EDGAR: a software framework for the comparative analysis of prokaryotic genomes

Blom J, Albaum S, Doppmeier D, Pühler A, Vorhölter F-J, Zakrzewski M, Goesmann A (2009)
BMC Bioinformatics 10(1): 154.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
Abstract / Bemerkung
Background:The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large groups of related genomes in a comparative approach. A main task in comparative genomics is the identification of orthologous genes in different genomes and the classification of genes as core genes or singletons. Results: To support these studies EDGAR – ''Efficient Database framework for comparative Genome Analyses using BLAST score Ratios'' – was developed. EDGAR is designed to automatically perform genome comparisons in a high throughput approach. Comparative analyses for 582 genomes across 75 genus groups taken from the NCBI genomes database were conducted with the software and the results were integrated into an underlying database. To demonstrate a specific application case, we analyzed ten genomes of the bacterial genus Xanthomonas, for which phylogenetic studies were awkward due to divergent taxonomic systems. The resultant phylogeny EDGAR provided was consistent with outcomes from traditional approaches performed recently and moreover, it was possible to root each strain with unprecedented accuracy. Conclusion: EDGAR provides novel analysis features and significantly simplifies the comparative analysis of related genomes. The software supports a quick survey of evolutionary relationships and simplifies the process of obtaining new biological insights into the differential gene content of kindred genomes. Visualization features, like synteny plots or Venn diagrams, are offered to the scientific community through a web-based and therefore platform independent user interface http://edgar.cebitec.uni-bielefeld.de webcite, where the precomputed data sets can be browsed.
BMC Bioinformatics
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Blom J, Albaum S, Doppmeier D, et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics. 2009;10(1): 154.
Blom, J., Albaum, S., Doppmeier, D., Pühler, A., Vorhölter, F. - J., Zakrzewski, M., & Goesmann, A. (2009). EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics, 10(1), 154. https://doi.org/10.1186/1471-2105-10-154
Blom, Jochen, Albaum, Stefan, Doppmeier, Daniel, Pühler, Alfred, Vorhölter, Frank-Jörg, Zakrzewski, Martha, and Goesmann, Alexander. 2009. “EDGAR: a software framework for the comparative analysis of prokaryotic genomes”. BMC Bioinformatics 10 (1): 154.
Blom, J., Albaum, S., Doppmeier, D., Pühler, A., Vorhölter, F. - J., Zakrzewski, M., and Goesmann, A. (2009). EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 10:154.
Blom, J., et al., 2009. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics, 10(1): 154.
J. Blom, et al., “EDGAR: a software framework for the comparative analysis of prokaryotic genomes”, BMC Bioinformatics, vol. 10, 2009, : 154.
Blom, J., Albaum, S., Doppmeier, D., Pühler, A., Vorhölter, F.-J., Zakrzewski, M., Goesmann, A.: EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics. 10, : 154 (2009).
Blom, Jochen, Albaum, Stefan, Doppmeier, Daniel, Pühler, Alfred, Vorhölter, Frank-Jörg, Zakrzewski, Martha, and Goesmann, Alexander. “EDGAR: a software framework for the comparative analysis of prokaryotic genomes”. BMC Bioinformatics 10.1 (2009): 154.
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The Sinorhizobium fredii HH103 Genome: A Comparative Analysis With S. fredii Strains Differing in Their Symbiotic Behavior With Soybean.
Vinardell JM, Acosta-Jurado S, Zehner S, Göttfert M, Becker A, Baena I, Blom J, Crespo-Rivas JC, Goesmann A, Jaenicke S, Krol E, McIntosh M, Margaret I, Pérez-Montaño F, Schneiker-Bekel S, Serranía J, Szczepanowski R, Buendía AM, Lloret J, Bonilla I, Pühler A, Ruiz-Sainz JE, Weidner S., Mol Plant Microbe Interact 28(7), 2015
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Draft Genome Sequence of Pseudomonas aeruginosa Strain WS136, a Highly Cytotoxic ExoS-Positive Wound Isolate Recovered from Pyoderma Gangrenosum.
Arnold M, Wibberg D, Blom J, Schatschneider S, Winkler A, Kutter Y, Rückert C, Albersmeier A, Albaum S, Goesmann A, Zange S, Heesemann J, Pühler A, Hogardt M, Vorhölter FJ., Genome Announc 3(4), 2015
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The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms.
