Presentations, Publications, Posters

Presentations

Comparative Genomics of Vibrio New: Reich CI; 2nd International Conference on the Biology of Vibrios (Vibrio2007), Paris, Nov. 28- Dec 1, 2007; view PowerPoint slideshow (24 slides, new window)
NMPDR - Tools for Expert Annotations New: McNeil LK; Invited seminar, University of Oklahoma Health Sciences Center, Oklahoma City, Oct. 22, 2007; view PowerPoint slideshow (28 slides with links, new window)

more >>

The SEED: Subsystem Annotation and the Generation of Testable Hypotheses: Reich CI; 2nd ASM Conference on Integrating Metabolism and Genomics (IMAGE2), Montreal, April 30 - May 3, 2007; view PowerPoint slideshow (25 slides, new window); pdf slides with notes (new window)
NMPDR - Connecting Bioinformatics to the Bench: McNeil LK; Computational Genomics Conference, Baltimore, Oct. 28 - 31, 2006; Conference tutorial was a live tour of this site. Linked here is the back-up slide presentation (25 slides).; view PowerPoint slideshow (new window)
Using NMPDR for Comparative Systems Biology of Re-emerging Pathogens: Overbeek R; Frontiers of Pharmacology and Toxicology , Chicago, Aug. 28 - 31, 2006; Chem Biol Interact. 2006 Jul 10;161(3):182 Abstract S11; view PowerPoint slideshow (new window); pdf 2 slides per page (new window)
Subsystems Annotation: NMPDR subsystems annotation presentation, 20 slides, Feb. 2006; view PowerPoint slideshow (new window); pdf slides with notes (new window)
Using NMPDR and GBrowse: NMPDR tutorial handout, illustrated, 14 pages with exercises; pdf handout (new window)

^top ◊posters

Publications

Describing our tools

New The RAST Server: rapid annotations using subsystems technology: Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O.; BMC Genomics. 2008 Feb 8;9:75. PMID: 18261238; This paper is the primary description of the RAST server, a fully automated service for annotating bacterial and archaeal genomes, including predictions of which subsystems are represented in the genome, and a reconstruction of the metabolic network.

The National Microbial Pathogen Database Resource (NMPDR): A genomics platform based on subsystem annotation

McNeil LK, Reich C, Aziz RK, Bartels D, Cohoon M, Disz T, Edwards RA, Gerdes SY, Hwang K, Kubal M, Margaryan GR, Meyer F, Mihalo W, Olsen GJ, Olson R, Osterman AL, Paarmann D, Paczian T, Parrello B, Pusch GD, Rodionov DA, Shi X, Vassieva O, Vonstein V, Zagnitko OP, Xia F, Zinner J, Overbeek R, Stevens R.

Nucleic Acids Res. 2007 Jan;35(Database issue):D347-53. [Epub 2006 Dec 1] icon

PMID: 17145713

This paper is the primary description of the data and tools available at NMPDR.

National Institute of Allergy and Infectious Diseases bioinformatics resource centers: new assets for pathogen informatics: Greene JM, Collins F, Lefkowitz EJ, Roos D, Scheuermann RH, Sobral B, Stevens R, White O, Di Francesco V.; Infect Immun. 2007 Jul;75(7):3212-9. [Epub 2007 Apr 9] PMID: 17420237; This paper describes eight Bioinformatics Resource Centers for Biodefense and Emerging/Re-Emerging Infectious Disease (BRCs), which are funded by NIAID to provide free access to integrated genomic data to aid in the discovery and development of innovative therapeutics, vaccines, and diagnostics.

Annotation of bacterial and archaeal genomes: improving accuracy and consistency: Overbeek R, Bartels D, Vonstein V, Meyer F.; Chem Rev. 2007 Aug;107(8):3431-47. [Epub 2007 Jul 21] PMID: 17658903; This paper reviews technology used to accurately find and characterize the functional elements coded by genome sequences.

The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes: Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V.; Nucleic Acids Res. 2005 Oct 7;33(17):5691-702. PMID: 16214803; In this paper, subsystems are defined, and the SEED annotation environment that supports the creation, curation, population and exchange of subsystems is described. The SEED is used by the NMPDR curation staff, and a public SEED is available for community annotation.

