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Pseudomonas bubulae sp. nov., isolated from beef.

Lick S, Kröckel L, Wibberg D, Winkler A, Blom J, Goesmann A, Kalinowski J.

Int J Syst Evol Microbiol. 2019 Oct 17. doi: 10.1099/ijsem.0.003751. [Epub ahead of print]


Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19T.

Suarez C, Ratering S, Hain T, Fritzenwanker M, Goesmann A, Blom J, Chakraborty T, Bunk B, Spröer C, Overmann J, Schnell S.

Int J Genomics. 2019 Sep 9;2019:7586430. doi: 10.1155/2019/7586430. eCollection 2019.


Whole-Genome Sequences of Clinical Enterobacter bugandensis Isolates from Germany.

Falgenhauer J, Imirzalioglu C, Falgenhauer L, Yao Y, Hauri AM, Erath B, Schwengers O, Goesmann A, Seifert H, Chakraborty T, Doijad S.

Microbiol Resour Announc. 2019 Jul 18;8(29). pii: e00465-19. doi: 10.1128/MRA.00465-19.


Codon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry.

López JL, Lozano MJ, Lagares A Jr, Fabre ML, Draghi WO, Del Papa MF, Pistorio M, Becker A, Wibberg D, Schlüter A, Pühler A, Blom J, Goesmann A, Lagares A.

MBio. 2019 May 28;10(3). pii: e00505-19. doi: 10.1128/mBio.00505-19.


Complete Genome Sequence of the Corallopyronin A-Producing Myxobacterium Corallococcus coralloides B035.

Bouhired S, Rupp O, Blom J, Schäberle TF, Schiefer A, Kehraus S, Pfarr K, Goesmann A, Hoerauf A, König G.

Microbiol Resour Announc. 2019 Apr 25;8(17). pii: e00050-19. doi: 10.1128/MRA.00050-19.


Fabry disease: Detection of Alu-mediated exon duplication by NGS.

Farr M, Ferreira S, Al-Dilaimi A, Bögeholz S, Goesmann A, Kalinowski J, Knabbe C, Faber L, Oliveira JP, Rudolph V.

Mol Cell Probes. 2019 Jun;45:79-83. doi: 10.1016/j.mcp.2019.03.008. Epub 2019 Mar 29.


Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling.

Gerresheim GK, Bathke J, Michel AM, Andreev DE, Shalamova LA, Rossbach O, Hu P, Glebe D, Fricke M, Marz M, Goesmann A, Kiniry SJ, Baranov PV, Shatsky IN, Niepmann M.

Int J Mol Sci. 2019 Mar 15;20(6). pii: E1321. doi: 10.3390/ijms20061321.


ADAR1 Is Required for Dendritic Cell Subset Homeostasis and Alveolar Macrophage Function.

Baal N, Cunningham S, Obermann HL, Thomas J, Lippitsch A, Dietert K, Gruber AD, Kaufmann A, Michel G, Nist A, Stiewe T, Rupp O, Goesmann A, Zukunft S, Fleming I, Bein G, Lohmeyer J, Bauer S, Hackstein H.

J Immunol. 2019 Feb 15;202(4):1099-1111. doi: 10.4049/jimmunol.1800269. Epub 2019 Jan 16.


Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response.

Schult F, Le TN, Albersmeier A, Rauch B, Blumenkamp P, van der Does C, Goesmann A, Kalinowski J, Albers SV, Siebers B.

Nucleic Acids Res. 2018 Aug 21;46(14):7179-7192. doi: 10.1093/nar/gky527.


Genome sequence of the endophytic strain Enterobacter sp. J49, a potential biofertilizer for peanut and maize.

Ludueña LM, Anzuay MS, Angelini JG, McIntosh M, Becker A, Rupp O, Goesmann A, Blom J, Fabra A, Taurian T.

Genomics. 2019 Jul;111(4):913-920. doi: 10.1016/j.ygeno.2018.05.021. Epub 2018 May 29.


A reference genome of the Chinese hamster based on a hybrid assembly strategy.

