Peer Bork

Summary

Affiliation: European Molecular Biology Laboratory
Country: Germany

Publications

  1. ncbi STITCH 3: zooming in on protein-chemical interactions
    Michael Kuhn
    Biotechnology Center, TU Dresden, 01062 Dresden, Germany
    Nucleic Acids Res 40:D876-80. 2012
  2. ncbi Prediction of effective genome size in metagenomic samples
    Jeroen Raes
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Genome Biol 8:R10. 2007
  3. ncbi High-resolution transcription atlas of the mitotic cell cycle in budding yeast
    Marina V Granovskaia
    EMBL European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr, Heidelberg, Germany
    Genome Biol 11:R24. 2010
  4. ncbi Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution
    Carlos Quijano
    Instituto de Investigaciones Biomedicas CSIC UAM, Arturo Duperier 4, 28029 Madrid, Spain
    Genome Biol 9:R176. 2008
  5. ncbi Circular reasoning rather than cyclic expression
    Lars Juhl Jensen
    Genome Biol 9:403. 2008
  6. ncbi Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
    Albert Pallejà
    Biochemistry and Biotechnology Department, Rovira i Virgili University, C Marcel li Domingo s n, 43007 Tarragona, Catalunya, Spain
    BMC Genomics 9:335. 2008
  7. ncbi Non-random retention of protein-coding overlapping genes in Metazoa
    Giulia Soldà
    1Department of Biology and Genetics for Medical Sciences, University of Milan, 20133 Milan, Italy
    BMC Genomics 9:174. 2008
  8. ncbi G2D: a tool for mining genes associated with disease
    Carolina Perez-Iratxeta
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, ON K1H 8L6, Ottawa, Canada
    BMC Genet 6:45. 2005
  9. ncbi DCD - a novel plant specific domain in proteins involved in development and programmed cell death
    Raimund Tenhaken
    Plant Molecular Biology, University of Frankfurt, Marie Curie Str, 9, 60439 Frankfurt, Germany
    BMC Bioinformatics 6:169. 2005
  10. ncbi Information extraction from full text scientific articles: where are the keywords?
    Parantu K Shah
    Biocomputing, European Molecular Biology Laboratory, Heidelberg, Germany
    BMC Bioinformatics 4:20. 2003

Collaborators

  • Christian von Mering
  • Lars Juhl Jensen
  • Pablo Minguez
  • Andreas Beyer
  • Michael Kuhn
  • Andrea Franceschini
  • Damian Szklarczyk
  • Carolina Perez-Iratxeta
  • Marina V Granovskaia
  • Giulia Soldà
  • Carlos Quijano
  • Albert Pallejà
  • Mikita Suyama
  • Jeroen Raes
  • Raimund Tenhaken
  • Miguel A Andrade
  • Parantu K Shah
  • Milan Simonovic
  • Alexander Roth
  • Jianyi Lin
  • Sune Frankild
  • Joern Toedling
  • Lars M Steinmetz
  • Monica Campillos
  • Ye Ning
  • Matthew E Ritchie
  • Wolfgang Huber
  • Jesus Lopez-Marti
  • Paride Pelucchi
  • Ermanno Rizzi
  • Pavel Tomancak
  • David Torrents
  • Maria Luisa Tenchini
  • Francesca D Ciccarelli
  • Marco Milan
  • Eoghan D Harrington
  • Alessandro Guffanti
  • Silvia Boi
  • Miguel Manzanares
  • Martin J Lercher
  • Jan O Korbel
  • Tobias Doerks
  • Matthias Wjst

