldblyum; C R Buell; K A Ketchum; J Lee; C M Ronning; H L Koo; K S Moffat; L A Cronin; M Shen; G Pai; S Van Aken; L Umayam; L J Tallon; J E Gill; M D Adams; A J Carrera; T H Creasy; H M Goodman; chris somerville; Gregory Paul Copenhaver; D Preuss; W C Nierman; Owen R White; Jonathan Eisen; Steven L Salzberg; Claire M Fraser-Liggett; J C Venter
Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.
Nature 1999;402(6763):761-8.
1999: Hervé Tettelin; Diana Radune; S Kasif; Hoda Khouri; Steven L Salzberg
Optimized multiplex PCR: efficiently closing a whole-genome shotgun sequencing project.
Genomics 1999;62(3):500-7.
1999: Arthur L Delcher; D Harmon; S Kasif; Owen R White; Steven L Salzberg
Improved microbial gene identification with GLIMMER.
Nucleic acids research 1999;27(23):4636-41.
1999: Owen R White; Jonathan Eisen; J F Heidelberg; E K Hickey; J D Peterson; R J Dodson; D H Haft; Michelle G Giglio; W C Nelson; D L Richardson; K S Moffat; H Qin; L Jiang; W Pamphile; M Crosby; M Shen; J J Vamathevan; P Lam; L McDonald; T Utterback; C Zalewski; K S Makarova; L Aravind; Mark J Daly; K W Minton; R D Fleischmann; K A Ketchum; K E Nelson; Steven L Salzberg; Hamilton O Smith; J C Venter; Claire M Fraser-Liggett
Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1.
Science (New York, N.Y.) 1999;286(5444):1571-7.
1999: Hamilton O Smith; Michelle G Giglio; Steven L Salzberg
DNA uptake signal sequences in naturally transformable bacteria.
Research in microbiology 1999;150(9-10):603-16.
1999: Steven L Salzberg; Mihaela Pertea; Arthur L Delcher; Malcolm J Gardner; Hervé Tettelin
Interpolated Markov models for eukaryotic gene finding.
Genomics 1999;59(1):24-31.
1999: Arthur L Delcher; S Kasif; Robert D Fleischmann; J Peterson; Owen R White; Steven L Salzberg
Alignment of whole genomes.
Nucleic acids research 1999;27(11):2369-76.
1999: Karen E Nelson; RA Clayton; Steven R Gill; Michelle G Giglio; Robert J Dodson; Daniel H Haft; EK Hickey; J D Peterson; William C Nelson; KA Ketchum; L McDonald; Teresa Utterback; JA Malek; K D Linher; M M Garrett; A M Stewart; M D Cotton; M S Pratt; C A Phillips; D Richardson; John F Heidelberg; Granger Sutton; Robert D Fleischmann; Jonathan Eisen; Owen R White; Steven L Salzberg; Hamilton O Smith; J Craig Venter; Claire M Fraser-Liggett
Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
Nature 1999;399(6734):323-9.
1998: Malcolm J Gardner; Hervé Tettelin; Daniel J Carucci; LM Cummings; L Aravind; E V Koonin; S Shallom; T Mason; K Yu; C Fujii; J Pederson; K Shen; J Jing; C Aston; Z Lai; David C Schwartz; Mihaela Pertea; Steven L Salzberg; L Zhou; Granger Sutton; R Clayton; Owen R White; Hamilton O Smith; Claire M Fraser-Liggett; Mark D Adams; J Craig Venter; Stephen L Hoffman
Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum.
Science (New York, N.Y.) 1998;282(5391):1126-32.
1998: Steven L Salzberg; A J Salzberg; A R Kerlavage; J F Tomb
Skewed oligomers and origins of replication.
Gene 1998;217(1-2):57-67.
1998: Claire M Fraser-Liggett; S J Norris; G M Weinstock; Owen R White; G G Sutton; R Dodson; Michelle G Giglio; E K Hickey; R Clayton; K A Ketchum; E Sodergren; J M Hardham; M P McLeod; Steven L Salzberg; J Peterson; Hanif Khalak; D Richardson; J K Howell; M Chidambaram; T Utterback; L McDonald; P Artiach; C Bowman; M D Cotton; C Fujii; S Garland; B Hatch; K Horst; K Roberts; M Sandusky; J Weidman; Hamilton O Smith; J C Venter
Complete genome sequence of Treponema pallidum, the syphilis spirochete.
Science (New York, N.Y.) 1998;281(5375):375-88.
1998: Steven L Salzberg; Arthur L Delcher; S Kasif; Owen R White
Microbial gene identification using interpolated Markov models.
Nucleic acids research 1998;26(2):544-8.
1998: Steven L Salzberg; Arthur L Delcher; Kenneth Fasman; J Henderson
A decision tree system for finding genes in DNA.
Journal of computational biology : a journal of computational molecular cell biology 1998;5(4):667-80.
1997: Claire M Fraser-Liggett; S Casjens; W M Huang; G G Sutton; R Clayton; Raju Lathigra; Owen R White; K A Ketchum; R Dodson; E K Hickey; Michelle G Giglio; B Dougherty; J F Tomb; R D Fleischmann; D Richardson; J Peterson; A R Kerlavage; John Quackenbush; Steven L Salzberg; Mark S Hanson; R van Vugt; N Palmer; M D Adams; J Gocayne; J Weidman; T Utterback; L Watthey; L McDonald; P Artiach; C Bowman; S Garland; C Fuji; M D Cotton; K Horst; K Roberts; B Hatch; Hamilton O Smith; J C Venter
Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi.
Nature 1997;390(6660):580-6.
1997: Steven L Salzberg
A method for identifying splice sites and translational start sites in eukaryotic mRNA.
Computer applications in the biosciences : CABIOS 1997;13(4):365-76.
1997: J Henderson; Steven L Salzberg; Kenneth Fasman
Finding genes in DNA with a Hidden Markov Model.
Journal of computational biology : a journal of computational molecular cell biology 1997;4(2):127-41.
1996: Steven L Salzberg; X Chen; J Henderson; K Fasman
Finding genes in DNA using decision trees and dynamic programming.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1996;4():201-10.
1995: Steven L Salzberg
Locating protein coding regions in human DNA using a decision tree algorithm.
Journal of computational biology : a journal of computational molecular cell biology 1995;2(3):473-85.
1992: Steven L Salzberg; S Cost
Predicting protein secondary structure with a nearest-neighbor algorithm.
Journal of molecular biology 1992;227(2):371-4.