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Alexander Goesmann

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Erwinia amylovora

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Sebastian Jünemann; Jörn Kalinowski; Alexander Mellmann; Karola Prior; Fritz Joachim Sedlazeck; Jens Stoye; Arndt von Haeseler; Andreas Albersmeier; Alexander Goesmann; Uwe John; Dag Harmsen
Updating benchtop sequencing performance comparison.
Samanta B de Campos; Roberto Farina; Alexander Goesmann; Sebastian Jaenicke; Sebastian Jünemann; Rafael Szczepanowski; Luciano K Vargas; Volker F Wendisch; Jung-Won Youn; Anelise Beneduzi; Luciane Maria Pereira Passaglia
Changes in root bacterial communities associated to two different development stages of canola (Brassica napus L. var oleifera) evaluated through next-generation sequencing technology.
Thomas Riedel; Meike Rohlfs; Stefan Spring; Jürgen Tomasch; Thorsten Brinkhoff; Heribert Cypionka; Anne Fiebig; Jed A Fuhrman; Alexander Goesmann; Markus Göker; Laura Gómez-Consarnau; José M González; Michael Jarek; Johannes Klein; Madeleine Martin; Irene Wagner-Döbler
Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.

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All Publications

2013: Sebastian Jünemann; Jörn Kalinowski; Alexander Mellmann; Karola Prior; Fritz Joachim Sedlazeck; Jens Stoye; Arndt von Haeseler; Andreas Albersmeier; Alexander Goesmann; Uwe John; Dag Harmsen
Updating benchtop sequencing performance comparison.
Nature biotechnology 2013;31(4):294-6.
2013: Samanta B de Campos; Roberto Farina; Alexander Goesmann; Sebastian Jaenicke; Sebastian Jünemann; Rafael Szczepanowski; Luciano K Vargas; Volker F Wendisch; Jung-Won Youn; Anelise Beneduzi; Luciane Maria Pereira Passaglia
Changes in root bacterial communities associated to two different development stages of canola (Brassica napus L. var oleifera) evaluated through next-generation sequencing technology.
Microbial ecology 2013;65(3):593-601.
2013: Thomas Riedel; Meike Rohlfs; Stefan Spring; Jürgen Tomasch; Thorsten Brinkhoff; Heribert Cypionka; Anne Fiebig; Jed A Fuhrman; Alexander Goesmann; Markus Göker; Laura Gómez-Consarnau; José M González; Michael Jarek; Johannes Klein; Madeleine Martin; Irene Wagner-Döbler
Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein.
PloS one 2013;8(3):e57487.
2013: Rachel A Mann; Kim M Plummer; Theo H M Smits; Steven V Beer; Jochen Blom; Andreas Bühlmann; Brion Duffy; Jürg E Frey; Alexander Goesmann; Joanne Luck; Brendan Rodoni
Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.
PloS one 2013;8(2):e55644.
2013: Moritz Fritzenwanker; Alexander Goesmann; Torsten Hain; Carsten Tobias Kuenne; Kurt Zimmermann; André Billion; Trinad Chakraborty; Eugen Domann
Complete Genome Sequence of the Probiotic Enterococcus faecalis Symbioflor 1 Clone DSM 16431.
Genome announcements 2013;1(1):.
2013: Carsten Tobias Kuenne; Mobarak Abu Mraheil; Axel Strittmatter; Sukhadeo Barbuddhe; André Billion; Rolf Daniel; Alexander Goesmann; Torsten Hain; Trinad Chakraborty
Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome.
BMC genomics 2013;14():47.
2012: Jessica Schneider; Christoph Schorsch; Rafael Szczepanowski; Andreas Tauch; Mike Farwick; Alexander Goesmann; Sebastian Jaenicke; Tim Köhler; Alfred Pühler; Christian Rückert; Steffen Schaffer; Heiko Andrea; Jochen Blom; Karina Brinkrolf
Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10.
Eukaryotic cell 2012;11(12):1582-3.
2012: Stefan Heinl; Burkhard Linke; Alfred Pühler; Jochen Blom; Felix Eikmeyer; Alexander Goesmann; Reingard Grabherr; Helmut Schwab; Rafael Szczepanowski; Daniel Wibberg; Andreas Schlüter
Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage.
Journal of biotechnology 2012;161(2):153-66.
2012: Melanie Zischka; Wolfgang Witte; Jochen Blom; Piotr W Dabrowski; Alexander Goesmann; Torsten Hain; Lars B Jensen; Carsten Tobias Kuenne; Jesper Larsen; Burkhard Linke; Andreas Nitsche; Guido Werner
Complete genome sequence of the porcine isolate Enterococcus faecalis D32.
Journal of bacteriology 2012;194(19):5490-1.
2012: Fabio Rezzonico; Brendan Rodoni; Andrea Braun-Kiewnick; Brion Duffy; Alexander Goesmann; Rachel A Mann; Theo H M Smits
Lipopolysaccharide biosynthesis genes discriminate between Rubus- and Spiraeoideae-infective genotypes of Erwinia amylovora.
Molecular plant pathology 2012;13(8):975-84.
2012: Michael T Rose; Terry J Rose; Tadashi Yoshihashi; Michael Frei; Alexander Goesmann; Heiko Neuweger; Juan Pariasca-Tanaka; Matthias Wissuwa
Root metabolic response of rice (Oryza sativa L.) genotypes with contrasting tolerance to zinc deficiency and bicarbonate excess.