Rupp O, Brinkrolf K, Buerth C, Kunigo M, Schneider J, Jaenicke S, Goesmann A, Pühler A, Jaeger KE, Ernst JF., J Biotechnol 211(), 2015
PMID: 26150016
Diversity and Global Distribution of IncL/M Plasmids Enabling Horizontal Dissemination of β-Lactam Resistance Genes among the Enterobacteriaceae.
Adamczuk M, Zaleski P, Dziewit L, Wolinowska R, Nieckarz M, Wawrzyniak P, Kieryl P, Plucienniczak A, Bartosik D., Biomed Res Int 2015(), 2015
PMID: 26236726
Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21.
Wibberg D, Tielen P, Narten M, Schobert M, Blom J, Schatschneider S, Meyer AK, Neubauer R, Albersmeier A, Albaum S, Jahn M, Goesmann A, Vorhölter FJ, Pühler A, Jahn D., Genome Announc 3(4), 2015
PMID: 26184943
Whole-genome analysis of Azoarcus sp. strain CIB provides genetic insights to its different lifestyles and predicts novel metabolic features.
Martín-Moldes Z, Zamarro MT, Del Cerro C, Valencia A, Gómez MJ, Arcas A, Udaondo Z, García JL, Nogales J, Carmona M, Díaz E., Syst Appl Microbiol 38(7), 2015
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Inside the Pan-genome - Methods and Software Overview.
Guimarães LC, Florczak-Wyspianska J, de Jesus LB, Viana MV, Silva A, Ramos RT, Soares Sde C, Soares Sde C., Curr Genomics 16(4), 2015
PMID: 27006628
Pan-Tetris: an interactive visualisation for Pan-genomes.
Hennig A, Bernhardt J, Nieselt K., BMC Bioinformatics 16 Suppl 11(), 2015
PMID: 26328606
Transcriptomic analysis of a moderately growing subisolate Botryococcus braunii 779 (Chlorophyta) in response to nitrogen deprivation.
Fang L, Sun D, Xu Z, He J, Qi S, Chen X, Chew W, Liu J., Biotechnol Biofuels 8(), 2015
PMID: 26322124
The complete genome, structural proteome, comparative genomics and phylogenetic analysis of a broad host lytic bacteriophage ϕD3 infecting pectinolytic Dickeya spp.
Czajkowski R, Ozymko Z, Siwinska J, Ossowicki A, de Jager V, Narajczyk M, Łojkowska E., Stand Genomic Sci 10(), 2015
PMID: 26405503
Adherence and invasive properties of Corynebacterium diphtheriae strains correlates with the predicted membrane-associated and secreted proteome.
Sangal V, Blom J, Sutcliffe IC, von Hunolstein C, Burkovski A, Hoskisson PA., BMC Genomics 16(), 2015
PMID: 26452736
Parallel computing in genomic research: advances and applications.
Ocaña K, de Oliveira D., Adv Appl Bioinform Chem 8(), 2015
PMID: 26604801
Draft Genome Sequence of the Commercial Biocontrol Strain Pantoea agglomerans P10c.
Smits TH, Rezzonico F, Blom J, Goesmann A, Abelli A, Kron Morelli R, Vanneste JL, Duffy B., Genome Announc 3(6), 2015
PMID: 26659685
Novel Routes for Improving Biocontrol Activity of Bacillus Based Bioinoculants.
Wu L, Wu HJ, Qiao J, Gao X, Borriss R., Front Microbiol 6(), 2015
PMID: 26696998
A molecular scheme for Yersinia enterocolitica patho-serotyping derived from genome-wide analysis.
Garzetti D, Susen R, Fruth A, Tietze E, Heesemann J, Rakin A., Int J Med Microbiol 304(3-4), 2014
PMID: 24246413
A lack of genetic basis for biovar differentiation in clinically important Corynebacterium diphtheriae from whole genome sequencing.
Sangal V, Burkovski A, Hunt AC, Edwards B, Blom J, Hoskisson PA., Infect Genet Evol 21(), 2014
PMID: 24200588
Whole-Genome Sequencing of Erwinia amylovora Strains from Mexico Detects Single Nucleotide Polymorphisms in rpsL Conferring Streptomycin Resistance and in the avrRpt2 Effector Altering Host Interactions.
