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2018

SSMART: Sequence-structure motif identification for RNA-binding proteins.
Munteanu, A. and Mukherjee, N. and Ohler, U.
Bioinformatics 11 June 2018 (In Press)

Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund, K. and Pereira, C. and Capella-Gutierrez, S. and Sousa da Silva, A. and Altenhoff, A. and Huerta-Cepas, J. and Muffato, M. and Patricio, M. and Vandepoele, K. and Ebersberger, I. and Blake, J. and Fernández Breis, J.T. and Boeckmann, B. and Gabaldón, T. and Sonnhammer, E. and Dessimoz, C. and Lewis, S.
Bioinformatics 34 (2): 323-329. 15 January 2018

2017

RTK: efficient rarefaction analysis of large datasets.
Saary, P. and Forslund, K. and Bork, P. and Hildebrand, F.
Bioinformatics 33 (16): 2594-2595. 15 August 2017

HLA-MA: simple yet powerful matching of samples using HLA typing results.
Messerschmidt, C. and Holtgrewe, M. and Beule, D.
Bioinformatics 33 (14): 2241-2242. 15 July 2017

RiboDiff: detecting changes of mRNA translation efficiency from ribosome footprints.
Zhong, Y. and Karaletsos, T. and Drewe, P. and Sreedharan, V.T. and Kuo, D. and Singh, K. and Wendel, H.G. and Raetsch, G.
Bioinformatics 33 (1): 139-141. 1 January 2017

2016

CART - a chemical annotation retrieval toolkit.
Deghou, S. and Zeller, G. and Iskar, M. and Driessen, M. and Castillo, M. and van Noort, V. and Bork, P.
Bioinformatics 32 (18): 2869-2871. 15 September 2016

Benchmarking the next generation of homology inference tools.
Saripella, G.V.a and Sonnhammer, E.L.L. and Forslund, K.
Bioinformatics 32 (17): 2636-2641. 1 September 2016

MOCAT2: a metagenomic assembly, annotation and profiling framework.
Kultima, J.R. and Coelho, L.P. and Forslund, K. and Huerta-Cepas, J. and Li, S.S. and Driessen, M. and Voigt, A.Y. and Zeller, G. and Sunagawa, S. and Bork, P.
Bioinformatics 32 (16): 2520-2523. 15 August 2016

An integer programming framework for inferring disease complexes from network data.
Mazza, A. and Klockmeier, K. and Wanker, E. and Sharan, R.
Bioinformatics 32 (12): i271-i277. 15 June 2016

An automated workflow for parallel processing of large multiview SPIM recordings.
Schmied, C. and Steinbach, P. and Pietzsch, T. and Preibisch, S. and Tomancak, P.
Bioinformatics 32 (7): 1112-1114. 1 April 2016

2015

Analysis of impedance-based cellular growth assays.
Witzel, F. and Fritsche-Guenther, R. and Lehmann, N. and Sieber, A. and Bluethgen, N.
Bioinformatics 31 (16): 2705-2712. 15 August 2015

genomation: a toolkit to summarize, annotate and visualize genomic intervals.
Akalin, A. and Franke, V. and Vlahoviček, K. and Mason, C.E. and Schübeler, D.
Bioinformatics 31 (7): 1127-1129. 1 April 2015

JAMM: a peak finder for joint analysis of NGS replicates.
Ibrahim, M.M. and Lacadie, S.A. and Ohler, U.
Bioinformatics 31 (1): 48-55. 1 January 2015

2014

Greater power and computational efficiency for kernel-based association testing of sets of genetic variants.
Lippert, C. and Xiang, J. and Horta, D. and Widmer, C. and Kadie, C. and Heckerman, D. and Listgarten, J.
Bioinformatics 30 (22): 3206-3214. 15 November 2014

Improved transcript isoform discovery using ORF graphs.
Majoros, W.H. and Lebeck, N. and Ohler, U. and Li, S.
Bioinformatics 30 (14): 1958-1964. 15 July 2014

CAFE: an R package for the detection of gross chromosomal abnormalities from gene expression microarray data.
Bollen, S. and Leddin, M. and Andrade-Navarro, M.A. and Mah, N.
Bioinformatics 30 (10): 1484-1485. 15 May 2014

2013

ACCUSA2: Multi-purpose SNV calling enhanced by probabilistic integration of quality scores.
Piechotta, M. and Dieterich, C.
Bioinformatics 29 (14): 1809-1810. 15 July 2013

Genome-wide identification and predictive modeling of tissue-specific alternative polyadenylation.
Hafez, D. and Ni, T. and Mukherjee, S. and Zhu, J. and Ohler, U.
Bioinformatics 29 (13): i108-i116. 1 July 2013

