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Ian Paulsen

Research Profile

Genes & Molecular Sequences

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Chemicals & Drugs

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Sequence Analysis, DNA

Physiology

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Bacterial Chromosomes

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Publications

TOP 3
Teresa A Kidarsa; Donald Y Kobayashi; Jeffrey S Buyer; Neal C Goebel; Aaron Johnson; Ian Paulsen; Daniel P Roberts; Brenda T Shaffer; T Mark Zabriskie; Joyce E Loper
Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces under the control of the global regulators GacA and RpoS.
Ingrid Keseler; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Amanda Mackie; Luis Muñiz-Rascado; Quang Ong; Suzanne Paley; Ian Paulsen; Martín Peralta-Gil; Alberto Santos-Zavaleta; Imke Schröder; Alexander G Shearer; Pallavi Subhraveti; Mike Travers; Deepika Weerasinghe; Verena Weiss; César Bonavides-Martínez; Julio Collado-Vides; Carol Fulcher; Socorro Gama-Castro; Robert P Gunsalus; Araceli M Huerta; Peter D Karp
EcoCyc: fusing model organism databases with systems biology.
C L Dupont; D A Johnson; Ian Paulsen; K Phillippy; B Brahamsha; Brian Palenik
Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102.

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All Publications

2013: Teresa A Kidarsa; Donald Y Kobayashi; Jeffrey S Buyer; Neal C Goebel; Aaron Johnson; Ian Paulsen; Daniel P Roberts; Brenda T Shaffer; T Mark Zabriskie; Joyce E Loper
Genes expressed by the biological control bacterium Pseudomonas protegens Pf-5 on seed surfaces under the control of the global regulators GacA and RpoS.
Environmental microbiology 2013;15(3):716-35.
2013: Ingrid Keseler; Anamika Kothari; Markus Krummenacker; Mario Latendresse; Amanda Mackie; Luis Muñiz-Rascado; Quang Ong; Suzanne Paley; Ian Paulsen; Martín Peralta-Gil; Alberto Santos-Zavaleta; Imke Schröder; Alexander G Shearer; Pallavi Subhraveti; Mike Travers; Deepika Weerasinghe; Verena Weiss; César Bonavides-Martínez; Julio Collado-Vides; Carol Fulcher; Socorro Gama-Castro; Robert P Gunsalus; Araceli M Huerta; Peter D Karp
EcoCyc: fusing model organism databases with systems biology.
Nucleic acids research 2013;41(Database issue):D605-12.
2012: C L Dupont; D A Johnson; Ian Paulsen; K Phillippy; B Brahamsha; Brian Palenik
Genetic identification of a high-affinity Ni transporter and the transcriptional response to Ni deprivation in Synechococcus sp. strain WH8102.
Applied and environmental microbiology 2012;78(22):7822-32.
2012: Lisa Zeigler Allen; Eric E Allen; Jonathan H Badger; Liam D H Elbourne; John P McCrow; Kenneth H Nealson; Ian Paulsen; Douglas B Rusch; Mathangi Thiagarajan; J Craig Venter; Shannon J Williamson; Andrew E Allen
Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic.
The ISME journal 2012;6(7):1403-14.
2011: Mark Eppinger; Scott Grayburn; Dieter Jahn; Mitrick A Johns; Sara S K Koenig; Kirthi K Kutumbaka; Vitaliy Lukyanchuk; Madeleine Martin; Ian Paulsen; Jacques Ravel; David R Riley; Mary J Rosovitz; Jürgen Seibel; Riaz Ul-Qamar; Barbara Ball; Rebekka Biedendieck; Christopher Braun; Erhard Bremer; Boyke Bunk; Sean Daugherty; Sourabh Dhingra; Janaka N Edirisinghe; Liam D H Elbourne; Heather Huot Creasy; Patricia S Vary
Genome sequences of the biotechnologically important Bacillus megaterium strains QM B1551 and DSM319.
Journal of bacteriology 2011;193(16):4199-213.
2011: Sujatha Subramoni; Juan F Gonzalez; Aaron Johnson; Christoph Keel; Joyce E Loper; Ian Paulsen; Maria Péchy-Tarr; Laurène Rochat; Vittorio Venturi
Bacterial subfamily of LuxR regulators that respond to plant compounds.
Applied and environmental microbiology 2011;77(13):4579-88.
2011: Ingrid Keseler; Julio Collado-Vides; Alberto Santos-Zavaleta; Martín Peralta-Gil; Socorro Gama-Castro; Luis Muñiz-Rascado; César Bonavides-Martinez; Suzanne Paley; Markus Krummenacker; Tomer Altman; Pallavi Kaipa; Aaron Spaulding; John Pacheco; Mario Latendresse; Carol Fulcher; Malabika Sarker; Alexander G Shearer; Amanda Mackie; Ian Paulsen; Robert P Gunsalus; Peter Karp
EcoCyc: a comprehensive database of Escherichia coli biology.
Nucleic acids research 2011;39(Database issue):D583-90.
2010: Martin Ostrowski; Sophie Mazard; Sasha G Tetu; Katherine Phillippy; Aaron Johnson; Brian Palenik; Ian Paulsen; David J Scanlan
PtrA is required for coordinate regulation of gene expression during phosphate stress in a marine Synechococcus.
The ISME journal 2010;4(7):908-21.
2010: Xizeng Mao; Victor Olman; Rhona Stuart; Ian Paulsen; Brian Palenik; Ying Xu
Computational prediction of the osmoregulation network in Synechococcus sp. WH8102.
BMC genomics 2010;11():291.
2010: Peter Karp; Suzanne Paley; Markus Krummenacker; Mario Latendresse; Joseph M Dale; Thomas J Lee; Pallavi Kaipa; Fred Gilham; Aaron Spaulding; Liviu Popescu; Tomer Altman; Ian Paulsen; Ingrid Keseler; Ron Caspi
Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.
Briefings in bioinformatics 2010;11(1):40-79.
2009: Vera Tai; Ian Paulsen; Katherine Phillippy; D Aaron Johnson; Brian Palenik
Whole-genome microarray analyses of Synechococcus-Vibrio interactions.
Environmental microbiology 2009;11(10):2698-709.
2009: Rhona K Stuart; Chris L Dupont; D Aaron Johnson; Ian Paulsen; Brian Palenik
Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains.
Applied and environmental microbiology 2009;75(15):5047-57.
