GenDB - an open source genome annotation system for prokaryote genomes

Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Pühler A (2003)
Nucleic Acids Research 31(8): 2187-2195.

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Meyer F, Goesmann A, McHardy AC, et al. GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Research. 2003;31(8):2187-2195.
Meyer, F., Goesmann, A., McHardy, A. C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., et al. (2003). GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Research, 31(8), 2187-2195. doi:10.1093/nar/gkg312
Meyer, F., Goesmann, A., McHardy, A. C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R., et al. (2003). GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Research 31, 2187-2195.
Meyer, F., et al., 2003. GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Research, 31(8), p 2187-2195.
F. Meyer, et al., “GenDB - an open source genome annotation system for prokaryote genomes”, Nucleic Acids Research, vol. 31, 2003, pp. 2187-2195.
Meyer, F., Goesmann, A., McHardy, A.C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R., Pühler, A.: GenDB - an open source genome annotation system for prokaryote genomes. Nucleic Acids Research. 31, 2187-2195 (2003).
Meyer, Folker, Goesmann, Alexander, McHardy, Alice C., Bartels, Daniela, Bekel, Thomas, Clausen, Jörn, Kalinowski, Jörn, Linke, Burkhard, Rupp, Oliver, Giegerich, Robert, and Pühler, Alfred. “GenDB - an open source genome annotation system for prokaryote genomes”. Nucleic Acids Research 31.8 (2003): 2187-2195.
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PMID: 27727519
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PMID: 25240439
Interclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment.
Hilker R, Munder A, Klockgether J, Losada PM, Chouvarine P, Cramer N, Davenport CF, Dethlefsen S, Fischer S, Peng H, Schönfelder T, Türk O, Wiehlmann L, Wölbeling F, Gulbins E, Goesmann A, Tümmler B., Environ Microbiol 17(1), 2015
PMID: 25156090
Chassis organism from Corynebacterium glutamicum--a top-down approach to identify and delete irrelevant gene clusters.
Unthan S, Baumgart M, Radek A, Herbst M, Siebert D, Brühl N, Bartsch A, Bott M, Wiechert W, Marin K, Hans S, Krämer R, Seibold G, Frunzke J, Kalinowski J, Rückert C, Wendisch VF, Noack S., Biotechnol J 10(2), 2015
PMID: 25139579
Complete genome sequence of the novel Porphyromonadaceae bacterium strain ING2-E5B isolated from a mesophilic lab-scale biogas reactor.
Hahnke S, Maus I, Wibberg D, Tomazetto G, Pühler A, Klocke M, Schlüter A., J Biotechnol 193(), 2015
PMID: 25444871
Complete genome sequence of the actinobacterium Streptomyces glaucescens GLA.O (DSM 40922) consisting of a linear chromosome and one linear plasmid.
Ortseifen V, Winkler A, Albersmeier A, Wendler S, Pühler A, Kalinowski J, Rückert C., J Biotechnol 194(), 2015
PMID: 25499805
The mannitol utilization system of the marine bacterium Zobellia galactanivorans.
Groisillier A, Labourel A, Michel G, Tonon T., Appl Environ Microbiol 81(5), 2015
PMID: 25548051
Genomic avenue to avian colisepticemia.
Huja S, Oren Y, Trost E, Brzuszkiewicz E, Biran D, Blom J, Goesmann A, Gottschalk G, Hacker J, Ron EZ, Dobrindt U., MBio 6(1), 2015
PMID: 25587010
Complete genome sequence of Streptomyces lividans TK24.
Rückert C, Albersmeier A, Busche T, Jaenicke S, Winkler A, Friðjónsson ÓH, Hreggviðsson GÓ, Lambert C, Badcock D, Bernaerts K, Anne J, Economou A, Kalinowski J., J Biotechnol 199(), 2015
PMID: 25680930
Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.
Bertelli C, Aeby S, Chassot B, Clulow J, Hilfiker O, Rappo S, Ritzmann S, Schumacher P, Terrettaz C, Benaglio P, Falquet L, Farinelli L, Gharib WH, Goesmann A, Harshman K, Linke B, Miyazaki R, Rivolta C, Robinson-Rechavi M, van der Meer JR, Greub G., Front Microbiol 6(), 2015
PMID: 25745418
Diversity and role of plasmids in adaptation of bacteria inhabiting the Lubin copper mine in Poland, an environment rich in heavy metals.
Dziewit L, Pyzik A, Szuplewska M, Matlakowska R, Mielnicki S, Wibberg D, Schlüter A, Pühler A, Bartosik D., Front Microbiol 6(), 2015
PMID: 26074880
Complete Sequence of Probiotic Symbioflor 2 Escherichia coli Strain G3/10 and Draft Sequences of Symbioflor 2 E. coli Strains G1/2, G4/9, G5, G6/7, and G8.
Zschüttig A, Auerbach C, Meltke S, Eichhorn C, Brandt M, Blom J, Goesmann A, Jarek M, Scharfe M, Zimmermann K, Wassenaar TM, Gunzer F., Genome Announc 3(2), 2015
PMID: 25745009
Genome Sequence of the Urethral Catheter Isolate Pseudomonas aeruginosa MH19.
Vorhölter FJ, Tielen P, Wibberg D, Narten M, Schobert M, Tüpker R, Blom J, Schatschneider S, Winkler A, Albersmeier A, Goesmann A, Pühler A, Jahn D., Genome Announc 3(2), 2015
PMID: 25767242
Improved genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 as established by deep mate-pair sequencing on the MiSeq (Illumina) system.
Wibberg D, Rupp O, Jelonek L, Kröber M, Verwaaijen B, Blom J, Winkler A, Goesmann A, Grosch R, Pühler A, Schlüter A., J Biotechnol 203(), 2015
PMID: 25801332
Complete genome sequence of the strain Defluviitoga tunisiensis L3, isolated from a thermophilic, production-scale biogas plant.
Maus I, Cibis KG, Wibberg D, Winkler A, Stolze Y, König H, Pühler A, Schlüter A., J Biotechnol 203(), 2015
PMID: 25801333
Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor.
Koeck DE, Ludwig W, Wanner G, Zverlov VV, Zverlov VV, Liebl W, Schwarz WH., Int J Syst Evol Microbiol 65(8), 2015
PMID: 25872956
Complete genome sequence of Paenibacillus riograndensis SBR5(T), a Gram-positive diazotrophic rhizobacterium.
Brito LF, Bach E, Kalinowski J, Rückert C, Wibberg D, Passaglia LM, Wendisch VF., J Biotechnol 207(), 2015
PMID: 25959170
Sphingopyxis fribergensis sp. nov., a soil bacterium with the ability to degrade styrene and phenylacetic acid.
Oelschlägel M, Rückert C, Kalinowski J, Schmidt G, Schlömann M, Tischler D., Int J Syst Evol Microbiol 65(9), 2015
PMID: 26040579
Endophytic Streptomyces in the traditional medicinal plant Arnica montana L.: secondary metabolites and biological activity.
Wardecki T, Brötz E, De Ford C, von Loewenich FD, Rebets Y, Tokovenko B, Luzhetskyy A, Merfort I., Antonie Van Leeuwenhoek 108(2), 2015
PMID: 26036671
Complete Genome Sequence of the Cyanogenic Phosphate-Solubilizing Pseudomonas sp. Strain CCOS 191, a Close Relative of Pseudomonas mosselii.
Smits TH, Pothier JF, Ruinelli M, Blom J, Frasson D, Koechli C, Fabbri C, Brandl H, Duffy B, Sievers M., Genome Announc 3(3), 2015
PMID: 26067963
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
PMID: 25675256
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
PMID: 26139712
Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system.
Pulgar R, Hödar C, Travisany D, Zuñiga A, Domínguez C, Maass A, González M, Cambiazo V., BMC Genomics 16(), 2015
PMID: 26141111
Potential Mechanism of Action of 3'-Demethoxy-6-O-demethyl-isoguaiacin on Methicillin Resistant Staphylococcus aureus.
Favela-Hernández JM, Clemente-Soto AF, Balderas-Rentería I, Garza-González E, Camacho-Corona Mdel R., Molecules 20(7), 2015
PMID: 26184132
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
Draft genome sequence of Talaromyces islandicus ("Penicillium islandicum") WF-38-12, a neglected mold with significant biotechnological potential.
Schafhauser T, Wibberg D, Rückert C, Winkler A, Flor L, van Pée KH, Fewer DP, Sivonen K, Jahn L, Ludwig-Müller J, Caradec T, Jacques P, Huijbers MM, van Berkel WJ, Weber T, Wohlleben W, Kalinowski J., J Biotechnol 211(), 2015
PMID: 26197417
Complete Genome Sequence of Acinetobacter baumannii CIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses.
Krahn T, Wibberg D, Maus I, Winkler A, Pühler A, Poirel L, Schlüter A., Genome Announc 3(4), 2015
PMID: 26227605
Genome-guided insight into the methylotrophy of Paracoccus aminophilus JCM 7686.
Dziewit L, Czarnecki J, Prochwicz E, Wibberg D, Schlüter A, Pühler A, Bartosik D., Front Microbiol 6(), 2015
PMID: 26347732
Serotype 1 and 8 Pneumococci Evade Sensing by Inflammasomes in Human Lung Tissue.
