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. ORCID: https://orcid.org/0000-0003-3980-6469, Kopp, W. ORCID: https://orcid.org/0000-0003-0376-0032, Lutsik, P. and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
BMC Bioinformatics 25 (1): 257. 6 August 2024

cDNA-detector: detection and removal of cDNA contamination in DNA sequencing libraries.
Qi, M. ORCID: https://orcid.org/0000-0002-8671-3110, Nayar, U. ORCID: https://orcid.org/0000-0002-9024-6084, Ludwig, L.S. ORCID: https://orcid.org/0000-0002-2916-2164, Wagle, N. and Rheinbay, E. ORCID: https://orcid.org/0000-0002-5566-6729
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. ORCID: https://orcid.org/0000-0003-3729-9002, Ørom, U.A.V. and Piro, R.M. ORCID: https://orcid.org/0000-0002-3066-7397
BMC Bioinformatics 22 (1): 368. 15 July 2021

Domainoid: domain-oriented orthology inference.
Persson, E. ORCID: https://orcid.org/0000-0003-0532-8251, Kaduk, M., Forslund, S.K. ORCID: https://orcid.org/0000-0003-4285-6993 and Sonnhammer, E.L.L.
BMC Bioinformatics 20 (1): 523. 28 October 2019

SigsPack, a package for cancer mutational signatures.
Schumann, F., Blanc, E. ORCID: https://orcid.org/0000-0002-4369-0254, Messerschmidt, C. ORCID: https://orcid.org/0000-0001-8632-656X, Blankenstein, T. ORCID: https://orcid.org/0000-0002-3357-4321, Busse, A. ORCID: https://orcid.org/0000-0002-3470-6947 and Beule, D. ORCID: https://orcid.org/0000-0002-3284-0632
BMC Bioinformatics 20 (1): 450. 2 September 2019

JACUSA: site-specific identification of RNA editing events from replicate sequencing data.
Piechotta, M., Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Dieterich, C. ORCID: https://orcid.org/0000-0001-9468-6311
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. ORCID: https://orcid.org/0000-0002-5890-5510 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. ORCID: https://orcid.org/0000-0003-3094-1031, 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. ORCID: https://orcid.org/0000-0002-5612-1720, Colomé-Tatché, M., Taudt, A., Rintisch, C., Schafer, S., Pravenec, M. ORCID: https://orcid.org/0000-0001-9197-5871, Hubner, N. ORCID: https://orcid.org/0000-0002-1218-6223, 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. ORCID: https://orcid.org/0000-0001-6650-1711
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. ORCID: https://orcid.org/0000-0002-1101-4091, 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. ORCID: https://orcid.org/0000-0001-6650-1711 and Fontaine, J.F. ORCID: https://orcid.org/0000-0002-1101-4091
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. ORCID: https://orcid.org/0000-0002-0468-0123, 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. ORCID: https://orcid.org/0000-0002-5260-2607, Fontaine, J.F. ORCID: https://orcid.org/0000-0002-1101-4091, Donnard, E.R., Stussi, F., Ortega, J.M. and Andrade-Navarro, M.A. ORCID: https://orcid.org/0000-0001-6650-1711
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. ORCID: https://orcid.org/0000-0002-1101-4091, Andrade-Navarro, M.A. ORCID: https://orcid.org/0000-0001-6650-1711 and Valencia, A.
BMC Bioinformatics 12 (Suppl 8): S3. 3 October 2011

Domain architecture conservation in orthologs.
Forslund, K. ORCID: https://orcid.org/0000-0003-4285-6993, 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. ORCID: https://orcid.org/0000-0002-1796-9606, 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. ORCID: https://orcid.org/0000-0002-5260-2607, Soldatos, T.G., Magalhaes, I.L., Pavlopoulos, G.A., Fontaine, J.F. ORCID: https://orcid.org/0000-0002-1101-4091, Andrade-Navarro, M.A. ORCID: https://orcid.org/0000-0001-6650-1711, 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. ORCID: https://orcid.org/0000-0002-0468-0128, Sharma, Y. and Lenhard, B.
BMC Bioinformatics 11 (Suppl 1): S59. 18 January 2010

Transcriptional regulation at a glance.
Sperling, S. ORCID: https://orcid.org/0000-0002-7135-3298
BMC Bioinformatics 8 (Suppl 6): S2. 27 September 2007

Integrated network reconstruction, visualization and analysis using YANAsquare.
Schwarz, R. ORCID: https://orcid.org/0000-0001-9155-4268, 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. ORCID: https://orcid.org/0000-0002-1796-9606, 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. ORCID: https://orcid.org/0000-0003-1471-1295, Skylar, O., Krueger, T., Fischer, J.J., Sperling, S. ORCID: https://orcid.org/0000-0002-7135-3298 and Huber, W.
BMC Bioinformatics 8 : 221. 26 June 2007

Optimized mixed Markov models for motif identification.
Huang, W., Umbach, D.M., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 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. ORCID: https://orcid.org/0000-0002-4048-3479
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. ORCID: https://orcid.org/0000-0002-7135-3298
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. ORCID: https://orcid.org/0000-0001-9155-4268, 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. ORCID: https://orcid.org/0000-0002-9746-4412, Galli, R., Mebus, S., Sperling, H.P., Lehrach, H. and Sperling, S. ORCID: https://orcid.org/0000-0002-7135-3298
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. ORCID: https://orcid.org/0000-0002-2627-833X
BMC Bioinformatics 4 : 64. 19 December 2003

Conservation of regulatory elements between two species of Drosophila.
Emberly, E., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 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. ORCID: https://orcid.org/0000-0002-2627-833X and Andrade, M.A. ORCID: https://orcid.org/0000-0001-6650-1711
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. ORCID: https://orcid.org/0000-0002-4785-4332, Vergassola, M., Gaul, U. and Siggia, E.D.
BMC Bioinformatics 3 : 30. 24 October 2002