2009: David J Scanlan; Martin Ostrowski; Sophie Mazard; Alexis Dufresne; Laurence Garczarek; Wolfgang Hess; Anton F Post; M Hagemann; Ian Paulsen; Frédéric Partensky
Ecological genomics of marine picocyanobacteria.
Microbiology and molecular biology reviews : MMBR 2009;73(2):249-99.
2009: Brian Palenik; Qinghu Ren; V Tai; Ian Paulsen
Coastal Synechococcus metagenome reveals major roles for horizontal gene transfer and plasmids in population diversity.
Environmental microbiology 2009;11(2):349-59.
2009: E V Thomas; K H Phillippy; B Brahamsha; David M Haaland; Jerilyn A Timlin; L D H Elbourne; Brian Palenik; Ian Paulsen
Statistical analysis of microarray data with replicated spots: a case study with synechococcus WH8102.
Comparative and functional genomics 2009;():950171.
2008: Andrew M Bailey; Ian Paulsen; Laura J V Piddock
RamA confers multidrug resistance in Salmonella enterica via increased expression of acrB, which is inhibited by chlorpromazine.
Antimicrobial agents and chemotherapy 2008;52(10):3604-11.
2008: Stefan M Sievert; Kathleen M Scott; Martin Klotz; Patrick S G Chain; Loren Hauser; James Hemp; Michael Hügler; Miriam Land; Alla Lapidus; Frank W Larimer; Susan Lucas; Stephanie Malfatti; Folker Meyer; Ian Paulsen; Qinghu Ren; Jörg Simon
Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans.
Applied and environmental microbiology 2008;74(4):1145-56.
2008: Daniel A Johnson; Sasha G Tetu; Katherine Phillippy; Joan Chen; Qinghu Ren; Ian Paulsen
High-throughput phenotypic characterization of Pseudomonas aeruginosa membrane transport genes.
PLoS genetics 2008;4(10):e1000211.
2008: Alexis Dufresne; Martin Ostrowski; David J Scanlan; Laurence Garczarek; Sophie Mazard; Brian P Palenik; Ian Paulsen; Nicole Tandeau de Marsac; Patrick Wincker; Carole Dossat; Steve Ferriera; Justin Johnson; Anton F Post; Wolfgang Hess; Frédéric Partensky
Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.
Genome biology 2008;9(5):R90.
2007: Kelly A Brayton; Audrey O T Lau; David R Herndon; Linda Hannick; Lowell S Kappmeyer; Shawn J Berens; Shelby L Bidwell; Wendy C Brown; Jonathan Crabtree; Doug Fadrosh; Tamara Feldblum; Heather A Forberger; Brian J Haas; Jeanne Freeman; Hoda Khouri; Hean Koo; David J Mann; Junzo Norimine; Ian Paulsen; Diana Radune; Qinghu Ren; Roger K Smith; Carlos Suarez; Owen R White; Jennifer Wortman; Donald P Knowles; Terry F McElwain; Vishvanath Nene
Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa.
PLoS pathogens 2007;3(10):1401-13.
2007: Sabeeha S Merchant; Simon E Prochnik; Olivier Vallon; Elizabeth H Harris; Steven J Karpowicz; George B Witman; Astrid Terry; Asaf Salamov; Lillian K Fritz-Laylin; Laurence Maréchal-Drouard; wallace marshall; Liang-Hu Qu; David Nelson; Anton A Sanderfoot; Martin H Spalding; Vladimir V Kapitonov; Qinghu Ren; Patrick Ferris; Erika Lindquist; Harris Shapiro; Susan M Lucas; Jane Grimwood; Jeremy Schmutz; Pierre Cardol; Heriberto Cerutti; Guillaume Chanfreau; Chun-Long Chen; Valérie Cognat; Martin T Croft; Rachel Dent; Susan Dutcher; Emilio Fernández; Fukuzawa Hideya; David González-Ballester; Diego González-Halphen; Armin Hallmann; Marc Hanikenne; Michael Hippler; William Inwood; Kamel Jabbari; Ming Kalanon; Richard Kuras; Paul A Lefebvre; Stéphane D Lemaire; Alexey V Lobanov; Martin Lohr; Andrea Manuell; Iris Meier; Laurens Mets; Maria Mittag; Telsa Mittelmeier; James V Moroney; Jeffrey Moseley; Carolyn Napoli; Aurora M Nedelcu; Krishna Niyogi; Sergey V Novoselov; Ian Paulsen; Greg Pazour; Saul Purton; Jean-Philippe Ral; Diego Mauricio Riaño-Pachón; Wayne Riekhof; Linda Rymarquis; Michael Schroda; David Stern; James G Umen; Robert Willows; Nedra Wilson; Sara Lana Zimmer; Jens Allmer; Janneke Balk; Katerina Bisova; Chong-Jian Chen; Marek Elias; Karla Gendler; Charles Hauser; Mary Rose Lamb; Heidi Ledford; Joanne C Long; Jun Minagawa; Mark Dudley Page; Junmin Pan; Wirulda Pootakham; Sanja Roje; Annkatrin Rose; Eric Stahlberg; Aimee M Terauchi; Pinfen Yang; Steven Ball; Chris Bowler; Carol L Dieckmann; Vadim N Gladyshev; Pamela Green; Richard Jorgensen; Stephen Mayfield; Bernd Mueller-Roeber; Sathish Rajamani; Richard T Sayre; Peter Brokstein; Inna Dubchak; David Goodstein; Leila Hornick; Y Wayne Huang; Jinal Jhaveri; Yigong Luo; Diego Martínez; Wing Chi Abby Ngau; Bobby Otillar; Alexander Poliakov; Aaron Porter; Lukasz Szajkowski; Gregory Werner; Kemin Zhou; Igor V Grigoriev; Daniel S Rokhsar; Arthur R Grossman
The Chlamydomonas genome reveals the evolution of key animal and plant functions.
Science (New York, N.Y.) 2007;318(5848):245-50.
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: Garry S A Myers; Dane Parker; Keith Al-Hasani; Ruth M Kennan; Torsten Seemann; Qinghu Ren; Jonathan H Badger; Jeremy D Selengut; Robert T Deboy; Hervé Tettelin; John D Boyce; Victoria P McCarl; Xiaoyan Han; William C Nelson; Ramana Madupu; Yasmin Mohamoud; Tara Holley; Nadia Fedorova; Hoda Khouri; Steven P Bottomley; Richard J Whittington; Ben Adler; J Glenn Songer; Julian I Rood; Ian Paulsen
Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.
Nature biotechnology 2007;25(5):569-75.