Planta 2012;236(4):959-73.
2012: Sabine Schork; Jochen Blom; Matthias Frosch; Alexander Goesmann; Alfred Pühler; Andreas Schlüter; Susanne Schneiker-Bekel; Christoph Schoen
Genome sequence of a Neisseria meningitidis capsule null locus strain from the clonal complex of sequence type 198.
Journal of bacteriology 2012;194(18):5144-5.
2012: Manuela Filippini; Alexander Goesmann; Sebastian Jaenicke; Weihong Qi; Theo H M Smits; Homayoun C Bagheri
Genome sequence of the filamentous bacterium Fibrisoma limi BUZ 3T.
Journal of bacteriology 2012;194(16):4445.
2012: Rachel A Mann; Kim M Plummer; Brendan C Rodoni; Steven V Beer; Jochen Blom; Andreas Bühlmann; Brion Duffy; Jürg E Frey; Alexander Goesmann; Joanne E Luck; Theo H M Smits
Comparative analysis of the Hrp pathogenicity island of Rubus- and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element.
Gene 2012;504(1):6-12.
2012: Christian Trötschel; Daniel Wolff; Simon Schröder; Stefan Albaum; Alexander Goesmann; Tim W Nattkemper; Ansgar Poetsch
Protein turnover quantification in a multilabeling approach: from data calculation to evaluation.
Molecular & cellular proteomics : MCP 2012;11(8):512-26.
2012: Manuela Filippini; Alexander Goesmann; Weihong Qi; Theo H M Smits; Jochen Blom; Homayoun C Bagheri
Genome sequence of Fibrella aestuarina BUZ 2(T), a filamentous marine bacterium.
Journal of bacteriology 2012;194(13):3555.
2012: Jessica Schneider; Andreas Tauch; Eva Trost; Alexander Goesmann; Sebastian Jaenicke; Volkmar Passoth; Oliver Rupp; Karina Brinkrolf
Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities.
FEMS yeast research 2012;12(3):382-6.
2012: Martha Zakrzewski; Søren Sørensen; Rafael Szczepanowski; Waleed Abu Al-Soud; Felix Eikmeyer; Alexander Goesmann; Sebastian Jaenicke; Sebastian Jünemann; Alfred Pühler; Andreas Schlüter
Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing.
Journal of biotechnology 2012;158(4):248-58.
2012: Matthias Hackl; Vaibhav Jadhav; Tobias Jakobi; Thomas Noll; Alfred Pühler; Oliver Rupp; Nicole Borth; Karina Brinkrolf; Alexander Goesmann; Johannes Grillari
Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines.
Journal of biotechnology 2012;158(3):151-5.
2012: De Maayer Pieter; Brion Duffy; Jürg E Frey; Alexander Goesmann; Fabio Rezzonico; Theo H M Smits; Stephanus N Venter; Jochen Blom; Andreas Bühlmann; Wai Yin Chan; Teresa A Coutinho
Complete genome sequence of clinical isolate Pantoea ananatis LMG 5342.
Journal of bacteriology 2012;194(6):1615-6.
2012: Antje Rademacher; Andreas Schlüter; Mandy Schönberg; Rafael Szczepanowski; Martha Zakrzewski; Alexander Goesmann; Alfred Pühler; Michael Klocke
Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing.
FEMS microbiology ecology 2012;79(3):785-99.
2012: Sebastian Jünemann; Karola Prior; Jens Stoye; Rafael Szczepanowski; Benjamin Ehmke; Alexander Goesmann; Inga Harks; Dag Harmsen
Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing.
PloS one 2012;7(8):e41606.
2012: Tim Kahlke; Nils Peder Willassen; Alexander Goesmann; Erik Hjerde; Peik Haugen
Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.
BMC genomics 2012;13():179.
2012: Torsten Hain; Ben Izar; Uwe Kärst; Carsten Tobias Kuenne; Rainer Merkl; Walid Mohamed; Mobarak Abu Mraheil; Sebastian Oehm; Alfred Pühler; Christophe Rusniok; Silke Schaffrath; Christiane Steinweg; Sonja Vorwerk; Eugen Domann; Patricia Garrido; Rohit Ghai; Philippe Glaser; Werner Goebel; Alexander Goesmann; André Billion; Carmen Buchrieser; Trinad Chakraborty
Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes.
BMC genomics 2012;13():144.
2012: Anke Zschüttig; Jochen Blom; Alexander Goesmann; Christoph Pöhlmann; Kurt Zimmermann; Florian Gunzer
Identification and characterization of microcin S, a new antibacterial peptide produced by probiotic Escherichia coli G3/10.
PloS one 2012;7(3):e33351.
2011: Jennifer Becker; Thomas Bekel; Nicole Borth; Alexander Goesmann; Johannes Grillari; Matthias Hackl; Tobias Jakobi; Christian Kaltschmidt; Thomas Noll; Alfred Pühler; Oliver Rupp; Jessica Schneider; Rafael Szczepanowski; Andreas Tauch; Karina Brinkrolf
Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing.
Journal of biotechnology 2011;156(3):227-35.
2011: José M González; Mónica González-Velázquez; Sebastian Jaenicke; Montserrat Coll-Lladó; Beatriz Fernández-Gómez; Antoni Fernàndez-Guerra; Alexander Goesmann; Laura Gómez-Consarnau; Jarone Pinhassi; Pere Puigbò; Carlos Pedrós-Alió
Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134.
