Publications of Bork Group in the journal "Bioinformatics".

Publications of Bork Group in the journal "Bioinformatics".

Authors in this color are/were of Bork Group. [Altmetric off].
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2022 1 publication(s).
35.
metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes.
Van Rossum T, Costea PI, Paoli L, Alves RJ, Thielemann R, Sunagawa S, Bork P
Bioinformatics.
2022 Jan 27; 38(4): 1162-1164. PubMed: 34791031.
Abstract + PDF
2020 1 publication(s).
34.
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.
Li YY, Kuhn M, Gavin AC, Bork P
Bioinformatics.
2020 Feb 15; 36(4): 1213-1218. PubMed: 31605112.
Abstract + PDF
2017 2 publication(s).
33.
MAPseq: highly efficient k-mer search with confidence estimates, for rRNA sequence analysis.
Matias Rodrigues JF, Schmidt TSB, Tackmann J, von Mering C
Bioinformatics.
2017 Dec 1; 33(23): 3808-3810. PubMed: 28961926.
Abstract + PDF
32.
RTK: efficient rarefaction analysis of large datasets.
Bioinformatics.
2017 Aug 15; 33(16): 2594-2595. PubMed: 28398468.
Abstract + PDF
2016 3 publication(s).
31.
CART - a chemical annotation retrieval toolkit.
Bioinformatics.
2016 Sep 15; 32(18): 2869-71. Epub 2016 Jun 2; PubMed: 27256313.
Abstract + PDF
30.
MOCAT2: a metagenomic assembly, annotation and profiling framework.
Bioinformatics.
2016 Aug 15; 32(16): 2520-3. Epub 2016 Apr 8; PubMed: 27153620.
Abstract + PDF
29.
Benchmarking the next generation of homology inference tools.
Saripella GV, Sonnhammer EL, Forslund K
Bioinformatics.
2016 Jun 1; [Epub ahead of print] PubMed: 27256311.
Abstract + PDF
2015 1 publication(s).
28.
Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images.
Coelho LP, Pato C, Friães A, Neumann A, von Köckritz-Blickwede M, Ramirez M, Carriço JA
Bioinformatics.
2015 Jul 15; 31(14): 2364-70. PubMed: 25792554.
Abstract
2013 1 publication(s).
27.
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Pacini C, Iorio F, Gonçalves E, Iskar M, Klabunde T, Bork P, Saez-Rodriguez J
Bioinformatics.
2013 Jan 1; 29(1): 132-4. Epub 2012 Nov 4; PubMed: 23129297.
Abstract + PDF
2010 3 publication(s).
26.
SmashCommunity: A metagenomic annotation and analysis tool.
Bioinformatics.
2010 Dec 1; 26(23): 2977-8. Epub 2010 Oct 19; PubMed: 20959381.
Abstract + PDF
25.
SmashCell: A software framework for the analysis of single-cell amplified genome sequences.
Bioinformatics.
2010 Dec 1; 26(23): 2979-80. Epub 2010 Oct 21; PubMed: 20966005.
Abstract + PDF
24.
AQUA: Automated quality improvement for multiple sequence alignments.
Muller J, Creevey CJ, Thompson JD, Arendt D, Bork P
Bioinformatics.
2010 Jan 15; 26(2): 263-5. Epub 2009 Nov 19; PubMed: 19926669.
Abstract + PDF
2009 1 publication(s).
23.
OnTheFly: A Tool for automated document-based text annotation, data linking and network generation.
Pavlopoulos GA, Pafilis E, Kuhn M, Hooper SD, Schneider R
Bioinformatics.
2009 Feb 17; 25(7): 977-8. PubMed: 19223449.
Abstract + PDF
2008 1 publication(s).
22.
Sircah: A tool for the detection and visualisation of alternative transcripts.
Bioinformatics.
2008 Sep 1; 24(17): 1959-60. Epub 2008 Jul 17; PubMed: 18635569.
Abstract + PDF
2007 1 publication(s).
21.
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Bioinformatics.
2007 Jan 1; 23(1): 127-8. Epub 2006 Oct 18; PubMed: 17050570.
Abstract + PDF
2006 2 publication(s).
20.
Extraction of regulatory gene/protein networks from Medline.
Saric J, Jensen LJ, Ouzounova R, Rojas I, Bork P
Bioinformatics.
2006 Mar 15; 22(6): 645-50. Epub 2005 Jul 26; PubMed: 16046493.
Abstract + PDF
19.
LSAT: learning about alternative transcripts in MEDLINE.
Bioinformatics.
2006 Apr 1; 22(7): 857-65. Epub 2006 Jan 12; PubMed: 16410322.
Abstract + PDF
2005 3 publication(s).
18.
The WHy domain mediates the response to desiccation in plants and bacteria.
Bioinformatics.
2005 Apr 15; 21(8): 1304-7. Epub 2004 Dec 14; PubMed: 15598830.
Abstract + PDF
17.