Fatykhova D, Rabes A, Machnik C, Guruprasad K, Pache F, Berg J, Toennies M, Bauer TT, Schneider P, Schimek M, Eggeling S, Mitchell TJ, Mitchell AM, Hilker R, Hain T, Suttorp N, Hippenstiel S, Hocke AC, Opitz B., PLoS One 10(8), 2015
PMID: 26317436
Complete Genome Sequence of the Clinical Strain Acinetobacter baumannii R2090 Carrying the Chromosomally Encoded Metallo-β-Lactamase Gene blaNDM-1.
Krahn T, Wibberg D, Maus I, Winkler A, Nordmann P, Pühler A, Poirel L, Schlüter A., Genome Announc 3(5), 2015
PMID: 26358593
Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels.
Sayavedra L, Kleiner M, Ponnudurai R, Wetzel S, Pelletier E, Barbe V, Satoh N, Shoguchi E, Fink D, Breusing C, Reusch TB, Rosenstiel P, Schilhabel MB, Becher D, Schweder T, Markert S, Dubilier N, Petersen JM., Elife 4(), 2015
PMID: 26371554
Intercellular wiring enables electron transfer between methanotrophic archaea and bacteria.
Wegener G, Krukenberg V, Riedel D, Tegetmeyer HE, Boetius A., Nature 526(7574), 2015
PMID: 26490622
The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract.
Wegmann U, MacKenzie DA, Zheng J, Goesmann A, Roos S, Swarbreck D, Walter J, Crossman LC, Juge N., BMC Genomics 16(), 2015
PMID: 26626322
Developing of the Computer Method for Annotation of Bacterial Genes.
Golyshev MA, Korotkov EV., Adv Bioinformatics 2015(), 2015
PMID: 26770195
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
Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium.
Humphreys CM, McLean S, Schatschneider S, Millat T, Henstra AM, Annan FJ, Breitkopf R, Pander B, Piatek P, Rowe P, Wichlacz AT, Woods C, Norman R, Blom J, Goesman A, Hodgman C, Barrett D, Thomas NR, Winzer K, Minton NP., BMC Genomics 16(), 2015
PMID: 26692227
Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates.
Wibberg D, Rupp O, Blom J, Jelonek L, Kröber M, Verwaaijen B, Goesmann A, Albaum S, Grosch R, Pühler A, Schlüter A., PLoS One 10(12), 2015
PMID: 26690577
Complete sequences of a novel blaNDM-1-harbouring plasmid from Providencia rettgeri and an FII-type plasmid from Klebsiella pneumoniae identified in Canada.
Mataseje LF, Boyd DA, Lefebvre B, Bryce E, Embree J, Gravel D, Katz K, Kibsey P, Kuhn M, Langley J, Mitchell R, Roscoe D, Simor A, Taylor G, Thomas E, Turgeon N, Mulvey MR, Canadian Nosocomial Infection Surveillance Program., J Antimicrob Chemother 69(3), 2014
PMID: 24275114
Permanent draft genomes of the two Rhodopirellula europaea strains 6C and SH398.
Richter-Heitmann T, Richter M, Klindworth A, Wegner CE, Frank CS, Glöckner FO, Harder J., Mar Genomics 13(), 2014
PMID: 24286834
Permanent draft genomes of the Rhodopirellula maiorica strain SM1.
Richter M, Richter-Heitmann T, Klindworth A, Wegner CE, Frank CS, Harder J, Glöckner FO., Mar Genomics 13(), 2014
PMID: 24286833
Permanent draft genome of Rhodopirellula sallentina SM41.
Wegner CE, Richter M, Richter-Heitmann T, Klindworth A, Frank CS, Glöckner FO, Harder J., Mar Genomics 13(), 2014
PMID: 24286832
Permanent draft genomes of the three Rhodopirellula baltica strains SH28, SWK14 and WH47.
Richter M, Richter-Heitmann T, Klindworth A, Wegner CE, Frank CS, Harder J, Glöckner FO., Mar Genomics 13(), 2014
PMID: 24286831
Permanent draft genome of Rhodopirellula rubra SWK7.
Klindworth A, Richter M, Richter-Heitmann T, Wegner CE, Frank CS, Harder J, Glöckner FO., Mar Genomics 13(), 2014
PMID: 24291061
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines.
Rupp O, Becker J, Brinkrolf K, Timmermann C, Borth N, Pühler A, Noll T, Goesmann A., PLoS One 9(1), 2014
PMID: 24427317
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
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
Complete genome sequence of the cyanide-degrading bacterium Pseudomonas pseudoalcaligenes CECT5344.
Wibberg D, Luque-Almagro VM, Igeño MI, Bremges A, Roldán MD, Merchán F, Sáez LP, Guijo MI, Manso MI, Macías D, Cabello P, Becerra G, Ibáñez MI, Carmona MI, Escribano MM, Castillo F, Sczyrba A, Moreno-Vivián C, Blasco R, Pühler A, Schlüter A., J Biotechnol 175(), 2014
PMID: 24553071
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
The gill chamber epibiosis of deep-sea shrimp Rimicaris exoculata: an in-depth metagenomic investigation and discovery of Zetaproteobacteria.
Jan C, Petersen JM, Werner J, Teeling H, Huang S, Glöckner FO, Golyshina OV, Dubilier N, Golyshin PN, Jebbar M, Cambon-Bonavita MA., Environ Microbiol 16(9), 2014
PMID: 24447589
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
Improving the genome annotation of the acarbose producer Actinoplanes sp. SE50/110 by sequencing enriched 5'-ends of primary transcripts.
Schwientek P, Neshat A, Kalinowski J, Klein A, Rückert C, Schneiker-Bekel S, Wendler S, Stoye J, Pühler A., J Biotechnol 190(), 2014
PMID: 24642337
Bioinformatics of prokaryotic RNAs.
Backofen R, Amman F, Costa F, Findeiß S, Richter AS, Stadler PF., RNA Biol 11(5), 2014
PMID: 24755880
Rhizobial plasmid pLPU83a is able to switch between different transfer machineries depending on its genomic background.
Torres Tejerizo G, Pistorio M, Althabegoiti MJ, Cervantes L, Wibberg D, Schlüter A, Pühler A, Lagares A, Romero D, Brom S., FEMS Microbiol Ecol 88(3), 2014
PMID: 24646299
IncH-type plasmid harboring bla CTX-M-15, bla DHA-1, and qnrB4 genes recovered from animal isolates.
Schlüter A, Nordmann P, Bonnin RA, Millemann Y, Eikmeyer FG, Wibberg D, Pühler A, Poirel L., Antimicrob Agents Chemother 58(7), 2014
PMID: 24752252
On the limits of computational functional genomics for bacterial lifestyle prediction.
Barbosa E, Röttger R, Hauschild AC, Azevedo V, Baumbach J., Brief Funct Genomics 13(5), 2014
PMID: 24855068
Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum.
Bachmann NL, Fraser TA, Bertelli C, Jelocnik M, Gillett A, Funnell O, Flanagan C, Myers GS, Timms P, Polkinghorne A., BMC Genomics 15(), 2014
PMID: 25106440
Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria.
Klippel B, Sahm K, Basner A, Wiebusch S, John P, Lorenz U, Peters A, Abe F, Takahashi K, Kaiser O, Goesmann A, Jaenicke S, Grote R, Horikoshi K, Antranikian G., Extremophiles 18(5), 2014
PMID: 25108363
Mycolic Acid Biosynthesis Genes in the Genome Sequence of Corynebacterium atypicum DSM 44849.
Tippelt A, Möllmann S, Albersmeier A, Jaenicke S, Rückert C, Tauch A., Genome Announc 2(4), 2014
PMID: 25146145
Complete genome sequence of Bacillus methanolicus MGA3, a thermotolerant amino acid producing methylotroph.
Irla M, Neshat A, Winkler A, Albersmeier A, Heggeset TM, Brautaset T, Kalinowski J, Wendisch VF, Rückert C., J Biotechnol 188(), 2014
PMID: 25152427
Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant.
Koeck DE, Wibberg D, Maus I, Winkler A, Albersmeier A, Zverlov VV, Zverlov VV, Liebl W, Pühler A, Schwarz WH, Schlüter A., J Biotechnol 188(), 2014
PMID: 25173616
A novel plasmid pEA68 of Erwinia amylovora and the description of a new family of plasmids.
Ismail E, Blom J, Bultreys A, Ivanović M, Obradović A, van Doorn J, Bergsma-Vlami M, Maes M, Willems A, Duffy B, Stockwell VO, Smits TH, Puławska J., Arch Microbiol 196(12), 2014
PMID: 25178659
Complete genome sequence of the actinobacterium Amycolatopsis japonica MG417-CF17(T) (=DSM 44213T) producing (S,S)-N,N'-ethylenediaminedisuccinic acid.
Stegmann E, Albersmeier A, Spohn M, Gert H, Weber T, Wohlleben W, Kalinowski J, Rückert C., J Biotechnol 189(), 2014
PMID: 25193710
Complete genome sequence of the methanogenic neotype strain Methanobacterium formicicum MF(T.).