Rupp O, MacDonald ML, Li S, Dhiman H, Polson S, Griep S, Heffner K, Hernandez I, Brinkrolf K, Jadhav V, Samoudi M, Hao H, Kingham B, Goesmann A, Betenbaugh MJ, Lewis NE, Borth N, Lee KH.

Biotechnol Bioeng. 2018 Aug;115(8):2087-2100. doi: 10.1002/bit.26722. Epub 2018 May 29.


Flexible metagenome analysis using the MGX framework.

Jaenicke S, Albaum SP, Blumenkamp P, Linke B, Stoye J, Goesmann A.

Microbiome. 2018 Apr 24;6(1):76. doi: 10.1186/s40168-018-0460-1.


Enterobacter bugandensis: a novel enterobacterial species associated with severe clinical infection.

Pati NB, Doijad SP, Schultze T, Mannala GK, Yao Y, Jaiswal S, Ryan D, Suar M, Gwozdzinski K, Bunk B, Mraheil MA, Marahiel MA, Hegemann JD, Spröer C, Goesmann A, Falgenhauer L, Hain T, Imirzalioglu C, Mshana SE, Overmann J, Chakraborty T.

Sci Rep. 2018 Mar 29;8(1):5392. doi: 10.1038/s41598-018-23069-z.


Listeria monocytogenes Induces a Virulence-Dependent microRNA Signature That Regulates the Immune Response in Galleria mellonella.

Mannala GK, Izar B, Rupp O, Schultze T, Goesmann A, Chakraborty T, Hain T.

Front Microbiol. 2017 Dec 12;8:2463. doi: 10.3389/fmicb.2017.02463. eCollection 2017.


Taxonomic analyses of members of the Streptomyces cinnabarinus cluster, description of Streptomyces cinnabarigriseus sp. nov. and Streptomyces davaonensis sp. nov.

Landwehr W, Kämpfer P, Glaeser SP, Rückert C, Kalinowski J, Blom J, Goesmann A, Mack M, Schumann P, Atasayar E, Hahnke RL, Rohde M, Martin K, Stadler M, Wink J.

Int J Syst Evol Microbiol. 2018 Jan;68(1):382-393. doi: 10.1099/ijsem.0.002519. Epub 2017 Dec 11.


Complete Genome Sequence of the Fruiting Myxobacterium Melittangium boletus DSM 14713.

Treuner-Lange A, Bruckskotten M, Rupp O, Goesmann A, Søgaard-Andersen L.

Genome Announc. 2017 Nov 9;5(45). pii: e01262-17. doi: 10.1128/genomeA.01262-17.


Temporal variation in brain transcriptome is associated with the expression of female mimicry as a sequential male alternative reproductive tactic in fish.

Cardoso SD, Gonçalves D, Goesmann A, Canário AVM, Oliveira RF.

Mol Ecol. 2018 Feb;27(3):789-803. doi: 10.1111/mec.14408. Epub 2017 Nov 29.


Streptomyces ciscaucasicus Sveshnikova et al. 1983 is a later subjective synonym of Streptomyces canus Heinemann et al. 1953.

Kämpfer P, Rückert C, Blom J, Goesmann A, Wink J, Kalinowski J, Glaeser SP.

Int J Syst Evol Microbiol. 2018 Jan;68(1):42-46. doi: 10.1099/ijsem.0.002418. Epub 2017 Nov 2.


Draft Genome Sequence of the Fruiting Myxobacterium Nannocystis exedens DSM 71.

Treuner-Lange A, Bruckskotten M, Rupp O, Goesmann A, Søgaard-Andersen L.

Genome Announc. 2017 Oct 26;5(43). pii: e01227-17. doi: 10.1128/genomeA.01227-17.


Whole-Genome Sequence of the Fruiting Myxobacterium Cystobacter fuscus DSM 52655.

Treuner-Lange A, Bruckskotten M, Rupp O, Goesmann A, Søgaard-Andersen L.

