Browse by Journal Title

2024

Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data.
Marot-Lassauzaie, V., Beneyto-Calabuig, S., Obermayer, B., Velten, L., Beule, D. and Haghverdi, L.
Bioinformatics 40 (9): btae512. September 2024

Metadata-guided feature disentanglement for functional genomics.
Rakowski, A., Monti, R., Huryn, V., Lemanczyk, M., Ohler, U. and Lippert, C.
Bioinformatics 40 (Suppl 2): ii4-ii10. September 2024

Compound-SNE: comparative alignment of t-SNEs for multiple single-cell omics data visualization.
Cess, C.G. and Haghverdi, L.
Bioinformatics : btae471. 25 July 2024 (In Press)

2023

PEDL+: Protein-centered relation extraction from PubMed at your fingertip.
Weber, L., Barth, F., Lorenz, L., Konrath, F., Huska, K., Wolf, J. and Leser, U.
Bioinformatics 39 (11): btad603. November 2023

SMITH: spatially constrained stochastic model for simulation of intra-tumour heterogeneity.
Streck, A., Kaufmann, T.L. and Schwarz, R.F.
Bioinformatics 39 (3): btad102. March 2023

2022

Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programming.
Breitenbach, T., Schmitt, M.J. and Dandekar, T.
Bioinformatics 38 (17): 4162-4171. 1 September 2022

ClearCNV: CNV calling from NGS panel data in the presence of ambiguity and noise.
May, V., Koch, L., Fischer-Zirnsak, B., Horn, D., Gehle, P., Kornak, U., Beule, D. and Holtgrewe, M.
Bioinformatics 38 (16): 3871-3876. 15 August 2022

On the relation between input and output distributions of scRNA-seq experiments.
Schwabe, D. and Falcke, M.
Bioinformatics 38 (5): 1336-1343. 1 March 2022

2021

ASHLEYS: automated quality control for single-cell Strand-seq data.
Eimer, C., Sanders, A.D., Korbel, J.O., Marschall, T. and Ebert, P.
Bioinformatics 37 (19): 3356-3357. 1 October 2021

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data.
Markowski, J., Kempfer, R., Kukalev, A., Irastorza-Azcarate, I., Loof, G., Kehr, B., Pombo, A., Rahmann, S. and Schwarz, R.F.
Bioinformatics 37 (19): 3128–3135. 1 October 2021

FRC-QE: a robust and comparable 3D microscopy image quality metric for cleared organoids.
Preusser, F., Dos Santos, N., Contzen, J., Stachelscheid, H., Costa, E.T., Mergenthaler, P. and Preibisch, S.
Bioinformatics 37 (18): 3088-3090. 15 September 2021

HunFlair: an easy-to-use tool for state-of-the-art biomedical named entity recognition.
Weber, L., Sänger, M., Münchmeyer, J., Habibi, M., Leser, U. and Akbik, A.
Bioinformatics 37 (17): 2792–2794. 1 September 2021

2020

PEDL: extracting protein-protein associations using deep language models and distant supervision.
Weber, L., Thobe, K., Migueles Lozano, O.A., Wolf, J. and Leser, U.
Bioinformatics 36 (Suppl 1): i490-i498. July 2020

Digestiflow: from BCL to FASTQ with ease.
Holtgrewe, M., Messerschmidt, C., Nieminen, M. and Beule, D.
Bioinformatics 36 (6): 1983-1985. 15 March 2020

VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing.
Bolognini, D., Sanders, A., Korbel, J.O., Magi, A., Benes, V. and Rausch, T.
Bioinformatics 36 (4): 1267-1269. 15 February 2020

Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features.
Li, Y., Kuhn, M., Gavin, A.C. and Bork, P.
Bioinformatics 36 (4): 1213-1218. 15 February 2020

breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data.
Porubsky, D., Sanders, A.D., Taudt, A., Colomé-Tatché, M., Lansdorp, P.M. and Guryev, V.
Bioinformatics 36 (4): 1260-1261. 15 February 2020

