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Personal Homepage of Prof. Dr. Alexander Goesmann



Heinrich-Buff-Ring 58

Raum: I 003

Tel.: +49 (0)641 99 35-800
Tel.: +49 (0)641 99 35-801 (Sekr.) 


2013 - present Professor of Bioinformatics and Systems Biology, Gießen University, Germany
2010 - 2013 Member of the CeBiTec board of directors, CeBiTec, Bielefeld University, Germany
2009 - 2013 Vice speaker of the Institute for Bioinformatics, CeBiTec, Bielefeld University, Germany
2007 - 2013 Leader of the Junior Research Group “Computational Genomics”, Institute for Bioinformatics, CeBiTec, Bielefeld University, Germany
2006 - 2013 Head of the Bioinformatics Resource Facility (BRF), CeBiTec, Bielefeld University, Germany
2004 - 2006 PostDoc at Bielefeld University, Germany
2004 PhD - Faculty of Technology, Bielefeld University, Bielefeld, Germany
2001 - 2006 Employment within the BMBF competence network for “Genome Research on Bacteria relevant for Agriculture, Environment and Biotechnology” (GenoMik) at Bielefeld University, Germany
2000 - 2001 PhD grant “Graduiertenkolleg Bioinformatik”, Bielefeld University, Germany
2000 Diploma - Informatics in the Natural Sciences, Faculty of Technology, Bielefeld University, Bielefeld, Germany
1993 School leaving examination (Abitur), Gymnasium Warstein
1974 Born in Warstein, Germany



Schwengers, O., Hoek, A., Fritzenwanker, M., Falgenhauer, L., Hain, T., Chakraborty, T. and Goesmann, A., 2020. ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates. PLoS Computational Biology, 16(3), DOI:10.1371/journal.pcbi.1007134.

Lick, S., Kröckel, L., Wibberg, D., Winkler, A., Blom, J., Goesmann, A. and Kalinowski, J., 2020. Pseudomonas bubulae sp. Nov., isolated from beef. International Journal of Systematic and Evolutionary Microbiology, 70(1), pp.292-301, DOI:10.1099/ijsem.0.003751.

Lick, S., Kröckel, L., Wibberg, D., Winkler, A., Blom, J., Bantleon, A., Goesmann, A. and Kalinowski, J., 2020. Pseudomonas carnis sp. Nov., isolated from meat. International Journal of Systematic and Evolutionary Microbiology, 70(3), pp.1528-1540, DOI:10.1099/ijsem.0.003928.

Sauerhering, L., Kupke, A., Meier, L., Dietzel, E., Hoppe, J., Gruber, A.D., Gattenloehner, S., Witte, B., Fink, L., Hofmann, N., Zimmermann, T., Goesmann, A., Nist, A., Stiewe, T., Becker, S., Herold, S. and Peteranderl, C., 2020. Cyclophilin Inhibitors Restrict Middle East Respiratory Syndrome Coronavirus Via Interferon λ In Vitro And In Mice. European Respiratory Journal, p.1901826, DOI:10.1183/13993003.01826-2019.

Schwengers, O., Barth, P., Falgenhauer, L., Hain, T., Chakraborty, T. and Goesmann, A., 2020. Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microbial genomics, DOI:10.1099/mgen.0.000398.


Suarez, C., Ratering, S., Hain, T., Fritzenwanker, M., Goesmann, A., Blom, J., Chakraborty, T., Bunk, B., Spröer, C., Overmann, J. and Schnell, S., 2019. Complete Genome Sequence of the Plant Growth-Promoting Bacterium Hartmannibacter diazotrophicus Strain E19T. International journal of genomics, p.7586430, DOI:10.1155/2019/7586430.

Ludueña, L.M., Anzuay, M.S., Angelini, J.G., McIntosh, M., Becker, A., Rupp, O., Goesmann, A., Blom, J., Fabra, A. and Taurian, T., 2019. Genome sequence of the endophytic strain Enterobacter sp. J49, a potential biofertilizer for peanut and maize. Genomics, 111(4), pp.913-920, DOI:10.1016/j.ygeno.2018.05.021.

Falgenhauer, J., Imirzalioglu, C., Falgenhauer, L., Yao, Y., Hauri, A.M., Erath, B., Schwengers, O., Goesmann, A., Seifert, H., Chakraborty, T. and Doijad, S., 2019. Whole-Genome Sequences of Clinical Enterobacter bugandensis Isolates from Germany. Microbiology Resource Announcements, 8(29), DOI:10.1128/mra.00465-19.

Farr, M., Ferreira, S., Al-Dilaimi, A., Bögeholz, S., Goesmann, A., Kalinowski, J., Knabbe, C., Faber, L., Oliveira, J.P. and Rudolph, V., 2019. Fabry disease: Detection of Alu-mediated exon duplication by NGS. Molecular and Cellular Probes, pp.79-83, DOI:10.1016/j.mcp.2019.03.008.

López, J.L., Lozano, M.J., Lagares, A., Fabre, M.L., Draghi, W.O., Del Papa, M.F., Pistorio, M., Becker, A., Wibberg, D., Schlüter, A., Pühler, A., Blom, J., Goesmann, A. and Lagares, A., 2019. Codon usage heterogeneity in the multipartite prokaryote genome: Selection-based coding bias associated with gene location, expression level, and ancestry. mBio, 10(3), DOI:10.1128/mBio.00505-19.

Bouhired, S., Rupp, O., Blom, J., Schäberle, T.F., Schiefer, A., Kehraus, S., Pfarr, K., Goesmann, A., Hoerauf, A. and König, G., 2019. Complete Genome Sequence of the Corallopyronin A-Producing Myxobacterium Corallococcus coralloides B035. Microbiology Resource Announcements, 8(17), DOI:10.1128/mra.00050-19.

Gerresheim, G.K., Bathke, J., Michel, A.M., Andreev, D.E., Shalamova, L.A., Rossbach, O., Hu, P., Glebe, D., Fricke, M., Marz, M., Goesmann, A., Kiniry, S.J., Baranov, P.V., Shatsky, I.N. and Niepmann, M., 2019. Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling. International journal of molecular sciences, 20(6), DOI:10.3390/ijms20061321.

Baal, N., Cunningham, S., Obermann, H., Thomas, J., Lippitsch, A., Dietert, K., Gruber, A.D., Kaufmann, A., Michel, G., Nist, A., Stiewe, T., Rupp, O., Goesmann, A., Zukunft, S., Fleming, I., Bein, G., Lohmeyer, J., Bauer, S. and Hackstein, H., 2019. ADAR1 Is Required for Dendritic Cell Subset Homeostasis and Alveolar Macrophage Function. Journal of immunology (Baltimore, Md. : 1950), 202(4), pp.1099-1111, DOI:10.4049/jimmunol.1800269.


Schult, F., Le, T.N., Albersmeier, A., Rauch, B., Blumenkamp, P., van der Does, C., Goesmann, A., Kalinowski, J., Albers, S. and Siebers, B., 2018. Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response. Nucleic acids research, 46(14), pp.7179-7192, DOI:10.1093/nar/gky527.

Pati, N.B., Doijad, S.P., Schultze, T., Mannala, G.K., Yao, Y., Jaiswal, S., Ryan, D., Suar, M., Gwozdzinski, K., Bunk, B., Mraheil, M.A., Marahiel, M.A., Hegemann, J.D., Spröer, C., Goesmann, A., Falgenhauer, L., Hain, T., Imirzalioglu, C., Mshana, S.E., Overmann, J. and Chakraborty, T., 2018. Enterobacter bugandensis: A novel enterobacterial species associated with severe clinical infection. Scientific Reports, 8(1), DOI:10.1038/s41598-018-23069-z.

Rupp, O., MacDonald, M.L., 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, M.J., Lewis, N.E., Borth, N. and Lee, K.H., 2018. A reference genome of the Chinese hamster based on a hybrid assembly strategy. Biotechnology and Bioengineering, 115(8), pp.2087-2100, DOI:10.1002/bit.26722.

Jaenicke, S., Albaum, S.P., Blumenkamp, P., Linke, B., Stoye, J. and Goesmann, A., 2018. Flexible metagenome analysis using the MGX framework. Microbiome, 6(1), p.76, DOI:10.1186/s40168-018-0460-1.

Kämpfer, P., Rückert, C., Blom, J., Goesmann, A., Wink, J., Kalinowski, J. and Glaeser, S.P., 2018. Streptomyces ciscaucasicus sveshnikova et al. 1983 is a later subjective synonym of streptomyces canus heinemann et al. 1953. International Journal of Systematic and Evolutionary Microbiology, 68(1), pp.42-46, DOI:10.1099/ijsem.0.002418.

Landwehr, W., Kämpfer, P., Glaeser, S.P., Rückert, C., Kalinowski, J., Blom, J., Goesmann, A., Mack, M., Schumann, P., Atasayar, E., Hahnke, R.L., Rohde, M., Martin, K., Stadler, M. and Wink, J., 2018. Taxonomic analyses of members of the streptomyces cinnabarinus cluster, description of streptomyces cinnabarigriseus sp. Nov. and streptomyces davaonensis sp. nov. International Journal of Systematic and Evolutionary Microbiology, 68(1), pp.382-393, DOI:10.1099/ijsem.0.002519.


Mannala, G.K., Izar, B., Rupp, O., Schultze, T., Goesmann, A., Chakraborty, T. and Hain, T., 2017. Listeria monocytogenes induces a virulence-dependent microRNA signature that regulates the immune response in Galleria mellonella. Frontiers in Microbiology, 8(DEC), DOI:10.3389/fmicb.2017.02463.

Golyshina, O.V., Tran, H., Reva, O.N., Lemak, S., Yakunin, A.F., Goesmann, A., Nechitaylo, T.Y., Lacono, V., Smedile, F., Slesarev, A., Rojo, D., Barbas, C., Ferrer, M., Yakimov, M.M. and Golyshin, P.N., 2017. Metabolic and evolutionary patterns in the extremely acidophilic archaeon Ferroplasma acidiphilum YT. Scientific Reports, 7(1), DOI:10.1038/s41598-017-03904-5.

Kämpfer, P., Rückert, C., Blom, J., Goesmann, A., Wink, J., Kalinowski, J. and Glaeser, S.P., 2017. 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. International Journal of Systematic and Evolutionary Microbiology, 67(8), pp.3111-3116, DOI:10.1099/ijsem.0.002110.

Yu, J., Blom, J., Glaeser, S.P., Jaenicke, S., Juhre, T., Rupp, O., Schwengers, O., Spänig, S. and Goesmann, A., 2017. A review of bioinformatics platforms for comparative genomics. Recent developments of the EDGAR 2.0 platform and its utility for taxonomic and phylogenetic studies., pp.2-9, DOI:10.1016/j.jbiotec.2017.07.010.

Jünemann, S., Kleinbölting, N., Jaenicke, S., Henke, C., Hassa, J., Nelkner, J., Stolze, Y., Albaum, S.P., Schlüter, A., Goesmann, A., Sczyrba, A. and Stoye, J., 2017. Bioinformatics for NGS-based metagenomics and the application to biogas research., pp.10-23, DOI:10.1016/j.jbiotec.2017.08.012.

Treuner-Lange, A., Bruckskotten, M., Rupp, O., Goesmann, A. and Søgaard-Andersen, L., 2017. Complete genome sequence of the fruiting myxobacterium Melittangium boletus DSM 14713. Genome Announcements, 5(45), DOI:10.1128/genomeA.01262-17.

