Konrad Förstner I am a researcher in the field of in bioinformatics / computational biology / systems biology. My methodical focus is the integration and interpretation of large data sets - mainly generated using high-throughput sequencing technologies but also text corpora - with the aim to translate them into biological and medical insights. As part of that I am advocating open science with all its facetes (data, publications, source code of research software, educational resources, publication metrics etc.) and am active in several groups/communites promoting this.

Short CV

  • Since 2018: Professor for Information Literacy at the TH Köln – University of Applied Sciences and Head of Information Services at ZB MED - Information Centre for Life Sciences (see research group page).
  • 2016 - 2018: Acting Head of the Core Unit Systems Medicine, University/Clinic of Würzburg
  • 2013 - 2018: Head of Bioinformatics, Core Unit Systems Medicine, University/Clinic of Würzburg
  • 2011 - 2013: Postdoc in the groups of Jörg Vogel and Cynthia Sharma, Institute of Molecular Infection Biology and Research Center for Infectious Diseases, University of Würzburg
  • 2009 - 2011: Entrepreneurial and freelancing work, Darmstadt/Berlin
  • 2004 - 2009: PhD (Bioinformatics/Computational biology) in the group of Peer Bork, EMBL, Heidelberg
  • 1999 - 2004: Studies of Biochemistry and Computer Science, University of Greifswald, including stays in Switzerland and USA


My ORCID identifier is 0000-0002-1481-2996 and further information/statistics regarding my publications can also be found on my Google Scholar, Impact Story and ResearchGate profile.

Several source code repositories are shared on GitHub.

Peer-Review activities are listed at Publons.

Slides of selected talks can be found at Speaker Deck.

I am co-host of the podcast Open Science Radio. As the name implies we cover open science and related topics.

Further information about previous positions and activities can be found at Xing and LinkedIn.

I'm on Twitter and Mastodon.


Detailed statistics can be found on my Google Scholar page.

The badges on the left side represent the altmetric score of each article.

Pre-prints submitted/underreview

Accepted/published after peer-review


The RNase YbeY is vital for ribosome maturation, stress resistance and virulence of the natural genetic engineer Agrobacterium tumefaciens. Philip Möller, Philip Busch, Beate Sauerbrei, Alexander Kraus, Konrad U. Förstner, Tuan-Nan Wen, Aaron Overlöper, Erh-Min Lai, Franz Narberhaus Journal of Bacteriology, 18 March 2019, Pubmed |
A non-coding RNA from the intercellular adhesion (ica) locus of Staphylococcus epidermidis controls polysaccharide intercellular adhesion (PIA)-mediated biofilm formation. Maike F. Lerch, Sonja M.K. Schoenfelder, Gabriella Marincola, Freya D. R. Wencker, Martin Eckart, Konrad U. Förstner, Cynthia M. Sharma, Kai M. Thormann, Martin Kucklick, Susanne Engelmann, Wilma Ziebuhr Molecular Microbiology, 15 March 2019, Pubmed | 10.1371/10.1111/mmi.14238
The small non-coding RNA RsaE influences extracellular matrix composition in Staphylococcus epidermidis biofilm communities. Sonja M. K. Schoenfelder, Claudia Lange, Srinivasa Abishek Prakash, Gabriella Marincola, Maike F. Lerch, Freya D. R. Wencker, Konrad U. Förstner, Cynthia M. Sharma, Wilma Ziebuhr PLOS Pathongens, 14 March 2019, Pubmed |
The Major RNA-Binding Protein ProQ Impacts Virulence Gene Expression in Salmonella enterica Serovar Typhimurium. Alexander J. Westermann, Elisa Venturini, Mikael E. Sellin, Konrad U. Förstner, Wolf-Dietrich Hardt, Jörg Vogel mBio, 2 Jan 2019, Pubmed |