Using our tools

New Cohesion Group Approach for Evolutionary Analysis of TyrA, a Protein Family with Wide-Ranging Substrate Specificities: Bonner CA, Disz T, Hwang K, Song J, Vonstein V, Overbeek R, Jensen RA.; Microbiol Mol Biol Rev. 2008 Mar;72(1):13-53 PMID: 18322033; This paper presents a comprehensive analysis of a dehydrogenase protein family (TyrA) as a prototype example of how a credible picture of evolutionary events can be deduced within the vertical trace of inheritance in combination with intervening events of lateral gene transfer (LGT). The TyrA subsystem as well as figures and tables supplemental to the paper are found in the SEED.

New Functional metagenomic profiling of nine biomes: Dinsdale EA, Edwards RA, Hall D, Angly F, Breitbart M, Brulc JM, Furlan M, Desnues C, Haynes M, Li L, McDaniel L, Moran MA, Nelson KE, Nilsson C, Olson R, Paul J, Brito BR, Ruan Y, Swan BK, Stevens R, Valentine DL, Thurber RV, Wegley L, White BA, Rohwer F.; Nature. 2008 Mar 12 [Epub ahead of print] PMID: 18337718; MG-RAST and our subsystems were used to reconstruct and compare the metabolism of different microbial environments.

The biological role of death and lysis in biofilm development: Bayles KW.; Nat Rev Microbiol. 2007 Sep;5(9):721-6. PMID: 17694072; This paper describes the functional roles, phylogenetic distribution, and biological importance of the murein hydrolase regulation and cell death subsystem, which was developed in conjunction with an NMPDR curator.

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation: Gupta N, Tanner S, Jaitly N, Adkins JN, Lipton M, Edwards R, Romine M, Osterman A, Bafna V, Smith RD, Pevzner PA.; Genome Res. 2007 Sep;17(9):1362-77. [Epub 2007 Aug 9] PMID: 17690205; In this paper, functional content of identified peptides was deduced from the categorized collection of annotated subsystems (pathways) provided by SEED.

Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations: de Crécy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD.; BMC Genomics. 2007 Jul 23;8:245. PMID: 17645794; In this paper, subsystem construction tools in the SEED and the Signature Genes tool at NMPDR were used to predict the pathways and to identify cases of missing genes for almost every step of the folate biosynthesis subsystem. Candidates for such missing genes in bacteria and plants were then predicted using comparative genomic tools, and representative candidates were tested experimentally.

Free methionine-(R)-sulfoxide reductase from Escherichia coli reveals a new GAF domain function: Lin Z, Johnson LC, Weissbach H, Brot N, Lively MO, Lowther WT.; Proc Natl Acad Sci U S A. 2007 Jun 5;104(23):9597-602. [Epub 2007 May 29] PMID: 17535911; In this paper, genomic context analysis was performed in the SEED.

Toward the automated generation of genome-scale metabolic networks in the SEED.: Dejongh M, Formsma K, Boillot P, Gould J, Rycenga M, Best A.; BMC Bioinformatics. 2007 8(1):139. [Epub 2007 Apr 26] PMID: 17462086; In this paper, genomes in the SEED were used to guide the automated generation of substantially complete metabolic networks from a collection of modular components called "scenarios."

The IclR-type transcriptional repressor LtbR regulates the expression of leucine and tryptophan biosynthesis genes in the amino acid producer Corynebacterium glutamicum: Brune I, Jochmann N, Brinkrolf K, Huser AT, Gerstmeir R, Eikmanns BJ, Kalinowski J, Puhler A, Tauch A.; J Bacteriol. 2007 Apr;189(7):2720-33. [Epub 2007 Jan 26] PMID: 17259312; In this paper, the SEED was used to compare the context of genes homologous with ltbR in sequenced genomes of bacteria belonging to the taxonomic class Actinobacteria.

Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate: Rodionov DA, Kurnasov OV, Stec B, Wang Y, Roberts MF, Osterman AL.; Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4279-84. [Epub 2007 Mar 2] PMID: 17360515; In this paper, the SEED was used used to predict two genes of this pathway that were previously missing and to create a subsystem that accurately describes the DIP biosynthesis pathway.