Applied and environmental microbiology 2011;77(24):8676-86.
2011: Joël F Pothier; Alfred Pühler; Theo H M Smits; Frank-Jörg Vorhölter; Jochen Blom; Alexander Goesmann; Brion Duffy
The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: complete sequence and comparative genomic analysis.
FEMS microbiology letters 2011;323(1):52-60.
2011: Isabel Margaret; Virginie Mittard-Runte; Christian Rückert; José E Ruiz-Sainz; José M Vinardell; Anke Becker; Jochen Blom; Ildefonso Bonilla; Alexander Goesmann; Michael Göttfert; Javier Lloret; Stefan Weidner
Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean.
Journal of biotechnology 2011;155(1):11-9.
2011: Susanne Schneiker-Bekel; Michael Stiens; Frank-Jörg Vorhölter; Stefan Weidner; Daniel Wibberg; Thomas Bekel; Jochen Blom; Alexander Goesmann; Burkhard Linke; Heiko Neuweger; Alfred Pühler; Andreas Schlüter
The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome.
Journal of biotechnology 2011;155(1):20-33.
2011: Daniel Wibberg; Rüdiger Schmitt; Susanne Schneiker-Bekel; Rafael Sczcepanowski; Joao Carlos Setubal; Jochen Blom; Alexander Goesmann; Sebastian Jaenicke; Florian Kollin; Alfred Pühler; Oliver Rupp; Birgit Scharf; Andreas Schlüter
Complete genome sequencing of Agrobacterium sp. H13-3, the former Rhizobium lupini H13-3, reveals a tripartite genome consisting of a circular and a linear chromosome and an accessory plasmid but lacking a tumor-inducing Ti-plasmid.
Journal of biotechnology 2011;155(1):50-62.
2011: Elizaveta Krol; Jörn Winnebald; Melanie J Barnett; Jan Baumbach; Alexander Berhörster; Jochen Blom; Alexander Goesmann; Anke Becker
RhizoRegNet--a database of rhizobial transcription factors and regulatory networks.
Journal of biotechnology 2011;155(1):127-34.
2011: Jessica Schneider; Andreas Tauch; Jochen Blom; Karina Brinkrolf; Sebastian Jaenicke; Burkhard Linke; Heiko Neuweger; Alexander Goesmann
RAPYD--rapid annotation platform for yeast data.
Journal of biotechnology 2011;155(1):118-26.
2011: Andreas Küberl; Ingund Anderl; Karina Brinkrolf; Anton Glieder; Alexander Goesmann; Tanja Hajek; Sebastian Jaenicke; Alfred Pühler; Jessica Schneider; Helmut Schwab; Rafael Szczepanowski; Gerhard G Thallinger; Daniel Wibberg; Harald Pichler
High-quality genome sequence of Pichia pastoris CBS7435.
Journal of biotechnology 2011;154(4):312-20.
2011: Vincent Thomas; Claire Bertelli; François Collyn; Nicola Casson; Amalio Telenti; Alexander Goesmann; Antony Croxatto; Gilbert Greub
Lausannevirus, a giant amoebal virus encoding histone doublets.
Environmental microbiology 2011;13(6):1454-66.
2011: Jochen Blom; Tobias Jakobi; Daniel Doppmeier; Sebastian Jaenicke; Jörn Kalinowski; Jens Stoye; Alexander Goesmann
Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming.
Bioinformatics (Oxford, England) 2011;27(10):1351-8.
2011: Matthias Hackl; Tobias Jakobi; Jochen Blom; Daniel Doppmeier; Karina Brinkrolf; Rafael Szczepanowski; Stephan H Bernhart; Juan Antonio Hernandez Bort; Matthias Wieser; Renate Kunert; Simon Jeffs; Ivo L Hofacker; Alexander Goesmann; Alfred Pühler; Nicole Borth; Christian Höner Zu Siederdissen; Johannes Grillari
Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering.
Journal of biotechnology 2011;153(1-2):62-75.
2011: Tristano Bacchetti De Gregoris; Oliver Rupp; Sven Klages; Florian Knaust; Thomas Bekel; Michael Kube; grant burgess; Maria Ina Arnone; Alexander Goesmann; Richard Reinhardt; Anthony S Clare
Deep sequencing of naupliar-, cyprid- and adult-specific normalised Expressed Sequence Tag (EST) libraries of the acorn barnacle Balanus amphitrite.
Biofouling 2011;27(4):367-74.
2011: Christoph Schoen; Jacqueline Weber-Lehmann; Jochen Blom; Biju Joseph; Alexander Goesmann; Axel Strittmatter; Matthias Frosch
Whole-genome sequence of the transformable Neisseria meningitidis serogroup A strain WUE2594.
Journal of bacteriology 2011;193(8):2064-5.
2011: Kerstin Brankatschk; Jochen Blom; Alexander Goesmann; Theo H M Smits; Brion Duffy
Genome of a European fresh-vegetable food safety outbreak strain of Salmonella enterica subsp. enterica serovar weltevreden.
Journal of bacteriology 2011;193(8):2066.
2011: Burkhard Linke; Robert Giegerich; Alexander Goesmann
Conveyor: a workflow engine for bioinformatic analyses.
Bioinformatics (Oxford, England) 2011;27(7):903-11.