Smits TH, Guerrero-Prieto VM, Hernández-Escarcega G, Blom J, Goesmann A, Rezzonico F, Duffy B, Stockwell VO., Genome Announc 2(1), 2014
PMID: 24459281
Characterization of the pyrophosphate-dependent 6-phosphofructokinase from Xanthomonas campestris pv. campestris.
Frese M, Schatschneider S, Voss J, Vorhölter FJ, Niehaus K., Arch Biochem Biophys 546(), 2014
PMID: 24508689
Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids.
Dziewit L, Czarnecki J, Wibberg D, Radlinska M, Mrozek P, Szymczak M, Schlüter A, Pühler A, Bartosik D., BMC Genomics 15(), 2014
PMID: 24517536
Genome sequence of the acid-tolerant strain Rhizobium sp. LPU83.
Wibberg D, Tejerizo GT, Del Papa MF, Martini C, Pühler A, Lagares A, Schlüter A, Pistorio M., J Biotechnol 176(), 2014
PMID: 24556327
Genome Sequence of the Acute Urethral Catheter Isolate Pseudomonas aeruginosa MH38.
Wibberg D, Tielen P, Blom J, Rosin N, Schobert M, Tüpker R, Schatschneider S, Spilker D, Albersmeier A, Goesmann A, Vorhölter FJ, Pühler A, Jahn D., Genome Announc 2(2), 2014
PMID: 24625869
Comparative genomics of the dairy isolate Streptococcus macedonicus ACA-DC 198 against related members of the Streptococcus bovis/Streptococcus equinus complex.
Papadimitriou K, Anastasiou R, Mavrogonatou E, Blom J, Papandreou NC, Hamodrakas SJ, Ferreira S, Renault P, Supply P, Pot B, Tsakalidou E., BMC Genomics 15(), 2014
PMID: 24713045
ReadXplorer--visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A., Bioinformatics 30(16), 2014
PMID: 24790157
Development and application of a multilocus sequence typing scheme for Streptococcus gallolyticus subsp. gallolyticus.
Dumke J, Hinse D, Vollmer T, Knabbe C, Dreier J., J Clin Microbiol 52(7), 2014
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Draft genome of formaldehyde-degrading strain, Pseudomonas monteilii IOFA19.
Liu Y, Chen X, Blom J, Yi Z, Wen J, Zeng R., Mar Genomics 15(), 2014
PMID: 24798874
Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle.
Załuga J, Stragier P, Baeyen S, Haegeman A, Van Vaerenbergh J, Maes M, De Vos P., BMC Genomics 15(), 2014
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A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus.
Kant R, Rintahaka J, Yu X, Sigvart-Mattila P, Paulin L, Mecklin JP, Saarela M, Palva A, von Ossowski I., PLoS One 9(7), 2014
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Relaxed selection drives a noisy noncoding transcriptome in members of the Mycobacterium tuberculosis complex.
Dinan AM, Tong P, Lohan AJ, Conlon KM, Miranda-CasoLuengo AA, Malone KM, Gordon SV, Loftus BJ., MBio 5(4), 2014
PMID: 25096875
Genome features of the endophytic actinobacterium Micromonospora lupini strain Lupac 08: on the process of adaptation to an endophytic life style?
Trujillo ME, Bacigalupe R, Pujic P, Igarashi Y, Benito P, Riesco R, Médigue C, Normand P., PLoS One 9(9), 2014
PMID: 25268993
Draft Genome Sequence of Pseudomonas aeruginosa Strain WS394, a Multidrug-Resistant and Highly Cytotoxic Wound Isolate from Chronic Ulcus Cruris.
Vorhölter FJ, Arnold M, Wibberg D, Blom J, Winkler A, Viehoever P, Albersmeier A, Goesmann A, Zange S, Heesemann J, Pühler A, Hogardt M., Genome Announc 2(6), 2014
PMID: 25523779
Draft whole genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.