Genome organization and DNA accessibility control antigenic variation in trypanosomes. Laura S. M. Müller, Raúl O. Cosentino, Konrad U. Förstner, Julien Guizetti, Carolin Wedel, Noam Kaplan, Christian J. Janzen, Panagiota Arampatzi, Jörg Vogel, Sascha Steinbiss, Thomas D. Otto, Antoine-Emmanuel Saliba, Robert P. Sebra, T. Nicolai Siegel Nature, 17 Oct 2018, Pubmed |
Cross-cleavage activity of Cas6b in crRNA processing of two different CRISPR-Cas systems in Methanosarcina mazei Gö1. Lisa Nickel, Andrea Ulbricht, Omer S. Alkhnbashi, Konrad U. Förstner, Liam Cassidy, Katrin Weidenbach, Rolf Backofen, Ruth A. Schmitz RNA Biology, 13 Sep 2018, Pubmed |
ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes.. Sung-Huan Yu Jörg Vogel Konrad U Förstner GigaScience, Volume 7, Issue 9, 1 September 2018, Pubmed |
[Pre-print] ANNOgesic: A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes. Sung-Huan Yu, Jörg Vogel, Konrad U. Förstner
Pre-print at bioRxiv | First submission: 2017-05-27
Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus. Kathrin S. Fröhlich, Konrad U. Förstner, Zemer Gitai Nucleic Acid Research, 2018 27 August, Pubmed |
RNase E cleavage shapes the transcriptome of Rhodobacter sphaeroides and strongly impacts phototrophic growth. Konrad U. Förstner*, Carina M. Reuscher*, Kerstin Haberzettl, Lennart Weber, Gabriele Klug, Life Science Alliance, 2018 1 August, (* contributed equally)
SuhB, a small non-coding RNA involved in catabolite repression of tetralin degradation genes in Sphingopyxis granuli strain TFA. Inmaculada García‐Romero, Konrad U. Förstner, Eduardo Santero, Belén Floriano Environmental Microbiology, 2018 July 22, Pubmed |
A New Bioactive Compound From the Marine Sponge-Derived Streptomyces sp. SBT348 Inhibits Staphylococcal Growth and Biofilm Formation. Srikkanth Balasubramanian, Joseph Skaf, Ulrike Holzgrabe, Richa Bharti, Konrad U. Förstner, Wilma Ziebuhr, Ute H. Humeida, Usama R. Abdelmohsen and Tobias A. Oelschlaeger, Frontiers in Microbiology, 2018 July 29;9:929, Pubmed |
The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ. Susanne Bury, Manonmani Soundararajan, Richa Bharti, Rudolf von Bünau, Konrad U. Förstner and Tobias A. Oelschlaeger, Frontiers in Microbiology, 2018 May 29;9:929, Pubmed |
A Novel Mechanism of Inactivating Antibacterial Nitro Compounds in the Human Pathogen Staphylococcus aureus by Overexpression of a NADH-dependent Flavin Nitroreductase. Ebaa M. El-Hossary, Konrad U. Förstner, Patrice François, Damien Baud , Karin Streker , Jacques Schrenzel, Knut Ohlsen, Ulrike Holzgrabe, Antimicrobial Agents Chemotherapy, 2018 Jan 25;62(2), Pubmed |


Insights into Microalga and Bacteria Interactions of Selected Phycosphere Biofilms Using Metagenomic, Transcriptomic, and Proteomic Approaches. Ines Krohn-Molt, Malik Alawi, Konrad U. Förstner, Alena Wiegandt, Lia Burkhardt, Daniela Indenbirken, Melanie Thieß, Adam Grundhoff, Julia Kehr, Andreas Tholey, Wolfgang R. Streit, Frontiers in Microbiology, 10 October 2017, Pubmed |
Differential effects of FTY720 on the B cell compartment in a mouse model of multiple sclerosis. Kathrin Bail, Quirin Notz, Damiano M. Rovituso, Andrea Schampel, Marie Wunsch, Tobias Koeniger, Verena Schropp, Richa Bharti, Claus-Juergen Scholz, Konrad U. Foerstner, Christoph Kleinschnitz, Stefanie Kuerten, Journal of Neuroinflammation, 2017, December, 14:148 Pubmed |
GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes. Carolin Wedel, Konrad U. Förstner, Ramona Derr, T. Nicolai Siegel, EMBO Journal, 2017 July Pubmed |
dRNA-seq Transcriptional Profiling of the FK506 Biosynthetic Gene Cluster in Streptomyces tsukubaensis NRRL18488 and General Analysis of the Transcriptome. Judith S. Bauer, Sven Fillinger, Konrad Förstner, Alexander Herbig, Adam C. Jones, Katrin Flinspach, Cynthia Sharma, Harald Gross, Kay Nieselt, Alexander K. Apel, RNA Biology, 2017, June Pubmed |
An RpoHI-dependent response promotes outgrowth after extended stationary phase in the alphaproteobacterium Rhodobacter sphaeroides. Bernhard Remes, Tom Rische-Grahl, Katrin M. H. Müller, Konrad U. Förstner, Sung-Huan Yu, Lennart Weber, Andreas Jäger, Verena Peuser, Gabriele Klug, Journal of Bacteriology, 2017, May Pubmed |
sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1. Daniela Prasse, Konrad U. Förstner, Dominik Jäger, Rolf Backofen, Ruth A. Schmitz, RNA Biology, 2017, March Pubmed |
APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. Malvika Sharan, Konrad U. Förstner, Ana Eulalio, Jörg Vogel, Nucleic Acids Research, 2017, March, Pubmed |
Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases. Daria Lavysh, Maria Sokolova, Marina Slashcheva, Konrad U. Förstner, Konstantin Severinov, mBio, 2017, 14 February, vol. 8 no. 1 e02041-16, Pubmed |
In Vivo Cleavage Map Illuminates the Central Role of RNase E in Coding and Non-coding RNA Pathways. Yanjie Chao, Lei Li, Dylan Girodat, Konrad U. Förstner, Nelly Said, Colin Corcoran, Michał Śmiga, Kai Papenfort, Richard Reinhardt, Hans-Joachim Wieden, Ben F. Luisi, Jörg Vogel, Molecular Cell, 2017, Jan 65;1:39-51 Pubmed |