2011: Luka Ausec; Alexander Goesmann; Andreas Schlüter; Martha Zakrzewski; Ines Mandic-Mulec
Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes.
PloS one 2011;6(10):e25724.
2011: Theo H M Smits; Virginia O Stockwell; Jochen Blom; Jürg E Frey; Alexander Goesmann; Carol A Ishimaru; Tim Kamber; Fabio Rezzonico; Brion Duffy
Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist Pantoea vagans C9-1.
PloS one 2011;6(7):e22247.
2011: Stefan Albaum; Dörte Becher; Alexander Goesmann; Hannes Hahne; Ute Haußmann; Andreas Otto; Ansgar Poetsch; Tim W Nattkemper
A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study.
Proteome science 2011;9():30.
2011: Biju Joseph; Roland F Schwarz; Burkhard Linke; Jochen Blom; Anke Becker; Heike Claus; Alexander Goesmann; Matthias Frosch; Tobias Müller; Ulrich Vogel; Christoph Schoen
Virulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome.
PloS one 2011;6(4):e18441.
2011: Sebastian Jaenicke; Christina Ander; Thomas Bekel; Regina Bisdorf; M Dröge; Karl-Heinz Gartemann; Sebastian Jünemann; Olaf Kaiser; Lutz Krause; Felix Tille; Martha Zakrzewski; Alfred Pühler; Andreas Schlüter; Alexander Goesmann
Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing.
PloS one 2011;6(1):e14519.
2010: Theo H M Smits; Fabio Rezzonico; Tim Kamber; Alexander Goesmann; Carol A Ishimaru; Virginia O Stockwell; Jürg E Frey; Brion Duffy
Genome sequence of the biocontrol agent Pantoea vagans strain C9-1.
Journal of bacteriology 2010;192(24):6486-7.
2010: Biju Joseph; Susanne Schneiker-Bekel; Anja Schramm-Glück; Jochen Blom; Heike Claus; Burkhard Linke; Roland F Schwarz; Anke Becker; Alexander Goesmann; Matthias Frosch; Christoph Schoen
Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence.
Journal of bacteriology 2010;192(20):5363-77.
2010: Theo H M Smits; Fabio Rezzonico; Cosima Pelludat; Alexander Goesmann; Jürg E Frey; Brion Duffy
Genomic and phenotypic characterization of a nonpigmented variant of Pantoea vagans biocontrol strain C9-1 lacking the 530-kb megaplasmid pPag3.
FEMS microbiology letters 2010;308(1):48-54.
2010: Theo H M Smits; Fabio Rezzonico; Tim Kamber; Jochen Blom; Alexander Goesmann; Jürg E Frey; Brion Duffy
Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp.
Molecular plant-microbe interactions : MPMI 2010;23(4):384-93.
2010: Nils Gehlenborg; Seán I O'Donoghue; Nitin S Baliga; Alexander Goesmann; Matthew A Hibbs; Hiroaki Kitano; Oliver Kohlbacher; Heiko Neuweger; Reinhard Schneider; Dan Tenenbaum; Anne-Claude Gavin
Visualization of omics data for systems biology.
Nature methods 2010;7(3 Suppl):S56-68.
2010: Christiane Steinweg; Carsten Tobias Kuenne; André Billion; Mobarak A Mraheil; Eugen Domann; Rohit Ghai; Sukhadeo B Barbuddhe; Uwe Kärst; Alexander Goesmann; Alfred Pühler; Bernd Weisshaar; Jürgen Wehland; Robert Lampidis; Jürgen Kreft; Werner Goebel; Trinad Chakraborty; Torsten Hain
Complete genome sequence of Listeria seeligeri, a nonpathogenic member of the genus Listeria.
Journal of bacteriology 2010;192(5):1473-4.
2010: Eva Trost; Lisa Ott; Jessica Schneider; Jasmin Schröder; Sebastian Jaenicke; Alexander Goesmann; Peter Husemann; Jens Stoye; Fernanda A Dorella; Flavia Souza Rocha; Siomar de Castro Soares; Vívian D'Afonseca; Anderson Miyoshi; Jeronimo Ruiz; Artur Silva; Vasco Azevedo; Andreas Burkovski; Nicole Guiso; Olivier F Join-Lambert; Samer Kayal; Andreas Tauch
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.
BMC genomics 2010;11():728.
2010: Kolja Henckel; Helge Küster; Leonhard J Stutz; Alexander Goesmann
MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula.
BMC research notes 2010;3():262.
2010: Carsten Tobias Kuenne; Sonja Voget; Jordan Pischimarov; Sebastian Oehm; Alexander Goesmann; Rolf Daniel; Torsten Hain; Trinad Chakraborty
Comparative analysis of plasmids in the genus Listeria.
PloS one 2010;5(9):.
2010: J Schneider; Frank-Jörg Vorhölter; Eva Trost; J Blom; Y R Musa; H Neuweger; Karsten Niehaus; S Schatschneider; Andreas Tauch; Alexander Goesmann
CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks.
Genetics and molecular research : GMR 2010;9(3):1660-72.
2010: Claire Bertelli; François Collyn; Antony Croxatto; Christian Rückert; Adam Polkinghorne; Carole Kebbi-Beghdadi; Alexander Goesmann; Lloyd Vaughan; Gilbert Greub
The Waddlia genome: a window into chlamydial biology.
PloS one 2010;5(5):e10890.