2007: Peter D Karp; Ingrid Keseler; Alexander Shearer; Mario Latendresse; Markus Krummenacker; Suzanne Paley; Ian Paulsen; Julio Collado-Vides; Socorro Gama-Castro; Martín Peralta-Gil; Alberto Santos-Zavaleta; Mónica I Peñaloza-Spínola; César Bonavides-Martinez; John Ingraham
Multidimensional annotation of the Escherichia coli K-12 genome.
Nucleic acids research 2007;35(22):7577-90.
2007: Qinghu Ren; Ian Paulsen
Large-scale comparative genomic analyses of cytoplasmic membrane transport systems in prokaryotes.
Journal of molecular microbiology and biotechnology 2007;12(3-4):165-79.
2007: Qinghu Ren; Kaixi Chen; Ian Paulsen
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels.
Nucleic acids research 2007;35(Database issue):D274-9.
2006: Kathleen M Scott; Stefan M Sievert; Fereniki N Abril; Lois A Ball; Chantell J Barrett; Rodrigo A Blake; Amanda J Boller; Patrick S G Chain; Justine A Clark; Carisa R Davis; Chris Detter; Kimberly F Do; Kimberly P Dobrinski; Brandon I Faza; Kelly A Fitzpatrick; Sharyn K Freyermuth; Tara L Harmer; Loren J Hauser; Michael Hügler; Cheryl A Kerfeld; Martin Klotz; William W Kong; Miriam Land; Alla Lapidus; Frank W Larimer; Dana L Longo; Susan Lucas; Stephanie A Malfatti; Steven E Massey; Darlene D Martin; zoe (mckiness) mccuddin; Folker Meyer; Jessica L Moore; Luis H Ocampo; John H Paul; Ian Paulsen; Douglas K Reep; Qinghu Ren; Rachel L Ross; Priscila Y Sato; Phaedra Thomas; Lance E Tinkham; Gary T Zeruth
The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2.
PLoS biology 2006;4(12):e383.
2006: Jonathan H Badger; Timothy R Hoover; Yves V Brun; Ronald M Weiner; Michael T Laub; Gladys Alexandre; Jan Mrázek; Qinghu Ren; Ian Paulsen; Karen E Nelson; Hoda Khouri; Diana Radune; Julia Sosa; Robert J Dodson; Steven A Sullivan; Mary J Rosovitz; Ramana Madupu; Lauren M Brinkac; A Scott Durkin; Sean C Daugherty; Sagar P Kothari; Michelle G Giglio; Liwei Zhou; Daniel H Haft; Jeremy D Selengut; Tanja M Davidsen; Qi Yang; Nikhat Zafar; Naomi L Ward
Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus.
Journal of bacteriology 2006;188(19):6841-50.
2006: Brian Palenik; Qinghu Ren; Chris L Dupont; Garry S A Myers; John F Heidelberg; Jonathan H Badger; Ramana Madupu; William C Nelson; Lauren M Brinkac; Robert J Dodson; A Scott Durkin; Sean C Daugherty; Steven A Sullivan; Hoda Khouri; Yasmin Mohamoud; Rebecca Halpin; Ian Paulsen
Genome sequence of Synechococcus CC9311: Insights into adaptation to a coastal environment.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(36):13555-9.
2006: Garry S A Myers; David Rasko; Jackie K Cheung; Jacques Ravel; Rekha Seshadri; Robert T DeBoy; Qinghu Ren; John Joseph Varga; Milena M Awad; Lauren M Brinkac; Sean C Daugherty; Daniel H Haft; Robert J Dodson; Ramana Madupu; William C Nelson; M J Rosovitz; Steven A Sullivan; Hoda Khouri; George I Dimitrov; Kisha L Watkins; Stephanie Mulligan; Jonathan Benton; Diana Radune; Derek J Fisher; Helen S Atkins; Tom Hiscox; B Helen Jost; Stephen J Billington; J Glenn Songer; Bruce A McClane; Richard Titball; Julian I Rood; Stephen B Melville; Ian Paulsen
Skewed genomic variability in strains of the toxigenic bacterial pathogen, Clostridium perfringens.
Genome research 2006;16(8):1031-40.
2006: Massoud Saidijam; Giulia Benedetti; Qinghu Ren; Zhiqiang Xu; Christopher J Hoyle; Sarah L Palmer; Alison Ward; Kim E Bettaney; Gerda Szakonyi; Johan Meuller; Scott Morrison; Martin K Pos; Patrick Butaye; Karl Walravens; Kate Langton; Richard B Herbert; Ronald A Skurray; Ian Paulsen; John O'Reilly; Nicholas G Rutherford; Marion H Brown; Roslyn M Bill; Peter J F Henderson
Microbial drug efflux proteins of the major facilitator superfamily.
Current drug targets 2006;7(7):793-811.
2006: Xuan Z Ding; Ian Paulsen; Apurba K Bhattacharjee; Mikeljon P Nikolich; Garry S A Myers; David L Hoover
A high efficiency cloning and expression system for proteomic analysis.
Proteomics 2006;6(14):4038-46.
2006: Dane Parker; Ruth M Kennan; Garry S A Myers; Ian Paulsen; J Glenn Songer; Julian I Rood
Regulation of type IV fimbrial biogenesis in Dichelobacter nodosus.
Journal of bacteriology 2006;188(13):4801-11.
2006: Daniel H Haft; Ian Paulsen; Naomi Ward; Jeremy D Selengut
Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic.
BMC biology 2006;4():29.
2006: Zhengchang Su; Fenglou Mao; Phuongan Dam; Hongwei Wu; Victor Olman; Ian Paulsen; Brian Palenik; Ying Xu
Computational inference and experimental validation of the nitrogen assimilation regulatory network in cyanobacterium Synechococcus sp. WH 8102.
Nucleic acids research 2006;34(3):1050-65.
2005: Marion Brodhagen; Ian Paulsen; Joyce E Loper
Reciprocal regulation of pyoluteorin production with membrane transporter gene expression in Pseudomonas fluorescens Pf-5.
Applied and environmental microbiology 2005;71(11):6900-9.
2005: Qinghu Ren; Ian Paulsen
Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes.
PLoS computational biology 2005;1(3):e27.