Detail Information

Publications12

  1. ncbi STITCH 3: zooming in on protein-chemical interactions
    Michael Kuhn
    Biotechnology Center, TU Dresden, 01062 Dresden, Germany
    Nucleic Acids Res 40:D876-80. 2012
    ..Combining the isomers increases the coverage, as interaction databases and publications found through text mining will often refer to compounds without specifying the stereoisomer. The database is accessible at http://stitch.embl.de/...
  2. ncbi Prediction of effective genome size in metagenomic samples
    Jeroen Raes
    European Molecular Biology Laboratory, Meyerhofstrasse 1, D 69117 Heidelberg, Germany
    Genome Biol 8:R10. 2007
    ..7 Mb; for bacteria in a nutrient-poor, organism-sparse ocean surface water sample, EGS is as low as 1.6 Mb. The method also permits evaluation of completion status and assembly bias in single-genome sequencing projects...
  3. ncbi High-resolution transcription atlas of the mitotic cell cycle in budding yeast
    Marina V Granovskaia
    EMBL European Molecular Biology Laboratory, Department of Genome Biology, Meyerhofstr, Heidelberg, Germany
    Genome Biol 11:R24. 2010
    ..To explore the complex transcriptome architecture underlying the budding yeast cell cycle, we used 8 bp tiling arrays to generate a 5 minute-resolution, strand-specific expression atlas of the whole genome...
  4. ncbi Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution
    Carlos Quijano
    Instituto de Investigaciones Biomedicas CSIC UAM, Arturo Duperier 4, 28029 Madrid, Spain
    Genome Biol 9:R176. 2008
    ..However, the contribution of gene duplication to gene order has not been analyzed in detail, as it is believed that co-expression due to recent duplicates would obscure other domains of co-expression...
  5. ncbi Circular reasoning rather than cyclic expression
    Lars Juhl Jensen
    Genome Biol 9:403. 2008
    ..A response to Combined analysis reveals a core set of cycling genes by Y Lu, S Mahony, PV Benos, R Rosenfeld, I Simon, LL Breeden and Z Bar-Joseph. Genome Biol 2007, 8:R146...
  6. ncbi Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?
    Albert Pallejà
    Biochemistry and Biotechnology Department, Rovira i Virgili University, C Marcel li Domingo s n, 43007 Tarragona, Catalunya, Spain
    BMC Genomics 9:335. 2008
    ..Here we examine the longest overlaps and assess whether they are the product of special functional constraints or of erroneous annotation...
  7. ncbi Non-random retention of protein-coding overlapping genes in Metazoa
    Giulia Soldà
    1Department of Biology and Genetics for Medical Sciences, University of Milan, 20133 Milan, Italy
    BMC Genomics 9:174. 2008
    ..Here we report a comparative analysis of overlaps between genes coding for well-annotated proteins in five metazoan genomes (human, mouse, zebrafish, fruit fly and worm)...
  8. ncbi G2D: a tool for mining genes associated with disease
    Carolina Perez-Iratxeta
    Ontario Genomics Innovation Centre, Ottawa Health Research Institute, ON K1H 8L6, Ottawa, Canada
    BMC Genet 6:45. 2005
    ..We previously developed an algorithm to prioritize genes on a chromosomal region according to their possible relation to an inherited disease using a combination of data mining on biomedical databases and gene sequence analysis...
  9. ncbi DCD - a novel plant specific domain in proteins involved in development and programmed cell death
    Raimund Tenhaken
    Plant Molecular Biology, University of Frankfurt, Marie Curie Str, 9, 60439 Frankfurt, Germany
    BMC Bioinformatics 6:169. 2005
    ..We delineate the NRP-gene in soybean, which is specifically induced during this programmed cell death and contains a novel protein domain, which is commonly found in different plant proteins...
  10. ncbi Information extraction from full text scientific articles: where are the keywords?
    Parantu K Shah
    Biocomputing, European Molecular Biology Laboratory, Heidelberg, Germany
    BMC Bioinformatics 4:20. 2003
    ..Several questions arise as to whether the effort of scanning full text articles is worthy, or whether the information that can be extracted from the different sections of an article can be relevant...
  11. ncbi STITCH 2: an interaction network database for small molecules and proteins
    Michael Kuhn
    Biotechnology Center, TU Dresden, 01062 Dresden, Germany
    Nucleic Acids Res 38:D552-6. 2010
    ..STITCH 2.0 connects proteins from 630 organisms to over 74,000 different chemicals, including 2200 drugs. STITCH can be accessed at http://stitch.embl.de/...
  12. ncbi STRING v9.1: protein-protein interaction networks, with increased coverage and integration
    Andrea Franceschini
    Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Switzerland
    Nucleic Acids Res 41:D808-15. 2013
    ....