The Absence of the N-acyl-homoserine-lactone Autoinducer Synthase Genes traI and ngrI Increases the Copy Number of the Symbiotic Plasmid in Sinorhizobium fredii NGR234. Jessica Grote, Dagmar Krysciak, Katrin Petersen, Simon Güllert, Christel Schmeisser, Konrad U. Förstner, Hari B. Krishnan, Harald Schwalbe, Nina Kubatova, Wolfgang R. Streit, Frontiers in Microbiology, 2016, Nov 18, Pubmed |
The primary transcriptome of the Escherichia coli O104:H4 pAA plasmid and novel insights into its virulence gene expression and regulation. Petya Berger, Michael Knödler, Konrad U. Förstner, Michael Berger, Christian Bertling, Cynthia M. Sharma, Jörg Vogel, Helge Karch, Ulrich Dobrindt, Alexander Mellmann, Scientific Reports, 2016, Oct 17;6:35307 Pubmed |
Grad-seq guides the discovery of ProQ as a major small RNA binding protein. Alexandre Smirnov, Konrad U. Förstner, Erik Holmqvist, Andreas Otto, Regina Günster, Dörte Becher, Richard Reinhardt, and Jörg Vogel, PNAS, 2016, Pubmed |
Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq). Julia Babski, Karina A. Haas, Daniela Näther-Schindler, Friedhelm Pfeiffer, Konrad U. Förstner, Matthias Hammelmann, Rolf Hilker, Anke Becker, Cynthia M. Sharma, Anita Marchfelder, Jörg Soppa, BMC Genomics, 2016 Aug 12; 17:629, Pubmed |
Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung. Jozef Dingemans, Pieter Monsieurs, Sung-Huan Yu, Aurélie Crabbé, Konrad U. Förstner, Anne Malfroot, Pierre Cornelis, Rob Van Houdt, mBio, 2016 Aug 2;7(4). pii: e00813-16 Pubmed |
Cis-encoded sRNAs, a conserved mechanism for repression of polysaccharide utilization in the Bacteroides. Yanlu Cao, Konrad U. Förstner, Jörg Vogel and C. Jeffrey Smith, Journal of Bacteriology, 2016, Jun 27; Pubmed |
Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein. Doreen Meier, Janis Kruse, Jann Buttlar, Michael Friedrich, Fides Zenk, Benjamin Boesler, Konrad U. Förstner, Christian Hammann, Wolfgang Nellen, PLOS Genetics, 2016, Jun 6;12(6):e1006057 Pubmed |
Natural mutations in a Staphylococcus aureus virulence regulator attenuate cytotoxicity but permit bacteremia and abscess formation. Sudip Das, Claudia Lindemann, Bernadette C. Young, Julius Muller, Babett Österreich, Nicola Ternette, Ann-Cathrin Winkler, Kerstin Paprotka, Richard Reinhardt, Konrad U. Förstner, Elizabeth Allen, Amy Flaxman, Yuko Yamaguchi, Christine S. Rollier, Pauline van Diemen, Sebastian Blättner, Christian W. Remmele, Martina Selle, Marcus Dittrich, Tobias Müller, Jörg Vogel, Knut Ohlsen, Derrick W. Crook, Ruth Massey, Daniel J. Wilson, Thomas Rudel, David H. Wyllie, and Martin J. Fraunholz, PNAS, 2016, 31;113(22):E3101-10 Pubmed |
Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation Jelena Čuklina, Julia Hahn, Maxim Imakaev, Ulrich Omasits, Konrad U. Förstner, Nikolay Ljubimov, Melanie Goebel, Gabriella Pessi, Hans-Martin Fischer, Christian H. Ahrens, Mikhail S. Gelfand, Elena Evguenieva-Hackenberg, BMC Genomics, 2016, 17:302
Pubmed |
Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions. Alexander J. Westermann, Konrad U. Förstner, Fabian Amman, Lars Barquist, Yanjie Chao, Leon N. Schulte, Lydia Müller, Richard Reinhardt, Peter F. Stadler, Jörg Vogel, Nature, 2016 Pubmed |