Treuner-Lange, A., Bruckskotten, M., Rupp, O., Goesmann, A. and Søgaard-Andersen, L., 2017. Complete Genome Sequence of the Fruiting Myxobacterium Myxococcus macrosporus Strain DSM 14697, Generated by PacBio Sequencing. Genome announcements, 5(40), DOI:10.1128/genomeA.01127-17.

Treuner-Lange, A., Bruckskotten, M., Rupp, O., Goesmann, A. and Søgaard-Andersen, L., 2017. Draft genome sequence of the fruiting myxobacterium Nannocystis exedens DSM 71. Genome Announcements, 5(43), DOI:10.1128/genomeA.01227-17.

Treuner-Lange, A., Bruckskotten, M., Rupp, O., Goesmann, A. and Søgaard-Andersen, L., 2017. Whole-Genome Sequence of the Fruiting Myxobacterium Cystobacter fuscus DSM 52655. Genome announcements, 5(43), DOI:10.1128/genomeA.01196-17.

Wibberg, D., Genzel, F., Verwaaijen, B., Blom, J., Rupp, O., Goesmann, A., Zrenner, R., Grosch, R., Pühler, A. and Schlüter, A., 2017. Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Archives of microbiology, 199(7), pp.1065-1068, DOI:10.1007/s00203-017-1394-x.

Serranía, J., Johner, T., Rupp, O., Goesmann, A. and Becker, A., 2017. Massive parallel insertion site sequencing of an arrayed Sinorhizobium meliloti signature-tagged mini-Tn 5 transposon mutant library. Journal of Biotechnology, pp.9-12, DOI:10.1016/j.jbiotec.2017.02.019.

Yu, J., Blom, J., Sczyrba, A. and Goesmann, A., 2017. Rapid protein alignment in the cloud: HAMOND combines fast DIAMOND alignments with Hadoop parallelism. Journal of Biotechnology, pp.58-60, DOI:10.1016/j.jbiotec.2017.02.020.

Schatschneider, S., Schneider, J., Blom, J., Létisse, F., Niehaus, K., Goesmann, A. and Vorhölter, F.J., 2017. Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium xanthomonas campestris., 163(8), pp.1117-1144, DOI:10.1099/mic.0.000473.

Jaeger, D., Winkler, A., Mussgnug, J.H., Kalinowski, J., Goesmann, A. and Kruse, O., 2017. Time-resolved transcriptome analysis and lipid pathway reconstruction of the oleaginous green microalga Monoraphidium neglectum reveal a model for triacylglycerol and lipid hyperaccumulation. Biotechnology for biofuels, 10(1), p.197, DOI:10.1186/s13068-017-0882-1.

Schmautz, Z., Graber, A., Jaenicke, S., Goesmann, A., Junge, R. and Smits, T.H., 2017. Microbial diversity in different compartments of an aquaponics system. Archives of Microbiology, 199(4), pp.613-620, DOI:10.1007/s00203-016-1334-1.

Ampattu, B.J., Hagmann, L., Liang, C., Dittrich, M., Schlüter, A., Blom, J., Krol, E., Goesmann, A., Becker, A., Dandekar, T., Müller, T. and Schoen, C., 2017. Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence. BMC Genomics, 18(1), DOI:10.1186/s12864-017-3616-7.

Cardoso, S.D., Gonçalves, D., Goesmann, A., Canário, A.V. and Oliveira, R.F., 2017. Temporal variation in brain transcriptome is associated with the expression of female mimicry as a sequential male alternative reproductive tactic in fish. Molecular Ecology, 27(3), pp.789-803, DOI:10.1111/mec.14408.

Klughammer, J., Dittrich, M., Blom, J., Mitesser, V., Vogel, U., Frosch, M., Goesmann, A., Müller, T. and Schoen, C., 2017. Comparative genome sequencing reveals within-host genetic changes in neisseria meningitidis during invasive disease. PLoS ONE, 12(1), DOI:10.1371/journal.pone.0169892.

Hersemann, L., Wibberg, D., Blom, J., Goesmann, A., Widmer, F., Vorhölter, F.J. and Kölliker, R., 2017. Comparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis. BMC Genomics, 18(1), DOI:10.1186/s12864-016-3422-7.

Petkauskaite, R., Blom, J., Goesmann, A. and Kuisiene, N., 2017. Draft genome sequence of pectic polysaccharide-degrading moderate thermophilic bacterium Geobacillus thermodenitrificans DSM 101594. Brazilian Journal of Microbiology, 48(1), pp.7-8, DOI:10.1016/j.bjm.2016.06.013.

Makarewicz, O., Lucas, M., Brandt, C., Herrmann, L., Albersmeier, A., Rückert, C., Blom, J., Goesmann, A., Van Der Linden, M., Kalinowski, J. and Pletz, M.W., 2017. Whole genome sequencing of 39 invasive Streptococcus pneumoniae sequence type 199 isolates revealed switches from serotype 19A to 15B. PLoS ONE, 12(1), DOI:10.1371/journal.pone.0169370.


Wegmann, U., Goesmann, A. and Carding, S.R., 2016. Complete Genome Sequence of Bacteroides ovatus V975. Genome Announcements, 4(6), DOI:10.1128/genomea.01335-16.

Langenkämper, D., Jakobi, T., Feld, D., Jelonek, L., Goesmann, A. and Nattkemper, T.W., 2016. Comparison of Acceleration Techniques for Selected Low-Level Bioinformatics Operations. Frontiers in genetics, 7(FEB), p.5, DOI:10.3389/fgene.2016.00005.

Blifernez-Klassen, O., Wibberg, D., Winkler, A., Blom, J., Goesmann, A., Kalinowski, J. and Kruse, O., 2016. Complete chloroplast and mitochondrial genome sequences of the hydrocarbon oil-producing green microalga Botryococcus braunii race B (Showa). Genome Announcements, 4(3), DOI:10.1128/genomeA.00524-16.

Jaenicke, S., Bunk, B., Wibberg, D., Spröer, C., Hersemann, L., Blom, J., Winkler, A., Schatschneider, S., Albaum, S.P., Kölliker, R., Goesmann, A., Pühler, A., Overmann, J. and Vorhölter, F.J., 2016. Complete genome sequence of the barley pathogen Xanthomonas translucens pv. translucens DSM 18974T (ATCC 19319T). Genome Announcements, 4(6), DOI:10.1128/genomeA.01334-16.

Bertelli, C., Cissé, O.H., Rusconi, B., Kebbi-Beghdadi, C., Croxatto, A., Goesmann, A., Collyn, F. and Greub, G., 2016. CRISPR system acquisition and evolution of an obligate intracellular chlamydia-related bacterium. Genome Biology and Evolution, 8(8), pp.2376-2386, DOI:10.1093/gbe/evw138.

Barbeyron, T., Thomas, F., Barbe, V., Teeling, H., Schenowitz, C., Dossat, C., Goesmann, A., Leblanc, C., Oliver Glöckner, F., Czjzek, M., Amann, R. and Michel, G., 2016. Habitat and taxon as driving forces of carbohydrate catabolism in marine heterotrophic bacteria: example of the model algae-associated bacterium Zobellia galactanivorans DsijT. Environmental Microbiology, 18(12), pp.4610-4627, DOI:10.1111/1462-2920.13584.

Franta, Z., Vogel, H., Lehmann, R., Rupp, O., Goesmann, A. and Vilcinskas, A., 2016. Next Generation Sequencing Identifies Five Major Classes of Potentially Therapeutic Enzymes Secreted by Lucilia sericata Medical Maggots. BioMed research international, p.8285428, DOI:10.1155/2016/8285428.

Hilker, R., Stadermann, K.B., Schwengers, O., Anisiforov, E., Jaenicke, S., Weisshaar, B., Zimmermann, T. and Goesmann, A., 2016. ReadXplorer 2-detailed read mapping analysis and visualization from one single source. Bioinformatics, 32(24), pp.3702-3708, DOI:10.1093/bioinformatics/btw541.

Maus, I., Koeck, D.E., Cibis, K.G., Hahnke, S., Kim, Y.S., Langer, T., Kreubel, J., Erhard, M., Bremges, A., Off, S., Stolze, Y., Jaenicke, S., Goesmann, A., Sczyrba, A., Scherer, P., König, H., Schwarz, W.H., Zverlov, V.V., Liebl, W., Pühler, A., Schlüter, A. and Klocke, M., 2016. Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates. Biotechnology for Biofuels, 9(1), DOI:10.1186/s13068-016-0581-3.

Morales, M., Sentchilo, V., Bertelli, C., Komljenovic, A., Kryuchkovc-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., Buendia, G.R., Pillard, L., Escoriza, A., Moritz, R., Schneider, C., Alfonso, E., Jeddou, F.B., Selmoni, O., Resch, G., Greub, G., Emery, O., Dubey, M., Pillonel, T., Robinson-Rechavi, M. and Van Der Meer, J.R., 2016. The genome of the toluene-degrading Pseudomonas veronii strain 1YdBTEX2 and its differential gene expression in contaminated sand. PLoS ONE, 11(11), DOI:10.1371/journal.pone.0165850.

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. and Kogel, K.H., 2016. 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. PLoS Pathogens, 12(10), DOI:10.1371/journal.ppat.1005901.

Flury, P., Aellen, N., Ruffner, B., Péchy-Tarr, M., Fataar, S., Metla, Z., Dominguez-Ferreras, A., Bloemberg, G., Frey, J., Goesmann, A., Raaijmakers, J.M., Duffy, B., Höfte, M., Blom, J., Smits, T.H.M., Keel, C. and Maurhofer, M., 2016. Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. The ISME journal, 10(10), pp.2527-42, DOI:10.1038/ismej.2016.5.

Falgenhauer, L., Waezsada, S.E., 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. and Chakraborty, T., 2016. Chromosomal locations of mcr-1 and blaCTX-M-15 in fluoroquinolone-resistant Escherichia coli ST410., 22(9), pp.1689-1691, DOI:10.3201/eid2209.160692.

Blom, J., Kreis, J., Spänig, S., Juhre, T., Bertelli, C., Ernst, C. and Goesmann, A., 2016. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic acids research, 44(W1), pp.W22-W28, DOI:10.1093/nar/gkw255.

Ghatak, S., Blom, J., Das, S., Sanjukta, R., Puro, K., Mawlong, M., Shakuntala, I., Sen, A., Goesmann, A., Kumar, A. and Ngachan, S.V., 2016. Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila. Antonie van Leeuwenhoek, 109(7), pp.945-56, DOI:10.1007/s10482-016-0693-6.

Falgenhauer, L., Imirzalioglu, C., Ghosh, H., Gwozdzinski, K., Schmiedel, J., Gentil, K., Bauerfeind, R., Kämpfer, P., Seifert, H., Michael, G.B., Schwarz, S., Pfeifer, Y., Werner, G., Pietsch, M., Roesler, U., Guerra, B., Fischer, J., Sharp, H., Käsbohrer, A., Goesmann, A., Hille, K., Kreienbrock, L. and Chakraborty, T., 2016. Circulation of clonal populations of fluoroquinolone-resistant CTX-M-15-producing Escherichia coli ST410 in humans and animals in Germany. International Journal of Antimicrobial Agents, 47(6), pp.457-465, DOI:10.1016/j.ijantimicag.2016.03.019.

Barbuddhe, S.B., Doijad, S.P., Goesmann, A., Hilker, R., Poharkar, K.V., Rawool, D.B., Kurkure, N.V., Kalorey, D.R., Malik, S.S., 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. and Chakraborty, T., 2016. Presence of a widely disseminated Listeria monocytogenes serotype 4b clone in India., 5(6), DOI:10.1038/emi.2016.55.