Maus I, Stantscheff R, Wibberg D, Stolze Y, Winkler A, Pühler A, König H, Schlüter A., J Biotechnol 192 Pt A(), 2014
PMID: 25270020
First draft genome sequence of the amylolytic Bacillus thermoamylovorans wild-type strain 1A1 isolated from a thermophilic biogas plant.
Koeck DE, Wibberg D, Maus I, Winkler A, Albersmeier A, Zverlov VV, Zverlov VV, Pühler A, Schwarz WH, Liebl W, Schlüter A., J Biotechnol 192 Pt A(), 2014
PMID: 25270021
Complete genome sequence of producer of the glycopeptide antibiotic Aculeximycin Kutzneria albida DSM 43870T, a representative of minor genus of Pseudonocardiaceae.
Rebets Y, Tokovenko B, Lushchyk I, Rückert C, Zaburannyi N, Bechthold A, Kalinowski J, Luzhetskyy A., BMC Genomics 15(), 2014
PMID: 25301375
Criblamydia sequanensis Harbors a Megaplasmid Encoding Arsenite Resistance.
Bertelli C, Goesmann A, Greub G., Genome Announc 2(5), 2014
PMID: 25342672
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
Chloride and organic osmolytes: a hybrid strategy to cope with elevated salinities by the moderately halophilic, chloride-dependent bacterium Halobacillus halophilus.
Saum SH, Pfeiffer F, Palm P, Rampp M, Schuster SC, Müller V, Oesterhelt D., Environ Microbiol 15(5), 2013
PMID: 22583374
Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure.
Ferrer M, Ruiz A, Lanza F, Haange SB, Oberbach A, Till H, Bargiela R, Campoy C, Segura MT, Richter M, von Bergen M, Seifert J, Suarez A., Environ Microbiol 15(1), 2013
PMID: 22891823
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
MetaSAMS--a novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets.
Zakrzewski M, Bekel T, Ander C, Pühler A, Rupp O, Stoye J, Schlüter A, Goesmann A., J Biotechnol 167(2), 2013
PMID: 23026555
Characterization of a mazEF toxin-antitoxin homologue from Staphylococcus equorum.
Schuster CF, Park JH, Prax M, Herbig A, Nieselt K, Rosenstein R, Inouye M, Bertram R., J Bacteriol 195(1), 2013
PMID: 23104807
Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14.
Wibberg D, Jelonek L, Rupp O, Hennig M, Eikmeyer F, Goesmann A, Hartmann A, Borriss R, Grosch R, Pühler A, Schlüter A., J Biotechnol 167(2), 2013
PMID: 23280342
Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids.
Dagan T, Roettger M, Stucken K, Landan G, Koch R, Major P, Gould SB, Goremykin VV, Rippka R, Tandeau de Marsac N, Gugger M, Lockhart PJ, Allen JF, Brune I, Maus I, Pühler A, Martin WF., Genome Biol Evol 5(1), 2013
PMID: 23221676
Complete Genome Sequence of the Probiotic Enterococcus faecalis Symbioflor 1 Clone DSM 16431.
Fritzenwanker M, Kuenne C, Billion A, Hain T, Zimmermann K, Goesmann A, Chakraborty T, Domann E., Genome Announc 1(1), 2013
PMID: 23405346
Ecology of marine Bacteroidetes: a comparative genomics approach.
Fernández-Gómez B, Richter M, Schüler M, Pinhassi J, Acinas SG, González JM, Pedrós-Alió C., ISME J 7(5), 2013
PMID: 23303374
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
Genome Sequence of Sinorhizobium meliloti Rm41.
Weidner S, Baumgarth B, Göttfert M, Jaenicke S, Pühler A, Schneiker-Bekel S, Serrania J, Szczepanowski R, Becker A., Genome Announc 1(1), 2013
PMID: 23405285
Characterization of a stable, metronidazole-resistant Clostridium difficile clinical isolate.
Lynch T, Chong P, Zhang J, Hizon R, Du T, Graham MR, Beniac DR, Booth TF, Kibsey P, Miller M, Gravel D, Mulvey MR, Canadian Nosocomial Infection Surveillance Program (CNISP)., PLoS One 8(1), 2013
PMID: 23349739
Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome.
Kuenne C, Billion A, Mraheil MA, Strittmatter A, Daniel R, Goesmann A, Barbuddhe S, Hain T, Chakraborty T., BMC Genomics 14(), 2013
PMID: 23339658
New insights into the archaeal diversity of a hypersaline microbial mat obtained by a metagenomic approach.
López-López A, Richter M, Peña A, Tamames J, Rosselló-Móra R., Syst Appl Microbiol 36(3), 2013
PMID: 23352736
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
Whole genome sequencing versus traditional genotyping for investigation of a Mycobacterium tuberculosis outbreak: a longitudinal molecular epidemiological study.
Roetzer A, Diel R, Kohl TA, Rückert C, Nübel U, Blom J, Wirth T, Jaenicke S, Schuback S, Rüsch-Gerdes S, Supply P, Kalinowski J, Niemann S., PLoS Med 10(2), 2013
PMID: 23424287
Community-wide plasmid gene mobilization and selection.
Sentchilo V, Mayer AP, Guy L, Miyazaki R, Green Tringe S, Barry K, Malfatti S, Goessmann A, Robinson-Rechavi M, van der Meer JR., ISME J 7(6), 2013
PMID: 23407308
Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.
Riedel T, Gómez-Consarnau L, Tomasch J, Martin M, Jarek M, González JM, Spring S, Rohlfs M, Brinkhoff T, Cypionka H, Göker M, Fiebig A, Klein J, Goesmann A, Fuhrman JA, Wagner-Döbler I., PLoS One 8(3), 2013
PMID: 23526944
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021.
Schlüter JP, Reinkensmeier J, Barnett MJ, Lang C, Krol E, Giegerich R, Long SR, Becker A., BMC Genomics 14(), 2013
PMID: 23497287
Predominant archaea in marine sediments degrade detrital proteins.
Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD, Stepanauskas R, Richter M, Kleindienst S, Lenk S, Schramm A, Jørgensen BB., Nature 496(7444), 2013
PMID: 23535597
The noncanonical type III secretion system of Xanthomonas translucens pv. graminis is essential for forage grass infection.
Wichmann F, Vorhölter FJ, Hersemann L, Widmer F, Blom J, Niehaus K, Reinhard S, Conradin C, Kölliker R., Mol Plant Pathol 14(6), 2013
PMID: 23578314
The genus Pseudovibrio contains metabolically versatile bacteria adapted for symbiosis.
Bondarev V, Richter M, Romano S, Piel J, Schwedt A, Schulz-Vogt HN., Environ Microbiol 15(7), 2013
PMID: 23601235
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
Comparative Genomics Reveal That Host-Innate Immune Responses Influence the Clinical Prevalence of Legionella pneumophila Serogroups.
Khan MA, Knox N, Prashar A, Alexander D, Abdel-Nour M, Duncan C, Tang P, Amatullah H, Dos Santos CC, Tijet N, Low DE, Pourcel C, Van Domselaar G, Terebiznik M, Ensminger AW, Guyard C., PLoS One 8(6), 2013
PMID: 23826259
Molecular characterization of a fungicidal endoglucanase from the cyanobacterium Calothrix elenkinii.
Natarajan C, Gupta V, Kumar K, Prasanna R., Biochem Genet 51(9-10), 2013
PMID: 23839085
Metabolic engineering of Bacillus subtilis for growth on overflow metabolites.
Kabisch J, Pratzka I, Meyer H, Albrecht D, Lalk M, Ehrenreich A, Schweder T., Microb Cell Fact 12(), 2013
PMID: 23886069
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
The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides.
Mann AJ, Hahnke RL, Huang S, Werner J, Xing P, Barbeyron T, Huettel B, Stüber K, Reinhardt R, Harder J, Glöckner FO, Amann RI, Teeling H., Appl Environ Microbiol 79(21), 2013
PMID: 23995932
Complete genome sequence of the hydrogenotrophic Archaeon Methanobacterium sp. Mb1 isolated from a production-scale biogas plant.
Maus I, Wibberg D, Stantscheff R, Cibis K, Eikmeyer FG, König H, Pühler A, Schlüter A., J Biotechnol 168(4), 2013
PMID: 24184088
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
Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique.
Pfeifer-Sancar K, Mentz A, Rückert C, Kalinowski J., BMC Genomics 14(), 2013
PMID: 24341750
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
Genomic content of uncultured Bacteroidetes from contrasting oceanic provinces in the North Atlantic Ocean.
Gómez-Pereira PR, Schüler M, Fuchs BM, Bennke C, Teeling H, Waldmann J, Richter M, Barbe V, Bataille E, Glöckner FO, Amann R., Environ Microbiol 14(1), 2012
PMID: 21895912
Unveiling microbial life in the new deep-sea hypersaline Lake Thetis. Part II: a metagenomic study.
Ferrer M, Werner J, Chernikova TN, Bargiela R, Fernández L, La Cono V, Waldmann J, Teeling H, Golyshina OV, Glöckner FO, Yakimov MM, Golyshin PN, MAMBA Scientific Consortium., Environ Microbiol 14(1), 2012
PMID: 22040283
Arabitol metabolism of Corynebacterium glutamicum and its regulation by AtlR.