Phenotypic heterogeneity affects Stenotrophomonas maltophilia K279a colony morphotypes and β-lactamase expression. Ebrahim M. Abda, Dagmar Krysciak, Ines Krohn-Molt, Uwe Mamat, Christel Schmeisser, Konrad U. Förstner, Ulrich E. Schaible, Thomas A. Kohl, Stefan Nieman, Wolfgang R. Streit, Frontiers in Microbiology, 6:1373, 2015 Pubmed |
dRNA-Seq Reveals Genomewide TSSs and Noncoding RNAs of Plant Beneficial Rhizobacterium Bacillus amyloliquefaciens. Ben Fan, Lei Li, Yanjie Chao, Konrad Förstner, Jörg Vogel, Rainer Borriss, Xiao-Qin Wu, PLOS ONE, November 5, 2015 Pubmed |
Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315. Andrea M. Sass, Heleen Van Acker, Konrad U. Förstner, Filip Van Nieuwerburgh, Dieter Deforce, Jörg Vogel, Tom Coenye, BMC Genomics, October 13, 2015, 16:775 Pubmed |
Differential RNA-seq of Vibrio cholerae identifies the VqmR small RNA as a regulator of biofilm formation. Kai Papenfort, Konrad U. Förstner, Jian-Ping Cong, Cynthia M. Sharma, Bonnie L. Bassler, PNAS, February 2, 2015 Pubmed |
Ten Simple Rules for Organizing an Unconference. Aidan Budd, Holger Dinkel, Manuel Corpas, Jonathan C. Fuller, Laura Rubinat, Damien P. Devos, Pierre H. Khoueiry, Konrad U. Förstner, Fotis Georgatos, Francis Rowland, Malvika Sharan, Janos X. Binder, Tom Grace, Karyn Traphagen, Adam Gristwood, Natasha T. Wood PLoS Comput Biol, 2015,11(1): e1003905. Pubmed |