2010: Max Farnbacher; Thomas Jahns; Dirk Willrodt; Rolf Daniel; Rainer Haas; Alexander Goesmann; Stefan Kurtz; Gabriele Rieder
Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8.
BMC genomics 2010;11():335.
2010: Ines Yang; Uwe John; Sára Beszteri; Gernot Glöckner; Bernd Krock; Alexander Goesmann; Allan D Cembella
Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum.
BMC genomics 2010;11():248.
2010: Eva Trost; Susanne Götker; Jessica Schneider; Susanne Schneiker-Bekel; Rafael Szczepanowski; Alexandra Tilker; Prisca Viehoever; Walter Arnold; Thomas Bekel; Jochen Blom; Karl-Heinz Gartemann; Burkhard Linke; Alexander Goesmann; Alfred Pühler; Sanjay K Shukla; Andreas Tauch
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.
BMC genomics 2010;11():91.
2010: Theo H M Smits; Sebastian Jaenicke; Fabio Rezzonico; Tim Kamber; Alexander Goesmann; Jürg E Frey; Brion Duffy
Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163T and comparative genomic insights into plant pathogenicity.
BMC genomics 2010;11():2.
2009: Stefan Albaum; Heiko Neuweger; Benjamin Fränzel; Sita Lange; Dominik Mertens; Christian Trötschel; Dirk Wolters; Jörn Kalinowski; Tim W Nattkemper; Alexander Goesmann
Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.
Bioinformatics (Oxford, England) 2009;25(23):3128-34.
2009: Udo Wegmann; Karin Overweg; Nikki Horn; Alexander Goesmann; Arjan Narbad; Michael J Gasson; Claire Shearman
Complete genome sequence of Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry.
Journal of bacteriology 2009;191(22):7142-3.
2009: Justina Krawczyk; Thomas A Kohl; Alexander Goesmann; Jörn Kalinowski; Jan Baumbach
From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet.
Nucleic acids research 2009;37(14):e97.
2009: Magdalena Kröber; Thomas Bekel; Naryttza N Diaz; Alexander Goesmann; Sebastian Jaenicke; Lutz Krause; Dimitri Miller; Kai J Runte; Prisca Viehöver; Alfred Pühler; Andreas Schlüter
Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing.
Journal of biotechnology 2009;142(1):38-49.
2009: Axel W Strittmatter; Heiko Liesegang; Ralf Rabus; Iwona Decker; Judith Amann; Sönke Andres; Anke Henne; W. Florian Fricke; Rosa Martinez-Arias; Daniela Bartels; Alexander Goesmann; Lutz Krause; Alfred Pühler; Hans-Peter Klenk; Michael Richter; Margarete Schüler; Frank Oliver Glöckner; Anke Meyerdierks; Gerhard Gottschalk; Rudolf Amann
Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide.
Environmental microbiology 2009;11(5):1038-55.
2009: Michael Dondrup; Andrea T Hüser; Dominik Mertens; Alexander Goesmann
An evaluation framework for statistical tests on microarray data.
Journal of biotechnology 2009;140(1-2):18-26.
2009: Thomas Bekel; Kolja Henckel; Helge Küster; Folker Meyer; Virginie Mittard Runte; Heiko Neuweger; Daniel Paarmann; Oliver Rupp; Martha Zakrzewski; Alfred Pühler; Jens Stoye; Alexander Goesmann
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.
Journal of biotechnology 2009;140(1-2):3-12.
2009: Anke Becker; Melanie J Barnett; Delphine Capela; Michael Dondrup; Paul-Bertram Kamp; Elizaveta Krol; Burkhard Linke; Silvia Rüberg; Kai Runte; Brenda K Schroeder; Stefan Weidner; Svetlana N Yurgel; Jacques Batut; Sharon R Long; Alfred Pühler; Alexander Goesmann
A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data.
Journal of biotechnology 2009;140(1-2):45-50.
2009: Wolfgang Gerlach; Sebastian Jünemann; Felix Tille; Alexander Goesmann; Jens Stoye
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads.
BMC bioinformatics 2009;10():430.
2009: Heiko Neuweger; Marcus Persicke; Stefan Albaum; Thomas Bekel; Michael Dondrup; Andrea T Hüser; Jörn Winnebald; Jessica Schneider; Jörn Kalinowski; Alexander Goesmann
Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example.
BMC systems biology 2009;3():82.
2009: Justina Krawczyk; Alexander Goesmann; Ralf Nolte; Martin Werber; Bernd Weisshaar
Trace2PS and FSA2PS: two software toolkits for converting trace and fsa files to PostScript format.
Source code for biology and medicine 2009;4():4.
2009: Jochen Blom; Stefan Albaum; Daniel Doppmeier; Alfred Pühler; Frank-Jörg Vorhölter; Martha Zakrzewski; Alexander Goesmann
EDGAR: a software framework for the comparative analysis of prokaryotic genomes.
BMC bioinformatics 2009;10():154.
2009: Naryttza N Diaz; Lutz Krause; Alexander Goesmann; Karsten Niehaus; Tim W Nattkemper
TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach.
BMC bioinformatics 2009;10():56.
2009: Kolja Henckel; Kai J Runte; Thomas Bekel; Michael Dondrup; Tobias Jakobi; Helge Küster; Alexander Goesmann
TRUNCATULIX--a data warehouse for the legume community.
BMC plant biology 2009;9():19.