Automated annotation of gene expression image sequences via non-parametric factor analysis and conditional random fields.
Pruteanu-Malinici, I. and Majoros, W.H. and Ohler, U.
Bioinformatics 29 (13): i27-i35. 1 July 2013

A powerful and efficient set test for genetic markers that handles confounders.
Listgarten, J. and Lippert, C. and Kang, E.Y. and Xiang, J. and Kadie, C.M. and Heckerman, D.
Bioinformatics 29 (12): 1526-1533. 15 June 2013

Detecting regulatory gene-environment interactions with unmeasured environmental factors.
Fusi, N. and Lippert, C. and Borgwardt, K. and Lawrence, N.D. and Stegle, O.
Bioinformatics 29 (11): 1382-1389. 1 June 2013

A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch, B. and Lippert, C. and Stegle, O. and Borgwardt, K.
Bioinformatics 29 (2): 206-214. 15 January 2013

2012

ImgLib2-generic image processing in Java.
Pietzsch, T. and Preibisch, S. and Tomancak, P. and Saalfeld, S.
Bioinformatics 28 (22): 3009-3011. 15 November 2012

2011

The GNAT library for local and remote gene mention normalization.
Hakenberg, J. and Gerner, M. and Haeussler, M. and Solt, I. and Plake, C. and Schroeder, M. and Gonzalez, G. and Nenadic, G. and Bergman, C.M.
Bioinformatics 27 (19): 2769-2771. 1 October 2011

PDBpaint, a visualization webservice to tag protein structures with sequence annotations.
Fournier, D. and Andrade-Navarro, M.A.
Bioinformatics 27 (18): 2605-2606. 15 September 2011

Tissue specific subnetworks and characteristics of publicly available human protein interaction databases.
Lopes, T.J. and Schaefer, M. and Shoemaker, J. and Matsuoka, Y. and Fontaine, J.F. and Neumann, G. and Andrade-Navarro, M.A. and Kawaoka, Y. and Kitano, H.
Bioinformatics 27 (17): 2414-2421. 1 September 2011

2010

SmashCommunity: A metagenomic annotation and analysis tool.
Arumugam, M. and Harrington, E.D. and Foerstner, K.U. and Raes, J. and Bork, P.
Bioinformatics 26 (23): 2977-2978. 1 December 2010

SmashCell: a software framework for the analysis of single-cell amplified genome sequences.
Harrington, E.D. and Arumugam, M. and Raes, J. and Bork, P. and Relman, D.A.
Bioinformatics 26 (23): 2979-2980. 1 December 2010

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.
Arunachalam, M. and Jayasurya, K. and Tomancak, P. and Ohler, U.
Bioinformatics 26 (17): 2109-2115. 1 September 2010

ACCUSA - Accurate SNP calling on draft genomes.
Froehler, S. and Dieterich, C.
Bioinformatics 26 (10): 1364-1365. 15 May 2010

Gene function prediction from synthetic lethality networks via ranking on demand.
Lippert, C. and Ghahramani, Z. and Borgwardt, K.M.
Bioinformatics 26 (7): 912-918. 1 April 2010

Extraction and comparison of gene expression patterns from 2D RNA in situ hybridization images.
Mace, D.L. and Varnado, N. and Zhang, W. and Frise, E. and Ohler, U.
Bioinformatics 26 (6): 761-769. 15 March 2010

AQUA: Automated quality improvement for multiple sequence alignments.
Muller, J. and Creevey, C.J. and Thompson, J.D. and Arendt, D. and Bork, P.
Bioinformatics 26 (2): 263-265. 15 January 2010

MicroRazerS: rapid alignment of small RNA reads.
Emde, A.K. and Grunert, M. and Weese, D. and Reinert, K. and Sperling, S.R.
Bioinformatics 26 (1): 123-124. 1 January 2010

2009

Benchmarking homology detection procedures with low complexity filters.
Forslund, K. and Sonnhammer, E.L.L.
Bioinformatics 25 (19): 2500-2505. 1 October 2009

Globally optimal stitching of tiled 3D microscopic image acquisitions.
Preibisch, S. and Saalfeld, S. and Tomancak, P.
Bioinformatics 25 (11): 1463-1465. 1 June 2009

Complexity reduction in context-dependent DNA substitution models.
Majoros, W.H. and Ohler, U.
Bioinformatics 25 (2): 175-182. 15 January 2009

2008

Sircah: a tool for the detection and visualization of alternative transcripts.
Harrington, E.D. and Bork, P.
Bioinformatics 24 (17): 1959-1960. 1 September 2008

Predicting protein function from domain content.
Forslund, K. and Sonnhammer, E.L.L.
Bioinformatics 24 (15): 1681-1687. 1 August 2008

