Intro

Konrad Förstner I am a scientist with an expertise in bioinformatics / computational biology / systems biology and am conducting research in the field of infection and RNA biology as head of bioinformatics at the Core Unit Systems Medicine, University of Würzburg, Germany. While my methodical focus is the integration and interpretation of large data sets - mainly generated with high-troughput sequencing technologies - I am working on a diverse set of biological questions. 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.

Links

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

Several source code repositories are located on GitHub.

Peer-Review activity are represented 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.

Random noise can be found on twitter and app.net.

Publications

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 of manuscripts

If my co-authors agree manuscripts of studies are submitted to a pre-print server like bioRxiv in order to make the results faster available for the scientific community.

APRICOT: an integrated computational pipeline for the sequence-based identification and characterization of RNA-binding proteins. Malvika Sharan, Konrad Ulrich Förstner, Ana Eulalio, Jörg Vogel
Pre-print at bioRxiv | First submitted: 2016-05-24 | Status: Under Review
READemption – A tool for the computational analysis of deep-sequencing-based transcriptome data. Konrad U. Förstner, Jörg Vogel, Cynthia M. Sharma
Pre-print at bioRxiv | First submitted: 2014-04-15 | Status: Published (see below)
Collaborative platforms for streamlining workflows in Open Science. Konrad U. Förstner, Gregor Hagedorn, Claudia Koltzenburg, M. Fabiana Kubke, Daniel Mietchen
Pre-print Nature Precedings | First submitted: 2011-06-27 | Status: Published (see below)

Accepted/published after peer-review

2016

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; DOI:10.1128/JB.00381-16
Pubmed | Full text at Journal of Bacteriology
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, DOI:10.1371/journal.pgen.1006057
Pubmed | Full text at PLOS Genetics
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, DOI:10.1073/pnas.1520255113
Pubmed | Full text at PNAS
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, DOI 10.1186/s12864-016-2602-9
Pubmed | Full text at BMC Genomics
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 | Full text at Nature

2015

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 | Full text at Frontiers in Microbiology
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 | Full text at PLOS ONE
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 | Full text at BMC Genomics
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

2014

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 | Full text at PubMedCentral
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

2013

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

2012

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

2011

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

2010

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

2008

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

2007

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

2006

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

2005

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

Software

  • READemption Github
  • APRICOT Github
  • PEAKachu Github
  • ANNOgesic 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

Data

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

Contact

Simply send me a friendly e-mail. If needed use my PGP key 0xc170f2f83e02d9a1 to encrypt the message. Find more crypto-goodness on keybase.

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