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: Ian Paulsen; Caroline M Press; Jacques Ravel; Donald Y Kobayashi; Garry S A Myers; Dmitri V Mavrodi; Robert T Deboy; Rekha Seshadri; Qinghu Ren; Ramana Madupu; Robert J Dodson; A Scott Durkin; Lauren M Brinkac; Sean C Daugherty; Steven A Sullivan; Mary J Rosovitz; Michelle G Giglio; Liwei Zhou; Davd J Schneider; Samuel Cartinhour; William C Nelson; Janice Weidman; Kisha Watkins; Kevin Tran; Hoda Khouri; Elizabeth A Pierson; Leland S Pierson; Linda S Thomashow; Joyce E Loper
Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5.
Nature biotechnology 2005;23(7):873-8.
2005: Steven R Gill; Derrick E Fouts; Gordon L Archer; Emmanuel F Mongodin; Robert T Deboy; Jacques Ravel; Ian Paulsen; James F Kolonay; Lauren M Brinkac; Maureen J Beanan; Robert J Dodson; Sean C Daugherty; Ramana Madupu; Samuel V Angiuoli; A Scott Durkin; Daniel H Haft; Jessica Vamathevan; Hoda Khouri; Teresa Utterback; Chris Lee; George Dimitrov; Lingxia Jiang; Haiying Qin; Janice Weidman; Kevin Tran; Kathy Kang; Ioana R Hance; Karen E Nelson; Claire M Fraser-Liggett
Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain.
Journal of bacteriology 2005;187(7):2426-38.
2005: Xuan Z Ding; Apurba Bhattacharjee; Mikeljon P Nikolich; Ian Paulsen; Garry S A Myers; Rekha Seshadri; David L Hoover
Cloning, expression, and purification of Brucella suis outer membrane proteins.
Protein expression and purification 2005;40(1):134-41.
2005: Asis Khan; Sonya Taylor; Chunlei Su; Aaron J Mackey; Jon Boyle; Robert Cole; Darius Glover; Keliang Tang; Ian Paulsen; Matthew Berriman; John C Boothroyd; Elmer R Pfefferkorn; J P Dubey; James W Ajioka; David S Roos; John C Wootton; L David Sibley
Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii.
Nucleic acids research 2005;33(9):2980-92.
2005: Ingrid Keseler; Julio Collado-Vides; Socorro Gama-Castro; John Ingraham; Suzanne Paley; Ian Paulsen; Martín Peralta-Gil; Peter D Karp
EcoCyc: a comprehensive database resource for Escherichia coli.
Nucleic acids research 2005;33(Database issue):D334-7.
2005: Dane Parker; Ruth M Kennan; Garry S A Myers; Ian Paulsen; Julian I Rood
Identification of a Dichelobacter nodosus ferric uptake regulator and determination of its regulatory targets.
Journal of bacteriology 2005;187(1):366-75.
2004: Mary Ann Moran; Alison Buchan; José M González; John F Heidelberg; William B Whitman; Ronald P Kiene; James R Henriksen; Gary M King; Robert Belas; Clay Fuqua; Lauren Brinkac; Matt Lewis; Shivani Johri; Bruce Weaver; Grace Pai; Jonathan Eisen; Elisha Rahe; Wade M Sheldon; Wenying Ye; Todd R Miller; Jane Carlton; David Rasko; Ian Paulsen; Qinghu Ren; Sean C Daugherty; Robert T Deboy; Robert J Dodson; A Scott Durkin; Ramana Madupu; William C Nelson; Steven A Sullivan; M J Rosovitz; Daniel H Haft; Jeremy Selengut; Naomi Ward
Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment.
Nature 2004;432(7019):910-3.
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: John F Heidelberg; Rekha Seshadri; Shelley A Haveman; Christopher L Hemme; Ian Paulsen; James F Kolonay; Jonathan Eisen; Naomi Ward; Barbara Methe; Lauren M Brinkac; Sean C Daugherty; Robert T Deboy; Robert J Dodson; A Scott Durkin; Ramana Madupu; William C Nelson; Steven A Sullivan; Derrick Fouts; Daniel H Haft; Jeremy Selengut; Jeremy D Peterson; Tanja M Davidsen; Nikhat Zafar; Liwei Zhou; Diana Radune; George Dimitrov; Mark Hance; Kevin Tran; Hoda Khouri; John Gill; Terry R Utterback; Tamara V Feldblyum; Judy D Wall; Gerrit Voordouw; Claire M Fraser-Liggett
The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough.
Nature biotechnology 2004;22(5):554-9.
2004: Rekha Seshadri; Garry S A Myers; Hervé Tettelin; Jonathan Eisen; John F Heidelberg; Robert J Dodson; Tanja M Davidsen; Robert T DeBoy; Derrick E Fouts; Dan H Haft; Jeremy Selengut; Qinghu Ren; Lauren M Brinkac; Ramana Madupu; Jamie Kolonay; Scott A Durkin; Sean C Daugherty; Jyoti Shetty; Alla Shvartsbeyn; Elizabeth Gebregeorgis; Keita Geer; Getahun Tsegaye; Joel Malek; Bola Ayodeji; Sofiya Shatsman; Michael P McLeod; David Smajs; Jerrilyn K Howell; Sangita Pal; Anita Amin; Pankaj Vashisth; Thomas Z McNeill; Qin Xiang; Erica Sodergren; Ernesto Baca; George M Weinstock; Steven J Norris; Claire M Fraser-Liggett; Ian Paulsen
Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(15):5646-51.
2004: J Craig Venter; Karin Remington; John F Heidelberg; Aaron L Halpern; Douglas B Rusch; Jonathan Eisen; Dongying Wu; Ian Paulsen; Karen E Nelson; William Nelson; Derrick E Fouts; Samuel Levy; Anthony H Knap; Michael W Lomas; Ken Nealson; Owen R White; Jeremy Peterson; Jeff Hoffman; Rachel Parsons; Holly Baden-Tillson; Cynthia Pfannkoch; Yu-Hui Rogers; Hamilton O Smith
Environmental genome shotgun sequencing of the Sargasso Sea.
Science (New York, N.Y.) 2004;304(5667):66-74.
2004: Martin Wu; Ling V Sun; Jessica Vamathevan; Markus Riegler; Robert T Deboy; Jeremy C Brownlie; Elizabeth A McGraw; William Martin; Christian Esser; Nahal Ahmadinejad; Christian Wiegand; Ramana Madupu; Maureen J Beanan; Lauren M Brinkac; Sean C Daugherty; A Scott Durkin; James F Kolonay; William C Nelson; Yasmin Mohamoud; Perris Lee; Kristi Berry; M Brook Young; Teresa Utterback; Janice Weidman; William C Nierman; Ian Paulsen; Karen E Nelson; Hervé Tettelin; Scott L O'Neill; Jonathan Eisen
Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.