An Open Science Peer Review Oath [v2; ref status: indexed,]. Jelena Aleksic, Adrian Alexa, Teresa K Attwood, Neil Chue Hong, Martin Dahlö, Robert Davey, Holger Dinkel, Konrad U Förstner, Ivo Grigorov, Jean-Karim Hériché, Leo Lahti, Dan MacLean, Michael L Markie, Jenny Molloy, Maria Victoria Schneider, Camille Scott, Richard Smith-Unna, Bruno Miguel Vieira, F1000Research, 2014, 3:271 Pubmed |
Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1. Benjamin Boesler, Doreen Meier, Konrad U. Foerstner, Michael Friedrich, Christian Hammann, Cynthia M. Sharma, Wolfgang Nellen J. Biol. Chem, 2014 Oct 28., Pubmed |
Profound Impact of Hfq on Nutrient Acquisition, Metabolism and Motility in the Plant Pathogen Agrobacterium tumefaciens. Philip Möller, Aaron Overlöper, Konrad U. Förstner, Tuan-Nan Wen, Cynthia M Sharma, Erh-Min Lai, Franz Narberhaus, PLoS One, 2014 Oct 17;9(10):e110427 Pubmed |
Global transcriptional start site mapping using dRNA-seq reveals novel antisense RNAs in Escherichia coli. Maureen K. Thomason, Thorsten Bischler, Sara K. Eisenbart, Konrad U. Förstner, Aixia Zhang, Alexander Herbig, Kay Nieselt, Cynthia M. Sharma, Gisela Storz, Journal of Bacteriology, 2014, Sept. 29, Pubmed |
Role of oxygen and the OxyR protein in the response to iron limitation in Rhodobacter sphaeroides. Bernhard Remes, Bork A. Berghoff, Konrad U. Förstner, Gabriele Klug, BMC Genomics, 2014, 15:794 Pubmed |
Evolution of Resistance to a Last-Resort Antibiotic in Staphylococcus aureus via Bacterial Competition. Gudrun Koch, Ana Yepes, Konrad U. Förstner, Charlotte Wermser, Stephanie T. Stengel, Jennifer Modamio, Knut Ohlsen, Kevin R. Foster, Daniel Lopez, Cell, 2014, 158, 5, p1060–1071 Pubmed |
Functional high-throughput screening identifies the miR-15 microRNA family as cellular restriction factors for Salmonella infection. Claire Maudet, Miguel Mano, Ushasree Sunkavalli, Malvika Sharan, Mauro Giacca, Konrad U. Förstner, Ana Eulalio, Nature Communications, 2014, 5, Article number: 4718, Pubmed |
Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis. Dominik Jäger, Konrad U. Förstner, Cynthia M. Sharma, Thomas J. Santangelo, John N. Reeve, BMC Genomics, 2014 Aug 16;15(1):684 Pubmed |
READemption – A tool for the computational analysis of deep-sequencing-based transcriptome data. Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma, Bioinformatics, August 13, 2014 Pubmed | | Pre-print at bioRxiv
Regulation of transcription termination by glucosylated hydroxymethyluracil, base J, in Leishmania major and Trypanosoma brucei. David Reynolds, Laura Cliffe1, Konrad U. Förstner, Chung-Chau Hon T. Nicolai Siegel, Robert Sabatini, Nucleic Acids Research, August 7, 2014 Pubmed |
RNA-seq in the broad host range strain Sinorhizobium fredii NGR234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a traI and ngrI deletion mutant. Krysciak D, Grote J, Rodriguez Orbegoso M, Utpatel C, Förstner KU, Li L, Schmeisser C, Krishnan HB, Streit WR, Appl Environ Microbiol., 2014 Jul 7. pii: AEM.01835-14 Pubmed |
RNase J is required for processing of a small number of RNAs in Rhodobacter sphaeroides. Rische-Grahl T, Weber L1, Remes B, Förstner KU, Klug G RNA Biol, 2014, Jun 12;11(7), Pubmed |


Target recognition, RNA methylation activity and transcriptional regulation of the Dictyostelium discoideum Dnmt2-homologue (DnmA). Mueller, S., Windhof, I., Maximov, V., Jurkowski, T.P., Jeltsch, A., Förstner, K., Sharma, C., Gräf, R., and Nellen, W Nucleic Acids Research. 2013, 41 (18):8434-8443 Pubmed |
Integrative "omics"-approach discovers dynamic and regulatory features of bacterial stress responses. Berghoff B.A, Konzer A., Mank N. N., Looso M., Rische T., Förstner K.U., Krüger M., Klug G. PLoS Genetics. 2013, Jun;9(6), Pubmed |
High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates. Dugar G, Herbig A, Förstner KU, Heidrich N, Reinhardt R, Nieselt K, Sharma CM. PLoS Genetics. 2013 May;9(5):e1003495 Pubmed |


Functional characterization of the RNA chaperone Hfq in opportunistic human pathogen Stenotrophomonas maltophilia. Roscetto E, Angrisano T, Costa V, Casalino M, Förstner KU, Sharma CM, Di Nocera PP, De Gregorio E. J Bacteriol. 2012 Aug 24 Pubmed |
The Primary Transcriptome of Barley Chloroplasts: Numerous Noncoding RNAs and the Dominating Role of the Plastid-Encoded RNA Polymerase. Zhelyazkova P, Sharma CM, Förstner KU, Liere K, Vogel J, Börner T. Plant Cell. 2012 Jan 20 Pubmed |


