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. My methodical focus is the integration and interpretation of large data sets - mainly generated using high-throughput sequencing technologies - with the aim to translate them into biological and medical insight. 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 academic CV

  • Since 2016: Acting Head of the Core Unit Systems Medicine, University/Clinic of Würzburg
  • Since 2014: Habilitant in the Deparment of Bioinformatics, University of Würzburg
  • Since 2013: 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

Links

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 profiles.

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.

Random noise can be found on twitter.

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 submitted/underreview

ANNOgesic: A Pipeline To Translate Bacterial/Archaeal RNA-Seq Data Into High-Resolution Genome Annotations. Sung-Huan Yu, Jörg Vogel, Konrad U. Förstner
Pre-print at bioRxiv | First submission: 2017-05-27

Accepted/published after peer-review

2017

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, DOI: 10.1186/s12974-017-0924-4
Pubmed | Full text at Journal of Neuroinflammation
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, DOI: 10.15252/embj.201695323
Pubmed | Full text at EMBO Journal
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, DOI: 10.1080/15476286.2017.1341020
Pubmed | Full text at RNA Biology
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, DOI: 10.1128/JB.00249-17
Pubmed | Full text at Journal of Bacteriology
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, DOI:10.1080/15476286.2017.1306170
Pubmed | Full text at RNA Biology
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, DOI:10.1093/nar/gkx137
Pubmed | Full text at Nucleic Acids Research
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, DOI:10.1128/mBio.02041-16
Pubmed | Full text at mBio
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, DOI:10.1016/j.molcel.2016.11.002
Pubmed | Full text at Molecular Cell

2016

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, DOI:10.3389/fmicb.2016.01858
Pubmed | Full text at Frontiers in Microbiology
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, DOI:10.1038/srep35307
Pubmed | Full text at Scientific Reports
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, DOI:10.1073/pnas.1609981113
Pubmed | Full text at PNAS
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, DOI:10.1186/s12864-016-2920-y
Pubmed | Full text at BMC Genomics
Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung. Jozef Dingemansa, 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, DOI:10.1128/mBio.00813-16
Pubmed | Full text at mBio
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, DOI:10.1038/nature16547
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, DOI:10.3389/fmicb.2015.01373
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, DOI:10.1371/journal.pone.0142002
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, DOI:10.1186/s12864-015-1993-3
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, DOI:10.1073/pnas.1500203112
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., DOI:10.1371/journal.pcbi.1003905 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, DOI:10.12688/f1000research.5686.2, DOI:10.12688/f1000research.5686.2 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., DOI:10.1074/jbc.M114.612663
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, DOI:10.1371/journal.pone.0110427
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, DOI:10.1128/JB.02096-14, DOI:10.1128/JB.02096-14
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, DOI:10.1186/1471-2164-15-794
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, DOi:10.1016/j.cell.2014.06.046
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, DOI:10.1038/ncomms5718
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, DOI:10.1186/1471-2164-15-684
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, DOI:10.1093/bioinformatics/btu533
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, Nucleic Acids Research, August 7, 2014, DOI:10.1093/nar/gku714
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, DOI:10.1128/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), DOI:10.4161/rna.29440
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 Nucleic Acids Research. 2013, 41 (18):8434-8443, DOI:10.1093/nar/gkt634
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), DOI:10.1371/journal.pgen.1003576
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, DOI:10.1371/journal.pgen.1003495
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, DOI:10.1128/JB.00746-12
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, DOI:10.1105/tpc.111.089441
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, DOI:10.1038/npre.2011.6066.1
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, DOI:10.1038/nature09944
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, DOI:10.1371/journal.pone.0003515, DOI:10.1371/journal.pone.0002607
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, DOI:10.1016/j.mib.2007.09.001
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, DOI:10.1038/sj.emboj.7601699
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, DOI:10.1016/j.ijmm.2005.11.011
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, DOI:10.1098/rstb.2005.1809
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, DOI:10.1038/sj.embor.7400538
PubMed | Full text at PubMed Central

Software

  • 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

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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