Laslo T, von Zaluskowski P, Gabris C, Lodd E, Rückert C, Dangel P, Kalinowski J, Auchter M, Seibold G, Eikmanns BJ., J Bacteriol 194(5), 2012
PMID: 22178972
Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones.
Grote J, Schott T, Bruckner CG, Glöckner FO, Jost G, Teeling H, Labrenz M, Jürgens K., Proc Natl Acad Sci U S A 109(2), 2012
PMID: 22203982
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
Genome sequence of Stenotrophomonas maltophilia RR-10, isolated as an endophyte from rice root.
Zhu B, Liu H, Tian WX, Fan XY, Li B, Zhou XP, Jin GL, Xie GL., J Bacteriol 194(5), 2012
PMID: 22328769
Complete genome sequence of clinical isolate Pantoea ananatis LMG 5342.
De Maayer P, Chan WY, Rezzonico F, Bühlmann A, Venter SN, Blom J, Goesmann A, Frey JE, Smits TH, Duffy B, Coutinho TA., J Bacteriol 194(6), 2012
PMID: 22374951
Genome sequence of the soybean symbiont Sinorhizobium fredii HH103.
Weidner S, Becker A, Bonilla I, Jaenicke S, Lloret J, Margaret I, Pühler A, Ruiz-Sainz JE, Schneiker-Bekel S, Szczepanowski R, Vinardell JM, Zehner S, Göttfert M., J Bacteriol 194(6), 2012
PMID: 22374952
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110.
Schwientek P, Szczepanowski R, Rückert C, Kalinowski J, Klein A, Selber K, Wehmeier UF, Stoye J, Pühler A., BMC Genomics 13(), 2012
PMID: 22443545
Identification and characterization of microcin S, a new antibacterial peptide produced by probiotic Escherichia coli G3/10.
Zschüttig A, Zimmermann K, Blom J, Goesmann A, Pöhlmann C, Gunzer F., PLoS One 7(3), 2012
PMID: 22479389
Characterization of the biosynthetic operon for the antibacterial peptide herbicolin in Pantoea vagans biocontrol strain C9-1 and incidence in Pantoea species.
Kamber T, Lansdell TA, Stockwell VO, Ishimaru CA, Smits TH, Duffy B., Appl Environ Microbiol 78(12), 2012
PMID: 22504810
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
Substrate-controlled succession of marine bacterioplankton populations induced by a phytoplankton bloom.
Teeling H, Fuchs BM, Becher D, Klockow C, Gardebrecht A, Bennke CM, Kassabgy M, Huang S, Mann AJ, Waldmann J, Weber M, Klindworth A, Otto A, Lange J, Bernhardt J, Reinsch C, Hecker M, Peplies J, Bockelmann FD, Callies U, Gerdts G, Wichels A, Wiltshire KH, Glöckner FO, Schweder T, Amann R., Science 336(6081), 2012
PMID: 22556258
Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.
Kahlke T, Goesmann A, Hjerde E, Willassen NP, Haugen P., BMC Genomics 13(), 2012
PMID: 22574681
IncP-1β plasmids of Comamonas sp. and Delftia sp. strains isolated from a wastewater treatment plant mediate resistance to and decolorization of the triphenylmethane dye crystal violet.
Stolze Y, Eikmeyer F, Wibberg D, Brandis G, Karsten C, Krahn I, Schneiker-Bekel S, Viehöver P, Barsch A, Keck M, Top EM, Niehaus K, Schlüter A., Microbiology 158(pt 8), 2012
PMID: 22653947
Phenylacetic acid catabolism and its transcriptional regulation in Corynebacterium glutamicum.
Chen X, Kohl TA, Rückert C, Rodionov DA, Li LH, Ding JY, Kalinowski J, Liu SJ., Appl Environ Microbiol 78(16), 2012
PMID: 22685150
Genome sequence of Fibrella aestuarina BUZ 2(T), a filamentous marine bacterium.
Filippini M, Qi W, Blom J, Goesmann A, Smits TH, Bagheri HC., J Bacteriol 194(13), 2012
PMID: 22689241
Biochemical and structural characterization of the complex agarolytic enzyme system from the marine bacterium Zobellia galactanivorans.
Hehemann JH, Correc G, Thomas F, Bernard T, Barbeyron T, Jam M, Helbert W, Michel G, Czjzek M., J Biol Chem 287(36), 2012
PMID: 22778272
Genome sequence of the filamentous bacterium Fibrisoma limi BUZ 3T.
Filippini M, Qi W, Jaenicke S, Goesmann A, Smits TH, Bagheri HC., J Bacteriol 194(16), 2012
PMID: 22843583
Genome sequence of a Neisseria meningitidis capsule null locus strain from the clonal complex of sequence type 198.
Schork S, Schlüter A, Blom J, Schneiker-Bekel S, Pühler A, Goesmann A, Frosch M, Schoen C., J Bacteriol 194(18), 2012
PMID: 22933768
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
Complete genome sequence of the hydrogenotrophic, methanogenic archaeon Methanoculleus bourgensis strain MS2(T), Isolated from a sewage sludge digester.
Maus I, Wibberg D, Stantscheff R, Eikmeyer FG, Seffner A, Boelter J, Szczepanowski R, Blom J, Jaenicke S, König H, Pühler A, Schlüter A., J Bacteriol 194(19), 2012
PMID: 22965103
Complete genome sequence of the porcine isolate Enterococcus faecalis D32.
Zischka M, Kuenne C, Blom J, Dabrowski PW, Linke B, Hain T, Nitsche A, Goesmann A, Larsen J, Jensen LB, Witte W, Werner G., J Bacteriol 194(19), 2012
PMID: 22965105
Fighting outbreaks with bacterial genomics: case review and workflow proposal.
Cheung MK, Kwan HS., Public Health Genomics 15(6), 2012
PMID: 23037860
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
The large universal Pantoea plasmid LPP-1 plays a major role in biological and ecological diversification.
De Maayer P, Chan WY, Blom J, Venter SN, Duffy B, Smits TH, Coutinho TA., BMC Genomics 13(), 2012
PMID: 23151240
whole-genome sequence of livestock-associated st398 methicillin-resistant staphylococcus aureus Isolated from Humans in Canada.
Golding GR, Bryden L, Levett PN, McDonald RR, Wong A, Graham MR, Tyler S, Van Domselaar G, Mabon P, Kent H, Butaye P, Smith TC, Kadlec K, Schwarz S, Weese SJ, Mulvey MR., J Bacteriol 194(23), 2012
PMID: 23144384
Genome sequence of the biocontrol agent Microbacterium barkeri strain 2011-R4.
Liu J, Zhou Q, Ibrahim M, Liu H, Jin G, Zhu B, Xie G., J Bacteriol 194(23), 2012
PMID: 23144410
Genome sequence of Clostridium tunisiense TJ, isolated from drain sediment from a pesticide factory.
Sun L, Wang Y, Yu C, Zhao Y, Gan Y., J Bacteriol 194(24), 2012
PMID: 23209212
Genome sequence of the human-pathogenic bacterium Vibrio vulnificus type strain ATCC 27562.
Li Z, Chen H, Chen X, Zhou T, Zhao L, Zhang C, Jin W., J Bacteriol 194(24), 2012
PMID: 23209214
Genome sequence of the pathogenic Herbaspirillum seropedicae strain Os34, isolated from rice roots.
Ye W, Ye S, Liu J, Chang S, Chen M, Zhu B, Guo L, An Q., J Bacteriol 194(24), 2012
PMID: 23209241
Genome sequence of the pathogenic Herbaspirillum seropedicae strain Os45, isolated from rice roots.
Zhu B, Ye S, Chang S, Chen M, Sun L, An Q., J Bacteriol 194(24), 2012
PMID: 23209242
Genome sequence of the human-pathogenetic bacterium Vibrio vulnificus B2.
Wang ZG, Wu Z, Xu SL, Zha J., J Bacteriol 194(24), 2012
PMID: 23209257
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
Gene sets for utilization of primary and secondary nutrition supplies in the distal gut of endangered Iberian lynx.
Alcaide M, Messina E, Richter M, Bargiela R, Peplies J, Huws SA, Newbold CJ, Golyshin PN, Simón MA, López G, Yakimov MM, Ferrer M., PLoS One 7(12), 2012
PMID: 23251564
Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges.
Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U., ISME J 5(1), 2011
PMID: 20613790
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
PMID: 20817842
A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T.
Schwibbert K, Marin-Sanguino A, Bagyan I, Heidrich G, Lentzen G, Seitz H, Rampp M, Schuster SC, Klenk HP, Pfeiffer F, Oesterhelt D, Kunte HJ., Environ Microbiol 13(8), 2011
PMID: 20849449
Genome sequence of Oceanicaulis sp. strain HTCC2633, isolated from the Western Sargasso Sea.
Oh HM, Kang I, Vergin KL, Lee K, Giovannoni SJ, Cho JC., J Bacteriol 193(1), 2011
PMID: 21036991
Genome sequence of strain HTCC2083, a novel member of the marine clade Roseobacter.