Collaborative platforms for streamlining workflows in Open Science. Konrad U. Förstner, Gregor Hagedorn, Claudia Koltzenburg, M Fabiana Kubke, Daniel Mietchen Proceedings of the 6th Open Knowledge Conference, Berlin, Germany, June 30 & July 1, 2011. Berlin, Germany, June 30 & July 1, 2011, | Wiki page at Species-ID | Nature Precedings
Enterotypes of the human gut microbiome. Manimozhiyan Arumugam, Jeroen Raes, Eric Pelletier, Denis Le Paslier, Takuji Yamada, Daniel R. Mende, Gabriel R. Fernandes, Julien Tap, Thomas Bruls, Jean-Michel M. Batto, Marcelo Bertalan, Natalia Borruel, Francesc Casellas, Leyden Fernandez, Laurent Gautier, Torben Hansen,Masahira Hattori, Tetsuya Hayashi, Michiel Kleerebezem, Ken Kurokawa, Marion Leclerc, Florence Levenez, Chaysavanh Manichanh, H. Bjørn Nielsen, Trine Nielsen, Nicolas Pons, Julie Poulain, Junjie Qin, Thomas Sicheritz-Ponten, Sebastian Tims, David Torrents, Edgardo Ugarte, Erwin G. Zoetendal, Jun Wang, Francisco Guarner, Oluf Pedersen, Willem M. de Vos, Søren Brunak, Joel Doré, María Antolín, François Artiguenave, Hervé M. Blottiere, Mathieu Almeida, Christian Brechot, Carlos Cara, Christian Chervaux, Antonella Cultrone, Christine Delorme, Gérard Denariaz, Rozenn Dervyn, Konrad U. Foerstner, Carsten Friss, Maarten van de Guchte, Eric Guedon, Florence Haimet, Wolfgang Huber, Johan van Hylckama-Vlieg, Alexandre Jamet, Catherine Juste, Ghalia Kaci, Jan Knol, Omar Lakhdari, Severine Layec, Karine Le Roux, EmmanuelleMaguin, Alexandre Mérieux, Raquel Melo Minardi, Christine M'rini, Jean Muller, Raish Oozeer, Julian Parkhill, Pierre Renault, Maria Rescigno, Nicolas Sanchez, Shinichi Sunagawa, Antonio Torrejon, Keith Turner, Gaetana Vandemeulebrouck, Encarna Varela, Yohanan Winogradsky, Georg Zeller, Jean Weissenbach, S. Dusko Ehrlich, Peer Bork Nature. 2011 Apr. 20 Pubmed |
Wikis in scholarly publishing. Daniel Mietchen, Gregor Hagedorn, Konrad U. Förstner, M Fabiana Kubke, Claudia Koltzenburg, Mark J. Hahnel, Lyubomir Penev. Information Services and Use 31(1-2) : 53–59 | Wiki page at Species-ID


SmashCommunity: A metagenomic annotation and analysis tool. Arumugam M, Harrington ED, Foerstner KU, Raes J, Bork P Bioinformatics. 2010 Oct 19 Pubmed |


A Nitrile Hydratase in the Eukaryote Monosiga brevicollis. Foerstner KU, Doerks T, Muller J, Raes J, Bork P. PloS ONE 2008;3(12):e3976 Pubmed |
A computational screen for type I polyketide synthases in metagenomics shotgun data. Foerstner KU, Doerks T, Creevey CJ, Doerks A, Bork P PloS ONE 2008;3(10):e3515 Pubmed |
A Molecular Study of Microbe Transfer between Distant Environments. Hooper SD, Raes J, Foerstner KU, Harrington ED, Dalevi D, Bork P PloS ONE 2008 3(7): e2607 Pubmed |


Get the most out of your metagenome: computational analysis of environmental sequence data. Raes J, Foerstner KU, Bork P Curr Opin Microbiol. 2007 Oct 11 Pubmed |
Splicing factors stimulate polyadenylation via USEs at non-canonical 3' end formation signals. Danckwardt S, Kaufmann I, Gentzel M, Foerstner KU, Gantzert AS, Gehring NH, Neu-Yilik G, Bork P, Keller W, Wilm M, Hentze MW, Kulozik AE EMBO J. 2007 Apr 26 Pubmed |


The sigmaB regulon in Staphylococcus aureus and its regulation. Pane-Farre J, Jonas B, Förstner K, Engelmann S, Hecker M Int J Med Microbiol. 2006 Aug ; 296(4-5): 237-58 Pubmed |
Comparative analysis of environmental sequences: potential and challenges. Foerstner KU, von Mering C, Bork P Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29; 361(1467): 519-23 Pubmed |


Environments shape the nucleotide composition of genomes. Foerstner KU, von Mering C, Hooper SD, Bork P EMBO Rep. 2005 Dec ; 6(12): 1208-13 PubMed |


  • READemption Github
  • APRICOT Github
  • COVERnant Github
  • ANNOgesic Github
  • PEAKachu Github

Open Educational Resources

A growing collection of open (CC-licensed) education resources. More coming soon ...

  • Introduction to the Unix Shell for biologists Github
  • Software Carpentry: Version Control with Git (2015) Github
  • RNA-Seq analysis with READemption - Setup and usage in the EGI Federated Cloud (2014) Github


  • Numerous RNA-Seq data sets deposited at NCBI GEO can be found via this query.


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