PLoS biology 2004;2(3):E69.
2004: Karen E Nelson; Derrick E Fouts; Emmanuel F Mongodin; Jacques Ravel; Robert T DeBoy; James F Kolonay; David Rasko; Samuel V Angiuoli; Steven R Gill; Ian Paulsen; Jeremy Peterson; Owen R White; William C Nelson; William Nierman; Maureen J Beanan; Lauren M Brinkac; Sean C Daugherty; Robert J Dodson; A Scott Durkin; Ramana Madupu; Daniel H Haft; Jeremy Selengut; Susan Van Aken; Hoda Khouri; Nadia Fedorova; Heather Forberger; Bao Tran; Sophia Kathariou; Laura D Wonderling; Gaylen A Uhlich; Darrell O Bayles; John B Luchansky; Claire M Fraser-Liggett
Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species.
Nucleic acids research 2004;32(8):2386-95.
2004: Qinghu Ren; Katherine H Kang; Ian Paulsen
TransportDB: a relational database of cellular membrane transport systems.
Nucleic acids research 2004;32(Database issue):D284-8.
2003: B A Methé; K E Nelson; Jonathan Eisen; Ian Paulsen; W Nelson; J F Heidelberg; D Wu; M Wu; N Ward; M J Beanan; R J Dodson; R Madupu; L M Brinkac; S C Daugherty; R T DeBoy; A S Durkin; Michelle G Giglio; J F Kolonay; S A Sullivan; D H Haft; J Selengut; T M Davidsen; N Zafar; Owen R White; B Tran; C Romero; H A Forberger; J Weidman; H Khouri; T V Feldblyum; T R Utterback; S E Van Aken; D R Lovley; Claire M Fraser-Liggett
Genome of Geobacter sulfurreducens: metal reduction in subsurface environments.
Science (New York, N.Y.) 2003;302(5652):1967-9.
2003: Ian Paulsen
Multidrug efflux pumps and resistance: regulation and evolution.
Current opinion in microbiology 2003;6(5):446-51.
2003: C Robin Buell; Vinita Joardar; Magdalen Lindeberg; Jeremy Selengut; Ian Paulsen; Michelle G Giglio; Robert J Dodson; Robert T Deboy; A Scott Durkin; James F Kolonay; Ramana Madupu; Sean Daugherty; Lauren Brinkac; Maureen J Beanan; Daniel H Haft; William C Nelson; Tanja Davidsen; Nikhat Zafar; Liwei Zhou; Jia Liu; Qiaoping Yuan; Hoda Khouri; Nadia Fedorova; Bao Tran; Daniel Russell; Kristi Berry; Teresa Utterback; Susan E Van Aken; Tamara V Feldblyum; Mark D'Ascenzo; Wen-Ling Deng; Adela R Ramos; James R Alfano; Samuel Cartinhour; Arun K Chatterjee; Terrence P Delaney; Sondra G Lazarowitz; Gregory B Martin; David J Schneider; Xiaoyan Tang; Carol Bender; Owen R White; Claire M Fraser-Liggett; Alan Collmer
The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(18):10181-6.
2003: Karen E Nelson; Robert D Fleischmann; Robert T Deboy; Ian Paulsen; Derrick E Fouts; Jonathan Eisen; Sean C Daugherty; Robert J Dodson; A Scott Durkin; Michelle G Giglio; Daniel H Haft; James F Kolonay; William C Nelson; Tanya Mason; Luke J Tallon; Jessica Gray; David Granger; Hervé Tettelin; Hong Dong; Jamie L Galvin; Margaret J Duncan; Floyd E Dewhirst; Claire M Fraser-Liggett
Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83.
Journal of bacteriology 2003;185(18):5591-601.
2003: Eric S Miller; John F Heidelberg; Jonathan Eisen; William C Nelson; A Scott Durkin; Ann Ciecko; Tamara Feldblyum; Owen R White; Ian Paulsen; William C Nierman; Jong Lee; Bridget Szczypinski; Claire M Fraser-Liggett
Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage.
Journal of bacteriology 2003;185(17):5220-33.
2003: Brian Palenik; B Brahamsha; Frank W Larimer; Miriam Land; Loren Hauser; Patrick S G Chain; Jane Lamerdin; Warren Regala; Eric E Allen; J McCarren; Ian Paulsen; A Dufresne; Frédéric Partensky; E A Webb; John B Waterbury
The genome of a motile marine Synechococcus.
Nature 2003;424(6952):1037-42.
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: Rekha Seshadri; Ian Paulsen; Jonathan Eisen; Timothy D Read; Karen E Nelson; William C Nelson; Naomi L Ward; Hervé Tettelin; Tanja M Davidsen; Maureen J Beanan; Robert T Deboy; Sean C Daugherty; Lauren M Brinkac; Ramana Madupu; Robert J Dodson; Hoda Khouri; Kathy H Lee; Heather A Carty; David Scanlan; Robert A Heinzen; Herbert A Thompson; James E Samuel; Claire M Fraser-Liggett; John F Heidelberg
Complete genome sequence of the Q-fever pathogen Coxiella burnetii.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(9):5455-60.
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: Ian Paulsen; L Banerjei; Garry S A Myers; K E Nelson; R Seshadri; T D Read; D E Fouts; Jonathan Eisen; S R Gill; J F Heidelberg; Hervé Tettelin; R J Dodson; L Umayam; L Brinkac; M Beanan; S Daugherty; R T DeBoy; S Durkin; J Kolonay; R Madupu; W Nelson; J Vamathevan; B Tran; J Upton; T Hansen; J Shetty; H Khouri; T Utterback; D Radune; K A Ketchum; B A Dougherty; Claire M Fraser-Liggett
Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis.
Science (New York, N.Y.) 2003;299(5615):2071-4.
2003: Jessica Kissinger; Bindu Gajria; Li Li; Ian Paulsen; David S Roos
ToxoDB: accessing the Toxoplasma gondii genome.
Nucleic acids research 2003;31(1):234-6.
2002: Richard C Essenberg; Rekha Seshadri; Karen Nelson; Ian Paulsen
Sugar metabolism by Brucellae.
Veterinary microbiology 2002;90(1-4):249-61.