Fischer, S., Klockgether, J., Morán Losada, P., Chouvarine, P., Cramer, N., Davenport, C.F., Dethlefsen, S., Dorda, M., Goesmann, A., Hilker, R., Mielke, S., Schönfelder, T., Suerbaum, S., Türk, O., Woltemate, S., Wiehlmann, L. and Tümmler, B., 2016. Intraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14. Environmental microbiology reports, 8(2), pp.227-34, DOI:10.1111/1758-2229.12372.

Glaeser, S.P., Imani, J., Alabid, I., Guo, H., Kumar, N., Kämpfer, P., Hardt, M., Blom, J., Goesmann, A., Rothballer, M., Hartmann, A. and Kogel, K.H., 2016. Non-pathogenic Rhizobium radiobacter F4 deploys plant beneficial activity independent of its host Piriformospora indica. ISME Journal, 10(4), pp.871-884, DOI:10.1038/ismej.2015.163.

Falgenhauer, L., Waezsada, S., Yao, Y., Imirzalioglu, C., Käsbohrer, A., Roesler, U., Michael, G.B., Schwarz, S., Werner, G., Kreienbrock, L., Chakraborty, T. and consortium, R., 2016. Colistin resistance gene mcr-1 in extended-spectrum β-lactamase-producing and carbapenemase-producing Gram-negative bacteria in Germany. The Lancet. Infectious diseases, 16(3), pp.282-3, DOI:10.1016/S1473-3099(16)00009-8.

Sobetzko, P., Jelonek, L., Strickert, M., Han, W., Goesmann, A. and Waldminghaus, T., 2016. DistAMo: A Web-Based Tool to Characterize DNA-Motif Distribution on Bacterial Chromosomes. Frontiers in microbiology, 7(MAR), p.283, DOI:10.3389/fmicb.2016.00283.

Wibberg, D., Andersson, L., Rupp, O., Goesmann, A., Pühler, A., Varrelmann, M., Dixelius, C. and Schlüter, A., 2016. Draft genome sequence of the sugar beet pathogen Rhizoctonia solani AG2-2IIIB strain BBA69670. Journal of biotechnology, pp.11-2, DOI:10.1016/j.jbiotec.2016.02.001.

Rezzonico, F., Smits, T.H.M., Born, Y., Blom, J., Frey, J.E., Goesmann, A., Cleenwerck, I., de Vos, P., Bonaterra, A., Duffy, B. and Montesinos, E., 2016. Erwinia gerundensis sp. nov., a cosmopolitan epiphyte originally isolated from pome fruit trees. International journal of systematic and evolutionary microbiology, 66(3), pp.1583-1592, DOI:10.1099/ijsem.0.000920.


Schultze, T., Hilker, R., Mannala, G.K., Gentil, K., Weigel, M., Farmani, N., Windhorst, A.C., Goesmann, A., Chakraborty, T. and Hain, T., 2015. A detailed view of the intracellular transcriptome of Listeria monocytogenes in murine macrophages using RNA-seq. Frontiers in Microbiology, 6(OCT), DOI:10.3389/fmicb.2015.01199.

Zschüttig, A., Auerbach, C., Meltke, S., Eichhorn, C., Brandt, M., Blom, J., Goesmann, A., Jarek, M., Scharfe, M., Zimmermann, K., Wassenaar, T.M. and Gunzer, F., 2015. 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. Genome Announcements, 3(2), DOI:10.1128/genomeA.01330-14.

Pauli, M., Chakarov, N., Rupp, O., Kalinowski, J., Goesmann, A., Sorenson, M.D., Krüger, O. and Hoffman, J.I., 2015. De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite. BMC Genomics, 16(1), DOI:10.1186/s12864-015-2254-1.

Wibberg, D., Rupp, O., Blom, J., Jelonek, L., Kröber, M., Verwaaijen, B., Goesmann, A., Albaum, S., Grosch, R., Pühler, A. and Schlüter, A., 2015. 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. PLoS ONE, 10(12), DOI:10.1371/journal.pone.0144769.

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. and Vorhölter, F.J., 2015. Draft genome sequence of Pseudomonas aeruginosa strain WS136, a highly cytotoxic ExoS-positive wound isolate recovered from pyoderma gangrenosum. Genome Announcements, 3(4), DOI:10.1128/genomeA.00680-15.

Smits, T.H., Rezzonico, F., Blom, J., Goesmann, A., Abelli, A., Morelli, R.K., Vanneste, J.L. and Duffy, B., 2015. Draft genome sequence of the commercial biocontrol strain Pantoea agglomerans P10c. Genome Announcements, 3(6), DOI:10.1128/genomeA.01448-15.

Wibberg, D., Tielen, P., Narten, M., Schobert, M., Blom, J., Schatschneider, S., Meyer, A.K., Neubauer, R., Albersmeier, A., Albaum, S., Jahn, M., Goesmann, A., Vorhölter, F.J., Pühler, A. and Jahn, D., 2015. Genome sequence of the urethral isolate Pseudomonas aeruginosa RN21. Genome Announcements, 3(4), DOI:10.1128/genomeA.00788-15.

Kessler, N., Bonte, A., Albaum, S.P., Mäder, P., Messmer, M., Goesmann, A., Niehaus, K., Langenkämper, G. and Nattkemper, T.W., 2015. Learning to classify organic and conventional wheat - A machine learning driven approach using the MeltDB 2.0 metabolomics analysis platform. Frontiers in Bioengineering and Biotechnology, 3(MAR), DOI:10.3389/fbioe.2015.00035.

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, W.H., Goesmann, A., Harshman, K., Linke, B., Miyazaki, R., Rivolta, C., Robinson-Rechavi, M., van der Meer, J.R. and Greub, G., 2015. Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: Training students and biological insights. Frontiers in Microbiology, 6(FEB), DOI:10.3389/fmicb.2015.00101.

Wegmann, U., MacKenzie, D.A., Zheng, J., Goesmann, A., Roos, S., Swarbreck, D., Walter, J., Crossman, L.C. and Juge, N., 2015. The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. BMC Genomics, 16(1), DOI:10.1186/s12864-015-2216-7.

Rupp, O., Brinkrolf, K., Buerth, C., Kunigo, M., Schneider, J., Jaenicke, S., Goesmann, A., Pühler, A., Jaeger, K.E. and Ernst, J.F., 2015. The structure of the Cyberlindnera jadinii genome and its relation to Candida utilis analyzed by the occurrence of single nucleotide polymorphisms. Journal of Biotechnology, pp.20-30, DOI:10.1016/j.jbiotec.2015.06.423.

Vinardell, J.M., Acosta-Jurado, S., Zehner, S., Göttfert, M., Becker, A., Baena, I., Blom, J., Crespo-Rivas, J.C., Goesmann, A., Jaenicke, S., Krol, E., McIntosh, M., Margaret, I., Pérez-Montaño, F., Schneiker-Bekel, S., Serranía, J., Szczepanowski, R., Buendía, A.M., Lloret, J., Bonilla, I., Pühler, A., Ruiz-Sainz, J.E. and Weidner, S., 2015. The Sinorhizobium fredii HH103 genome: A comparative analysis with S. fredii strains differing in their symbiotic behavior with soybean. Molecular Plant-Microbe Interactions, 28(7), pp.811-824, DOI:10.1094/MPMI-12-14-0397-FI.

Wibberg, D., Rupp, O., Jelonek, L., Kröber, M., Verwaaijen, B., Blom, J., Winkler, A., Goesmann, A., Grosch, R., Pühler, A. and Schlüter, A., 2015. 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. Journal of Biotechnology, pp.19-21, DOI:10.1016/j.jbiotec.2015.03.005.

Chakarov, N., Linke, B., Boerner, M., Goesmann, A., Krüger, O. and Hoffman, J.I., 2015. Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite. Molecular Ecology, 24(6), pp.1355-1363, DOI:10.1111/mec.13115.

Zischka, M., Künne, C.T., Blom, J., Wobser, D., Sakinç, T., Schmidt-Hohagen, K., Dabrowski, P.W., Nitsche, A., Hübner, J., Hain, T., Chakraborty, T., Linke, B., Goesmann, A., Voget, S., Daniel, R., Schomburg, D., Hauck, R., Hafez, H.M., Tielen, P., Jahn, D., Solheim, M., Sadowy, E., Larsen, J., Jensen, L.B., Ruiz-Garbajosa, P., Quiñones Pérez, D., Mikalsen, T., Bender, J., Steglich, M., Nübel, U., Witte, W. and Werner, G., 2015. Comprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40. BMC Genomics, 16(1), DOI:10.1186/s12864-015-1367-x.

Vorhölter, F., Tielen, P., Wibberg, D., Narten, M., Schobert, M., Tüpker, R., Blom, J., Schatschneider, S., Winkler, A., Albersmeier, A., Goesmann, A., Pühler, A. and Jahn, D., 2015. Genome Sequence of the Urethral Catheter Isolate Pseudomonas aeruginosa MH19. Genome announcements, 3(2), DOI:10.1128/genomeA.00115-15.

Doijad, S., Weigel, M., Barbuddhe, S., Blom, J., Goesmann, A., Hain, T. and Chakraborty, T., 2015. Phylogenomic grouping of listeria monocytogenes. Canadian Journal of Microbiology, 61(9), pp.637-646, DOI:10.1139/cjm-2015-0281.

Miyazaki, R., Bertelli, C., Benaglio, P., Canton, J., De Coi, N., Gharib, W.H., Gjoksi, B., Goesmann, A., Greub, G., Harshman, K., Linke, B., Mikulic, J., Mueller, L., Nicolas, D., Robinson-Rechavi, M., Rivolta, C., Roggo, C., Roy, S., Sentchilo, V., Siebenthal, A.V., Falquet, L. and van der Meer, J.R., 2015. Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environmental Microbiology, 17(1), pp.91-104, DOI:10.1111/1462-2920.12498.

Huja, S., Oren, Y., Trost, E., Brzuszkiewicz, E., Biran, D., Blom, J., Goesmann, A., Gottschalk, G., Hacker, J., Ron, E.Z. and Dobrindt, U., 2015. Genomic avenue to avian colisepticemia. mBio, 6(1), DOI:10.1128/mBio.01681-14.

Hilker, R., Munder, A., Klockgether, J., Losada, P.M., Chouvarine, P., Cramer, N., Davenport, C.F., Dethlefsen, S., Fischer, S., Peng, H., Schönfelder, T., Türk, O., Wiehlmann, L., Wölbeling, F., Gulbins, E., Goesmann, A. and Tümmler, B., 2015. Interclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment. Environmental Microbiology, 17(1), pp.29-46, DOI:10.1111/1462-2920.12606.


Langenkämper, D., Goesmann, A. and Nattkemper, T.W., 2014. AKE - the Accelerated -mer Exploration web-tool for rapid taxonomic classification and visualization. BMC Bioinformatics, 15(1), DOI:10.1186/s12859-014-0384-0.

Bertelli, C., Goesmann, A. and Greub, G., 2014. Criblamydia sequanensis harbors a megaplasmid encoding arsenite resistance. Genome Announcements, 2(5), DOI:10.1128/genomeA.00949-14.

