Literature DB >> 17420237

National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics.

John M Greene1, Frank Collins, Elliot J Lefkowitz, David Roos, Richard H Scheuermann, Bruno Sobral, Rick Stevens, Owen White, Valentina Di Francesco.   

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Year:  2007        PMID: 17420237      PMCID: PMC1932942          DOI: 10.1128/IAI.00105-07

Source DB:  PubMed          Journal:  Infect Immun        ISSN: 0019-9567            Impact factor:   3.441


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  10 in total

1.  Mauve: multiple alignment of conserved genomic sequence with rearrangements.

Authors:  Aaron C E Darling; Bob Mau; Frederick R Blattner; Nicole T Perna
Journal:  Genome Res       Date:  2004-07       Impact factor: 9.043

2.  Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics.

Authors:  Daniel H Haft; Jeremy D Selengut; Lauren M Brinkac; Nikhat Zafar; Owen White
Journal:  Bioinformatics       Date:  2004-09-03       Impact factor: 6.937

3.  The pathogen resource integration center: implications for Rickettsial research.

Authors:  Mark E Hance; Michael J Czar; Abdu Azad; Anjan Purkayastha; Eric E Snyder; Oswald R Crasta; Joao C Setubal; Bruno W Sobral
Journal:  Ann N Y Acad Sci       Date:  2005-12       Impact factor: 5.691

4.  Expansion of the BioCyc collection of pathway/genome databases to 160 genomes.

Authors:  Peter D Karp; Christos A Ouzounis; Caroline Moore-Kochlacs; Leon Goldovsky; Pallavi Kaipa; Dag Ahrén; Sophia Tsoka; Nikos Darzentas; Victor Kunin; Núria López-Bigas
Journal:  Nucleic Acids Res       Date:  2005-10-24       Impact factor: 16.971

5.  OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups.

Authors:  Feng Chen; Aaron J Mackey; Christian J Stoeckert; David S Roos
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

6.  ASAP: a resource for annotating, curating, comparing, and disseminating genomic data.

Authors:  Jeremy D Glasner; Michael Rusch; Paul Liss; Guy Plunkett; Eric L Cabot; Aaron Darling; Bradley D Anderson; Paul Infield-Harm; Michael C Gilson; Nicole T Perna
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

7.  Reactome: a knowledgebase of biological pathways.

Authors:  G Joshi-Tope; M Gillespie; I Vastrik; P D'Eustachio; E Schmidt; B de Bono; B Jassal; G R Gopinath; G R Wu; L Matthews; S Lewis; E Birney; L Stein
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

8.  Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource.

Authors:  Elliot J Lefkowitz; Chris Upton; Shankar S Changayil; Charles Buck; Paula Traktman; R Mark L Buller
Journal:  Nucleic Acids Res       Date:  2005-01-01       Impact factor: 16.971

9.  The immune epitope database and analysis resource: from vision to blueprint.

Authors:  Bjoern Peters; John Sidney; Phil Bourne; Huynh-Hoa Bui; Soeren Buus; Grace Doh; Ward Fleri; Mitch Kronenberg; Ralph Kubo; Ole Lund; David Nemazee; Julia V Ponomarenko; Muthu Sathiamurthy; Stephen Schoenberger; Scott Stewart; Pamela Surko; Scott Way; Steve Wilson; Alessandro Sette
Journal:  PLoS Biol       Date:  2005-03       Impact factor: 8.029

10.  The genome Assembly Archive: a new public resource.

Authors:  Steven L Salzberg; Deanna Church; Michael DiCuccio; Eugene Yaschenko; James Ostell
Journal:  PLoS Biol       Date:  2004-09-14       Impact factor: 8.029

  10 in total
  33 in total

Review 1.  Applications for T-cell epitope queries and tools in the Immune Epitope Database and Analysis Resource.

Authors:  Yohan Kim; Alessandro Sette; Bjoern Peters
Journal:  J Immunol Methods       Date:  2010-10-31       Impact factor: 2.303

2.  Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation.

Authors:  Samuel V Angiuoli; Aaron Gussman; William Klimke; Guy Cochrane; Dawn Field; George Garrity; Chinnappa D Kodira; Nikos Kyrpides; Ramana Madupu; Victor Markowitz; Tatiana Tatusova; Nick Thomson; Owen White
Journal:  OMICS       Date:  2008-06

3.  David Roos. Interview by H. Craig Mak.

Authors:  David Roos
Journal:  Nat Biotechnol       Date:  2011-02       Impact factor: 54.908

Review 4.  PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species.

Authors:  Joseph J Gillespie; Alice R Wattam; Stephen A Cammer; Joseph L Gabbard; Maulik P Shukla; Oral Dalay; Timothy Driscoll; Deborah Hix; Shrinivasrao P Mane; Chunhong Mao; Eric K Nordberg; Mark Scott; Julie R Schulman; Eric E Snyder; Daniel E Sullivan; Chunxia Wang; Andrew Warren; Kelly P Williams; Tian Xue; Hyun Seung Yoo; Chengdong Zhang; Yan Zhang; Rebecca Will; Ronald W Kenyon; Bruno W Sobral
Journal:  Infect Immun       Date:  2011-09-06       Impact factor: 3.441

Review 5.  A systems biological view of intracellular pathogens.

Authors:  Daniel P Beiting; David S Roos
Journal:  Immunol Rev       Date:  2011-03       Impact factor: 12.988

6.  Pathema: a clade-specific bioinformatics resource center for pathogen research.

Authors:  Lauren M Brinkac; Tanja Davidsen; Erin Beck; Anuradha Ganapathy; Elisabet Caler; Robert J Dodson; A Scott Durkin; Derek M Harkins; Hernan Lorenzi; Ramana Madupu; Yinong Sebastian; Susmita Shrivastava; Mathangi Thiagarajan; Joshua Orvis; Jaideep P Sundaram; Jonathon Crabtree; Kevin Galens; Yongmei Zhao; Jason M Inman; Robert Montgomery; Seth Schobel; Kevin Galinsky; David M Tanenbaum; Adam Resnick; Nikhat Zafar; Owen White; Granger Sutton
Journal:  Nucleic Acids Res       Date:  2009-10-20       Impact factor: 16.971

Review 7.  Design and utilization of epitope-based databases and predictive tools.

Authors:  Nima Salimi; Ward Fleri; Bjoern Peters; Alessandro Sette
Journal:  Immunogenetics       Date:  2010-03-06       Impact factor: 2.846

8.  IC50-to-Ki: a web-based tool for converting IC50 to Ki values for inhibitors of enzyme activity and ligand binding.

Authors:  R Z Cer; U Mudunuri; R Stephens; F J Lebeda
Journal:  Nucleic Acids Res       Date:  2009-04-24       Impact factor: 16.971

9.  Human genomics and preparedness for infectious threats.

Authors:  Nicole F Dowling; Marta Gwinn; Alison Mawle
Journal:  Genome Med       Date:  2009-12-29       Impact factor: 11.117

10.  Can an infectious disease genomics project predict and prevent the next pandemic?

Authors:  Rajesh Gupta; Mark H Michalski; Frank R Rijsberman
Journal:  PLoS Biol       Date:  2009-10-26       Impact factor: 8.029

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