2002: K E Nelson; C Weinel; Ian Paulsen; R J Dodson; H Hilbert; V A P Martins dos Santos; D E Fouts; S R Gill; Mihai Pop; M Holmes; L Brinkac; M Beanan; R T DeBoy; S Daugherty; J Kolonay; R Madupu; W Nelson; Owen R White; J Peterson; H Khouri; I Hance; P Chris Lee; E Holtzapple; D Scanlan; K Tran; A Moazzez; T Utterback; M Rizzo; K Lee; D Kosack; D Moestl; Holger Wedler; J Lauber; D Stjepandic; J Hoheisel; M Straetz; S Heim; C Kiewitz; Jonathan Eisen; K N Timmis; A Düsterhöft; B Tümmler; Claire M Fraser-Liggett
Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440.
Environmental microbiology 2002;4(12):799-808.
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: John F Heidelberg; Ian Paulsen; Karen E Nelson; Eric J Gaidos; William C Nelson; Timothy D Read; Jonathan Eisen; Rekha Seshadri; Naomi Ward; Barbara Methe; Rebecca A Clayton; Terry Meyer; Alexandre Tsapin; James Scott; Maureen Beanan; Lauren Brinkac; Sean Daugherty; Robert T DeBoy; Robert J Dodson; A Scott Durkin; Daniel H Haft; James F Kolonay; Ramana Madupu; Jeremy D Peterson; Lowell A Umayam; Owen R White; Alex M Wolf; Jessica Vamathevan; Janice Weidman; Marjorie Impraim; Kathy Lee; Kristy Berry; Chris Lee; Jacob Mueller; Hoda Khouri; John Gill; Terry R Utterback; Lisa A McDonald; Tamara V Feldblyum; Hamilton O Smith; J Craig Venter; Kenneth H Nealson; Claire M Fraser-Liggett
Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis.
Nature biotechnology 2002;20(11):1118-23.
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: Hervé Tettelin; Vega Masignani; Michael J Cieslewicz; Jonathan Eisen; Scott Peterson; Michael R Wessels; Ian Paulsen; Karen E Nelson; Immaculada Margarit; Timothy D Read; Lawrence C Madoff; Alex M Wolf; Maureen J Beanan; Lauren M Brinkac; Sean C Daugherty; Robert T DeBoy; A Scott Durkin; James F Kolonay; Ramana Madupu; Matthew R Lewis; Diana Radune; Nadezhda B Fedorova; David Scanlan; Hoda Khouri; Stephanie Mulligan; Heather A Carty; Robin T Cline; Susan E Van Aken; John Gill; Maria Scarselli; Marirosa Mora; Emilia T Iacobini; Cecilia Brettoni; Giuliano Galli; Massimo Mariani; Filippo Vegni; Domenico Maione; Daniela Rinaudo; Rino Rappuoli; John L Telford; Dennis L Kasper; Guido Grandi; Claire M Fraser-Liggett
Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(19):12391-6.
2002: Jonathan Eisen; Karen E Nelson; Ian Paulsen; John F Heidelberg; Martin Wu; Robert J Dodson; Robert Deboy; Michelle G Giglio; William C Nelson; Daniel H Haft; Erin K Hickey; Jeremy D Peterson; A Scott Durkin; James L Kolonay; Fan Yang; Ingeborg Holt; Lowell A Umayam; Tanya Mason; Michael Brenner; Terrance P Shea; Debbie Parksey; William C Nierman; Tamara V Feldblyum; Cheryl L Hansen; M Brook Craven; Diana Radune; Jessica Vamathevan; Hoda Khouri; Owen R White; Tanja M Gruber; Karen A Ketchum; J Craig Venter; Hervé Tettelin; Donald A Bryant; Claire M Fraser-Liggett
The complete genome sequence of Chlorobium tepidum TLS, a photosynthetic, anaerobic, green-sulfur bacterium.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(14):9509-14.
2002: John A Quan; Barbara L Schneider; Ian Paulsen; Mamoru Yamada; Nicholas M Kredich; Milton H Saier
Regulation of carbon utilization by sulfur availability in Escherichia coli and Salmonella typhimurium.
Microbiology (Reading, England) 2002;148(Pt 1):123-31.
2002: Milton H Saier; Seth R Goldman; Randal R Maile; Matthew S Moreno; Walter Weyler; Nelson Yang; Ian Paulsen
Transport capabilities encoded within the Bacillus subtilis genome.
Journal of molecular microbiology and biotechnology 2002;4(1):37-67.
2002: Peter D Karp; Monica Riley; Milton H Saier; Ian Paulsen; Julio Collado-Vides; Suzanne Paley; Alida Pellegrini-Toole; César Bonavides; Socorro Gama-Castro
The EcoCyc Database.
Nucleic acids research 2002;30(1):56-8.
2001: D W Wood; Joao Setubal; R Kaul; D E Monks; J P Kitajima; V K Okura; Y Zhou; L Chen; Gwen Wood; N F Almeida; L Woo; Y Chen; Ian Paulsen; Jonathan Eisen; Peter Karp; D Bovee; P Chapman; J Clendenning; G Deatherage; W Gillet; C Grant; T Kutyavin; R Levy; M J Li; E McClelland; A Palmieri; C Raymond; G Rouse; C Saenphimmachak; Z Wu; P Romero; D Gordon; S Zhang; H Yoo; Y Tao; P Biddle; M Jung; W Krespan; M Perry; B Gordon-Kamm; L Liao; S Kim; C Hendrick; Z Y Zhao; M Dolan; F Chumley; S V Tingey; J F Tomb; M P Gordon; M V Olson; E W Nester
The genome of the natural genetic engineer Agrobacterium tumefaciens C58.
Science (New York, N.Y.) 2001;294(5550):2317-23.
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: M H Saier; Ian Paulsen
Phylogeny of multidrug transporters.
Seminars in cell & developmental biology 2001;12(3):205-13.
2001: Ian Paulsen; J Chen; K E Nelson; M H Saier
Comparative genomics of microbial drug efflux systems.
Journal of molecular microbiology and biotechnology 2001;3(2):145-50.
2001: Ian Paulsen; K Lewis
Microbial multidrug efflux: introduction.
Journal of molecular microbiology and biotechnology 2001;3(2):143-4.
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: Daniel H Haft; B J Loftus; D L Richardson; F Yang; Jonathan Eisen; Ian Paulsen; Owen R White
TIGRFAMs: a protein family resource for the functional identification of proteins.
Nucleic acids research 2001;29(1):41-3.
2000: Milton H Saier; Ian Paulsen
Whole genome analyses of transporters in spirochetes: Borrelia burgdorferi and Treponema pallidum.