Kang I, Vergin KL, Oh HM, Choi A, Giovannoni SJ, Cho JC., J Bacteriol 193(1), 2011
PMID: 21036993
Complete genome sequence of strain HTCC2170, a novel member of the genus Maribacter in the family Flavobacteriaceae.
Oh HM, Kang I, Yang SJ, Jang Y, Vergin KL, Giovannoni SJ, Cho JC., J Bacteriol 193(1), 2011
PMID: 21037013
Genome sequence of the Marine Janibacter Sp. Strain HTCC2649.
Thrash JC, Cho JC, Bertagnolli AD, Ferriera S, Johnson J, Vergin KL, Giovannoni SJ., J Bacteriol 193(2), 2011
PMID: 21075932
Genome sequence of an Erwinia amylovora strain with pathogenicity restricted to Rubus plants.
Powney R, Smits TH, Sawbridge T, Frey B, Blom J, Frey JE, Plummer KM, Beer SV, Luck J, Duffy B, Rodoni B., J Bacteriol 193(3), 2011
PMID: 21131493
The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages.
Mraheil MA, Billion A, Mohamed W, Mukherjee K, Kuenne C, Pischimarov J, Krawitz C, Retey J, Hartsch T, Chakraborty T, Hain T., Nucleic Acids Res 39(10), 2011
PMID: 21278422
Genome of a European fresh-vegetable food safety outbreak strain of Salmonella enterica subsp. enterica serovar weltevreden.
Brankatschk K, Blom J, Goesmann A, Smits TH, Duffy B., J Bacteriol 193(8), 2011
PMID: 21296964
Whole-genome sequence of the transformable Neisseria meningitidis serogroup A strain WUE2594.
Schoen C, Weber-Lehmann J, Blom J, Joseph B, Goesmann A, Strittmatter A, Frosch M., J Bacteriol 193(8), 2011
PMID: 21296965
Lausannevirus, a giant amoebal virus encoding histone doublets.
Thomas V, Bertelli C, Collyn F, Casson N, Telenti A, Goesmann A, Croxatto A, Greub G., Environ Microbiol 13(6), 2011
PMID: 21392201
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
Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome.
Joseph B, Schwarz RF, Linke B, Blom J, Becker A, Claus H, Goesmann A, Frosch M, Müller T, Vogel U, Schoen C., PLoS One 6(4), 2011
PMID: 21541312
Genome sequence of the Enterobacter mori type strain, LMG 25706, a pathogenic bacterium of Morus alba L.
Zhu B, Zhang GQ, Lou MM, Tian WX, Li B, Zhou XP, Wang GF, Liu H, Xie GL, Jin GL., J Bacteriol 193(14), 2011
PMID: 21602328
Genome-wide analysis of mobile genetic element insertion sites.
Rawal K, Ramaswamy R., Nucleic Acids Res 39(16), 2011
PMID: 21609951
The complete genome sequence of Clostridium botulinum F str. 230613, insertion sites, and recombination of BoNT gene clusters.
Tian RM, Li T, Hou XJ, Wang Q, Cai K, Liu YN, Gao X, Liu H, Xiao L, Tu W, Shi J, Cao WC, Wang H., Genome 54(7), 2011
PMID: 21696262
Taxonomic and functional metagenomic profiling of the microbial community in the anoxic sediment of a sub-saline shallow lake (Laguna de Carrizo, Central Spain).
Ferrer M, Guazzaroni ME, Richter M, García-Salamanca A, Yarza P, Suárez-Suárez A, Solano J, Alcaide M, van Dillewijn P, Molina-Henares MA, López-Cortés N, Al-Ramahi Y, Guerrero C, Acosta A, de Eugenio LI, Martínez V, Marques S, Rojo F, Santero E, Genilloud O, Pérez-Pérez J, Rosselló-Móra R, Ramos JL., Microb Ecol 62(4), 2011
PMID: 21735153
Genome sequence of the nonpathogenic Listeria monocytogenes serovar 4a strain M7.
Chen J, Xia Y, Cheng C, Fang C, Shan Y, Jin G, Fang W., J Bacteriol 193(18), 2011
PMID: 21742872
Genome sequence of the rice-pathogenic bacterium Acidovorax avenae subsp. avenae RS-1.
Xie GL, Zhang GQ, Liu H, Lou MM, Tian WX, Li B, Zhou XP, Zhu B, Jin GL., J Bacteriol 193(18), 2011
PMID: 21742879
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
Simple high-throughput annotation pipeline (SHAP).
DeMaere MZ, Lauro FM, Thomas T, Yau S, Cavicchioli R., Bioinformatics 27(17), 2011
PMID: 21775307
The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis.
Pothier JF, Vorhölter FJ, Blom J, Goesmann A, Pühler A, Smits TH, Duffy B., FEMS Microbiol Lett 323(1), 2011
PMID: 21732961
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
The discovery of novel protein-coding features in mouse genome based on mass spectrometry data.
Xing XB, Li QR, Sun H, Fu X, Zhan F, Huang X, Li J, Chen CL, Shyr Y, Zeng R, Li YX, Xie L., Genomics 98(5), 2011
PMID: 21840390
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
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium.
Ansong C, Tolić N, Purvine SO, Porwollik S, Jones M, Yoon H, Payne SH, Martin JL, Burnet MC, Monroe ME, Venepally P, Smith RD, Peterson SN, Heffron F, McClelland M, Adkins JN., BMC Genomics 12(), 2011
PMID: 21867535
Draft genome sequence of Caminibacter mediatlanticus strain TB-2, an epsilonproteobacterium isolated from a deep-sea hydrothermal vent.
Giovannelli D, Ferriera S, Johnson J, Kravitz S, Pérez-Rodríguez I, Ricci J, O'Brien C, Voordeckers JW, Bini E, Vetriani C., Stand Genomic Sci 5(1), 2011
PMID: 22180817
Antibiosis activity of Pantoea agglomerans biocontrol strain E325 against Erwinia amylovora on apple flower stigmas.
Pusey PL, Stockwell VO, Reardon CL, Smits TH, Duffy B., Phytopathology 101(10), 2011
PMID: 21679036
The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota.
Siebers B, Zaparty M, Raddatz G, Tjaden B, Albers SV, Bell SD, Blombach F, Kletzin A, Kyrpides N, Lanz C, Plagens A, Rampp M, Rosinus A, von Jan M, Makarova KS, Klenk HP, Schuster SC, Hensel R., PLoS One 6(10), 2011
PMID: 22003381
Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134.
González JM, Pinhassi J, Fernández-Gómez B, Coll-Lladó M, González-Velázquez M, Puigbò P, Jaenicke S, Gómez-Consarnau L, Fernàndez-Guerra A, Goesmann A, Pedrós-Alió C., Appl Environ Microbiol 77(24), 2011
PMID: 22003006
Comparative genomics of Vibrio cholerae from Haiti, Asia, and Africa.
Reimer AR, Van Domselaar G, Stroika S, Walker M, Kent H, Tarr C, Talkington D, Rowe L, Olsen-Rasmussen M, Frace M, Sammons S, Dahourou GA, Boncy J, Smith AM, Mabon P, Petkau A, Graham M, Gilmour MW, Gerner-Smidt P, V. cholerae Outbreak Genomics Task Force., Emerg Infect Dis 17(11), 2011
PMID: 22099115
Conservation and Occurrence of Trans-Encoded sRNAs in the Rhizobiales.
Reinkensmeier J, Schlüter JP, Giegerich R, Becker A., Genes (Basel) 2(4), 2011
PMID: 24710299
SalmonDB: a bioinformatics resource for Salmo salar and Oncorhynchus mykiss.
Di Génova A, Aravena A, Zapata L, González M, Maass A, Iturra P., Database (Oxford) 2011(), 2011
PMID: 22120661
Erwinia amylovora novel plasmid pEI70: complete sequence, biogeography, and role in aggressiveness in the fire blight phytopathogen.
Llop P, Cabrefiga J, Smits TH, Dreo T, Barbé S, Pulawska J, Bultreys A, Blom J, Duffy B, Montesinos E, López MM., PLoS One 6(12), 2011
PMID: 22174857
Megx.net: integrated database resource for marine ecological genomics.
Kottmann R, Kostadinov I, Duhaime MB, Buttigieg PL, Yilmaz P, Hankeln W, Waldmann J, Glöckner FO., Nucleic Acids Res 38(database issue), 2010
PMID: 19858098
Metagenome and mRNA expression analyses of anaerobic methanotrophic archaea of the ANME-1 group.
Meyerdierks A, Kube M, Kostadinov I, Teeling H, Glöckner FO, Reinhardt R, Amann R., Environ Microbiol 12(2), 2010
PMID: 19878267
Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity.
Smits TH, Jaenicke S, Rezzonico F, Kamber T, Goesmann A, Frey JE, Duffy B., BMC Genomics 11(), 2010
PMID: 20047678
Simple sequence repeats in Helicobacter canadensis and their role in phase variable expression and C-terminal sequence switching.
Snyder LA, Loman NJ, Linton JD, Langdon RR, Weinstock GM, Wren BW, Pallen MJ., BMC Genomics 11(), 2010
PMID: 20105305
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
High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak.
Gilmour MW, Graham M, Van Domselaar G, Tyler S, Kent H, Trout-Yakel KM, Larios O, Allen V, Lee B, Nadon C., BMC Genomics 11(), 2010
PMID: 20167121
An Ergatis-based prokaryotic genome annotation web server.