Genome Announc. 2017 Oct 26;5(43). pii: e01196-17. doi: 10.1128/genomeA.01196-17.


Complete Genome Sequence of the Fruiting Myxobacterium Myxococcus macrosporus Strain DSM 14697, Generated by PacBio Sequencing.

Treuner-Lange A, Bruckskotten M, Rupp O, Goesmann A, Søgaard-Andersen L.

Genome Announc. 2017 Oct 5;5(40). pii: e01127-17. doi: 10.1128/genomeA.01127-17.


Bioinformatics for NGS-based metagenomics and the application to biogas research.

Jünemann S, Kleinbölting N, Jaenicke S, Henke C, Hassa J, Nelkner J, Stolze Y, Albaum SP, Schlüter A, Goesmann A, Sczyrba A, Stoye J.

J Biotechnol. 2017 Nov 10;261:10-23. doi: 10.1016/j.jbiotec.2017.08.012. Epub 2017 Aug 18. Review.


Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation.

Jaeger D, Winkler A, Mussgnug JH, Kalinowski J, Goesmann A, Kruse O.

Biotechnol Biofuels. 2017 Aug 14;10:197. doi: 10.1186/s13068-017-0882-1. eCollection 2017.


Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris.

Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ.

Microbiology. 2017 Aug;163(8):1117-1144. doi: 10.1099/mic.0.000473. Epub 2017 Aug 10. Review.


Streptomyces phaeopurpureus Shinobu 1957 (Approved Lists 1980) and Streptomyces griseorubiginosus (Ryabova and Preobrazhenskaya 1957) Pridham et al. 1958 (Approved Lists 1980) are heterotypic subjective synonyms.

Kämpfer P, Rückert C, Blom J, Goesmann A, Wink J, Kalinowski J, Glaeser SP.

Int J Syst Evol Microbiol. 2017 Aug;67(8):3111-3116. doi: 10.1099/ijsem.0.002110. Epub 2017 Aug 10.


A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies.

Yu J, Blom J, Glaeser SP, Jaenicke S, Juhre T, Rupp O, Schwengers O, Spänig S, Goesmann A.

J Biotechnol. 2017 Nov 10;261:2-9. doi: 10.1016/j.jbiotec.2017.07.010. Epub 2017 Jul 10. Review.


Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT.

Golyshina OV, Tran H, Reva ON, Lemak S, Yakunin AF, Goesmann A, Nechitaylo TY, LaCono V, Smedile F, Slesarev A, Rojo D, Barbas C, Ferrer M, Yakimov MM, Golyshin PN.

Sci Rep. 2017 Jun 16;7(1):3682. doi: 10.1038/s41598-017-03904-5.


Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3.

Wibberg D, Genzel F, Verwaaijen B, Blom J, Rupp O, Goesmann A, Zrenner R, Grosch R, Pühler A, Schlüter A.

Arch Microbiol. 2017 Sep;199(7):1065-1068. doi: 10.1007/s00203-017-1394-x. Epub 2017 Jun 8.


Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence.

Ampattu BJ, Hagmann L, Liang C, Dittrich M, Schlüter A, Blom J, Krol E, Goesmann A, Becker A, Dandekar T, Müller T, Schoen C.

BMC Genomics. 2017 Apr 7;18(1):282. doi: 10.1186/s12864-017-3616-7.


Massive parallel insertion site sequencing of an arrayed Sinorhizobium meliloti signature-tagged mini-Tn 5 transposon mutant library.

Serrania J, Johner T, Rupp O, Goesmann A, Becker A.

J Biotechnol. 2017 Sep 10;257:9-12. doi: 10.1016/j.jbiotec.2017.02.019. Epub 2017 Feb 21.


Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism.

Yu J, Blom J, Sczyrba A, Goesmann A.

J Biotechnol. 2017 Sep 10;257:58-60. doi: 10.1016/j.jbiotec.2017.02.020. Epub 2017 Feb 21.


Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease.

Klughammer J, Dittrich M, Blom J, Mitesser V, Vogel U, Frosch M, Goesmann A, Müller T, Schoen C.