Journal of molecular microbiology and biotechnology 2000;2(4):393-9.
2000: Ian Paulsen; Jonathan Reizer; R Z Jin; E C Lin; Milton H Saier
Functional genomic studies of dihydroxyacetone utilization in Escherichia coli.
Microbiology (Reading, England) 2000;146 ( Pt 10)():2343-4.
2000: Karen E Nelson; Ian Paulsen; John F Heidelberg; Claire M Fraser-Liggett
Status of genome projects for nonpathogenic bacteria and archaea.
Nature biotechnology 2000;18(10):1049-54.
2000: C Kendall Stover; X Q Pham; Alice L Erwin; S D Mizoguchi; Paul Warrener; M J Hickey; F S Brinkman; W O Hufnagle; D J Kowalik; M Lagrou; R L Garber; L Goltry; E Tolentino; S Westbrock-Wadman; Y Yuan; Linnea Brody; S N Coulter; K R Folger; A Kas; K Larbig; R Lim; K Smith; D Spencer; G K Wong; Z Wu; Ian Paulsen; J Reizer; M H Saier; R E Hancock; S Lory; M V Olson
Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen.
Nature 2000;406(6799):959-64.
2000: Ian Paulsen; L Nguyen; M K Sliwinski; R Rabus; M H Saier
Microbial genome analyses: comparative transport capabilities in eighteen prokaryotes.
Journal of molecular biology 2000;301(1):75-100.
2000: Donald Lee Jack; Ian Paulsen; Milton H Saier
The amino acid/polyamine/organocation (APC) superfamily of transporters specific for amino acids, polyamines and organocations.
Microbiology (Reading, England) 2000;146 ( Pt 8)():1797-814.
2000: L Nguyen; Ian Paulsen; Jason Tchieu; C J Hueck; Milton H Saier
Phylogenetic analyses of the constituents of Type III protein secretion systems.
Journal of molecular microbiology and biotechnology 2000;2(2):125-44.
2000: Donald Lee Jack; M L Storms; Jason Tchieu; Ian Paulsen; Milton H Saier
A broad-specificity multidrug efflux pump requiring a pair of homologous SMR-type proteins.
Journal of bacteriology 2000;182(8):2311-3.
2000: Peter D Karp; Monica Riley; Milton H Saier; Ian Paulsen; Suzanne Paley; Alida Pellegrini-Toole
The EcoCyc and MetaCyc databases.
Nucleic acids research 2000;28(1):56-9.
1999: François Verrey; Donald Lee Jack; Ian Paulsen; M H Saier; R Pfeiffer
New glycoprotein-associated amino acid transporters.
The Journal of membrane biology 1999;172(3):181-92.
1999: Milton H Saier; J T Beatty; A Goffeau; KT Harley; W H Heijne; S C Huang; Donald Lee Jack; P S Jähn; K Lew; J Liu; SS Pao; Ian Paulsen; TT Tseng; P S Virk
The major facilitator superfamily.
Journal of molecular microbiology and biotechnology 1999;1(2):257-79.
1999: Milton H Saier; Ian Paulsen
Paralogous genes encoding transport proteins in microbial genomes.
Research in microbiology 1999;150(9-10):689-99.
1999: R Rabus; Jonathan Reizer; Ian Paulsen; Milton H Saier
Enzyme I(Ntr) from Escherichia coli. A novel enzyme of the phosphoenolpyruvate-dependent phosphotransferase system exhibiting strict specificity for its phosphoryl acceptor, NPr.
The Journal of biological chemistry 1999;274(37):26185-91.
1999: Elie Dassa; Maurice Hofnung; Ian Paulsen; M H Saier
The Escherichia coli ABC transporters: an update.
Molecular microbiology 1999;32(4):887-9.
1999: Milton H Saier; B H Eng; S Fard; J Garg; D A Haggerty; W J Hutchinson; Donald Lee Jack; Eric C Lai; H J Liu; D P Nusinew; A M Omar; SS Pao; Ian Paulsen; J A Quan; M Sliwinski; TT Tseng; S Wachi; G B Young
Phylogenetic characterization of novel transport protein families revealed by genome analyses.
Biochimica et biophysica acta 1999;1422(1):1-56.
1999: Bernadette A Mitchell; Ian Paulsen; Marion H Brown; Ronald A Skurray
Bioenergetics of the staphylococcal multidrug export protein QacA. Identification of distinct binding sites for monovalent and divalent cations.
The Journal of biological chemistry 1999;274(6):3541-8.
1999: Marion H Brown; Ian Paulsen; Ronald A Skurray
The multidrug efflux protein NorM is a prototype of a new family of transporters.
Molecular microbiology 1999;31(1):394-5.
1998: Steve Grkovic; Marion H Brown; N J Roberts; Ian Paulsen; Ronald A Skurray
QacR is a repressor protein that regulates expression of the Staphylococcus aureus multidrug efflux pump QacA.
The Journal of biological chemistry 1998;273(29):18665-73.
1998: Ian Paulsen; Marion H Brown; Ronald A Skurray
Characterization of the earliest known Staphylococcus aureus plasmid encoding a multidrug efflux system.
Journal of bacteriology 1998;180(13):3477-9.
1998: Ian Paulsen; M K Sliwinski; B Nelissen; A Goffeau; M H Saier
Unified inventory of established and putative transporters encoded within the complete genome of Saccharomyces cerevisiae.
FEBS letters 1998;430(1-2):116-25.
1998: Ian Paulsen; M K Sliwinski; Milton H Saier
Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities.
Journal of molecular biology 1998;277(3):573-92.
1998: SS Pao; Ian Paulsen; Milton H Saier
Major facilitator superfamily.
Microbiology and molecular biology reviews : MMBR 1998;62(1):1-34.
1998: Milton H Saier; Ian Paulsen; M K Sliwinski; SS Pao; Ronald A Skurray; H Nikaido
Evolutionary origins of multidrug and drug-specific efflux pumps in bacteria.
FASEB journal : official publication of the Federation of American Societies for Experimental Biology 1998;12(3):265-74.
1998: Ian Paulsen; S Chauvaux; P Choi; Milton H Saier
Characterization of glucose-specific catabolite repression-resistant mutants of Bacillus subtilis: identification of a novel hexose:H+ symporter.
Journal of bacteriology 1998;180(3):498-504.
1998: S Chauvaux; Ian Paulsen; Milton H Saier
CcpB, a novel transcription factor implicated in catabolite repression in Bacillus subtilis.