2008: Eckhard Strauch; Jens A Hammerl; Antje Konietzny; Susanne Schneiker-Bekel; Walter Arnold; Alexander Goesmann; Alfred Pühler; Lothar Beutin
Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7.
Infection and immunity 2008;76(12):5466-77.
2008: Heiko Neuweger; Stefan Albaum; Michael Dondrup; Marcus Persicke; Tony Watt; Karsten Niehaus; Jens Stoye; Alexander Goesmann
MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
Bioinformatics (Oxford, England) 2008;24(23):2726-32.
2008: Lutz Krause; Naryttza N Diaz; Robert A Edwards; Karl-Heinz Gartemann; Holger Krömeke; Heiko Neuweger; Alfred Pühler; Kai J Runte; Andreas Schlüter; Jens Stoye; Rafael Szczepanowski; Andreas Tauch; Alexander Goesmann
Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor.
Journal of biotechnology 2008;136(1-2):91-101.
2008: Andreas Schlüter; Lutz Krause; Rafael Szczepanowski; Alexander Goesmann; Alfred Pühler
Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant.
Journal of biotechnology 2008;136(1-2):65-76.
2008: Andreas Schlüter; Thomas Bekel; Naryttza N Diaz; Michael Dondrup; Rudolf Eichenlaub; Karl-Heinz Gartemann; Irene Krahn; Lutz Krause; Holger Krömeke; Olaf Kruse; Jan H Mussgnug; Heiko Neuweger; Karsten Niehaus; Alfred Pühler; Kai J Runte; Rafael Szczepanowski; Andreas Tauch; Alexandra Tilker; Prisca Viehöver; Alexander Goesmann
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
Journal of biotechnology 2008;136(1-2):77-90.
2008: Rafael Szczepanowski; Thomas Bekel; Alexander Goesmann; Lutz Krause; Holger Krömeke; Olaf Kaiser; Wolfgang Eichler; Alfred Pühler; Andreas Schlüter
Insight into the plasmid metagenome of wastewater treatment plant bacteria showing reduced susceptibility to antimicrobial drugs analysed by the 454-pyrosequencing technology.
Journal of biotechnology 2008;136(1-2):54-64.
2008: Michael Stiens; Anke Becker; Thomas Bekel; Victoria Gödde; Alexander Goesmann; Karsten Niehaus; Susanne Schneiker-Bekel; Werner Selbitschka; Stefan Weidner; Andreas Schlüter; Alfred Pühler
Comparative genomic hybridisation and ultrafast pyrosequencing revealed remarkable differences between the Sinorhizobium meliloti genomes of the model strain Rm1021 and the field isolate SM11.
Journal of biotechnology 2008;136(1-2):31-7.
2008: Andreas Tauch; Jessica Schneider; Rafael Szczepanowski; Alexandra Tilker; Prisca Viehoever; Karl-Heinz Gartemann; Walter Arnold; Jochen Blom; Karina Brinkrolf; Iris Brune; Susanne Götker; Bernd Weisshaar; Alexander Goesmann; M Dröge; Alfred Pühler
Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids.
Journal of biotechnology 2008;136(1-2):22-30.
2008: Andreas Tauch; Eva Trost; Alexandra Tilker; Ulrike Ludewig; Susanne Schneiker; Alexander Goesmann; Walter Arnold; Thomas Bekel; Karina Brinkrolf; Iris Brune; Susanne Götker; Jörn Kalinowski; Paul-Bertram Kamp; Francisco Pereira Lobo; Prisca Viehoever; Bernd Weisshaar; Francisco Soriano; M Dröge; Alfred Pühler
The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing.
Journal of biotechnology 2008;136(1-2):11-21.
2008: Sebastian Oehm; David Gilbert; Andreas Tauch; Jens Stoye; Alexander Goesmann
Comparative Pathway Analyzer--a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms.
Nucleic acids research 2008;36(Web Server issue):W433-7.
2008: Lutz Krause; Naryttza N Diaz; Alexander Goesmann; Scott Kelley; Tim W Nattkemper; Forest Rohwer; Robert A Edwards; Jens Stoye
Phylogenetic classification of short environmental DNA fragments.
Nucleic acids research 2008;36(7):2230-9.
2008: Frank-Jörg Vorhölter; Susanne Schneiker; Alexander Goesmann; Lutz Krause; Thomas Bekel; Olaf Kaiser; Burkhard Linke; Thomas Patschkowski; Christian Rückert; Joachim Schmid; Vishaldeep Kaur Sidhu; Volker Sieber; Andreas Tauch; Steven Alexander Watt; Bernd Weisshaar; Anke Becker; Karsten Niehaus; Alfred Pühler
The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis.
Journal of biotechnology 2008;134(1-2):33-45.
2008: Christoph Schoen; Jochen Blom; Heike Claus; Anja Schramm-Glück; Petra Brandt; Tobias Müller; Alexander Goesmann; Biju Joseph; Sebastian Konietzny; Oliver Kurzai; Corinna Schmitt; Torben Friedrich; Burkhard Linke; Ulrich Vogel; Matthias Frosch
Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(9):3473-8.