Vorhölter, F.J., Arnold, M., Wibberg, D., Blom, J., Winkler, A., Viehoever, P., Albersmeier, A., Goesmann, A., Zange, S., Heesemann, J., Pühler, A. and Hogardt, M., 2014. Draft genome sequence of Pseudomonas aeruginosa strain WS394, a multidrug-resistant and highly cytotoxic wound isolate from chronic ulcus cruris. Genome Announcements, 2(6), DOI:10.1128/genomeA.01325-14.

Christiansen, G., Goesmann, A. and Kurmayer, R., 2014. Elucidation of insertion elements carried on plasmids and in vitro construction of shuttle vectors from the toxic cyanobacterium Planktothrix. Applied and Environmental Microbiology, 80(16), pp.4887-4897, DOI:10.1128/AEM.01188-14.

Wibberg, D., Tielen, P., Blom, J., Rosin, N., Schobert, M., Tüpker, R., Schatschneider, S., Spilker, D., Albersmeier, A., Goesmann, A., Vorhölter, F.J., Pühler, A. and Jahn, D., 2014. Genome sequence of the acute urethral catheter isolate Pseudomonas aeruginosa MH38. Genome Announcements, 2(2), DOI:10.1128/genomeA.00161-14.

Bonte, A., Neuweger, H., Goesmann, A., Thonar, C., Mäder, P., Langenkämper, G. and Niehaus, K., 2014. Metabolite profiling on wheat grain to enable a distinction of samples from organic and conventional farming systems. Journal of the Science of Food and Agriculture, 94(13), pp.2605-2612, DOI:10.1002/jsfa.6566.

Dohm, J.C., Minoche, A.E., Holtgräwe, D., Capella-Gutiérrez, S., Zakrzewski, F., Tafer, H., Rupp, O., Sörensen, T.R., Stracke, R., Reinhardt, R., Goesmann, A., Kraft, T., Schulz, B., Stadler, P.F., Schmidt, T., Gabaldón, T., Lehrach, H., Weisshaar, B. and Himmelbauer, H., 2014. The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). Nature, 505(7484), pp.546-549, DOI:10.1038/nature12817.

Wibberg, D., Jelonek, L., Rupp, O., Kröber, M., Goesmann, A., Grosch, R., Pühler, A. and Schlüter, A., 2014. Transcriptome analysis of the phytopathogenic fungus Rhizoctonia solani AG1-IB 7/3/14 applying high-throughput sequencing of expressed sequence tags (ESTs). Fungal Biology, 118(9), pp.800-813, DOI:10.1016/j.funbio.2014.06.007.

Kessler, N., Walter, F., Persicke, M., Albaum, S.P., Kalinowski, J., Goesmann, A., Niehaus, K. and Nattkemper, T.W., 2014. Allocator: An interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis. PLoS ONE, 9(11), DOI:10.1371/journal.pone.0113909.

Jakobi, T., Brinkrolf, K., Tauch, A., Noll, T., Stoye, J., Pühler, A. and Goesmann, A., 2014. Discovery of transcription start sites in the Chinese hamster genome by next-generation RNA sequencing. Journal of Biotechnology, pp.64-75, DOI:10.1016/j.jbiotec.2014.07.437.

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. and Antranikian, G., 2014. Carbohydrate-active enzymes identified by metagenomic analysis of deep-sea sediment bacteria. Extremophiles, 18(5), pp.853-863, DOI:10.1007/s00792-014-0676-3.

Wegmann, U., Louis, P., Goesmann, A., Henrissat, B., Duncan, S.H. and Flint, H.J., 2014. Complete genome of a new Firmicutes species belonging to the dominant human colonic microbiota ('Ruminococcus bicirculans') reveals two chromosomes and a selective capacity to utilize plant glucans. Environmental microbiology, 16(9), pp.2879-90, DOI:10.1111/1462-2920.12217.

Jünemann, S., Prior, K., Albersmeier, A., Albaum, S., Kalinowski, J., Goesmann, A., Stoye, J. and Harmsen, D., 2014. GABenchToB: A genome assembly benchmark tuned on bacteria and benchtop sequencers. PLoS ONE, 9(9), DOI:10.1371/journal.pone.0107014.

Rückert, C., Szczepanowski, R., Albersmeier, A., Goesmann, A., Fischer, N., Steinkämper, A., Pühler, A., Biener, R., Schwartz, D. and Kalinowski, J., 2014. Complete genome sequence of the actinobacterium Actinoplanes friuliensis HAG 010964, producer of the lipopeptide antibiotic friulimycin. Journal of Biotechnology, 178(1), pp.41-42, DOI:10.1016/j.jbiotec.2014.03.011.

Becker, J., Timmermann, C., Rupp, O., Albaum, S.P., Brinkrolf, K., Goesmann, A., Pühler, A., Tauch, A. and Noll, T., 2014. Transcriptome analyses of CHO cells with the next-generation microarray CHO41K: Development and validation by analysing the influence of the growth stimulating substance IGF-1 substitute LongR3. Journal of Biotechnology, 178(1), pp.23-31, DOI:10.1016/j.jbiotec.2014.02.021.

Rupp, O., Becker, J., Brinkrolf, K., Timmermann, C., Borth, N., Pühler, A., Noll, T. and Goesmann, A., 2014. Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PLoS ONE, 9(1), DOI:10.1371/journal.pone.0085568.

Tielen, P., Wibberg, D., Blom, J., Rosin, N., Meyer, A., Bunk, B., Schobert, M., Tupker, R., Schatschneider, S., Ruckert, C., Albersmeier, A., Goesmann, A., Vorholter, F., Jahn, D. and Puhler, A., 2014. Genome Sequence of the Small-Colony Variant Pseudomonas aeruginosa MH27, Isolated from a Chronic Urethral Catheter Infection. Genome Announcements, 2(1), DOI:10.1128/genomea.01174-13.

Smits, T.H.M., Guerrero-Prieto, V.M., Hernandez-Escarcega, G., Blom, J., Goesmann, A., Rezzonico, F., Duffy, B. and Stockwell, V.O., 2014. 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. Genome Announcements, 2(1), DOI:10.1128/genomea.01229-13.


Köhler, K.A.K., Rückert, C., Schatschneider, S., Vorhölter, F., Szczepanowski, R., Blank, L.M., Niehaus, K., Goesmann, A., Pühler, A., Kalinowski, J. and Schmid, A., 2013. Complete genome sequence of Pseudomonas sp. strain VLB120 a solvent tolerant, styrene degrading bacterium, isolated from forest soil. Journal of biotechnology, 168(4), pp.729-30, DOI:10.1016/j.jbiotec.2013.10.016.

Rückert, C., Szczepanowski, R., Albersmeier, A., Goesmann, A., Iftime, D., Musiol, E.M., Blin, K., Wohlleben, W., Pühler, A., Kalinowski, J. and Weber, T., 2013. Complete genome sequence of the kirromycin producer Streptomyces collinus Tü 365 consisting of a linear chromosome and two linear plasmids. Journal of biotechnology, 168(4), pp.739-40, DOI:10.1016/j.jbiotec.2013.10.004.

Bogen, C., Al-Dilaimi, A., Albersmeier, A., Wichmann, J., Grundmann, M., Rupp, O., Lauersen, K.J., Blifernez-Klassen, O., Kalinowski, J., Goesmann, A., Mussgnug, J.H. and Kruse, O., 2013. Reconstruction of the lipid metabolism for the microalga Monoraphidium neglectum from its genome sequence reveals characteristics suitable for biofuel production. BMC Genomics, 14(1), DOI:10.1186/1471-2164-14-926.

Jünemann, S., Sedlazeck, F.J., Prior, K., Albersmeier, A., John, U., Kalinowski, J., Mellmann, A., Goesmann, A., Von Haeseler, A., Stoye, J. and Harmsen, D., 2013. Updating benchtop sequencing performance comparison., 31(4), pp.294-296, DOI:10.1038/nbt.2522.

Kessler, N., Neuweger, H., Bonte, A., Langenkämper, G., Niehaus, K., Nattkemper, T.W. and Goesmann, A., 2013. MeltDB 2.0-advances of the metabolomics software system. Bioinformatics (Oxford, England), 29(19), pp.2452-9, DOI:10.1093/bioinformatics/btt414.

Smits, T.H., Rezzonico, F., López, M.M., Blom, J., Goesmann, A., Frey, J.E. and Duffy, B., 2013. Phylogenetic position and virulence apparatus of the pear flower necrosis pathogen Erwinia piriflorinigrans CFBP 5888T as assessed by comparative genomics. Systematic and Applied Microbiology, 36(7), pp.449-456, DOI:10.1016/j.syapm.2013.04.003.

Vences, M., Susanne Hauswaldt, J., Steinfartz, S., Rupp, O., Goesmann, A., Künzel, S., Orozco-terWengel, P., Vieites, D.R., Nieto-Roman, S., Haas, S., Laugsch, C., Gehara, M., Bruchmann, S., Pabijan, M., Ludewig, A.K., Rudert, D., Angelini, C., Borkin, L.J., Crochet, P.A., Crottini, A., Dubois, A., Ficetola, G.F., Galán, P., Geniez, P., Hachtel, M., Jovanovic, O., Litvinchuk, S.N., Lymberakis, P., Ohler, A. and Smirnov, N.A., 2013. Radically different phylogeographies and patterns of genetic variation in two European brown frogs, genus Rana. Molecular Phylogenetics and Evolution, 68(3), pp.657-670, DOI:10.1016/j.ympev.2013.04.014.

Brinkrolf, K., Rupp, O., Laux, H., Kollin, F., Ernst, W., Linke, B., Kofler, R., Romand, S., Hesse, F., Budach, W.E., Galosy, S., Müller, D., Noll, T., Wienberg, J., Jostock, T., Leonard, M., Grillari, J., Tauch, A., Goesmann, A., Helk, B., Mott, J.E., Pühler, A. and Borth, N., 2013. Chinese hamster genome sequenced from sorted chromosomes., 31(8), pp.694-695, DOI:10.1038/nbt.2645.

Wibberg, D., Jelonek, L., Rupp, O., Hennig, M., Eikmeyer, F., Goesmann, A., Hartmann, A., Borriss, R., Grosch, R., Pühler, A. and Schlüter, A., 2013. Establishment and interpretation of the genome sequence of the phytopathogenic fungus Rhizoctonia solani AG1-IB isolate 7/3/14. Journal of biotechnology, 167(2), pp.142-55, DOI:10.1016/j.jbiotec.2012.12.010.

Zakrzewski, M., Bekel, T., Ander, C., Pühler, A., Rupp, O., Stoye, J., Schlüterd, A. and Goesmann, A., 2013. MetaSAMS-A novel software platform for taxonomic classification, functional annotation and comparative analysis of metagenome datasets. Journal of Biotechnology, 167(2), pp.156-165, DOI:10.1016/j.jbiotec.2012.09.013.

Toepel, J., Illmer-Kephalides, M., Jaenicke, S., Straube, J., May, P., Goesmann, A. and Kruse, O., 2013. New insights into Chlamydomonas reinhardtii hydrogen production processes by combined microarray/RNA-seq transcriptomics. Plant biotechnology journal, 11(6), pp.717-33, DOI:10.1111/pbi.12062.

de Campos, S.B., Youn, J., Farina, R., Jaenicke, S., Jünemann, S., Szczepanowski, R., Beneduzi, A., Vargas, L.K., Goesmann, A., Wendisch, V.F. and Passaglia, L.M.P., 2013. 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, 65(3), pp.593-601, DOI:10.1007/s00248-012-0132-9.