Discovery of a new prokaryotic type I GTP cyclohydrolase family: El Yacoubi B, Bonnett S, Anderson JN, Swairjo MA, Iwata-Reuyl D, de Crecy-Lagard V.; J Biol Chem. 2006 Dec 8;281(49):37586-93. [Epub 2006 Oct 10] PMID: 17032654; In this paper, the signature genes tool of NMPDR was used in conjunction with comparative genome analysis and a detailed reconstruction of the Folate Biosynthesis Subsystem in the SEED.

Experimental and computational assessment of conditionally essential genes in Escherichia coli: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S.; J Bacteriol. 2006 Dec;188(23):8259-71. [Epub 2006 Sep 29] PMID: 17012394; In this paper, essential genes of E. coli were analyzed in terms of metabolic subsystems across multiple genomes using the SEED.

The thioredoxin domain of Neisseria gonorrhoeae PilB can use electrons from DsbD to reduce downstream methionine sulfoxide reductases: Brot N, Collet JF, Johnson LC, Jonsson TJ, Weissbach H, Lowther WT.; J Biol Chem. 2006 Oct 27;281(43):32668-75. [Epub 2006 Aug 22] PMID: 16926157; In this paper, gene cluster analysis was performed using the SEED.

Essential genes on metabolic maps: Gerdes S, Edwards R, Kubal M, Fonstein M, Stevens R, Osterman A.; Curr Opin Biotechnol. 2006 Oct;17(5):448-56. [Epub 2006 Sep 15] PMID: 16978855; In this paper, the genomic scale screens for essential genes that are displayed on the Essential Genes page are reviewed and discussed in the context of comparative analysis of subsystems.
Supplemental data tables

more >>

Comparative genomics and experimental characterization of N-acetylglucosamine utilization pathway of Shewanella oneidensis: Yang C, Rodionov DA, Li X, Laikova ON, Gelfand MS, Zagnitko OP, Romine MF, Obraztsova AY, Nealson KH, Osterman AL.; J Biol Chem. 2006 Oct 6;281(40):29872-85. [Epub 2006 Jul 20] PMID: 16857666; In this paper, comparative genome analysis and a detailed reconstruction of the chitin and GlcNAc utilization subsystem and regulatory network in most proteobacteria was performed in the SEED.

Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover: Anderson KL, Roberts C, Disz T, Vonstein V, Hwang K, Overbeek R, Olson PD, Projan SJ, Dunman PM.; J Bacteriol. 2006 Oct;188(19):6739-56 PMID: 16980476; NMPDR team members used bioinformatics to produce supplemental file 1 - Table S8, Characterization of small stable RNA molecules identified in this study.

Crystal structure of a type III pantothenate kinase: insight into the mechanism of an essential coenzyme A biosynthetic enzyme universally distributed in bacteria: Yang K, Eyobo Y, Brand LA, Martynowski D, Tomchick D, Strauss E, Zhang H.; J Bacteriol. 2006 Aug;188(15):5532-40. PMID: 16855243; In this paper, a comprehensive survey of the phylogenetic distribution of type I, II and III PanKs in more than 300 complete or nearly complete genomes from the Archaea, Eukarya, and 13 major groups of Bacteria was performed in the SEED.

Comparative genomics of NAD biosynthesis in cyanobacteria: Gerdes SY, Kurnasov OV, Shatalin K, Polanuyer B, Sloutsky R, Vonstein V, Overbeek R, Osterman AL.; J Bacteriol. 2006 Apr;188(8):3012-23. PMID: 16585762; In this paper, comparative genome analysis and a detailed reconstruction of the NAD(P) metabolic subsystem was performed in the SEED.

A hidden metabolic pathway exposed: Osterman A.; Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5637-8. [Epub 2006 Apr 4] PMID: 16595627; In this paper, comparative genome analysis and the construction of a subsystem for pyrimidine utilization was performed in the SEED.