2018

SSMART: Sequence-structure motif identification for RNA-binding proteins.
Munteanu, A., Mukherjee, N. and Ohler, U.
Bioinformatics 34 (23): 3990-3998. 1 December 2018

Strand-seq enables reliable separation of long reads by chromosome via expectation maximization.
Ghareghani, M., Porubskỳ, D., Sanders, A.D., Meiers, S., Eichler, E.E., Korbel, J.O. and Marschall, T.
Bioinformatics 34 (13): i115-i123. 1 July 2018

FunImageJ: a lisp framework for scientific image processing.
Harrington, K.I.S., Rueden, C.T. and Eliceiri, K.W.
Bioinformatics 34 (5): 899-900. 1 March 2018

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

2017

Partitioned learning of deep Boltzmann machines for SNP data.
Hess, M., Lenz, S., Blätte, T.J., Bullinger, L. and Binder, H.
Bioinformatics 33 (20): 3173-3180. October 2017

RTK: efficient rarefaction analysis of large datasets.
Saary, P., Forslund, K., 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., 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., Karaletsos, T., Drewe, P., Sreedharan, V.T., Kuo, D., Singh, K., Wendel, H.G. and Raetsch, G.
Bioinformatics 33 (1): 139-141. 1 January 2017

2016

CART - a chemical annotation retrieval toolkit.
Deghou, S., Zeller, G., Iskar, M., Driessen, M., Castillo, M., 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., 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., Coelho, L.P., Forslund, K., Huerta-Cepas, J., Li, S.S., Driessen, M., Voigt, A.Y., Zeller, G., 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., Klockmeier, K., Wanker, E. and Sharan, R.
Bioinformatics 32 (12): i271-i277. 15 June 2016

GiANT: gene set uncertainty in enrichment analysis.
Schmid, F., Schmid, M., Müssel, C., Sträng, J.E., Buske, C., Bullinger, L., Kraus, J.M. and Kestler, H.A.
Bioinformatics 32 (12): 1891-1894. 15 June 2016

destiny: diffusion maps for large-scale single-cell data in R.
Angerer, P., Haghverdi, L., Büttner, M., Theis, F.J., Marr, C. and Buettner, F.
Bioinformatics 32 (8): 1241-1243. 15 April 2016

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

2015

Diffusion maps for high-dimensional single-cell analysis of differentiation data.
Haghverdi, L., Buettner, F. and Theis, F.J.
Bioinformatics 31 (18): 2989-2998. 15 September 2015

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

Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data.
Ocone, A., Haghverdi, L., Mueller, N.S. and Theis, F.J.
Bioinformatics 31 (12): i89-i96. 15 June 2015

genomation: a toolkit to summarize, annotate and visualize genomic intervals.
Akalin, A., Franke, V., Vlahoviček, K., 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., Lacadie, S.A. and Ohler, U.
Bioinformatics 31 (1): 48-55. 1 January 2015

2014

PHOXTRACK-a tool for interpreting comprehensive datasets of post-translational modifications of proteins.
Weidner, C., Fischer, C. and Sauer, S.
Bioinformatics 30 (23): 3410-3411. 1 December 2014

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

Improved transcript isoform discovery using ORF graphs.
Majoros, W.H., Lebeck, N., 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., Leddin, M., 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., Ni, T., Mukherjee, S., 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., 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., Lippert, C., Kang, E.Y., Xiang, J., 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., Lippert, C., Borgwardt, K., 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., Lippert, C., Stegle, O. and Borgwardt, K.
Bioinformatics 29 (2): 206-214. 15 January 2013

2012

ImgLib2-generic image processing in Java.
Pietzsch, T., Preibisch, S., 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., Gerner, M., Haeussler, M., Solt, I., Plake, C., Schroeder, M., Gonzalez, G., 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., Schaefer, M., Shoemaker, J., Matsuoka, Y., Fontaine, J.F., Neumann, G., Andrade-Navarro, M.A., Kawaoka, Y. and Kitano, H.
Bioinformatics 27 (17): 2414-2421. 1 September 2011