2008: Karl-Heinz Gartemann; Birte Abt; Thomas Bekel; Annette Burger; Jutta Engemann; Monika Flügel; Lars Gaigalat; Alexander Goesmann; Ines Gräfen; Jörn Kalinowski; Olaf Kaup; Oliver Kirchner; Lutz Krause; Burkhard Linke; Alice C McHardy; Folker Meyer; Sandra Pohle; Christian Rückert; Susanne Schneiker; Eva-Maria Zellermann; Alfred Pühler; Rudolf Eichenlaub; Olaf Kaiser; Daniela Bartels
The genome sequence of the tomato-pathogenic actinomycete Clavibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity.
Journal of bacteriology 2008;190(6):2138-49.
2007: Christine Meisinger-Henschel; Michaela Schmidt; Susanne Lukassen; Burkhard Linke; Lutz Krause; Sebastian Konietzny; Alexander Goesmann; Paul Howley; Paul Chaplin; Mark Suter; Jürgen Hausmann
Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara.
The Journal of general virology 2007;88(Pt 12):3249-59.
2007: Martin Iain Bahl; Lars Hestbjerg Hansen; Alexander Goesmann; Søren J Sørensen
The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established alpha, beta and delta sub-groups.
Plasmid 2007;58(1):31-43.
2007: Udo Wegmann; Mary O'Connell-Motherway; Aldert L Zomer; Girbe Buist; Claire Shearman; Carlos Canchaya; Marco Ventura; Alexander Goesmann; Michael J Gasson; Oscar P Kuipers; Douwe van Sinderen; Jan Kok
Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363.
Journal of bacteriology 2007;189(8):3256-70.
2007: Heiko Neuweger; Jan Baumbach; Stefan Albaum; Thomas Bekel; Michael Dondrup; Andrea T Hüser; Jörn Kalinowski; Sebastian Oehm; Alfred Pühler; Sven Rahmann; Jochen Weile; Alexander Goesmann
CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data.
BMC systems biology 2007;1():55.
2007: Helge Küster; Anke Becker; Christian Firnhaber; Natalija Hohnjec; Katja Manthey; Andreas M Perlick; Thomas Bekel; Michael Dondrup; Kolja Henckel; Alexander Goesmann; Folker Meyer; Daniel Wipf; Natalia Requena; Ulrich Hildebrandt; Rüdiger Hampp; Uwe Nehls; Franziska Krajinski; Philipp Franken; Alfred Pühler
Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses.
Phytochemistry 2007;68(1):19-32.
2006: Andrea Krause; Adarsh Ramakumar; Daniela Bartels; Federico Battistoni; Thomas Bekel; Jens Boch; Melanie Böhm; Frauke Friedrich; Thomas Hurek; Lutz Krause; Burkhard Linke; Alice C McHardy; Abhijit Sarkar; Susanne Schneiker; Arshad Ali Syed; Rudolf Thauer; Frank-Jörg Vorhölter; Stefan Weidner; Alfred Pühler; Barbara Reinhold-Hurek; Olaf Kaiser; Alexander Goesmann
Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72.
Nature biotechnology 2006;24(11):1385-91.
2006: Torsten Hain; Christiane Steinweg; Carsten Tobias Kuenne; André Billion; Rohit Ghai; Som Subhra Chatterjee; Eugen Domann; Uwe Kärst; Alexander Goesmann; Thomas Bekel; Daniela Bartels; Olaf Kaiser; Folker Meyer; Alfred Pühler; Bernd Weisshaar; Jürgen Wehland; Chunguang Liang; Thomas Dandekar; Robert Lampidis; Jürgen Kreft; Werner Goebel; Trinad Chakraborty
Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes.
Journal of bacteriology 2006;188(21):7405-15.
2006: Susanne Schneiker; Vítor A P Martins Dos Santos; Daniela Bartels; Thomas Bekel; Martina Brecht; Jens Buhrmester; Tatyana N Chernikova; Renata Denaro; Manuel Ferrer; Christoph Gertler; Alexander Goesmann; Olga V Golyshina; Filip Kaminski; Amit N Khachane; Siegmund Lang; Burkhard Linke; Alice C McHardy; Folker Meyer; Taras Nechitaylo; Alfred Pühler; Daniela Regenhardt; Oliver Rupp; Julia S Sabirova; Werner Selbitschka; Michail M Yakimov; Kenneth N Timmis; Frank-Jörg Vorhölter; Stefan Weidner; Olaf Kaiser; Peter N Golyshin
Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis.
Nature biotechnology 2006;24(8):997-1004.
2005: Frank Thieme; Ralf Koebnik; Thomas Bekel; Carolin Berger; Jens Boch; Daniela Büttner; Camila Caldana; Lars Gaigalat; Alexander Goesmann; Sabine Kay; Oliver Kirchner; Christa Lanz; Burkhard Linke; Alice C McHardy; Folker Meyer; Gerhard Mittenhuber; Dietrich H Nies; Ulla Niesbach-Klösgen; Thomas Patschkowski; Christian Rückert; Oliver Rupp; Susanne Schneiker; Stephan C Schuster; Frank-Jörg Vorhölter; Ernst Weber; Alfred Pühler; Ulla Bonas; Daniela Bartels; Olaf Kaiser
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.
Journal of bacteriology 2005;187(21):7254-66.
2005: Alexander Goesmann; Burkhard Linke; Daniela Bartels; Michael Dondrup; Lutz Krause; H Neuweger; S Oehm; T Paczian; Andreas Wilke; Folker Meyer
BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser.
Nucleic acids research 2005;33(Web Server issue):W710-6.