Functional genomics and expression analysis of the Corynebacterium glutamicum fpr2-cysIXHDNYZ gene cluster involved in assimilatory sulphate reduction: Ruckert C, Koch DJ, Rey DA, Albersmeier A, Mormann S, Puhler A, Kalinowski J.; BMC Genomics. 2005 Sep 13;6:121. PMID: 16159395; In this paper, genomic context analysis was performed in the SEED.

Low-molecular-weight protein tyrosine phosphatases of Bacillus subtilis: Musumeci L, Bongiorni C, Tautz L, Edwards RA, Osterman A, Perego M, Mustelin T, Bottini N.; J Bacteriol. 2005 Jul;187(14):4945-56. PMID: 15995210; In this paper, genomic context analysis was performed in the SEED.

Automatic detection of subsystem/pathway variants in genome analysis: Ye Y, Osterman A, Overbeek R, Godzik A.; Bioinformatics. 2005 Jun;21 Suppl 1:i478-86. PMID: 15961494; In this paper, genomic context analysis was performed in the SEED.

Mosaic prophages with horizontally acquired genes account for the emergence and diversification of the globally disseminated M1T1 clone of Streptococcus pyogenes: Aziz RK, Edwards RA, Taylor WW, Low DE, McGeer A, Kotb M.; J Bacteriol. 2005 May;187(10):3311-8. PMID: 15866915; In this paper, genomic context analysis was performed in the SEED.

^top

Posters

Comparative Genomics of Vibrio

Reich CI, McNeil LK, Olsen GJ.

15th International Conference on Microbial Genomes, College Park, MD, Sept. 16 - 20, 2007

pdf poster, 17 letter size pages in new window

Also presented at:

14th Annual Midwest Microbial Pathogenesis Conference, Chicago, IL, Sept. 28 - 30, 2007

Comparative genomics of microbial heme biosynthesis: Subsystem approach: Gerdes S, Vavilin D, Vermaas W, Dailey T, Dailey H, and Overbeek R.; 15th International Conference on Microbial Genomes, College Park, MD, Sept. 16 - 20, 2007; pdf poster, 1 letter size page in new window

Using the NMPDR to suggest a host-pathogen interaction: McNeil LK, Osterman AL, Reich CI, Overbeek R, Vonstein V, Stevens R.; 6th Microbial Pathogenesis and Host Response, Cold Spring Harbor Laboratory, NY, Sept. 15 - 19, 2007; pdf poster, 13 letter size pages in new window

Core genomes and signature genes that define Streptococcus pyogenes

Aziz RK, McNeil LK, Kamal I, Kotb M, Stevens R.

UT-ORNL-KBRIN Bioinformatics Summit, Paris Lake, TN, April 13 - 15, 2007

pdf poster, 12 letter size pages in new window

Also presented at:

10th Annual Conference on New and Reemerging Infectious Diseases, Urbana, IL, April 19 - 20, 2007

more >>

The National Microbial Pathogen Data Resource (NMPDR): A Bioinformatics Platform for Research Support

McNeil LK, Reich CI, Overbeek R, Stevens R.

14th International Conference on Microbial Genomes, Lake Arrowhead, CA, Sept. 24 - 28, 2006

pdf poster, 12 letter size pages in new window

Also presented at:

13th Annual Midwest Microbial Pathogenesis Conference, Cincinnati, OH, Oct. 20 - 22, 2006

Novel Bioinformatics Tools: Using The NMPDR and The SEED Subsystems Approach for Comparative Genomics and Understanding Streptococcal Virulence

Aziz RK, McNeil LK, Kubal M, Overbeek R, Stevens R, Vonstein V, Kotb M.

The 7th International Conference on the Genetics of Streptococci, Lactococci and Enterococci, Saint Malo, FRANCE, June 18 - 21, 2006

pdf poster, one letter size page in new window

Also presented at:

National Conference on Gram-positive Pathogens, Omaha, NE, Oct. 15 - 18, 2006

Subsystems-based genome annotation and analysis in the SEED.

Gerdes S, McNeil LK, Overbeek R, Osterman A, Stevens R.

First International Biocurator Meeting, Asilomar, CA, Dec. 8 - 11, 2005

pdf poster, one letter size page in new window