Hemmerich C, Buechlein A, Podicheti R, Revanna KV, Dong Q., Bioinformatics 26(8), 2010
PMID: 20194626
Identification, characterization, and regulation of a novel antifungal chitosanase gene (cho) in Anabaena spp.
Gupta V, Prasanna R, Natarajan C, Srivastava AK, Sharma J., Appl Environ Microbiol 76(9), 2010
PMID: 20228117
Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina.
Gallo G, Renzone G, Alduina R, Stegmann E, Weber T, Lantz AE, Thykaer J, Sangiorgi F, Scaloni A, Puglia AM., Proteomics 10(7), 2010
PMID: 20049855
Livestock-associated methicillin-resistant Staphylococcus aureus sequence type 398 in humans, Canada.
Golding GR, Bryden L, Levett PN, McDonald RR, Wong A, Wylie J, Graham MR, Tyler S, Van Domselaar G, Simor AE, Gravel D, Mulvey MR., Emerg Infect Dis 16(4), 2010
PMID: 20350371
Genome sequence of Lentisphaera araneosa HTCC2155T, the type species of the order Lentisphaerales in the phylum Lentisphaerae.
Thrash JC, Cho JC, Vergin KL, Morris RM, Giovannoni SJ., J Bacteriol 192(11), 2010
PMID: 20363947
Genomic and phenotypic characterization of a nonpigmented variant of Pantoea vagans biocontrol strain C9-1 lacking the 530-kb megaplasmid pPag3.
Smits TH, Rezzonico F, Pelludat C, Goesmann A, Frey JE, Duffy B., FEMS Microbiol Lett 308(1), 2010
PMID: 20487014
Genome sequence of the novel marine member of the Gammaproteobacteria strain HTCC5015.
Thrash JC, Stingl U, Cho JC, Ferriera S, Johnson J, Vergin KL, Giovannoni SJ., J Bacteriol 192(14), 2010
PMID: 20472792
Genome sequences of strains HTCC2148 and HTCC2080, belonging to the OM60/NOR5 clade of the Gammaproteobacteria.
Thrash JC, Cho JC, Ferriera S, Johnson J, Vergin KL, Giovannoni SJ., J Bacteriol 192(14), 2010
PMID: 20472793
SOBA: sequence ontology bioinformatics analysis.
Moore B, Fan G, Eilbeck K., Nucleic Acids Res 38(web server issue), 2010
PMID: 20494974
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
PMID: 20507619
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
PMID: 20531937
Life cycle analysis of the model organism Rhodopirellula baltica SH 1(T) by transcriptome studies.
Wecker P, Klockow C, Schüler M, Dabin J, Michel G, Glöckner FO., Microb Biotechnol 3(5), 2010
PMID: 21255355
Genome (re-)annotation and open-source annotation pipelines.
Siezen RJ, van Hijum SA., Microb Biotechnol 3(4), 2010
PMID: 21255336
Genome sequence of the oligotrophic marine Gammaproteobacterium HTCC2143, isolated from the Oregon Coast.
Oh HM, Kang I, Ferriera S, Giovannoni SJ, Cho JC., J Bacteriol 192(17), 2010
PMID: 20601481
Complete genome sequence of Croceibacter atlanticus HTCC2559T.
Oh HM, Kang I, Ferriera S, Giovannoni SJ, Cho JC., J Bacteriol 192(18), 2010
PMID: 20639333
Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence.
Joseph B, Schneiker-Bekel S, Schramm-Glück A, Blom J, Claus H, Linke B, Schwarz RF, Becker A, Goesmann A, Frosch M, Schoen C., J Bacteriol 192(20), 2010
PMID: 20709895
Genome sequences of Pelagibaca bermudensis HTCC2601T and Maritimibacter alkaliphilus HTCC2654T, the type strains of two marine Roseobacter genera.
Thrash JC, Cho JC, Ferriera S, Johnson J, Vergin KL, Giovannoni SJ., J Bacteriol 192(20), 2010
PMID: 20729358
Comparative analysis of plasmids in the genus Listeria.
Kuenne C, Voget S, Pischimarov J, Oehm S, Goesmann A, Daniel R, Hain T, Chakraborty T., PLoS One 5(9), 2010
PMID: 20824078
Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism.
Gärdes A, Kaeppel E, Shehzad A, Seebah S, Teeling H, Yarza P, Glöckner FO, Grossart HP, Ullrich MS., Stand Genomic Sci 3(2), 2010
PMID: 21304739
Genome sequence of the marine alphaproteobacterium HTCC2150, assigned to the Roseobacter clade.
Kang I, Oh HM, Vergin KL, Giovannoni SJ, Cho JC., J Bacteriol 192(23), 2010
PMID: 20889754
Genome sequence of the biocontrol agent Pantoea vagans strain C9-1.
Smits TH, Rezzonico F, Kamber T, Goesmann A, Ishimaru CA, Stockwell VO, Frey JE, Duffy B., J Bacteriol 192(24), 2010
PMID: 20952567
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
PMID: 21192786
Genomic islands of Pseudomonas aeruginosa.
Battle SE, Rello J, Hauser AR., FEMS Microbiol Lett 290(1), 2009
PMID: 19025565
Genome analysis of the meat starter culture bacterium Staphylococcus carnosus TM300.
Rosenstein R, Nerz C, Biswas L, Resch A, Raddatz G, Schuster SC, Götz F., Appl Environ Microbiol 75(3), 2009
PMID: 19060169
A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data.
Becker A, Barnett MJ, Capela D, Dondrup M, Kamp PB, Krol E, Linke B, Rüberg S, Runte K, Schroeder BK, Weidner S, Yurgel SN, Batut J, Long SR, Pühler A, Goesmann A., J Biotechnol 140(1-2), 2009
PMID: 19103235
WeGAS: a web-based microbial genome annotation system.
Lee D, Seo H, Park C, Park K., Biosci Biotechnol Biochem 73(1), 2009
PMID: 19129632
Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.
Strittmatter AW, Liesegang H, Rabus R, Decker I, Amann J, Andres S, Henne A, Fricke WF, Martinez-Arias R, Bartels D, Goesmann A, Krause L, Pühler A, Klenk HP, Richter M, Schüler M, Glöckner FO, Meyerdierks A, Gottschalk G, Amann R., Environ Microbiol 11(5), 2009
PMID: 19187283
Complete genome sequence of Erythrobacter litoralis HTCC2594.
Oh HM, Giovannoni SJ, Ferriera S, Johnson J, Cho JC., J Bacteriol 191(7), 2009
PMID: 19168610
The Genome Reverse Compiler: an explorative annotation tool.
Warren AS, Setubal JC., BMC Bioinformatics 10(), 2009
PMID: 19173744
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Jünemann S, Kahlke T, Kleindt CK, Küster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Pühler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
Comparative analysis of magnetosome gene clusters in magnetotactic bacteria provides further evidence for horizontal gene transfer.
Jogler C, Kube M, Schübbe S, Ullrich S, Teeling H, Bazylinski DA, Reinhardt R, Schüler D., Environ Microbiol 11(5), 2009
PMID: 19220405
The Sequence Analysis and Management System -- SAMS-2.0: data management and sequence analysis adapted to changing requirements from traditional sanger sequencing to ultrafast sequencing technologies.
Bekel T, Henckel K, Küster H, Meyer F, Mittard Runte V, Neuweger H, Paarmann D, Rupp O, Zakrzewski M, Pühler A, Stoye J, Goesmann A., J Biotechnol 140(1-2), 2009
PMID: 19297685
The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.
Woo PC, Lau SK, Tse H, Teng JL, Curreem SO, Tsang AK, Fan RY, Wong GK, Huang Y, Loman NJ, Snyder LA, Cai JJ, Huang JD, Mak W, Pallen MJ, Lok S, Yuen KY., PLoS Genet 5(3), 2009
PMID: 19283063
EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter FJ, Zakrzewski M, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19457249
Genome sequence of the emerging pathogen Helicobacter canadensis.
Loman NJ, Snyder LA, Linton JD, Langdon R, Lawson AJ, Weinstock GM, Wren BW, Pallen MJ., J Bacteriol 191(17), 2009
PMID: 19542273
Construction of an adult barnacle (Balanus amphitrite) cDNA library and selection of reference genes for quantitative RT-PCR studies.
Bacchetti De Gregoris T, Borra M, Biffali E, Bekel T, Burgess JG, Kirby RR, Clare AS., BMC Mol Biol 10(), 2009
PMID: 19552808
Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii.
Berglund EC, Frank AC, Calteau A, Vinnere Pettersson O, Granberg F, Eriksson AS, Näslund K, Holmberg M, Lindroos H, Andersson SG., PLoS Genet 5(7), 2009
PMID: 19578403
Transcriptional response of the model planctomycete Rhodopirellula baltica SH1(T) to changing environmental conditions.
Wecker P, Klockow C, Ellrott A, Quast C, Langhammer P, Harder J, Glöckner FO., BMC Genomics 10(), 2009
PMID: 19725962
Context-driven discovery of gene cassettes in mobile integrons using a computational grammar.