2007

Comparison of human protein-protein interaction maps.
Futschik, M.E. and Chaurasia, G. and Herzel, H.
Bioinformatics 23 (5): 605-611. March 2007

Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE.
Dietter, J. and Mattheisen, M. and Fuerst, R. and Rueschendorf, F. and Wienker, T.F. and Strauch, K.
Bioinformatics 23 (1): 64-70. 1 January 2007

Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation.
Letunic, I. and Bork, P.
Bioinformatics 23 (1): 127-128. 1 January 2007

2006

Quantification of transcription factor expression from Arabidopsis images.
Mace, D.L. and Lee, J.Y. and Twigg, R.W. and Colinas, J. and Benfey, P.N. and Ohler, U.
Bioinformatics 22 (14): e323-231. 15 July 2006

Informative priors based on transcription factor structural class improve de novo motif discovery.
Narlikar, L. and Gordan, R. and Ohler, U. and Hartemink, A.J.
Bioinformatics 22 (14): e384-392. 15 July 2006

LSAT: learning about alternative transcripts in MEDLINE.
Shah, P.K. and Bork, P.
Bioinformatics 22 (7): 857-865. 1 April 2006

Extraction of regulatory gene/protein networks from Medline.
Saric, J. and Jensen, L.J. and Ouzounova, R. and Rojas, I. and Bork, P.
Bioinformatics 22 : 645-650. 15 March 2006

2005

Medusa: a simple tool for interaction graph analysis.
Hooper, S.D. and Bork, P.
Bioinformatics 21 (24): 4432-4433. 27 September 2005

The WHy domain mediates the response to desiccation in plants and bacteria.
Ciccarelli, F.D. and Bork, P.
Bioinformatics 21 : 1304-1307. 1 January 2005

ALOHOMORA: a tool for linkage analysis using 10K SNP array data.
Rueschendorf, F. and Nuernberg, P.
Bioinformatics 21 : 2123-2125. 1 January 2005

GandrKB - ontological microarray annotation and visualization.
Schober, D. and Leser, U. and Zenke, M. and Reich, J.
Bioinformatics 21 (11): 2785-2786. 1 January 2005

HaploPainter: a tool for drawing pedigrees with complex haplotypes.
Thiele, H. and Nuernberg, P.
Bioinformatics 21 (8): 1730-1732. 1 January 2005

Comparison of computational methods for the identification of cell cycle regulated genes.
de Lichtenberg, U. and Jensen, L.J. and Fausboll, A. and Jensen, T.S. and Bork, P. and Brunak, S.
Bioinformatics 21 : 1164-1171. 1 January 2005

SITEBLAST - rapid and sensitive local alignment of genomic sequences employing motif anchors.
Michael, M. and Dieterich, C. and Vingron, M.
Bioinformatics 21 (9): 2093-2094. 2005

2004

VisRD-visual recombination detection.
Forslund, K. and Huson, D.H. and Moulton, V.
Bioinformatics 20 (18): 3654-3655. 12 December 2004

BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments.
Suyama, M. and Torrents, D. and Bork, P.
Bioinformatics 20 : 1968-1970. 12 August 2004

Functional inference from non-random distributions of conserved predicted transcription factor binding sites.
Dieterich, C. and Rahmann, S. and Vingron, M.
Bioinformatics 20 (Suppl 1): i109-i115. 4 August 2004

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
Crass, T. and Antes, I. and Basekow, R. and Bork, P. and Buning, C. and Christensen, M. and Claussen, H. and Ebeling, C. and Ernst, P. and Gailus-Durner, V. and Glatting, K.H. and Gohla, R. and Goessling, F. and Grote, K. and Heidtke, K. and Herrmann, A. and O'Keeffe, S. and Kiesslich, O. and Kolibal, S. and Korbel, J.O. and Lengauer, T. and Liebich, I. and van der Linden, M. and Luz, H. and Meissner, K. and von Mering, C. and Mevissen, H.T. and Mewes, H.W. and Michael, H. and Mokrejs, M. and Mueller, T. and Pospisil, H. and Rarey, M. and Reich, J.G. and Schneider, R. and Schomburg, D. and Schulze-Kremer, S. and Schwarzer, K. and Sommer, I. and Springstubbe, S. and Suhai, S. and Thoppae, G. and Vingron, M. and Warfsmann, J. and Werner, T. and Wetzler, D. and Wingender, E. and Zimmer, R.
Bioinformatics 20 (2): 268-270. 1 January 2004

Gene annotation from scientific literature using mappings between keyword systems.
Perez, A.J. and Perez-Iratxeta, C. and Bork, P. and Thode, G. and Andrade-Navarro, M.A.
Bioinformatics 20 (13): 2084-2091. 1 January 2004