Journal of bacteriology 1998;180(3):491-7.
1997: Ian Paulsen; J H Park; P S Choi; Milton H Saier
A family of gram-negative bacterial outer membrane factors that function in the export of proteins, carbohydrates, drugs and heavy metals from gram-negative bacteria.
FEMS microbiology letters 1997;156(1):1-8.
1997: Ian Paulsen; A M Beness; Milton H Saier
Computer-based analyses of the protein constituents of transport systems catalysing export of complex carbohydrates in bacteria.
Microbiology (Reading, England) 1997;143 ( Pt 8)():2685-99.
1997: Ian Paulsen; Milton H Saier
A novel family of ubiquitous heavy metal ion transport proteins.
The Journal of membrane biology 1997;156(2):99-103.
1997: M H Saier; Ian Paulsen; A Matin
A bacterial model system for understanding multi-drug resistance.
Microbial drug resistance (Larchmont, N.Y.) 1997;3(4):289-95.
1997: André Goffeau; J Park; Ian Paulsen; J L Jonniaux; T Dinh; P Mordant; M H Saier
Multidrug-resistant transport proteins in yeast: complete inventory and phylogenetic characterization of yeast open reading frames with the major facilitator superfamily.
Yeast (Chichester, England) 1997;13(1):43-54.
1996: Ian Paulsen; M H Brown; R A Skurray
Proton-dependent multidrug efflux systems.
Microbiological reviews 1996;60(4):575-608.
1996: A Leelaporn; Neville Firth; Ian Paulsen; Ronald A Skurray
IS257-mediated cointegration in the evolution of a family of staphylococcal trimethoprim resistance plasmids.
Journal of bacteriology 1996;178(20):6070-3.
1996: Ian Paulsen
Carbon metabolism and its regulation in Streptomyces and other high GC gram-positive bacteria.
Research in microbiology 1996;147(6-7):535-41.
1996: Ian Paulsen; Marion H Brown; T G Littlejohn; B A Mitchell; Ronald A Skurray
Multidrug resistance proteins QacA and QacB from Staphylococcus aureus: membrane topology and identification of residues involved in substrate specificity.
Proceedings of the National Academy of Sciences of the United States of America 1996;93(8):3630-5.
1996: Ian Paulsen; Ronald A Skurray; R Tam; M H Saier; R J Turner; Joel Weiner; E B Goldberg; L L Grinius
The SMR family: a novel family of multidrug efflux proteins involved with the efflux of lipophilic drugs.
Molecular microbiology 1996;19(6):1167-75.
1996: Milton H Saier; S Chauvaux; Gregory Cook; Josef Deutscher; Ian Paulsen; Jonathan Reizer; J J Ye
Catabolite repression and inducer control in Gram-positive bacteria.
Microbiology (Reading, England) 1996;142 ( Pt 2)():217-30.
1996: Jonathan Reizer; Ian Paulsen; A Reizer; Fritz M Titgemeyer; Milton H Saier
Novel phosphotransferase system genes revealed by bacterial genome analysis: the complete complement of pts genes in mycoplasma genitalium.
Microbial & comparative genomics 1996;1(3):151-64.
1996: A Blair; L Ngo; J Park; Ian Paulsen; Milton H Saier
Phylogenetic analyses of the homologous transmembrane channel-forming proteins of the F0F1-ATPases of bacteria, chloroplasts and mitochondria.
Microbiology (Reading, England) 1996;142 ( Pt 1)():17-32.
1995: B H Dagnall; Ian Paulsen; M H Saier
The DAG family of glycosyl hydrolases combines two previously identified protein families.
The Biochemical journal 1995;311 ( Pt 1)():349-50.
1995: A Leelaporn; Neville Firth; Ian Paulsen; A Hettiaratchi; Ronald A Skurray
Multidrug resistance plasmid pSK108 from coagulase-negative staphylococci; relationships to Staphylococcus aureus qacC plasmids.
Plasmid 1995;34(1):62-7.
1995: Ian Paulsen; Marion H Brown; S J Dunstan; Ronald A Skurray
Molecular characterization of the staphylococcal multidrug resistance export protein QacC.
Journal of bacteriology 1995;177(10):2827-33.
1994: Ian Paulsen; Ronald A Skurray
The POT family of transport proteins.
Trends in biochemical sciences 1994;19(10):404.
1994: T Dinh; Ian Paulsen; Milton H Saier
A family of extracytoplasmic proteins that allow transport of large molecules across the outer membranes of gram-negative bacteria.
Journal of bacteriology 1994;176(13):3825-31.
1994: Ian Paulsen; M T Gillespie; T G Littlejohn; O Hanvivatvong; S J Rowland; Keith G H Dyke; Ronald A Skurray
Characterisation of sin, a potential recombinase-encoding gene from Staphylococcus aureus.
Gene 1994;141(1):109-14.
1994: A Leelaporn; Ian Paulsen; J M Tennent; T G Littlejohn; Ronald A Skurray
Multidrug resistance to antiseptics and disinfectants in coagulase-negative staphylococci.
Journal of medical microbiology 1994;40(3):214-20.
1993: Neville Firth; K P Ridgway; M E Byrne; P D Fink; L Johnson; Ian Paulsen; Ronald A Skurray
Analysis of a transfer region from the staphylococcal conjugative plasmid pSK41.
Gene 1993;136(1-2):13-25.
1993: Ian Paulsen; T G Littlejohn; P Rådström; L Sundström; Ola Sköld; Göte Swedberg; Ronald A Skurray
The 3' conserved segment of integrons contains a gene associated with multidrug resistance to antiseptics and disinfectants.
Antimicrobial agents and chemotherapy 1993;37(4):761-8.
1993: Ian Paulsen; Ronald A Skurray
Topology, structure and evolution of two families of proteins involved in antibiotic and antiseptic resistance in eukaryotes and prokaryotes--an analysis.
Gene 1993;124(1):1-11.
1992: T G Littlejohn; Ian Paulsen; M T Gillespie; J M Tennent; M Midgley; I G Jones; A S Purewal; Ronald A Skurray
Substrate specificity and energetics of antiseptic and disinfectant resistance in Staphylococcus aureus.
FEMS microbiology letters 1992;74(2-3):259-65.
1992: Jeffrey K Griffith; M E Baker; D A Rouch; M G Page; R A Skurray; Ian Paulsen; K F Chater; S A Baldwin; P J Henderson
Membrane transport proteins: implications of sequence comparisons.
Current opinion in cell biology 1992;4(4):684-95.