Hi! I'm Konrad.

About Me

I am scientist with an expertise in bioinformatics and systems biology. While my technical focus is the intergration and interpretation of large data sets - mainly generated with high-troughput sequencing technologies - I am working on a collection of diverse biological questions. Currently, I am leading the RNA-Seq and Bioinformatics group of the Core Unit Systems Medicine of the University of Würzburg, Germany. I am advocating openess of source code, science, data, education, content - basically everything - and am an active member of the Open Science group of Open Knowledge.

Publications

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 | Full text at PNAS
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 | Full text at PLoS Comput Biol
An Open Science Peer Review Oath [v2; ref status: indexed, http://f1000r.es/4wf]. 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 | Full text at F1000Research
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 | Full text at J. Biol. Chem
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 | Full text at PLoS One
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 | Full text at JBac
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 | Full text at BMC Genomics
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 | Full text at Cell
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 | Full text at Nature Communications
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 | Full text at BMC Genomics
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 | Full text at Bioinformatics | 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, Nucl. Acids Res., August 7, 2014
Pubmed | Full text at NAR
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 Nucl. Acids Res. 2013, 41 (18):8434-8443
Pubmed | Full text at NAR
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 | Full text at PLoS Genetics
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 | Full text at PLoS Genetics
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 | Full text at Journal of Bacteriology
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 | Full text at Plant Cell
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.
PDF, 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, PDF
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,
PDF file, 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 | Full text at Bioinformatics
Computational analysis of metagenomic data: delineation of compositional features and screens for desirable enzymes. Foerstner KU, my PhD thesis (cumulative dissertation), 2008,
PDF file
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 | Full text at PloS ONE
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 | Full text at PloS ONE
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 | Full text at PloS ONE
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 | PDF
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 | Full text at PubMed Central
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 | Full text at PubMed Central
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 | Full text at PubMed Central

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