Riedel, T., Gómez-Consarnau, L., Tomasch, J., Martin, M., Jarek, M., González, J.M., Spring, S., Rohlfs, M., Brinkhoff, T., Cypionka, H., Göker, M., Fiebig, A., Klein, J., Goesmann, A., Fuhrman, J.A. and Wagner-Döbler, I., 2013. Genomics and physiology of a marine flavobacterium encoding a proteorhodopsin and a xanthorhodopsin-like protein. PloS one, 8(3), p.e57487, DOI:10.1371/journal.pone.0057487.

Mann, R.A., Smits, T.H., Bühlmann, A., Blom, J., Goesmann, A., Frey, J.E., Plummer, K.M., Beer, S.V., Luck, J., Duffy, B. and Rodoni, B., 2013. Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core. PLoS ONE, 8(2), DOI:10.1371/journal.pone.0055644.

Fritzenwanker, M., Kuenne, C., Billion, A., Hain, T., Zimmermann, K., Goesmann, A., Chakraborty, T. and Domann, E., 2013. Complete Genome Sequence of the Probiotic Enterococcus faecalis Symbioflor 1 Clone DSM 16431. Genome announcements, 1(1), DOI:10.1128/genomeA.00165-12.

Kuenne, C., Billion, A., Mraheil, M.A., Strittmatter, A., Daniel, R., Goesmann, A., Barbuddhe, S., Hain, T. and Chakraborty, T., 2013. Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. BMC genomics, 14(1), p.47, DOI:10.1186/1471-2164-14-47.


Schneider, J., Andrea, H., Blom, J., Jaenicke, S., Rückert, C., Schorsch, C., Szczepanowski, R., Farwick, M., Goesmann, A., Pühler, A., Schaffer, S., Tauch, A., Köhler, T. and Brinkrolf, K., 2012. Draft genome sequence of Wickerhamomyces ciferrii NRRL Y-1031 F-60-10. Eukaryotic Cell, 11(12), pp.1582-1583, DOI:10.1128/EC.00258-12.

Rose, M.T., Rose, T.J., Pariasca-Tanaka, J., Yoshihashi, T., Neuweger, H., Goesmann, A., Frei, M. and Wissuwa, M., 2012. Root metabolic response of rice (Oryza sativa L.) genotypes with contrasting tolerance to zinc deficiency and bicarbonate excess. Planta, 236(4), pp.959-973, DOI:10.1007/s00425-012-1648-4.

Zischka, M., Kuenne, C., Blom, J., Dabrowski, P.W., Linke, B., Hain, T., Nitsche, A., Goesmann, A., Larsen, J., Jensen, L.B., Witte, W. and Werner, G., 2012. Complete genome sequence of the porcine isolate Enterococcus faecalis D32., 194(19), pp.5490-5491, DOI:10.1128/JB.01298-12.

Heinl, S., Wibberg, D., Eikmeyer, F., Szczepanowski, R., Blom, J., Linke, B., Goesmann, A., Grabherr, R., Schwab, H., Pühler, A. and Schlüter, A., 2012. Insights into the completely annotated genome of Lactobacillus buchneri CD034, a strain isolated from stable grass silage. Journal of Biotechnology, 161(2), pp.153-166, DOI:10.1016/j.jbiotec.2012.03.007.

Rezzonico, F., Braun-Kiewnick, A., Mann, R.A., Rodoni, B., Goesmann, A., Duffy, B. and Smits, T.H., 2012. Lipopolysaccharide biosynthesis genes discriminate between Rubus- and Spiraeoideae-infective genotypes of Erwinia amylovora. Molecular Plant Pathology, 13(8), pp.975-984, DOI:10.1111/j.1364-3703.2012.00807.x.

Schork, S., Schlüter, A., Blom, J., Schneiker-Bekel, S., Pühler, A., Goesmann, A., Frosch, M. and Schoen, C., 2012. Genome sequence of a Neisseria meningitidis capsule null locus strain from the clonal complex of sequence type 198., 194(18), pp.5144-5145, DOI:10.1128/JB.01099-12.

Jünemann, S., Prior, K., Szczepanowski, R., Harks, I., Ehmke, B., Goesmann, A., Stoye, J. and Harmsen, D., 2012. Bacterial community shift in treated periodontitis patients revealed by ion torrent 16S rRNA gene amplicon sequencing. PloS one, 7(8), p.e41606, DOI:10.1371/journal.pone.0041606.

Mann, R.A., Blom, J., Bühlmann, A., Plummer, K.M., Beer, S.V., Luck, J.E., Goesmann, A., Frey, J.E., Rodoni, B.C., Duffy, B. and Smits, T.H.M., 2012. 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, 504(1), pp.6-12, DOI:10.1016/j.gene.2012.05.002.

Filippini, M., Qi, W., Jaenicke, S., Goesmann, A., Smits, T.H. and Bagheri, H.C., 2012. Genome sequence of the Filamentous bacterium Fibrisoma limi BUZ 3T., 194(16), pp.4445-4445, DOI:10.1128/JB.00869-12.

Trötschel, C., Albaum, S.P., Wolff, D., Schrod, S., Goesmanns, A., Nattkemper, T.W. and Poetsch, A., 2012. Protein turnover quantification in a multilabeling approach: From data calculation to evaluation. Molecular and Cellular Proteomics, 11(8), pp.512-526, DOI:10.1074/mcp.M111.014134.

Filippini, M., Qi, W., Blom, J., Goesmann, A., Smits, T.H. and Bagheri, H.C., 2012. Genome sequence of Fibrella aestuarina BUZ 2T, a filamentous: Marine bacterium., 194(13), p.3555, DOI:10.1128/JB.00550-12.

Schneider, J., Rupp, O., Trost, E., Jaenicke, S., Passoth, V., Goesmann, A., Tauch, A. and Brinkrolf, K., 2012. Genome sequence of Wickerhamomyces anomalus DSM 6766 reveals genetic basis of biotechnologically important antimicrobial activities. FEMS Yeast Research, 12(3), pp.382-386, DOI:10.1111/j.1567-1364.2012.00791.x.

Kahlke, T., Goesmann, A., Hjerde, E., Willassen, N.P. and Haugen, P., 2012. Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation. BMC Genomics, 13(1), DOI:10.1186/1471-2164-13-179.

Brankatschk, K., Blom, J., Goesmann, A., Smits, T.H. and Duffy, B., 2012. Comparative genomic analysis of Salmonella enterica subsp. enterica serovar Weltevreden foodborne strains with other serovars. International Journal of Food Microbiology, 155(3), pp.247-256, DOI:10.1016/j.ijfoodmicro.2012.01.024.

Hain, T., Ghai, R., Billion, A., Kuenne, C.T., Steinweg, C., Izar, B., Mohamed, W., Mraheil, M.A., Domann, E., Schaffrath, S., Kärst, U., Goesmann, A., Oehm, S., Pühler, A., Merkl, R., Vorwerk, S., Glaser, P., Garrido, P., Rusniok, C., Buchrieser, C., Goebel, W. and Chakraborty, T., 2012. Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics, 13(1), DOI:10.1186/1471-2164-13-144.

Hackl, M., Jadhav, V., Jakobi, T., Rupp, O., Brinkrolf, K., Goesmann, A., Pühler, A., Noll, T., Borth, N. and Grillari, J., 2012. Computational identification of microRNA gene loci and precursor microRNA sequences in CHO cell lines. Journal of Biotechnology, 158(3), pp.151-155, DOI:10.1016/j.jbiotec.2012.01.019.

Zakrzewski, M., Goesmann, A., Jaenicke, S., Jünemann, S., Eikmeyer, F., Szczepanowski, R., Al-Soud, W.A., Sørensen, S., Pühler, A. and Schlüter, A., 2012. Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. Journal of Biotechnology, 158(4), pp.248-258, DOI:10.1016/j.jbiotec.2012.01.020.

Rademacher, A., Zakrzewski, M., Schlüter, A., Schönberg, M., Szczepanowski, R., Goesmann, A., Pühler, A. and Klocke, M., 2012. Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing. FEMS Microbiology Ecology, 79(3), pp.785-799, DOI:10.1111/j.1574-6941.2011.01265.x.

De Maayer, P., Chan, W.Y., Rezzonico, F., Bühlmann, A., Venter, S.N., Blom, J., Goesmann, A., Frey, J.E., Smits, T.H., Duffy, B. and Coutinho, T.A., 2012. Complete genome sequence of clinical isolate pantoea ananatis LMG 5342., 194(6), pp.1615-1616, DOI:10.1128/JB.06715-11.

Zschüttig, A., Zimmermann, K., Blom, J., Goesmann, A., Pöhlmann, C. and Gunzer, F., 2012. Identification and characterization of microcin S, a new antibacterial peptide produced by probiotic Escherichia coli G3/10. PLoS ONE, 7(3), DOI:10.1371/journal.pone.0033351.


González, J.M., Pinhassi, J., Fernández-Gómez, B., Coll-Lladó, M., González-Velázquez, M., Puigbò, P., Jaenicke, S., Gómez-Consarnau, L., Fernàndez-Guerra, A., Goesmann, A. and Pedrós-Alió, C., 2011. Genomics of the proteorhodopsin-containing marine flavobacterium Dokdonia sp. strain MED134. Applied and Environmental Microbiology, 77(24), pp.8676-8686, DOI:10.1128/AEM.06152-11.

Smits, T.H., Rezzonico, F., Kamber, T., Blom, J., Goesmann, A., Ishimaru, C.A., FreyJü, J.E., Stockwell, V.O. and Duffy, B., 2011. Metabolic versatility and antibacterial metabolite biosynthesis are distinguishing genomic features of the fire blight antagonist pantoea vagans C9-1. PLoS ONE, 6(7), DOI:10.1371/journal.pone.0022247.

Becker, J., Timmermann, C., Jakobi, T., Rupp, O., Szczepanowski, R., Hackl, M., Goesmann, A., Tauch, A., Borth, N., Grillari, J., Pühler, A., Noll, T. and Brinkrolf, K., 2011. Next-generation sequencing of the CHO cell transcriptome. BMC Proceedings, 5(S8), DOI:10.1186/1753-6561-5-s8-p6.

Becker, J., Hackl, M., Rupp, O., Jakobi, T., Schneider, J., Szczepanowski, R., Bekel, T., Borth, N., Goesmann, A., Grillari, J., Kaltschmidt, C., Noll, T., Pühler, A., Tauch, A. and Brinkrolf, K., 2011. Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. Journal of Biotechnology, 156(3), pp.227-235, DOI:10.1016/j.jbiotec.2011.09.014.

Joseph, B., Schwarz, R.F., Linke, B., Blom, J., Becker, A., Claus, H., Goesmann, A., Frosch, M., Müller, T., Vogel, U. and Schoen, C., 2011. Virulence evolution of the human pathogen neisseria meningitidis by recombination in the core and accessory genome. PLoS ONE, 6(4), DOI:10.1371/journal.pone.0018441.

Toepel, J., Albaum, S.P., Arvidsson, S., Goesmann, A., la Russa, M., Rogge, K. and Kruse, O., 2011. Construction and evaluation of a whole genome microarray of Chlamydomonas reinhardtii. BMC Genomics, DOI:10.1186/1471-2164-12-579.

Ausec, L., Zakrzewski, M., Goesmann, A., Schlüter, A. and Mandic-Mulec, I., 2011. Bioinformatic analysis reveals high diversity of bacterial genes for laccase-like enzymes. PLoS ONE, 6(10), DOI:10.1371/journal.pone.0025724.