2003

A comprehensive set of protein complexes in yeast: mining large scale protein-protein interaction screens.
Krause, R. and von Mering, C. and Bork, P.
Bioinformatics 19 : 1901-1908. 12 October 2003

Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites.
Dieterich, C. and Herwig, R. and Vingron, M.
Bioinformatics 19 (Suppl 2): ii50-ii56. October 2003

Evaluation of annotation strategies using an entire genome sequence.
Iliopoulos, I. and Tsoka, S. and Andrade, M.A. and Enright, A.J. and Carroll, M. and Poullet, P. and Promponas, V. and Liakopoulos, T. and Palaios, G. and Pasquier, C. and Hamodrakas, S. and Tamames, J. and Yagnik, A.T. and Tramontano, A. and Devos, D. and Blaschke, C. and Valencia, A. and Brett, D. and Martin, D. and Leroy, C. and Rigoutsos, I. and Sander, C. and Ouzounis, C.A.
Bioinformatics 19 (6): 717-726. 12 April 2003

Prediction of human protein function according to Gene Ontology categories.
Jensen, L.J. and Gupta, R. and Staerfeldt, H.H. and Brunak, S.
Bioinformatics 19 : 635-642. 22 March 2003

2002

Comparative analysis of protein interaction networks.
Bork, P.
Bioinformatics 18 Suppl 2 : S64. 1 October 2002

Comparative ab initio prediction of gene structures using pair HMMs.
Meyer, I.M. and Durbin, R.
Bioinformatics 18 (10): 1309-1318. October 2002

Exploring the pathway structure of metabolism: decomposition into subnetworks and application to Mycoplasma pneumoniae.
Schuster, S. and Pfeiffer, T. and Moldenhauer, F. and Koch, I. and Dandekar, T.
Bioinformatics 18 (2): 351-361. 1 January 2002

Annotating regulatory DNA based on man-mouse genomic comparison.
Dieterich, C. and Cusack, B. and Wang, H. and Rateitschak, K. and Krause, A. and Vingron, M.
Bioinformatics 18 (Suppl 2): S84-S90. 2002

2001

Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition.
Ohler, U. and Niemann, H and Liao, G.C. and Rubin, G.M.
Bioinformatics 17 Suppl 1 : S199-206. 2001

2000

NAIL - Network Analysis Interface for Linking HMMER results.
Sanchez-Pulido, L. and Yuan, Y.P. and Andrade, M.A. and Bork, P.
Bioinformatics 16 (7): 656-657. 1 July 2000

1999

Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries.
Eisenhaber, F. and Bork, P.
Bioinformatics 15 : 528-535. 1 July 1999

Automated genome sequence analysis and annotation.
Andrade, M.A. and Brown, N.P. and Leroy, C. and Hoersch, S. and de Daruvar, A. and Reich, C. and Franchini, A. and Tamames, J. and Valencia, A. and Ouzounis, C. and Sander, C.
Bioinformatics 15 (5): 391-412. May 1999

Interpolated markov chains for eukaryotic promoter recognition.
Ohler, U. and Harbeck, S. and Niemann, H. and Noeth, E. and Reese, M.G.
Bioinformatics 15 (5): 362-369. May 1999

Associative database of protein sequences.
Hanke, J. and Lehmann, G. and Bork, P. and Reich, J.
Bioinformatics 15 : 741-748. 1 January 1999

METATOOL: for studying metabolic networks.
Pfeiffer, T. and Sanchez-Valdenebro, I. and Nuno, J.C. and Montero, F. and Schuster, S.
Bioinformatics 15 : 251-257. 1 January 1999

1998

Frame: detection of genomic sequencing errors.
Brown, N.P. and Sander, C. and Bork, P.
Bioinformatics 14 : 367-371. 1 January 1998

Systematic genomic screening and analysis of mRNA in untranslated regions and mRNA precursors: combining experimental and computational approaches.
Dandekar, T. and Beyer, K. and Bork, P. and Kenealy, M.R. and Pantopoulos, K. and Hentze, M. and Sonntag-Buck, V. and Flouriot, G. and Gannon, F. and Keller, W. and Schreiber, S.
Bioinformatics 14 : 271-278. 1 January 1998

POPSIM: a general population simulation program.
Hampe, J. and Wienker, T.F. and Schreiber, S. and Nuernberg, P.
Bioinformatics 14 : 458-464. 1 January 1998

Towards detection of orthologues in sequence databases.
Yuan, Y.P. and Eulenstein, O. and Vingron, M. and Bork, P.
Bioinformatics 14 : 285-289. 1 January 1998

Automatic extraction of keywords from scientific text: application to the knowledge domain of protein families.
Andrade, M.A. and Valencia, A.
Bioinformatics 14 (7): 600-607. 1998

This list was generated on Thu Oct 18 02:26:06 2018 CEST.
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