2005: Andreas Tauch; Olaf Kaiser; Torsten Hain; Alexander Goesmann; Bernd Weisshaar; Andreas Albersmeier; Thomas Bekel; Nicole Bischoff; Iris Brune; Trinad Chakraborty; Jörn Kalinowski; Folker Meyer; Oliver Rupp; Susanne Schneiker; Prisca Viehoever; Alfred Pühler
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
Journal of bacteriology 2005;187(13):4671-82.
2005: Daniela Bartels; Sebastian Kespohl; Stefan Albaum; Tanja Drüke; Alexander Goesmann; Julia Herold; Olaf Kaiser; Alfred Pühler; Friedhelm Pfeiffer; Günter Raddatz; Jens Stoye; Folker Meyer; Stephan C Schuster
BACCardI--a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison.
Bioinformatics (Oxford, England) 2005;21(7):853-9.
2004: Rafael Szczepanowski; Irene Krahn; Burkhard Linke; Alexander Goesmann; Alfred Pühler; Andreas Schlüter
Antibiotic multiresistance plasmid pRSB101 isolated from a wastewater treatment plant is related to plasmids residing in phytopathogenic bacteria and carries eight different resistance determinants including a multidrug transport system.
Microbiology (Reading, England) 2004;150(Pt 11):3613-30.
2004: Alice C McHardy; Alexander Goesmann; Alfred Pühler; Folker Meyer
Development of joint application strategies for two microbial gene finders.
Bioinformatics (Oxford, England) 2004;20(10):1622-31.
2004: Joakim Westberg; Anja Persson; Anders Holmberg; Alexander Goesmann; Joakim Lundeberg; Karl-Erik Johansson; Bertil Pettersson; Mathias Uhlén
The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP).
Genome research 2004;14(2):221-7.
2004: Snjezana Rendulic; Pratik Jagtap; Andrea Rosinus; Mark Eppinger; Claudia Baar; Christa Lanz; Heike Keller; Carey Lambert; Katy J Evans; Alexander Goesmann; Folker Meyer; R Elizabeth Sockett; Stephan C Schuster
A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective.
Science (New York, N.Y.) 2004;303(5658):689-92.
2003: Alexander Goesmann; Burkhard Linke; Oliver Rupp; Lutz Krause; Daniela Bartels; Michael Dondrup; Alice C McHardy; Andreas Wilke; Alfred Pühler; Folker Meyer
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.
Journal of biotechnology 2003;106(2-3):157-67.
2003: Andreas Wilke; Christian Rückert; Daniela Bartels; Michael Dondrup; Alexander Goesmann; Andrea T Hüser; Sebastian Kespohl; Burkhard Linke; Martina Mahne; Alice C McHardy; Alfred Pühler; Folker Meyer
Bioinformatics support for high-throughput proteomics.
Journal of biotechnology 2003;106(2-3):147-56.
2003: Michael Dondrup; Alexander Goesmann; Daniela Bartels; Jörn Kalinowski; Lutz Krause; Burkhard Linke; Oliver Rupp; Alexander Sczyrba; Alfred Pühler; Folker Meyer
EMMA: a platform for consistent storage and efficient analysis of microarray data.
Journal of biotechnology 2003;106(2-3):135-46.
2003: Olaf Kaiser; Daniela Bartels; Thomas Bekel; Alexander Goesmann; Sebastian Kespohl; Alfred Pühler; Folker Meyer
Whole genome shotgun sequencing guided by bioinformatics pipelines--an optimized approach for an established technique.
Journal of biotechnology 2003;106(2-3):121-33.
2003: Jörn Kalinowski; Brigitte Bathe; Daniela Bartels; Nicole Bischoff; Michael Bott; Andreas Burkovski; Nicole Dusch; Lothar Eggeling; Bernhard J Eikmanns; Lars Gaigalat; Alexander Goesmann; Michael Hartmann; Klaus Huthmacher; Reinhard Krämer; Burkhard Linke; Alice C McHardy; Folker Meyer; Bettina Möckel; Walter Pfefferle; Alfred Pühler; Daniel A Rey; Christian Rückert; Oliver Rupp; Hermann Sahm; Volker F Wendisch; Iris Wiegräbe; Andreas Tauch
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Journal of biotechnology 2003;104(1-3):5-25.
2003: Folker Meyer; Alexander Goesmann; Alice C McHardy; Daniela Bartels; Thomas Bekel; Jörn Clausen; Jörn Kalinowski; Burkhard Linke; Oliver Rupp; Robert Giegerich; Alfred Pühler
GenDB--an open source genome annotation system for prokaryote genomes.
Nucleic acids research 2003;31(8):2187-95.
2003: Andreas Tauch; Andreas Schlüter; Nicole Bischoff; Alexander Goesmann; Folker Meyer; Alfred Pühler
The 79,370-bp conjugative plasmid pB4 consists of an IncP-1beta backbone loaded with a chromate resistance transposon, the strA-strB streptomycin resistance gene pair, the oxacillinase gene bla(NPS-1), and a tripartite antibiotic efflux system of the resistance-nodulation-division family.
Molecular genetics and genomics : MGG 2003;268(5):570-84.
2002: Alexander Goesmann; Martin Haubrock; Folker Meyer; Jörn Kalinowski; Robert Giegerich
PathFinder: reconstruction and dynamic visualization of metabolic pathways.
Bioinformatics (Oxford, England) 2002;18(1):124-9.