Tsafnat G, Coiera E, Partridge SR, Schaeffer J, Iredell JR., BMC Bioinformatics 10(), 2009
PMID: 19735578
Complete genome sequence of Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry.
Wegmann U, Overweg K, Horn N, Goesmann A, Narbad A, Gasson MJ, Shearman C., J Bacteriol 191(22), 2009
PMID: 19767436
Complete genome sequence of Robiginitalea biformata HTCC2501.
Oh HM, Giovannoni SJ, Lee K, Ferriera S, Johnson J, Cho JC., J Bacteriol 191(22), 2009
PMID: 19767438
Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.
Albaum SP, Neuweger H, Fränzel B, Lange S, Mertens D, Trötschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A., Bioinformatics 25(23), 2009
PMID: 19808875
Plastid genomes of two brown algae, Ectocarpus siliculosus and Fucus vesiculosus: further insights on the evolution of red-algal derived plastids.
Le Corguillé G, Pearson G, Valente M, Viegas C, Gschloessl B, Corre E, Bailly X, Peters AF, Jubin C, Vacherie B, Cock JM, Leblanc C., BMC Evol Biol 9(), 2009
PMID: 19835607
MicroScope: a platform for microbial genome annotation and comparative genomics.
Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, Lajus A, Rouy Z, Roche D, Salvignol G, Scarpelli C, Médigue C., Database (Oxford) 2009(), 2009
PMID: 20157493
Genome of the epsilonproteobacterial chemolithoautotroph Sulfurimonas denitrificans.
Sievert SM, Scott KM, Klotz MG, Chain PS, Hauser LJ, Hemp J, Hügler M, Land M, Lapidus A, Larimer FW, Lucas S, Malfatti SA, Meyer F, Paulsen IT, Ren Q, Simon J, USF Genomics Class., Appl Environ Microbiol 74(4), 2008
PMID: 18065616
The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity.
Gartemann KH, Abt B, Bekel T, Burger A, Engemann J, Flügel M, Gaigalat L, Goesmann A, Gräfen I, Kalinowski J, Kaup O, Kirchner O, Krause L, Linke B, McHardy A, Meyer F, Pohle S, Rückert C, Schneiker S, Zellermann EM, Pühler A, Eichenlaub R, Kaiser O, Bartels D., J Bacteriol 190(6), 2008
PMID: 18192381
LeARN: a platform for detecting, clustering and annotating non-coding RNAs.
Noirot C, Gaspin C, Schiex T, Gouzy J., BMC Bioinformatics 9(), 2008
PMID: 18194551
The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
Vorhölter FJ, Schneiker S, Goesmann A, Krause L, Bekel T, Kaiser O, Linke B, Patschkowski T, Rückert C, Schmid J, Sidhu VK, Sieber V, Tauch A, Watt SA, Weisshaar B, Becker A, Niehaus K, Pühler A., J Biotechnol 134(1-2), 2008
PMID: 18304669
The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation.
Yu C, Zavaljevski N, Desai V, Johnson S, Stevens FJ, Reifman J., BMC Bioinformatics 9(), 2008
PMID: 18221520
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 9(), 2008
PMID: 18261238
Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis.
Schoen C, Blom J, Claus H, Schramm-Glück A, Brandt P, Müller T, Goesmann A, Joseph B, Konietzny S, Kurzai O, Schmitt C, Friedrich T, Linke B, Vogel U, Frosch M., Proc Natl Acad Sci U S A 105(9), 2008
PMID: 18305155
The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing.
Tauch A, Trost E, Tilker A, Ludewig U, Schneiker S, Goesmann A, Arnold W, Bekel T, Brinkrolf K, Brune I, Götker S, Kalinowski J, Kamp PB, Lobo FP, Viehoever P, Weisshaar B, Soriano F, Dröge M, Pühler A., J Biotechnol 136(1-2), 2008
PMID: 18367281
Comparative genomics of the pIPO2/pSB102 family of environmental plasmids: sequence, evolution, and ecology of pTer331 isolated from Collimonas fungivorans Ter331.
Mela F, Fritsche K, Boersma H, van Elsas JD, Bartels D, Meyer F, de Boer W, van Veen JA, Leveau JH., FEMS Microbiol Ecol 66(1), 2008
PMID: 18355297
Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids.
Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehoever P, Gartemann KH, Arnold W, Blom J, Brinkrolf K, Brune I, Götker S, Weisshaar B, Goesmann A, Dröge M, Pühler A., J Biotechnol 136(1-2), 2008
PMID: 18430482
JCoast - a biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes.
Richter M, Lombardot T, Kostadinov I, Kottmann R, Duhaime MB, Peplies J, Glöckner FO., BMC Bioinformatics 9(), 2008
PMID: 18380896
Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11.
Stiens M, Becker A, Bekel T, Gödde V, Goesmann A, Niehaus K, Schneiker-Bekel S, Selbitschka W, Weidner S, Schlüter A, Pühler A., J Biotechnol 136(1-2), 2008
PMID: 18562031
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
Schlüter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Krömeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Pühler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehöver P, Goesmann A., J Biotechnol 136(1-2), 2008
PMID: 18597880
Genome analysis of the proteorhodopsin-containing marine bacterium Polaribacter sp. MED152 (Flavobacteria).
González JM, Fernández-Gómez B, Fernàndez-Guerra A, Gómez-Consarnau L, Sánchez O, Coll-Lladó M, Del Campo J, Escudero L, Rodríguez-Martínez R, Alonso-Sáez L, Latasa M, Paulsen I, Nedashkovskaya O, Lekunberri I, Pinhassi J, Pedrós-Alió C., Proc Natl Acad Sci U S A 105(25), 2008
PMID: 18552178
Genome information management and integrated data analysis with HaloLex.
Pfeiffer F, Broicher A, Gillich T, Klee K, Mejía J, Rampp M, Oesterhelt D., Arch Microbiol 190(3), 2008
PMID: 18592220
Identification and characterization of genes underlying chitinolysis in Collimonas fungivorans Ter331.
Fritsche K, de Boer W, Gerards S, van den Berg M, van Veen JA, Leveau JH., FEMS Microbiol Ecol 66(1), 2008
PMID: 18671744
MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
PMID: 18765459
Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7.
Strauch E, Hammerl JA, Konietzny A, Schneiker-Bekel S, Arnold W, Goesmann A, Pühler A, Beutin L., Infect Immun 76(12), 2008
PMID: 18824528
The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae.
Gross R, Guzman CA, Sebaihia M, dos Santos VA, Pieper DH, Koebnik R, Lechner M, Bartels D, Buhrmester J, Choudhuri JV, Ebensen T, Gaigalat L, Herrmann S, Khachane AN, Larisch C, Link S, Linke B, Meyer F, Mormann S, Nakunst D, Rückert C, Schneiker-Bekel S, Schulze K, Vorhölter FJ, Yevsa T, Engle JT, Goldman WE, Pühler A, Göbel UB, Goesmann A, Blöcker H, Kaiser O, Martinez-Arias R., BMC Genomics 9(), 2008
PMID: 18826580
An introduction to metabolic networks and their structural analysis.
Lacroix V, Cottret L, Thébault P, Sagot MF., IEEE/ACM Trans Comput Biol Bioinform 5(4), 2008
PMID: 18989046
Peak intensity prediction in MALDI-TOF mass spectrometry: a machine learning study to support quantitative proteomics.
Timm W, Scherbart A, Böcker S, Kohlbacher O, Nattkemper TW., BMC Bioinformatics 9(), 2008
PMID: 18937839
EnGenIUS -- Environmental Genome Informational Utility System.
Kaplarevic M, Murray AE, Cary SC, Gao GR., J Bioinform Comput Biol 6(6), 2008
PMID: 19090024
Genome and proteome characterization of the psychrophilic Flavobacterium bacteriophage 11b.
Borriss M, Lombardot T, Glöckner FO, Becher D, Albrecht D, Schweder T., Extremophiles 11(1), 2007
PMID: 16932843
Novel macrolide resistance module carried by the IncP-1beta resistance plasmid pRSB111, isolated from a wastewater treatment plant.
Szczepanowski R, Krahn I, Bohn N, Pühler A, Schlüter A., Antimicrob Agents Chemother 51(2), 2007
PMID: 17101677
Discovering drug targets through the web.
Wishart DS., Comp Biochem Physiol Part D Genomics Proteomics 2(1), 2007
PMID: 20483274
Restauro-G: a rapid genome re-annotation system for comparative genomics.
Tamaki S, Arakawa K, Kono N, Tomita M., Genomics Proteomics Bioinformatics 5(1), 2007
PMID: 17572364
Characterization of a marine gammaproteobacterium capable of aerobic anoxygenic photosynthesis.
Fuchs BM, Spring S, Teeling H, Quast C, Wulf J, Schattenhofer M, Yan S, Ferriera S, Johnson J, Glöckner FO, Amann R., Proc Natl Acad Sci U S A 104(8), 2007
PMID: 17299055
Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363.
Wegmann U, O'Connell-Motherway M, Zomer A, Buist G, Shearman C, Canchaya C, Ventura M, Goesmann A, Gasson MJ, Kuipers OP, van Sinderen D, Kok J., J Bacteriol 189(8), 2007
PMID: 17307855
Comparative genome analysis of four magnetotactic bacteria reveals a complex set of group-specific genes implicated in magnetosome biomineralization and function.