Luque-Almagro VM, Acera F, Igeño MI, Wibberg D, Roldán MD, Sáez LP, Hennig M, Quesada A, Huertas MJ, Blom J, Merchán F, Escribano MP, Jaenicke S, Estepa J, Guijo MI, Martínez-Luque M, Macías D, Szczepanowski R, Becerra G, Ramirez S, Carmona MI, Gutiérrez O, Manso I, Pühler A, Castillo F, Moreno-Vivián C, Schlüter A, Blasco R., Environ Microbiol 15(1), 2013
PMID: 22998548
Erwinia amylovora loop-mediated isothermal amplification (LAMP) assay for rapid pathogen detection and on-site diagnosis of fire blight.
Bühlmann A, Pothier JF, Rezzonico F, Smits TH, Andreou M, Boonham N, Duffy B, Frey JE., J Microbiol Methods 92(3), 2013
PMID: 23275135
The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains.
Soares SC, Silva A, Trost E, Blom J, Ramos R, Carneiro A, Ali A, Santos AR, Pinto AC, Diniz C, Barbosa EG, Dorella FA, Aburjaile F, Rocha FS, Nascimento KK, Guimarães LC, Almeida S, Hassan SS, Bakhtiar SM, Pereira UP, Abreu VA, Schneider MP, Miyoshi A, Tauch A, Azevedo V., PLoS One 8(1), 2013
PMID: 23342011
Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.
Mann RA, Smits TH, Bühlmann A, Blom J, Goesmann A, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B., PLoS One 8(2), 2013
PMID: 23409014
Detecting sequence homology at the gene cluster level with MultiGeneBlast.
Medema MH, Takano E, Breitling R., Mol Biol Evol 30(5), 2013
PMID: 23412913
Dialects of the DNA uptake sequence in Neisseriaceae.
Frye SA, Nilsen M, Tønjum T, Ambur OH., PLoS Genet 9(4), 2013
PMID: 23637627
Complete Genome Sequence of Corynebacterium urealyticum Strain DSM 7111, Isolated from a 9-Year-Old Patient with Alkaline-Encrusted Cystitis.
Guimarães LC, Soares SC, Albersmeier A, Blom J, Jaenicke S, Azevedo V, Soriano F, Tauch A, Trost E., Genome Announc 1(3), 2013
PMID: 23704183
Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics.
Smits TH, Rezzonico F, López MM, Blom J, Goesmann A, Frey JE, Duffy B., Syst Appl Microbiol 36(7), 2013
PMID: 23726521
Dynamic protein phosphorylation during the growth of Xanthomonas campestris pv. campestris B100 revealed by a gel-based proteomics approach.
Musa YR, Bäsell K, Schatschneider S, Vorhölter FJ, Becher D, Niehaus K., J Biotechnol 167(2), 2013
PMID: 23792782
Novel configurations of type I and II CRISPR-Cas systems in Corynebacterium diphtheriae.
Sangal V, Fineran PC, Hoskisson PA., Microbiology 159(pt 10), 2013
PMID: 23904149
Draft genome sequence of the cellulolytic Clostridium thermocellum wild-type strain BC1 playing a role in cellulosic biomass degradation.
Koeck DE, Wibberg D, Koellmeier T, Blom J, Jaenicke S, Winkler A, Albersmeier A, Zverlov VV, Zverlov VV, Pühler A, Schwarz WH, Schlüter A., J Biotechnol 168(1), 2013
PMID: 23968723
Comparative genome analysis of Enterobacter cloacae.
Liu WY, Wong CF, Chung KM, Jiang JW, Leung FC., PLoS One 8(9), 2013
PMID: 24069314
Novel configurations of type I and II CRISPR-Cas systems in Corynebacterium diphtheriae.
Sangal V, Fineran PC, Hoskisson PA., Microbiology 159(10), 2013
PMID: 28206911
Draft genome sequence of Sinorhizobium meliloti RU11/001, a model organism for flagellum structure, motility and chemotaxis.
Wibberg D, Blom J, Rückert C, Winkler A, Albersmeier A, Pühler A, Schlüter A, Scharf BE., J Biotechnol 168(4), 2013
PMID: 24184089
Draft genome sequence of Xanthomonas fragariae reveals reductive evolution and distinct virulence-related gene content.
Vandroemme J, Cottyn B, Baeyen S, De Vos P, Maes M., BMC Genomics 14(), 2013
PMID: 24274055
Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production.