PLoS One. 2017 Jan 12;12(1):e0169892. doi: 10.1371/journal.pone.0169892. eCollection 2017.


Microbial diversity in different compartments of an aquaponics system.

Schmautz Z, Graber A, Jaenicke S, Goesmann A, Junge R, Smits TH.

Arch Microbiol. 2017 May;199(4):613-620. doi: 10.1007/s00203-016-1334-1. Epub 2017 Jan 10.


Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis.

Hersemann L, Wibberg D, Blom J, Goesmann A, Widmer F, Vorhölter FJ, Kölliker R.

BMC Genomics. 2017 Jan 5;18(1):35. doi: 10.1186/s12864-016-3422-7.


Whole Genome Sequencing of 39 Invasive Streptococcus pneumoniae Sequence Type 199 Isolates Revealed Switches from Serotype 19A to 15B.

Makarewicz O, Lucas M, Brandt C, Herrmann L, Albersmeier A, Rückert C, Blom J, Goesmann A, van der Linden M, Kalinowski J, Pletz MW.

PLoS One. 2017 Jan 3;12(1):e0169370. doi: 10.1371/journal.pone.0169370. eCollection 2017.


Complete Genome Sequence of Bacteroides ovatus V975.

Wegmann U, Goesmann A, Carding SR.

Genome Announc. 2016 Dec 1;4(6). pii: e01335-16. doi: 10.1128/genomeA.01335-16.


Complete Genome Sequence of the Barley Pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T).

Jaenicke S, Bunk B, Wibberg D, Spröer C, Hersemann L, Blom J, Winkler A, Schatschneider S, Albaum SP, Kölliker R, Goesmann A, Pühler A, Overmann J, Vorhölter FJ.

Genome Announc. 2016 Dec 1;4(6). pii: e01334-16. doi: 10.1128/genomeA.01334-16.


Draft genome sequence of pectic polysaccharide-degrading moderate thermophilic bacterium Geobacillus thermodenitrificans DSM 101594.

Petkauskaite R, Blom J, Goesmann A, Kuisiene N.

Braz J Microbiol. 2017 Jan - Mar;48(1):7-8. doi: 10.1016/j.bjm.2016.06.013. Epub 2016 Sep 21.


The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand.

Morales M, Sentchilo V, Bertelli C, Komljenovic A, Kryuchkova-Mostacci N, Bourdilloud A, Linke B, Goesmann A, Harshman K, Segers F, Delapierre F, Fiorucci D, Seppey M, Trofimenco E, Berra P, El Taher A, Loiseau C, Roggero D, Sulfiotti M, Etienne A, Ruiz Buendia G, Pillard L, Escoriza A, Moritz R, Schneider C, Alfonso E, Ben Jeddou F, Selmoni O, Resch G, Greub G, Emery O, Dubey M, Pillonel T, Robinson-Rechavi M, van der Meer JR.

PLoS One. 2016 Nov 3;11(11):e0165850. doi: 10.1371/journal.pone.0165850. eCollection 2016.


ReadXplorer 2-detailed read mapping analysis and visualization from one single source.

Hilker R, Stadermann KB, Schwengers O, Anisiforov E, Jaenicke S, Weisshaar B, Zimmermann T, Goesmann A.

Bioinformatics. 2016 Dec 15;32(24):3702-3708. Epub 2016 Aug 18.


Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans DsijT.

Barbeyron T, Thomas F, Barbe V, Teeling H, Schenowitz C, Dossat C, Goesmann A, Leblanc C, Oliver Glöckner F, Czjzek M, Amann R, Michel G.

Environ Microbiol. 2016 Dec;18(12):4610-4627. doi: 10.1111/1462-2920.13584. Epub 2016 Nov 13.


An RNAi-Based Control of Fusarium graminearum Infections Through Spraying of Long dsRNAs Involves a Plant Passage and Is Controlled by the Fungal Silencing Machinery.