Comparison of computational methods for the identification of cell cycle-regulated genes.
de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S
Bioinformatics.
2005 Apr 1; 21(7): 1164-71. Epub 2004 Oct 28; PubMed: 15513999.
Abstract + PDF
16.
Medusa: a simple tool for interaction graph analysis.
Bioinformatics.
2005 Dec 15; 21(24): 4432-3. Epub 2005 Sep 27; PubMed: 16188923.
Abstract + PDF
2004 3 publication(s).
15.
The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
Crass T, Antes I, Basekow R, Bork P, Buning C, Christensen M, Claussen H, Ebeling C, Ernst P, Gailus-Durner V, Glatting KH, Gohla R, Gössling F, Grote K, Heidtke K, Herrmann A, O'Keeffe S, Kiesslich O, Kolibal S, Korbel JO, Lengauer T, Liebich I, van der Linden M, Luz H, Meissner K, von Mering C, Mevissen HT, Mewes HW, Michael H, Mokrejs M, Müller T, Pospisil H, Rarey M, Reich JG, Schneider R, Schomburg D, Schulze-Kremer S, Schwarzer K, Sommer I, Springstubbe S, Suhai S, Thoppae G, Vingron M, Warfsmann J, Werner T, Wetzler D, Wingender E, Zimmer R
Bioinformatics.
2004 Jan 22; 20(2): 268-70. PubMed: 14734319.
Abstract + PDF
14.
Gene annotation from scientific literature using mappings between keyword systems.
Pérez AJ, Perez-Iratxeta C, Bork P, Thode G, Andrade MA
Bioinformatics.
2004 Sep 1; 20(13): 2084-91. Epub 2004 Apr 1; PubMed: 15059832.
Abstract + PDF
13.
BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
Bioinformatics.
2004 Aug 12; 20(12): 1968-70. Epub 2004 Mar 22; PubMed: 15037510.
Abstract + PDF
2003 2 publication(s).
12.
Evaluation of annotation strategies using an entire genome sequence.
Iliopoulos I, Tsoka S, Andrade MA, Enright AJ, Carroll M, Poullet P, Promponas V, Liakopoulos T, Palaios G, Pasquier C, Hamodrakas S, Tamames J, Yagnik AT, Tramontano A, Devos DP, Blaschke C, Valencia A, Brett D, Martin D, Leroy C, Rigoutsos I, Sander C, Ouzounis CA
Bioinformatics.
2003 Apr 12; 19(6): 717-26. PubMed: 12691983.
Abstract + PDF
11.
A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
Bioinformatics.
2003 Oct 12; 19(15): 1901-8. PubMed: 14555622.
Abstract + PDF
2002 1 publication(s).
10.
Comparative analysis of protein interaction networks.
Bioinformatics.
2002; 18 Suppl 2: S64. PubMed: 12385984.
Abstract + PDF
2000 1 publication(s).
9.
NAIL-Network Analysis Interface for Linking HMMER results.
Bioinformatics.
2000 Jul; 16(7): 656-7. PubMed: 11038338.
Abstract + PDF
1999 3 publication(s).
8.
Automated genome sequence analysis and annotation.
Andrade MA, Brown NP, Leroy C, Hoersch S, de Daruvar A, Reich C, Franchini A, Tamames J, Valencia A, Ouzounis C, Sander C
Bioinformatics.
1999 May; 15(5): 391-412. PubMed: 10366660.
Abstract + PDF
7.
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
Bioinformatics.
1999 Jul-Aug; 15(7-8): 528-35. PubMed: 10487860.
Abstract + PDF
6.
Associative database of protein sequences.
Hanke J, Lehmann G, Bork P, Reich JG
Bioinformatics.
1999 Sep; 15(9): 741-8. PubMed: 10498774.
Abstract + PDF
1998 5 publication(s).
5.
Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
Andrade MA, Valencia A
Bioinformatics.
1998; 14(7): 600-7. PubMed: 9730925.
Abstract
4.
Frame: detection of genomic sequencing errors.
Brown NP, Sander C, Bork P
Bioinformatics.
1998; 14(4): 367-71. PubMed: 9632832.
Abstract + PDF
3.
Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Dandekar T, Beyer K, Bork P, Kenealy MR, Pantopoulos K, Hentze M, Sonntag-Buck V, Flouriot G, Gannon F, Schreiber S
Bioinformatics.
1998; 14(3): 271-8. PubMed: 9614270.
Abstract + PDF
2.
Computational space reduction and parallelization of a new clustering approach for large groups of sequences.
Trelles O, Andrade MA, Valencia A, Zapata EL, Carazo JM
Bioinformatics.
1998 Jun; 14(5): 439-51. PubMed: 9682057.
Abstract
1.
Towards detection of orthologues in sequence databases.
Yuan YP, Eulenstein O, Vingron M, Bork P
Bioinformatics.
1998; 14(3): 285-9. PubMed: 9614272.
Abstract + PDF