Bogen C, Al-Dilaimi A, Albersmeier A, Wichmann J, Grundmann M, Rupp O, Lauersen KJ, Blifernez-Klassen O, Kalinowski J, Goesmann A, Mussgnug JH, Kruse O., BMC Genomics 14(), 2013
PMID: 24373495
Genome wide identification of Acidithiobacillus ferrooxidans (ATCC 23270) transcription factors and comparative analysis of ArsR and MerR metal regulators.
Hödar C, Moreno P, di Genova A, Latorre M, Reyes-Jara A, Maass A, González M, Cambiazo V., Biometals 25(1), 2012
PMID: 21830017
Genomics and current genetic understanding of Erwinia amylovora and the fire blight antagonist Pantoea vagans
Kamber T, Smits THM, Rezzonico F, Duffy B., Trees (Berl West) 26(1), 2012
PMID: IND44798016
Genomes-based phylogeny of the genus Xanthomonas.
Rodriguez-R LM, Grajales A, Arrieta-Ortiz ML, Salazar C, Restrepo S, Bernal A., BMC Microbiol 12(), 2012
PMID: 22443110
Pangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia.
Trost E, Blom J, Soares Sde C, Huang IH, Al-Dilaimi A, Schröder J, Jaenicke S, Dorella FA, Rocha FS, Miyoshi A, Azevedo V, Schneider MP, Silva A, Camello TC, Sabbadini PS, Santos CS, Santos LS, Hirata R, Mattos-Guaraldi AL, Efstratiou A, Schmitt MP, Ton-That H, Tauch A., J Bacteriol 194(12), 2012
PMID: 22505676
Complete genome sequence, lifestyle, and multi-drug resistance of the human pathogen Corynebacterium resistens DSM 45100 isolated from blood samples of a leukemia patient.
Schröder J, Maus I, Meyer K, Wördemann S, Blom J, Jaenicke S, Schneider J, Trost E, Tauch A., BMC Genomics 13(), 2012
PMID: 22524407
Lipopolysaccharide biosynthesis genes discriminate between Rubus- and Spiraeoideae-infective genotypes of Erwinia amylovora.
Rezzonico F, Braun-Kiewnick A, Mann RA, Rodoni B, Goesmann A, Duffy B, Smits TH., Mol Plant Pathol 13(8), 2012
PMID: 22583486
Complete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae.
Strobel T, Al-Dilaimi A, Blom J, Gessner A, Kalinowski J, Luzhetska M, Pühler A, Szczepanowski R, Bechthold A, Rückert C., BMC Genomics 13(), 2012
PMID: 22958348
Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin.
Jankowitsch F, Schwarz J, Rückert C, Gust B, Szczepanowski R, Blom J, Pelzer S, Kalinowski J, Mack M., J Bacteriol 194(24), 2012
PMID: 23043000
Genome sequence of the plant growth promoting strain Bacillus amyloliquefaciens subsp. plantarum B9601-Y2 and expression of mersacidin and other secondary metabolites.
He P, Hao K, Blom J, Rückert C, Vater J, Mao Z, Wu Y, Hou M, He P, He Y, Borriss R., J Biotechnol 164(2), 2012
PMID: 23357245
Relationship of Bacillus amyloliquefaciens clades associated with strains DSM 7T and FZB42T: a proposal for Bacillus amyloliquefaciens subsp. amyloliquefaciens subsp. nov. and Bacillus amyloliquefaciens subsp. plantarum subsp. nov. based on complete genome sequence comparisons.
Borriss R, Chen XH, Rueckert C, Blom J, Becker A, Baumgarth B, Fan B, Pukall R, Schumann P, Spröer C, Junge H, Vater J, Pühler A, Klenk HP., Int J Syst Evol Microbiol 61(pt 8), 2011
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Comparative genomics of Lactobacillus.
Kant R, Blom J, Palva A, Siezen RJ, de Vos WM., Microb Biotechnol 4(3), 2011
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The genome of Akkermansia muciniphila, a dedicated intestinal mucin degrader, and its use in exploring intestinal metagenomes.
van Passel MW, Kant R, Zoetendal EG, Plugge CM, Derrien M, Malfatti SA, Chain PS, Woyke T, Palva A, de Vos WM, Smidt H., PLoS One 6(3), 2011
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Pathogenomics of Xanthomonas: understanding bacterium-plant interactions.