Koch A, Biedenkopf D, Furch A, Weber L, Rossbach O, Abdellatef E, Linicus L, Johannsmeier J, Jelonek L, Goesmann A, Cardoza V, McMillan J, Mentzel T, Kogel KH.

PLoS Pathog. 2016 Oct 13;12(10):e1005901. doi: 10.1371/journal.ppat.1005901. eCollection 2016 Oct.


Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates.

Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, König H, Schwarz WH, Zverlov VV, Liebl W, Pühler A, Schlüter A, Klocke M.

Biotechnol Biofuels. 2016 Aug 11;9:171. doi: 10.1186/s13068-016-0581-3. eCollection 2016.


CRISPR System Acquisition and Evolution of an Obligate Intracellular Chlamydia-Related Bacterium.

Bertelli C, Cissé OH, Rusconi B, Kebbi-Beghdadi C, Croxatto A, Goesmann A, Collyn F, Greub G.

Genome Biol Evol. 2016 Aug 25;8(8):2376-86. doi: 10.1093/gbe/evw138.


Chromosomal Locations of mcr-1 and bla CTX-M-15 in Fluoroquinolone-Resistant Escherichia coli ST410.

Falgenhauer L, Waezsada SE, Gwozdzinski K, Ghosh H, Doijad S, Bunk B, Spröer C, Imirzalioglu C, Seifert H, Irrgang A, Fischer J, Guerra B, Käsbohrer A, Overmann J, Goesmann A, Chakraborty T.

Emerg Infect Dis. 2016 Sep;22(9):1689-91. doi: 10.3201/eid2209.160692. Epub 2016 Sep 15. No abstract available.


Complete Chloroplast and Mitochondrial Genome Sequences of the Hydrocarbon Oil-Producing Green Microalga Botryococcus braunii Race B (Showa).

Blifernez-Klassen O, Wibberg D, Winkler A, Blom J, Goesmann A, Kalinowski J, Kruse O.

Genome Announc. 2016 Jun 9;4(3). pii: e00524-16. doi: 10.1128/genomeA.00524-16.


Presence of a widely disseminated Listeria monocytogenes serotype 4b clone in India.

Barbuddhe SB, Doijad SP, Goesmann A, Hilker R, Poharkar KV, Rawool DB, Kurkure NV, Kalorey DR, Malik SS, Shakuntala I, Chaudhari S, Waskar V, D'Costa D, Kolhe R, Arora R, Roy A, Raorane A, Kale S, Pathak A, Negi M, Kaur S, Waghmare R, Warke S, Shoukat S, Harish B, Poojary A, Madhavaprasad C, Nagappa K, Das S, Zende R, Garg S, Bhosle S, Radriguez S, Paturkar A, Fritzenwanker M, Ghosh H, Hain T, Chakraborty T.

Emerg Microbes Infect. 2016 Jun 8;5:e55. doi: 10.1038/emi.2016.55. No abstract available.


Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany.

Falgenhauer L, Imirzalioglu C, Ghosh H, Gwozdzinski K, Schmiedel J, Gentil K, Bauerfeind R, Kämpfer P, Seifert H, Michael GB, Schwarz S, Pfeifer Y, Werner G, Pietsch M, Roesler U, Guerra B, Fischer J, Sharp H, Käsbohrer A, Goesmann A, Hille K, Kreienbrock L, Chakraborty T.

Int J Antimicrob Agents. 2016 Jun;47(6):457-65. doi: 10.1016/j.ijantimicag.2016.03.019. Epub 2016 May 12.


Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots.

Franta Z, Vogel H, Lehmann R, Rupp O, Goesmann A, Vilcinskas A.

Biomed Res Int. 2016;2016:8285428. doi: 10.1155/2016/8285428. Epub 2016 Mar 28.


EDGAR 2.0: an enhanced software platform for comparative gene content analyses.

Blom J, Kreis J, Spänig S, Juhre T, Bertelli C, Ernst C, Goesmann A.

Nucleic Acids Res. 2016 Jul 8;44(W1):W22-8. doi: 10.1093/nar/gkw255. Epub 2016 Apr 20.

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