Pothier, J.F., Vorhölter, F.J., Blom, J., Goesmann, A., Pühler, A., Smits, T.H. and Duffy, B., 2011. The ubiquitous plasmid pXap41 in the invasive phytopathogen Xanthomonas arboricola pv. pruni: Complete sequence and comparative genomic analysis. FEMS Microbiology Letters, 323(1), pp.52-60, DOI:10.1111/j.1574-6968.2011.02352.x.

Wibberg, D., Blom, J., Jaenicke, S., Kollin, F., Rupp, O., Scharf, B., Schneiker-Bekel, S., Sczcepanowski, R., Goesmann, A., Setubal, J.C., Schmitt, R., Pühler, A. and Schlüter, A., 2011. 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, 155(1), pp.50-62, DOI:10.1016/j.jbiotec.2011.01.010.

Schneider, J., Blom, J., Jaenicke, S., Linke, B., Brinkrolf, K., Neuweger, H., Tauch, A. and Goesmann, A., 2011. RAPYD - Rapid Annotation Platform for Yeast Data. Journal of Biotechnology, 155(1), pp.118-126, DOI:10.1016/j.jbiotec.2010.10.076.

Krol, E., Blom, J., Winnebald, J., Berhörster, A., Barnett, M.J., Goesmann, A., Baumbach, J. and Becker, A., 2011. RhizoRegNet-a database of rhizobial transcription factors and regulatory networks. Journal of biotechnology, 155(1), pp.127-34, DOI:10.1016/j.jbiotec.2010.11.004.

Margaret, I., Becker, A., Blom, J., Bonilla, I., Goesmann, A., Göttfert, M., Lloret, J., Mittard-Runte, V., Rückert, C., Ruiz-Sainz, J.E., Vinardell, J.M. and Weidner, S., 2011. Symbiotic properties and first analyses of the genomic sequence of the fast growing model strain Sinorhizobium fredii HH103 nodulating soybean. Journal of Biotechnology, 155(1), pp.11-19, DOI:10.1016/j.jbiotec.2011.03.016.

Schneiker-Bekel, S., Wibberg, D., Bekel, T., Blom, J., Linke, B., Neuweger, H., Stiens, M., Vorhölter, F.J., Weidner, S., Goesmann, A., Pühler, A. and Schlüter, A., 2011. The complete genome sequence of the dominant Sinorhizobium meliloti field isolate SM11 extends the S. meliloti pan-genome. Journal of Biotechnology, 155(1), pp.20-33, DOI:10.1016/j.jbiotec.2010.12.018.

Küberl, A., Schneider, J., Thallinger, G.G., Anderl, I., Wibberg, D., Hajek, T., Jaenicke, S., Brinkrolf, K., Goesmann, A., Szczepanowski, R., Pühler, A., Schwab, H., Glieder, A. and Pichler, H., 2011. High-quality genome sequence of Pichia pastoris CBS7435. Journal of Biotechnology, 154(4), pp.312-320, DOI:10.1016/j.jbiotec.2011.04.014.

Albaum, S.P., Hahne, H., Otto, A., Haußmann, U., Becher, D., Poetsch, A., Goesmann, A. and Nattkemper, T.W., 2011. A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: An application study. Proteome Science, DOI:10.1186/1477-5956-9-30.

Thomas, V., Bertelli, C., Collyn, F., Casson, N., Telenti, A., Goesmann, A., Croxatto, A. and Greub, G., 2011. Lausannevirus, a giant amoebal virus encoding histone doublets. Environmental Microbiology, 13(6), pp.1454-1466, DOI:10.1111/j.1462-2920.2011.02446.x.

Linke, B., Giegerich, R. and Goesmann, A., 2011. Conveyor: a workflow engine for bioinformatic analyses. Bioinformatics (Oxford, England), 27(7), pp.903-11, DOI:10.1093/bioinformatics/btr040.

de Gregoris, T.B., Rupp, O., Klages, S., Knaust, F., Bekel, T., Kube, M., Burgess, J.G., Arnone, M.I., Goesmann, A., Reinhardt, R. and Clare, A.S., 2011. Deep sequencing of naupliar-, cyprid- and adult-specific normalised expressed sequence tag (EST) libraries of the acorn barnacle Balanus amphitrite. Biofouling, 27(4), pp.367-374, DOI:10.1080/08927014.2011.577211.

Brankatschk, K., Blom, J., Goesmann, A., Smits, T.H. and Duffy, B., 2011. Genome of a European fresh-vegetable food safety outbreak strain of Salmonella enterica subsp. enterica Serovar Weltevreden. Journal of Bacteriology, 193(8), p.2066, DOI:10.1128/JB.00123-11.

Hackl, M., Jakobi, T., Blom, J., Doppmeier, D., Brinkrolf, K., Szczepanowski, R., Bernhart, S.H., Höner Zu Siederdissen, C., Bort, J.A.H., Wieser, M., Kunert, R., Jeffs, S., Hofacker, I.L., Goesmann, A., Pühler, A., Borth, N. and Grillari, J., 2011. Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering. Journal of biotechnology, 153(1-2), pp.62-75, DOI:10.1016/j.jbiotec.2011.02.011.

Schoen, C., Weber-Lehmann, J., Blom, J., Joseph, B., Goesmann, A., Strittmatter, A. and Frosch, M., 2011. Whole-genome sequence of the transformable Neisseria meningitidis Serogroup a strain WUE2594., 193(8), pp.2064-2065, DOI:10.1128/JB.00084-11.

Blom, J., Jakobi, T., Doppmeier, D., Jaenicke, S., Kalinowski, J., Stoye, J. and Goesmann, A., 2011. Exact and complete short-read alignment to microbial genomes using Graphics Processing Unit programming. Bioinformatics, 27(10), pp.1351-1358, DOI:10.1093/bioinformatics/btr151.

Jaenicke, S., Ander, C., Bekel, T., Bisdorf, R., Dröge, M., Gartemann, K., Jünemann, S., Kaiser, O., Krause, L., Tille, F., Zakrzewski, M., Pühler, A., Schlüter, A. and Goesmann, A., 2011. Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PloS one, 6(1), p.e14519, DOI:10.1371/journal.pone.0014519.


Smits, T.H., Rezzonico, F., Kamber, T., Goesmann, A., Ishimaru, C.A., Stockwell, V.O., Frey, J.E. and Duffy, B., 2010. Genome sequence of the biocontrol agent Pantoea vagans strain C9-1. Journal of Bacteriology, 192(24), pp.6486-6487, DOI:10.1128/JB.01122-10.

Trost, E., Ott, L., Schneider, J., Schröder, J., Jaenicke, S., Goesmann, A., Husemann, P., Stoye, J., Dorella, F.A., Rocha, F.S., de Castro Soares, S., D'Afonseca, V., Miyoshi, A., Ruiz, J., Silva, A., Azevedo, V., Burkovski, A., Guiso, N., Join-Lambert, O.F., Kayal, S. and Tauch, A., 2010. 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, 11(1), DOI:10.1186/1471-2164-11-728.

Bertelli, C., Collyn, F., Croxatto, A., Rückert, C., Polkinghorne, A., Kebbi-Beghdadi, C., Goesmann, A., Vaughan, L. and Greub, G., 2010. The waddlia genome: A window into chlamydial biology. PLoS ONE, 5(5), DOI:10.1371/journal.pone.0010890.

Gehlenborg, N., O'Donoghue, S.I., Baliga, N.S., Goesmann, A., Hibbs, M.A., Kitano, H., Kohlbacher, O., Neuweger, H., Schneider, R., Tenenbaum, D. and Gavin, A.C., 2010. Visualization of omics data for systems biology., 7(3), pp.S56-S68, DOI:10.1038/nmeth.1436.

Joseph, B., Schneiker-Bekel, S., Schramm-Glück, A., Blom, J., Claus, H., Linke, B., Schwarz, R.F., Becker, A., Goesmann, A., Frosch, M. and Schoen, C., 2010. Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence. Journal of Bacteriology, 192(20), pp.5363-5377, DOI:10.1128/JB.00883-10.

Henckel, K., Küster, H., Stutz, L.J. and Goesmann, A., 2010. MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. BMC research notes, p.262, DOI:10.1186/1756-0500-3-262.

Kuenne, C., Voget, S., Pischimarov, J., Oehm, S., Goesmann, A., Daniel, R., Hain, T. and Chakraborty, T., 2010. Comparative analysis of plasmids in the genus Listeria. PloS one, 5(9), pp.1-7, DOI:10.1371/journal.pone.0012511.

Schneider, J., Vorhölter, F., Trost, E., Blom, J., Musa, Y.R., Neuweger, H., Niehaus, K., Schatschneider, S., Tauch, A. and Goesmann, A., 2010. CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks. Genetics and molecular research : GMR, 9(3), pp.1660-72, DOI:10.4238/vol9-3gmr901.

Smits, T.H., Rezzonico, F., Pelludat, C., Goesmann, A., Frey, J.E. and Duffy, B., 2010. Genomic and phenotypic characterization of a nonpigmented variant of Pantoea vagans biocontrol strain C9-1 lacking the 530-kb megaplasmid pPag3. FEMS Microbiology Letters, 308(1), pp.48-54, DOI:10.1111/j.1574-6968.2010.01994.x.

Farnbacher, M., Jahns, T., Willrodt, D., Daniel, R., Haas, R., Goesmann, A., Kurtz, S. and Rieder, G., 2010. Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8. BMC Genomics, 11(1), DOI:10.1186/1471-2164-11-335.

Yang, I., John, U., Beszteri, S., Glöckner, G., Krock, B., Goesmann, A. and Cembella, A.D., 2010. Comparative gene expression in toxic versus non-toxic strains of the marine dinoflagellate Alexandrium minutum. BMC Genomics, 11(1), DOI:10.1186/1471-2164-11-248.

Smits, T.H.M., Rezzonico, F., Kamber, T., Blom, J., Goesmann, A., Frey, J.E. and Duffy, B., 2010. Complete genome sequence of the fire blight pathogen Erwinia amylovora CFBP 1430 and comparison to other Erwinia spp. Molecular plant-microbe interactions : MPMI, 23(4), pp.384-93, DOI:10.1094/MPMI-23-4-0384.

Steinweg, C., Kuenne, C.T., Billion, A., Mraheil, M.A., Domann, E., Ghai, R., Barbuddhe, S.B., Kärst, U., Goesmann, A., Pühler, A., Weisshaar, B., Wehland, J., Lampidis, R., Kreft, J., Goebel, W., Chakraborty, T. and Hain, T., 2010. Complete genome sequence of Listeria seeligeri, a nonpathogenic member of the genus Listeria. Journal of bacteriology, 192(5), pp.1473-4, DOI:10.1128/JB.01415-09.

Trost, E., Götker, S., Schneider, J., Schneiker-Bekel, S., Szczepanowski, R., Tilker, A., Viehoever, P., Arnold, W., Bekel, T., Blom, J., Gartemann, K.H., Linke, B., Goesmann, A., Pühler, A., Shukla, S.K. and Tauch, A., 2010. 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, 11(1), DOI:10.1186/1471-2164-11-91.

Smits, T.H., Jaenicke, S., Rezzonico, F., Kamber, T., Goesmann, A., Frey, J.E. and Duffy, B., 2010. Complete genome sequence of the fire blight pathogen Erwinia pyrifoliae DSM 12163Tand comparative genomic insights into plant pathogenicity. BMC Genomics, 11(1), DOI:10.1186/1471-2164-11-2.


Corti, D. and Castro, R., 2009. Chapter 5. Fire Danger, Fire Detection, Quantification of Burned Areas and Description of Post-Fire Vegetation in the Central Area of Chile., pp.1-257, DOI:10.1007/978-3-642-01754-4.