Ryan RP, Vorhölter FJ, Potnis N, Jones JB, Van Sluys MA, Bogdanove AJ, Dow JM., Nat Rev Microbiol 9(5), 2011
PMID: 21478901
Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist Pantoea vagans C9-1.
Smits TH, Rezzonico F, Kamber T, Blom J, Goesmann A, Ishimaru CA, Frey JE, Stockwell VO, Duffy B., PLoS One 6(7), 2011
PMID: 21789243
Comparative analysis of two complete Corynebacterium ulcerans genomes and detection of candidate virulence factors.
Trost E, Al-Dilaimi A, Papavasiliou P, Schneider J, Viehoever P, Burkovski A, Soares SC, Almeida SS, Dorella FA, Miyoshi A, Azevedo V, Schneider MP, Silva A, Santos CS, Santos LS, Sabbadini P, Dias AA, Hirata R, Mattos-Guaraldi AL, Tauch A., BMC Genomics 12(), 2011
PMID: 21801446
Complete genome and comparative analysis of Streptococcus gallolyticus subsp. gallolyticus, an emerging pathogen of infective endocarditis.
Hinse D, Vollmer T, Rückert C, Blom J, Kalinowski J, Knabbe C, Dreier J., BMC Genomics 12(), 2011
PMID: 21824414
The genomics of Acinetobacter baumannii: insights into genome plasticity, antimicrobial resistance and pathogenicity.
Imperi F, Antunes LC, Blom J, Villa L, Iacono M, Visca P, Carattoli A., IUBMB Life 63(12), 2011
PMID: 22034231
Calculating orthologs in bacteria and Archaea: a divide and conquer approach.
Halachev MR, Loman NJ, Pallen MJ., PLoS One 6(12), 2011
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Phylogenetic comparative assembly.
Husemann P, Stoye J., Algorithms Mol Biol 5(), 2010
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[The next generation sequencing technology and its application in cancer research].
Chen C, Wan H, Zhou Q., Zhongguo Fei Ai Za Zhi 13(2), 2010
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Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion.
Trost E, Götker S, Schneider J, Schneiker-Bekel S, Szczepanowski R, Tilker A, Viehoever P, Arnold W, Bekel T, Blom J, Gartemann KH, Linke B, Goesmann A, Pühler A, Shukla SK, Tauch A., BMC Genomics 11(), 2010
PMID: 20137072
DraGnET: software for storing, managing and analyzing annotated draft genome sequence data.
Duncan S, Sirkanungo R, Miller L, Phillips GJ., BMC Bioinformatics 11(), 2010
PMID: 20175920
Discovery of Phytophthora infestans genes expressed in planta through mining of cDNA libraries.
Sierra R, Rodríguez-R LM, Chaves D, Pinzón A, Grajales A, Rojas A, Mutis G, Cárdenas M, Burbano D, Jiménez P, Bernal A, Restrepo S., PLoS One 5(3), 2010
PMID: 20352100
Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8.
Farnbacher M, Jahns T, Willrodt D, Daniel R, Haas R, Goesmann A, Kurtz S, Rieder G., BMC Genomics 11(), 2010
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The Waddlia genome: a window into chlamydial biology.
Bertelli C, Collyn F, Croxatto A, Rückert C, Polkinghorne A, Kebbi-Beghdadi C, Goesmann A, Vaughan L, Greub G., PLoS One 5(5), 2010
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The complete genome sequence of Corynebacterium pseudotuberculosis FRC41 isolated from a 12-year-old girl with necrotizing lymphadenitis reveals insights into gene-regulatory networks contributing to virulence.
Trost E, Ott L, Schneider J, Schröder J, Jaenicke S, Goesmann A, Husemann P, Stoye J, Dorella FA, Rocha FS, Soares Sde C, D'Afonseca V, Miyoshi A, Ruiz J, Silva A, Azevedo V, Burkovski A, Guiso N, Join-Lambert OF, Kayal S, Tauch A., BMC Genomics 11(), 2010
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Passing GO (gene ontology) in plant pathogen biology: a report from the Xanthomonas Genomics Conference.
Ryan RP, Koebnik R, Szurek B, Boureau T, Bernal A, Bogdanove A, Dow JM., Cell Microbiol 11(12), 2009
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