Richter M, Kube M, Bazylinski DA, Lombardot T, Glöckner FO, Reinhardt R, Schüler D., J Bacteriol 189(13), 2007
PMID: 17449609
Comparative genomic analysis for the presence of potential enterococcal virulence factors in the probiotic Enterococcus faecalis strain Symbioflor 1.
Domann E, Hain T, Ghai R, Billion A, Kuenne C, Zimmermann K, Chakraborty T., Int J Med Microbiol 297(7-8), 2007
PMID: 17466591
Microbial genome data resources.
Markowitz VM., Curr Opin Biotechnol 18(3), 2007
PMID: 17467973
Ecological genomics of marine Roseobacters.
Moran MA, Belas R, Schell MA, González JM, Sun F, Sun S, Binder BJ, Edmonds J, Ye W, Orcutt B, Howard EC, Meile C, Palefsky W, Goesmann A, Ren Q, Paulsen I, Ulrich LE, Thompson LS, Saunders E, Buchan A., Appl Environ Microbiol 73(14), 2007
PMID: 17526795
IncP-1-beta plasmid pGNB1 isolated from a bacterial community from a wastewater treatment plant mediates decolorization of triphenylmethane dyes.
Schlüter A, Krahn I, Kollin F, Bönemann G, Stiens M, Szczepanowski R, Schneiker S, Pühler A., Appl Environ Microbiol 73(20), 2007
PMID: 17675426
Fosmids of novel marine Planctomycetes from the Namibian and Oregon coast upwelling systems and their cross-comparison with planctomycete genomes.
Woebken D, Teeling H, Wecker P, Dumitriu A, Kostadinov I, Delong EF, Amann R, Glöckner FO., ISME J 1(5), 2007
PMID: 18043661
Insights into the genome of large sulfur bacteria revealed by analysis of single filaments.
Mussmann M, Hu FZ, Richter M, de Beer D, Preisler A, Jørgensen BB, Huntemann M, Glöckner FO, Amann R, Koopman WJ, Lasken RS, Janto B, Hogg J, Stoodley P, Boissy R, Ehrlich GD., PLoS Biol 5(9), 2007
PMID: 17760503
Genomic and biochemical studies demonstrating the absence of an alkane-producing phenotype in Vibrio furnissii M1.
Wackett LP, Frias JA, Seffernick JL, Sukovich DJ, Cameron SM., Appl Environ Microbiol 73(22), 2007
PMID: 17921268
Annotation, comparison and databases for hundreds of bacterial genomes.
Médigue C, Moszer I., Res Microbiol 158(10), 2007
PMID: 18031997
Complete genome sequence of the myxobacterium Sorangium cellulosum.
Schneiker S, Perlova O, Kaiser O, Gerth K, Alici A, Altmeyer MO, Bartels D, Bekel T, Beyer S, Bode E, Bode HB, Bolten CJ, Choudhuri JV, Doss S, Elnakady YA, Frank B, Gaigalat L, Goesmann A, Groeger C, Gross F, Jelsbak L, Jelsbak L, Kalinowski J, Kegler C, Knauber T, Konietzny S, Kopp M, Krause L, Krug D, Linke B, Mahmud T, Martinez-Arias R, McHardy AC, Merai M, Meyer F, Mormann S, Muñoz-Dorado J, Perez J, Pradella S, Rachid S, Raddatz G, Rosenau F, Rückert C, Sasse F, Scharfe M, Schuster SC, Suen G, Treuner-Lange A, Velicer GJ, Vorhölter FJ, Weissman KJ, Welch RD, Wenzel SC, Whitworth DE, Wilhelm S, Wittmann C, Blöcker H, Pühler A, Müller R., Nat Biotechnol 25(11), 2007
PMID: 17965706
CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data.
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Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis.
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Tanaka N, Abe T, Miyazaki S, Sugawara H., BMC Bioinformatics 7(), 2006
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Barrett CL, Kim TY, Kim HU, Palsson BØ, Lee SY., Curr Opin Biotechnol 17(5), 2006
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Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes.
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Woyke T, Teeling H, Ivanova NN, Huntemann M, Richter M, Gloeckner FO, Boffelli D, Anderson IJ, Barry KW, Shapiro HJ, Szeto E, Kyrpides NC, Mussmann M, Amann R, Bergin C, Ruehland C, Rubin EM, Dubilier N., Nature 443(7114), 2006
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Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.
Krause A, Ramakumar A, Bartels D, Battistoni F, Bekel T, Boch J, Böhm M, Friedrich F, Hurek T, Krause L, Linke B, McHardy AC, Sarkar A, Schneiker S, Syed AA, Thauer R, Vorhölter FJ, Weidner S, Pühler A, Reinhold-Hurek B, Kaiser O, Goesmann A., Nat Biotechnol 24(11), 2006
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The genome of deep-sea vent chemolithoautotroph Thiomicrospira crunogena XCL-2.
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Towards the proteome of the marine bacterium Rhodopirellula baltica: mapping the soluble proteins.
Gade D, Theiss D, Lange D, Mirgorodskaya E, Lombardot T, Glöckner FO, Kube M, Reinhardt R, Amann R, Lehrach H, Rabus R, Gobom J., Proteomics 5(14), 2005
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Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis.
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Clustered genes related to sulfate respiration in uncultured prokaryotes support the theory of their concomitant horizontal transfer.
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Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.
Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Büttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klösgen U, Patschkowski T, Rückert C, Rupp O, Schneiker S, Schuster SC, Vorhölter FJ, Weber E, Pühler A, Bonas U, Bartels D, Kaiser O., J Bacteriol 187(21), 2005
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Metagenomics: DNA sequencing of environmental samples.
Tringe SG, Rubin EM., Nat Rev Genet 6(11), 2005
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Meyerdierks A, Kube M, Lombardot T, Knittel K, Bauer M, Glöckner FO, Reinhardt R, Amann R., Environ Microbiol 7(12), 2005
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The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP).
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Pharmacogenomic strategies against resistance development in microbial infections.
Ziebuhr W, Xiao K, Coulibaly B, Schwarz R, Dandekar T., Pharmacogenomics 5(4), 2004
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Complete genome sequence of the marine planctomycete Pirellula sp. strain 1.
Glöckner FO, Kube M, Bauer M, Teeling H, Lombardot T, Ludwig W, Gade D, Beck A, Borzym K, Heitmann K, Rabus R, Schlesner H, Amann R, Reinhardt R., Proc Natl Acad Sci U S A 100(14), 2003
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The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Krämer R, Linke B, McHardy AC, Meyer F, Möckel B, Pfefferle W, Pühler A, Rey DA, Rückert C, Rupp O, Sahm H, Wendisch VF, Wiegräbe I, Tauch A., J Biotechnol 104(1-3), 2003
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Genome-based analysis of biosynthetic aminotransferase genes of Corynebacterium glutamicum.
McHardy AC, Tauch A, Rückert C, Pühler A, Kalinowski J., J Biotechnol 104(1-3), 2003
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Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H(2)-based ithoautotrophy and anaerobiosis.
Schwartz E, Henne A, Cramm R, Eitinger T, Friedrich B, Gottschalk G., J Mol Biol 332(2), 2003
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Complete genome sequence and analysis of Wolinella succinogenes.
Baar C, Eppinger M, Raddatz G, Simon J, Lanz C, Klimmek O, Nandakumar R, Gross R, Rosinus A, Keller H, Jagtap P, Linke B, Meyer F, Lederer H, Schuster SC., Proc Natl Acad Sci U S A 100(20), 2003
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Characterization of a spontaneous nonmagnetic mutant of Magnetospirillum gryphiswaldense reveals a large deletion comprising a putative magnetosome island.
Schübbe S, Kube M, Scheffel A, Wawer C, Heyen U, Meyerdierks A, Madkour MH, Mayer F, Reinhardt R, Schüler D., J Bacteriol 185(19), 2003
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Acidobacteria form a coherent but highly diverse group within the bacterial domain: evidence from environmental genomics.
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Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique.
Kaiser O, Bartels D, Bekel T, Goesmann A, Kespohl S, Pühler A, Meyer F., J Biotechnol 106(2-3), 2003
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EMMA: a platform for consistent storage and efficient analysis of microarray data.
Dondrup M, Goesmann A, Bartels D, Kalinowski J, Krause L, Linke B, Rupp O, Sczyrba A, Pühler A, Meyer F., J Biotechnol 106(2-3), 2003
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Bioinformatics support for high-throughput proteomics.
Wilke A, Rückert C, Bartels D, Dondrup M, Goesmann A, Hüser AT, Kespohl S, Linke B, Mahne M, McHardy A, Pühler A, Meyer F., J Biotechnol 106(2-3), 2003
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Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Pühler A, Meyer F., J Biotechnol 106(2-3), 2003
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A conspicuous nickel protein in microbial mats that oxidize methane anaerobically.
Krüger M, Meyerdierks A, Glöckner FO, Amann R, Widdel F, Kube M, Reinhardt R, Kahnt J, Böcher R, Thauer RK, Shima S., Nature 426(6968), 2003
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