2010

SmashCommunity: A metagenomic annotation and analysis tool.
Arumugam, M., Harrington, E.D., Foerstner, K.U., 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., Arumugam, M., Raes, J., 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., Jayasurya, K., 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., 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., Varnado, N., Zhang, W., Frise, E. and Ohler, U.
Bioinformatics 26 (6): 761-769. 15 March 2010

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

MicroRazerS: rapid alignment of small RNA reads.
Emde, A.K., Grunert, M., Weese, D., 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., 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., Chaurasia, G. and Herzel, H.
Bioinformatics 23 (5): 605-611. March 2007

Linkage analysis using sex-specific recombination fractions with GENEHUNTER-MODSCORE.
Dietter, J., Mattheisen, M., Fuerst, R., Rueschendorf, F., 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., Lee, J.Y., Twigg, R.W., Colinas, J., 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., Gordan, R., 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., Jensen, L.J., Ouzounova, R., 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., Leser, U., 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., Jensen, L.J., Fausboll, A., Jensen, T.S., 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., Dieterich, C. and Vingron, M.
Bioinformatics 21 (9): 2093-2094. 2005

2004

VisRD-visual recombination detection.
Forslund, K., 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., 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., 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., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., Claussen, H., Ebeling, C., Ernst, P., Gailus-Durner, V., Glatting, K.H., Gohla, R., Goessling, F., Grote, K., Heidtke, K., Herrmann, A., O'Keeffe, S., Kiesslich, O., Kolibal, S., Korbel, J.O., Lengauer, T., Liebich, I., van der Linden, M., Luz, H., Meissner, K., von Mering, C., Mevissen, H.T., Mewes, H.W., Michael, H., Mokrejs, M., Mueller, T., Pospisil, H., Rarey, M., Reich, J.G., 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. and Zimmer, R.
Bioinformatics 20 (2): 268-270. 1 January 2004

Gene annotation from scientific literature using mappings between keyword systems.
Perez, A.J., Perez-Iratxeta, C., Bork, P., 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., 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., Herwig, R. and Vingron, M.
Bioinformatics 19 (Suppl 2): ii50-ii56. October 2003

Evaluation of annotation strategies using an entire genome sequence.
Iliopoulos, I., Tsoka, S., Andrade, M.A., Enright, A.J., Carroll, M., Poullet, P., Promponas, V., Liakopoulos, T., Palaios, G., Pasquier, C., Hamodrakas, S., Tamames, J., Yagnik, A.T., Tramontano, A., Devos, D., Blaschke, C., Valencia, A., Brett, D., Martin, D., Leroy, C., Rigoutsos, I., 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., Gupta, R., 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., Pfeiffer, T., Moldenhauer, F., Koch, I. and Dandekar, T.
Bioinformatics 18 (2): 351-361. 1 January 2002

Annotating regulatory DNA based on man-mouse genomic comparison.
Dieterich, C., Cusack, B., Wang, H., Rateitschak, K., 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., Niemann, H, 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., Yuan, Y.P., 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., Brown, N.P., Leroy, C., Hoersch, S., de Daruvar, A., Reich, C., Franchini, A., Tamames, J., Valencia, A., Ouzounis, C. and Sander, C.
Bioinformatics 15 (5): 391-412. May 1999

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

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

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

1998

Frame: detection of genomic sequencing errors.
Brown, N.P., 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., Beyer, K., Bork, P., Kenealy, M.R., Pantopoulos, K., Hentze, M., Sonntag-Buck, V., Flouriot, G., Gannon, F., Keller, W. and Schreiber, S.
Bioinformatics 14 : 271-278. 1 January 1998

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

Towards detection of orthologues in sequence databases.
Yuan, Y.P., Eulenstein, O., 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