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Article

scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data.
Jeong, Y., Ronen, J., Kopp, W., Lutsik, P. and Akalin, A.
BMC Bioinformatics 25 (1): 257. 6 August 2024

cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries.
Qi, M., Nayar, U., Ludwig, L.S., Wagle, N. and Rheinbay, E.
BMC Bioinformatics 22 (1): 611. 24 December 2021

SPLICE-q: a Python tool for genome-wide quantification of splicing efficiency.
de Melo Costa, V.R., Pfeuffer, J., Louloupi, A., Ørom, U.A.V. and Piro, R.M.
BMC Bioinformatics 22 (1): 368. 15 July 2021

Domainoid: domain-oriented orthology inference.
Persson, E., Kaduk, M., Forslund, S.K. and Sonnhammer, E.L.L.
BMC Bioinformatics 20 (1): 523. 28 October 2019

SigsPack, a package for cancer mutational signatures.
Schumann, F., Blanc, E., Messerschmidt, C., Blankenstein, T., Busse, A. and Beule, D.
BMC Bioinformatics 20 (1): 450. 2 September 2019

JACUSA: site-specific identification of RNA editing events from replicate sequencing data.
Piechotta, M., Wyler, E., Ohler, U., Landthaler, M. and Dieterich, C.
BMC Bioinformatics 18 (1): 7. 3 January 2017

Integrating multiple molecular sources into a clinical risk prediction signature by extracting complementary information.
Hieke, S., Benner, A., Schlenl, R.F., Schumacher, M., Bullinger, L. and Binder, H.
BMC Bioinformatics 17 (1): 327. 30 August 2016

2D and 3D similarity landscape analysis identifies PARP as a novel off-target for the drug Vatalanib.
Gohlke, B.O., Overkamp, T., Richter, A., Richter, A., Daniel, P.T., Gillissen, B. and Preissner, R.
BMC Bioinformatics 16 (1): 308. 24 September 2015

histoneHMM: Differential analysis of histone modifications with broad genomic footprints.
Heinig, M., Colomé-Tatché, M., Taudt, A., Rintisch, C., Schafer, S., Pravenec, M., Hubner, N., Vingron, M. and Johannes, F.
BMC Bioinformatics 16 : 60. 22 February 2015

A novel approach for protein subcellular location prediction using amino acid exposure.
Mer, A.S. and Andrade-Navarro, M.A.
BMC Bioinformatics 14 (1): 342. 28 November 2013

CELDA - an ontology for the comprehensive representation of cells in complex systems.
Seltmann, S., Stachelscheid, H., Damaschun, A., Jansen, L., Lekschas, F., Fontaine, J.F., Nguyen-Dobinsky, T.N., Leser, U. and Kurtz, A.
BMC Bioinformatics 14 : 228. 17 July 2013

Using cited references to improve the retrieval of related biomedical documents.
Ortuno, F.M., Rojas, I., Andrade-Navarro, M.A. and Fontaine, J.F.
BMC Bioinformatics 14 : 113. 27 March 2013

An optimized algorithm for detecting and annotating regional differential methylation.
Li, S., Garrett-Bakelman, F.E., Akalin, A., Zumbo, P., Levine, R., To, B.L., Lewis, I.D., Brown, A.L., D'Andrea, R.J., Melnick, A. and Mason, C.E.
BMC Bioinformatics 14 (Suppl 5): S10. 2013

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries.
Barbosa-Silva, A., Fontaine, J.F., Donnard, E.R., Stussi, F., Ortega, J.M. and Andrade-Navarro, M.A.
BMC Bioinformatics 12 (1): 435. 9 November 2011

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text.
Krallinger, M., Vazquez, M., Leitner, F., Salgado, D., Chatr-Aryamontri, A., Winter, A., Perfetto, L., Briganti, L., Licata, L., Iannuccelli, M., Castagnoli, L., Cesareni, G., Tyers, M., Schneider, G., Rinaldi, F., Leaman, R., Gonzalez, G., Matos, S., Kim, S., Wilbur, W.J., Rocha, L., Shatkay, H., Tendulkar, A.V., Agarwal, S., Liu, F., Wang, X., Rak, R., Noto, K., Elkan, C., Lu, Z., Dogan, R.I., Fontaine, J.F., Andrade-Navarro, M.A. and Valencia, A.
BMC Bioinformatics 12 (Suppl 8): S3. 3 October 2011

Domain architecture conservation in orthologs.
Forslund, K., Pekkari, I. and Sonnhammer, E.L.L.
BMC Bioinformatics 12 : 326. 5 August 2011

GPCR-SSFE: a comprehensive database of G-protein-coupled receptor template predictions and homology models.
Worth, C.L., Kreuchwig, A., Kleinau, G. and Krause, G.
BMC Bioinformatics 12 : 185. 23 May 2011

LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships.
Barbosa-Silva, A., Soldatos, T.G., Magalhaes, I.L., Pavlopoulos, G.A., Fontaine, J.F., Andrade-Navarro, M.A., Schneider, R. and Ortega, J.M.
BMC Bioinformatics 11 (1): 70. 1 February 2010

Translog, a web browser for studying the expression divergence of homologous genes.
Dong, X., Akalin, A., Sharma, Y. and Lenhard, B.
BMC Bioinformatics 11 (Suppl 1): S59. 18 January 2010

Transcriptional regulation at a glance.
Sperling, S.
BMC Bioinformatics 8 (Suppl 6): S2. 27 September 2007

Integrated network reconstruction, visualization and analysis using YANAsquare.
Schwarz, R., Liang, C., Kaleta, C., Kuehnel, M., Hoffmann, E., Kuznetsov, S., Hecker, M., Griffiths, G., Schuster, S. and Dandekar, T.
BMC Bioinformatics 8 : 313. 28 August 2007

Genome bioinformatic analysis of nonsynonymous SNPs.
Burke, D.F., Worth, C.L., Priego, E.M., Cheng, T., Smink, L.J., Todd, J.A. and Blundell, T.L.
BMC Bioinformatics 8 : 301. 20 August 2007

Ringo--an R/Bioconductor package for analyzing ChIP-chip readouts.
Toedling, J., Skylar, O., Krueger, T., Fischer, J.J., Sperling, S. and Huber, W.
BMC Bioinformatics 8 : 221. 26 June 2007

Optimized mixed Markov models for motif identification.
Huang, W., Umbach, D.M., Ohler, U. and Li, L.
BMC Bioinformatics 7 : 279. 2 June 2006

Transformation and other factors of the peptide mass spectrometry pairwise peak-list comparison process.
Wolski, W.E., Lalowski, M., Martus, P., Herwig, R., Giavalisco, P., Gobom, J., Sickmann, A., Lehrach, H. and Reinert, K.
BMC Bioinformatics 6 : 285. 30 November 2005

A linear memory algorithm for Baum-Welch training.
Miklos, I. and Meyer, I.M.
BMC Bioinformatics 6 : 231. 19 September 2005

Chromosomal clustering of a human transcriptome reveals regulatory background.
Vogel, J.H., von Heydebreck, A., Purmann, A. and Sperling, S.
BMC Bioinformatics 6 : 230. 19 September 2005

Calibration of mass spectrometric peptide mass fingerprint data without specific external or internal calibrants.
Wolski, W.E., Lalowski, M., Jungblut, P. and Reinert, K.
BMC Bioinformatics 6 : 203. 15 August 2005

DCD - a novel plant specific domain in proteins involved in development and programmed cell death.
Tenhaken, R., Doerks, T. and Bork, P.
BMC Bioinformatics 6 : 169. 11 July 2005

YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.
Schwarz, R., Musch, P., von Kamp, A., Engels, B., Schirmer, H., Schuster, S. and Dandekar, T.
BMC Bioinformatics 6 : 135. 1 June 2005

CGHPRO - a comprehensive data analysis tool for array CGH.
Chen, W., Erdogan, F., Ropers, H.H., Lenzner, S. and Ullmann, R.
BMC Bioinformatics 6 : 85. 2005

Ab initio identification of putative human transcription factor binding sites by comparative genomics.
Cora, D., Herrmann, C., Dieterich, C., Di Cunto, F., Provero, P. and Caselle, M.
BMC Bioinformatics 6 2005

d-matrix - database exploration, visualization and analysis.
Seelow, D., Galli, R., Mebus, S., Sperling, H.P., Lehrach, H. and Sperling, S.
BMC Bioinformatics 5 : 168. 28 October 2004

PASBio: predicate-argument structures for event extraction in molecular biology.
Wattarujeekrit, T., Shah, P.K. and Collier, N.
BMC Bioinformatics 5 : 155. 19 October 2004

The PAM domain, a multi-protein complex-associated module with an all-alpha-helix fold.
Ciccarelli, F.D., Izaurralde, E. and Bork, P.
BMC Bioinformatics 4 : 64. 19 December 2003

Conservation of regulatory elements between two species of Drosophila.
Emberly, E., Rajewsky, N. and Siggia, E.D.
BMC Bioinformatics 4 : 57. 20 November 2003

Information extraction from full text scientific articles: Where are the keywords?
Shah, P., Perez-Iratxeta, C., Bork, P. and Andrade, M.A.
BMC Bioinformatics 4 (1): 20. 29 May 2003

Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.
Rajewsky, N., Vergassola, M., Gaul, U. and Siggia, E.D.
BMC Bioinformatics 3 : 30. 24 October 2002