Albaum, S.P., Neuweger, H., Fränzel, B., Lange, S., Mertens, D., Trötschel, C., Wolters, D., Kalinowski, J., Nattkemper, T.W. and Goesmann, A., 2009. Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics (Oxford, England), 25(23), pp.3128-34, DOI:10.1093/bioinformatics/btp568.

Henckel, K., Runte, K.J., Bekel, T., Dondrup, M., Jakobi, T., Küster, H. and Goesmann, A., 2009. Truncatulix - A data warehouse for the legume community. BMC Plant Biology, DOI:10.1186/1471-2229-9-19.

Gerlach, W., Jünemann, S., Tille, F., Goesmann, A. and Stoye, J., 2009. WebCARMA: A web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics, DOI:10.1186/1471-2105-10-430.

Wegmann, U., Overweg, K., Horn, N., Goesmann, A., Narbad, A., Gasson, M.J. and Shearman, C., 2009. Complete genome sequence of Lactobacillus johnsonii FI9785, a competitive exclusion agent against pathogens in poultry. Journal of Bacteriology, 191(22), pp.7142-7143, DOI:10.1128/JB.01182-09.

Neuweger, H., Persicke, M., Albaum, S.P., Bekel, T., Dondrup, M., Hüser, A.T., Winnebald, J., Schneider, J., Kalinowski, J. and Goesmann, A., 2009. 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, p.82, DOI:10.1186/1752-0509-3-82.

Krawczyk, J., Goesmann, A., Nolte, R., Werber, M. and Weisshaar, B., 2009. Trace2PS and FSA2PS: Two software toolkits for converting trace and fsa files to PostScript format., DOI:10.1186/1751-0473-4-4.

Kröber, M., Bekel, T., Diaz, N.N., Goesmann, A., Jaenicke, S., Krause, L., Miller, D., Runte, K.J., Viehöver, P., Pühler, A. and Schlüter, A., 2009. 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, 142(1), pp.38-49, DOI:10.1016/j.jbiotec.2009.02.010.

Blom, J., Albaum, S.P., Doppmeier, D., Pühler, A., Vorhölter, F.J., Zakrzewski, M. and Goesmann, A., 2009. EDGAR: A software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics, DOI:10.1186/1471-2105-10-154.

Strittmatter, A.W., Liesegang, H., Rabus, R., Decker, I., Amann, J., Andres, S., Henne, A., Fricke, W.F., Martinez-Arias, R., Bartels, D., Goesmann, A., Krause, L., Pühler, A., Klenk, H.P., Richter, M., Schüler, M., Glöckner, F.O., Meyerdierks, A., Gottschalk, G. and Amann, R., 2009. Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environmental Microbiology, 11(5), pp.1038-1055, DOI:10.1111/j.1462-2920.2008.01825.x.

Becker, A., Barnett, M.J., Capela, D., Dondrup, M., Kamp, P.B., Krol, E., Linke, B., Rüberg, S., Runte, K., Schroeder, B.K., Weidner, S., Yurgel, S.N., Batut, J., Long, S.R., Pühler, A. and Goesmann, A., 2009. A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data. Journal of Biotechnology, 140(1-2), pp.45-50, DOI:10.1016/j.jbiotec.2008.11.006.

Dondrup, M., Hüser, A.T., Mertens, D. and Goesmann, A., 2009. An evaluation framework for statistical tests on microarray data. Journal of Biotechnology, 140(1-2), pp.18-26, DOI:10.1016/j.jbiotec.2009.01.009.

Bekel, T., Henckel, K., Küster, H., Meyer, F., Mittard Runte, V., Neuweger, H., Paarmann, D., Rupp, O., Zakrzewski, M., Pühler, A., Stoye, J. and Goesmann, A., 2009. 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, 140(1-2), pp.3-12, DOI:10.1016/j.jbiotec.2009.01.006.

Dondrup, M., Albaum, S.P., Griebel, T., Henckel, K., Jünemann, S., Kahlke, T., Kleindt, C.K., Küster, H., Linke, B., Mertens, D., Mittard-Runte, V., Neuweger, H., Runte, K.J., Tauch, A., Tille, F., Pühler, A. and Goesmann, A., 2009. EMMA 2 - A MAGE-compliant system for the collaborative analysis and integration of microarray data. BMC Bioinformatics, DOI:10.1186/1471-2105-10-50.

Diaz, N.N., Krause, L., Goesmann, A., Niehaus, K. and Nattkemper, T.W., 2009. TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics, DOI:10.1186/1471-2105-10-56.


Strauch, E., Hammerl, J.A., Konietzny, A., Schneiker-Bekel, S., Arnold, W., Goesmann, A., Pühler, A. and Beutin, L., 2008. Bacteriophage 2851 is a prototype phage for dissemination of the Shiga toxin variant gene 2c in Escherichia coli O157:H7. Infection and Immunity, 76(12), pp.5466-5477, DOI:10.1128/IAI.00875-08.

Oehm, S., Gilbert, D., Tauch, A., Stoye, J. and Goesmann, A., 2008. Comparative Pathway Analyzer-a web server for comparative analysis, clustering and visualization of metabolic networks in multiple organisms. Nucleic acids research, 36(Web Server issue), DOI:10.1093/nar/gkn284.

Neuweger, H., Albaum, S.P., Dondrup, M., Persicke, M., Watt, T., Niehaus, K., Stoye, J. and Goesmann, A., 2008. MeltDB: A software platform for the analysis and integration of metabolomics experiment data. Bioinformatics, 24(23), pp.2726-2732, DOI:10.1093/bioinformatics/btn452.

Gross, R., Guzman, C.A., Sebaihia, M., Martins dos Santos, V.A., Pieper, D.H., Koebnik, R., Lechner, M., Bartels, D., Buhrmester, J., Choudhuri, J.V., Ebensen, T., Gaigalat, L., Herrmann, S., Khachane, A.N., Larisch, C., Link, S., Linke, B., Meyer, F., Mormann, S., Nakunst, D., Rückert, C., Schneiker-Bekel, S., Schulze, K., Vorhölter, F.J., Yevsa, T., Engle, J.T., Goldman, W.E., Pühler, A., Göbel, U.B., Goesmann, A., Blöcker, H., Kaiser, O. and Martinez-Arias, R., 2008. The missing link: Bordetella petrii is endowed with both the metabolic versatility of environmental bacteria and virulence traits of pathogenic Bordetellae. BMC Genomics, DOI:10.1186/1471-2164-9-449.

Stiens, M., Becker, A., Bekel, T., Gödde, V., Goesmann, A., Niehaus, K., Schneiker-Bekel, S., Selbitschka, W., Weidner, S., Schlüter, A. and Pühler, A., 2008. 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, 136(1-2), pp.31-37, DOI:10.1016/j.jbiotec.2008.04.014.

Schlüter, A., Krause, L., Szczepanowski, R., Goesmann, A. and Pühler, A., 2008. Genetic diversity and composition of a plasmid metagenome from a wastewater treatment plant. Journal of biotechnology, 136(1-2), pp.65-76, DOI:10.1016/j.jbiotec.2008.03.017.

Szczepanowski, R., Bekel, T., Goesmann, A., Krause, L., Krömeke, H., Kaiser, O., Eichler, W., Pühler, A. and Schlüter, A., 2008. 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, 136(1-2), pp.54-64, DOI:10.1016/j.jbiotec.2008.03.020.

Krause, L., Diaz, N.N., Edwards, R.A., Gartemann, K.H., Krömeke, H., Neuweger, H., Pühler, A., Runte, K.J., Schlüter, A., Stoye, J., Szczepanowski, R., Tauch, A. and Goesmann, A., 2008. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. Journal of Biotechnology, 136(1-2), pp.91-101, DOI:10.1016/j.jbiotec.2008.06.003.

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, P.B., Lobo, F.P., Viehoever, P., Weisshaar, B., Soriano, F., Dröge, M. and Pühler, A., 2008. The lifestyle of Corynebacterium urealyticum derived from its complete genome sequence established by pyrosequencing. Journal of Biotechnology, 136(1-2), pp.11-21, DOI:10.1016/j.jbiotec.2008.02.009.

Schlüter, A., Bekel, T., Diaz, N.N., Dondrup, M., Eichenlaub, R., Gartemann, K., Krahn, I., Krause, L., Krömeke, H., Kruse, O., Mussgnug, J.H., Neuweger, H., Niehaus, K., Pühler, A., Runte, K.J., Szczepanowski, R., Tauch, A., Tilker, A., Viehöver, P. and Goesmann, A., 2008. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. Journal of biotechnology, 136(1-2), pp.77-90, DOI:10.1016/j.jbiotec.2008.05.008.

Tauch, A., Schneider, J., Szczepanowski, R., Tilker, A., Viehoever, P., Gartemann, K.H., Arnold, W., Blom, J., Brinkrolf, K., Brune, I., Götker, S., Weisshaar, B., Goesmann, A., Dröge, M. and Pühler, A., 2008. Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. Journal of Biotechnology, 136(1-2), pp.22-30, DOI:10.1016/j.jbiotec.2008.03.004.

Krause, L., Diaz, N.N., Goesmann, A., Kelley, S., Nattkemper, T.W., Rohwer, F., Edwards, R.A. and Stoye, J., 2008. Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Research, 36(7), pp.2230-2239, DOI:10.1093/nar/gkn038.

Vorhölter, F., Schneiker, S., Goesmann, A., Krause, L., Bekel, T., Kaiser, O., Linke, B., Patschkowski, T., Rückert, C., Schmid, J., Sidhu, V.K., Sieber, V., Tauch, A., Watt, S.A., Weisshaar, B., Becker, A., Niehaus, K. and Pühler, A., 2008. The genome of Xanthomonas campestris pv. campestris B100 and its use for the reconstruction of metabolic pathways involved in xanthan biosynthesis. Journal of biotechnology, 134(1-2), pp.33-45, DOI:10.1016/j.jbiotec.2007.12.013.

Gartemann, K.H., 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., Sehneiker, S., Zeilermann, E.M., Pühler, A., Eichenlaub, R., Kaiser, O. and Bartels, D., 2008. The genome sequence of the tomato-pathogenic actinomycete Chvibacter michiganensis subsp. michiganensis NCPPB382 reveals a large island involved in pathogenicity. Journal of Bacteriology, 190(6), pp.2138-2149, DOI:10.1128/JB.01595-07.

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. and Frosch, M., 2008. 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, 105(9), pp.3473-3478, DOI:10.1073/pnas.0800151105.


Meisinger-Henschel, C., Schmidt, M., Lukassen, S., Linke, B., Krause, L., Konietzny, S., Goesmann, A., Howley, P., Chaplin, P., Suter, M. and Hausmann, J., 2007. Genomic sequence of chorioallantois vaccinia virus Ankara, the ancestor of modified vaccinia virus Ankara. The Journal of general virology, 88(Pt 12), pp.3249-59, DOI:10.1099/vir.0.83156-0.

Schneiker, S., Perlova, O., Kaiser, O., Gerth, K., Alici, A., Altmeyer, M.O., Bartels, D., Bekel, T., Beyer, S., Bode, E., Bode, H.B., Bolten, C.J., Choudhuri, J.V., Doss, S., Elnakady, Y.A., 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, A.C., Merai, M., Meyer, F., Mormann, S., Mũoz-Dorado, J., Perez, J., Pradella, S., Rachid, S., Raddatz, G., Rosenau, F., Rückert, C., Sasse, F., Scharfe, M., Schuster, S.C., Suen, G., Treuner-Lange, A., Velicer, G.J., Vorhölter, F.J., Weissman, K.J., Welch, R.D., Wenzel, S.C., Whitworth, D.E., Wilhelm, S., Wittmann, C., Blöcker, H., Pühler, A. and Müller, R., 2007. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nature Biotechnology, 25(11), pp.1281-1289, DOI:10.1038/nbt1354.

Neuweger, H., Baumbach, J., Albaum, S., Bekel, T., Dondrup, M., Hüser, A.T., Kalinowski, J., Oehm, S., Pühler, A., Rahmann, S., Weile, J. and Goesmann, A., 2007. CoryneCenter - An online resource for the integrated analysis of corynebacterial genome and transcriptome data. BMC Systems Biology, DOI:10.1186/1752-0509-1-55.

Moran, M.A., Belas, R., Schell, M.A., González, J.M., Sun, F., Sun, S., Binder, B.J., Edmonds, J., Ye, W., Orcutt, B., Howard, E.C., Meile, C., Palefsky, W., Goesmann, A., Ren, Q., Paulsen, I., Ulrich, L.E., Thompson, L.S., Saunders, E. and Buchan, A., 2007. Ecological genomics of marine roseobacters. Applied and Environmental Microbiology, 73(14), pp.4559-4569, DOI:10.1128/AEM.02580-06.

Bahl, M.I., Hansen, L.H., Goesmann, A. and Sørensen, S.J., 2007. The multiple antibiotic resistance IncP-1 plasmid pKJK5 isolated from a soil environment is phylogenetically divergent from members of the previously established α, β and δ sub-groups. Plasmid, 58(1), pp.31-43, DOI:10.1016/j.plasmid.2006.11.007.

Wegmann, U., O'Connell-Motherway, M., Zomer, A., Buist, G., Shearman, C., Canchaya, C., Ventura, M., Goesmann, A., Gasson, M.J., Kuipers, O.P., Van Sinderen, D. and Kok, J., 2007. Complete genome sequence of the prototype lactic acid bacterium Lactococcus lactis subsp. cremoris MG1363. Journal of Bacteriology, 189(8), pp.3256-3270, DOI:10.1128/JB.01768-06.

Küster, H., Becker, A., Firnhaber, C., Hohnjec, N., Manthey, K., Perlick, A.M., Bekel, T., Dondrup, M., Henckel, K., Goesmann, A., Meyer, F., Wipf, D., Requena, N., Hildebrandt, U., Hampp, R., Nehls, U., Krajinski, F., Franken, P. and Pühler, A., 2007. Development of bioinformatic tools to support EST-sequencing, in silico- and microarray-based transcriptome profiling in mycorrhizal symbioses. Phytochemistry, 68(1), pp.19-32, DOI:10.1016/j.phytochem.2006.09.026.


Krause, A., Ramakumar, A., Bartels, D., Battistoni, F., Bekel, T., Boch, J., Böhm, M., Friedrich, F., Hurek, T., Krause, L., Linke, B., McHardy, A.C., Sarkar, A., Schneiker, S., Syed, A.A., Thauer, R., Vorhölter, F., Weidner, S., Pühler, A., Reinhold-Hurek, B., Kaiser, O. and Goesmann, A., 2006. Complete genome of the mutualistic, N2-fixing grass endophyte Azoarcus sp. strain BH72. Nature biotechnology, 24(11), pp.1385-91, DOI:10.1038/nbt1243.

Hain, T., Steinweg, C., Kuenne, C.T., Billion, A., Ghai, R., Chatterjee, S.S., Domann, E., Karst, U., Goesmann, A., Bekel, T., Bartels, D., Kaiser, O., Meyer, F., Pühler, A., Weisshaar, B., Wehland, J., Liang, C., Dandekar, T., Lampidis, R., Kreft, J., Goebel, W. and Chakraborty, T., 2006. Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to listeria monocytogenes. Journal of Bacteriology, 188(21), pp.7405-7415, DOI:10.1128/JB.00758-06.

Schneiker, S., Dos Santos, V.A., Bartels, D., Bekel, T., Brecht, M., Buhrmester, J., Chernikova, T.N., Denaro, R., Ferrer, M., Gertler, C., Goesmann, A., Golyshina, O.V., Kaminski, F., Khachane, A.N., Lang, S., Linke, B., McHardy, A.C., Meyer, F., Nechitaylo, T., Pühler, A., Regenhardt, D., Rupp, O., Sabirova, J.S., Selbitschka, W., Yakimov, M.M., Timmis, K.N., Vorhölter, F.J., Weidner, S., Kaiser, O. and Golyshin, P.N., 2006. Genome sequence of the ubiquitous hydrocarbon-degrading marine bacterium Alcanivorax borkumensis. Nature Biotechnology, 24(8), pp.997-1004, DOI:10.1038/nbt1232.


Overbeek, R., Begley, T., Butler, R.M., Choudhuri, J.V., Chuang, H.Y., Cohoon, M., de Crécy-Lagard, V., Diaz, N., Disz, T., Edwards, R., Fonstein, M., Frank, E.D., Gerdes, S., Glass, E.M., Goesmann, A., Hanson, A., Iwata-Reuyl, D., Jensen, R., Jamshidi, N., Krause, L., Kubal, M., Larsen, N., Linke, B., McHardy, A.C., Meyer, F., Neuweger, H., Olsen, G., Olson, R., Osterman, A., Portnoy, V., Pusch, G.D., Rodionov, D.A., Rül;ckert, C., Steiner, J., Stevens, R., Thiele, I., Vassieva, O., Ye, Y., Zagnitko, O. and Vonstein, V., 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Research, 33(17), pp.5691-5702, DOI:10.1093/nar/gki866.

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, A.C., Meyer, F., Mittenhuber, G., Nies, D.H., Niesbach-Klösgen, U., Patschkowski, T., Rückert, C., Rupp, O., Schneiker, S., Schuster, S.C., Vorhölter, F.J., Weber, E., Pühler, A., Bonas, U., Bartels, D. and Kaiser, O., 2005. Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence. Journal of Bacteriology, 187(21), pp.7254-7266, DOI:10.1128/JB.187.21.7254-7266.2005.

Goesmann, A., Linke, B., Bartels, D., Dondrup, M., Krause, L., Neuweger, H., Oehm, S., Paczian, T., Wilke, A. and Meyer, F., 2005. BRIGEP - The BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Research, 33(SUPPL. 2), DOI:10.1093/nar/gki400.

Tauch, A., Kaiser, O., Hain, T., Goesmann, A., Weisshaar, B., Albersmeier, A., Bekel, T., Bischoff, N., Brune, I., Chakraborty, T., Kalinowski, J., Meyer, F., Rupp, O., Schneiker, S., Viehoever, P. and Pühler, A., 2005. 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, 187(13), pp.4671-4682, DOI:10.1128/JB.187.13.4671-4682.2005.

Bartels, D., Kespohl, S., Albaum, S., Drüke, T., Goesmann, A., Herold, J., Kaiser, O., Pühler, A., Pfeiffer, F., Raddatz, G., Stoye, J., Meyer, F. and Schuster, S.C., 2005. BACCardl - A tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison. Bioinformatics, 21(7), pp.853-859, DOI:10.1093/bioinformatics/bti091.


Szczepanowski, R., Krahn, I., Linke, B., Goesmann, A., Pühler, A. and Schlüter, A., 2004. 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, 150(11), pp.3613-3630, DOI:10.1099/mic.0.27317-0.

McHardy, A.C., Goesmann, A., Pühler, A. and Meyer, F., 2004. Development of joint application strategies for two microbial gene finders. Bioinformatics (Oxford, England), 20(10), pp.1622-31, DOI:10.1093/bioinformatics/bth137.

Westberg, J., Persson, A., Holmberg, A., Goesmann, A., Lundeberg, J., Johansson, K.E., Pettersson, B. and Uhlén, M., 2004. The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Research, 14(2), pp.221-227, DOI:10.1101/gr.1673304.

Rendulic, S., Jagtap, P., Rosinus, A., Eppinger, M., Baar, C., Lanz, C., Keller, H., Lambert, C., Evans, K.J., Goesmann, A., Meyer, F., Sockett, R.E. and Schuster, S.C., 2004. A predator unmasked: life cycle of Bdellovibrio bacteriovorus from a genomic perspective. Science (New York, N.Y.), 303(5658), pp.689-92, DOI:10.1126/science.1093027.


Wilke, A., Rückert, C., Bartels, D., Dondrup, M., Goesmann, A., Hüser, A.T., Kespohl, S., Linke, B., Mahne, M., McHardy, A., Pühler, A. and Meyer, F., 2003. Bioinformatics support for high-throughput proteomics. Journal of biotechnology, 106(2-3), pp.147-56, DOI:10.1016/j.jbiotec.2003.08.009.

Goesmann, A., Linke, B., Rupp, O., Krause, L., Bartels, D., Dondrup, M., McHardy, A.C., Wilke, A., Pühler, A. and Meyer, F., 2003. Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology. Journal of Biotechnology, 106(2-3), pp.157-167, DOI:10.1016/j.jbiotec.2003.08.007.

Dondrup, M., Goesmann, A., Bartels, D., Kalinowski, J., Krause, L., Linke, B., Rupp, O., Sczyrba, A., Pühler, A. and Meyer, F., 2003. EMMA: a platform for consistent storage and efficient analysis of microarray data. Journal of biotechnology, 106(2-3), pp.135-46, DOI:10.1016/j.jbiotec.2003.08.010.

Kaiser, O., Bartels, D., Bekel, T., Goesmann, A., Kespohl, S., Pühler, A. and Meyer, F., 2003. Whole genome shotgun sequencing guided by bioinformatics pipelines-an optimized approach for an established technique. Journal of biotechnology, 106(2-3), pp.121-33, DOI:10.1016/j.jbiotec.2003.08.008.

Kalinowski, J., Bathe, B., Bartels, D., Bischoff, N., Bott, M., Burkovski, A., Dusch, N., Eggeling, L., Eikmanns, B.J., Gaigalat, L., Goesmann, A., Hartmann, M., Huthmacher, K., Krämer, R., Linke, B., McHardy, A.C., Meyer, F., Möckel, B., Pfefferle, W., Pühler, A., Rey, D.A., Rückert, C., Rupp, O., Sahm, H., Wendisch, V.F., Wiegräbe, I. and Tauch, A., 2003. 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, 104(1-3), pp.5-25, DOI:10.1016/S0168-1656(03)00154-8.

Meyer, F., Goesmann, A., McHardy, A.C., Bartels, D., Bekel, T., Clausen, J., Kalinowski, J., Linke, B., Rupp, O., Giegerich, R. and Pühler, A., 2003. GenDB - An open source genome annotation system for prokaryote genomes. Nucleic Acids Research, 31(8), pp.2187-2195, DOI:10.1093/nar/gkg312.

Tauch, A., Schlüter, A., Bischoff, N., Goesmann, A., Meyer, F. and Pühler, A., 2003. 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 resi. Molecular genetics and genomics : MGG, 268(5), pp.570-84, DOI:10.1007/s00438-002-0785-z.


Goesmann, A., Haubrock, M., Meyer, F., Kalinowski, J. and Giegerich, R., 2002. PathFinder: reconstruction and dynamic visualization of metabolic pathways. Bioinformatics (Oxford, England), 18(1), pp.124-9, DOI:10.1093/bioinformatics/18.1.124.