Publications

2015

  • Scheurwegs Elyne, Luyckx Kim, Luyten Leon, Daelemans Walter, Van den Bulcke Tim.- Data integration of structured and unstructured sources for assigning clinical codes to patient stays. Journal of the American Medical Informatics Association http://dx.doi.org/10.1093/jamia/ocv115
  • de Vijlder Thomas, Valkenborg Dirk, Dewaele Debbie, Remmerie Noor, Laukens Kris, Witters Erwin.- A generic approach for shotgun analysis of the soluble proteome of plant cell suspension cultures. Journal of chromatography: B: analytical technologies in the biomedical and life sciences 974(2015), p. 48-56 http://dx.doi.org/doi:10.1016/j.jchromb.2014.10.024
  • Naulaerts Stefan, Meysman Pieter, Bittremieux Wout, Vu Trung N., Vanden Berghe Wim, Goethals Bart, Laukens Kris.- A primer to frequent itemset mining for bioinformatics. Briefings in bioinformatics 16:2(2015), p. 216-231 http://dx.doi.org/doi:10.1093/bib/bbt074
  • Laukens Kris, Naulaerts Stefan, Vanden Berghe Wim.- Bioinformatics approaches for the functional interpretation of protein lists : from ontology term enrichment to network analysis. Proteomics 15:5-6(2015), p. 981-996 http://dx.doi.org/doi:10.1002/pmic.201400296 
  • Meysman Pieter, Zhou Cheng, Cule Boris, Goethals Bart, Laukens Kris.- Mining the entire Protein DataBank for frequent spatially cohesive amino acid patterns. BioData Mining 8(2015), 4 http://dx.doi.org/doi:10.1186/s13040-015-0038-4 
  • Meysman Pieter, Ogunjimi Benson, Naulaerts Stefan, Beutels Philippe, van Tendeloo Vigor, Laukens Kris.- Varicella-zoster virus-derived major histocompatibility complex class I-restricted peptide affinity Is a determining factor in the HLA risk profile for the development of postherpetic neuralgia. Journal of virology 89:2(2015), p. 962-969 http://dx.doi.org/doi:10.1128/JVI.02500-14
  • Bittremieux Wout, Willems Hanny, Kelchtermans Pieter, Martens Lennart, Laukens Kris, Valkenborg Dirk.- iMonDB : mass spectrometry quality control through instrument monitoring. Journal of proteome research 14:5(2015), p. 2360-2366 http://dx.doi.org/doi:10.1021/acs.jproteome.5b00127 
  • Hendrickx Tayena, Cule Boris, Meysman Pieter, Naulaerts Stefan, Laukens Kris, Goethals Bart.- Mining association rules in graphs based on frequent cohesive itemsets. Proceedings of the 19th Pacific-Asia Conference on Knowledge Discovery and Data Mining, May 19-22, 2015, Ho Chi Minh City, Vietnam - S.l., 2015 

2014

  • Geert Vandeweyer, Lut Van Laer, Bart Loeys, Tim Van den Bulcke, Frank Kooy. - VariantDB: a flexible annotation and filtering portal for next generation sequencing data. Genome Medicine DOI: 10.1186/s13073-014-0074-6
  • Meysman Pieter, Sonego Paolo, Bianco Luca, Laukens Kris, et al..- COLOMBOS v2.0 : an ever expanding collection of bacterial expression compendia. Nucleic acids research 42:D1(2014), p. D649-D653 http://dx.doi.org/doi:10.1093/nar/gkt1086 
  • Milenkovic Dragan, Vanden Berghe Wim, Boby Céline, Declerck Ken, Szarc vel Szic Katarzyna, Laukens Kris, et al..- Dietary flavanols modulate the transcription of genes associated with cardiovascular pathology without changes in their DNA methylation state. PLoS ONE 9:4(2014), e95527 http://dx.doi.org/doi:10.1371/journal.pone.0095527 
  • Zhou Cheng, Goethals Bart, Meysman Pieter, Laukens Kris, Cule Boris.- Discovery of spatially cohesive itemsets in three-dimensional protein structures. IEEE/ACM transactions on computational biology and bioinformatics / Institute of Electrical and Electronics Engineers [New York, N.Y.] - ISSN 1545-5963 - 11:5(2014), p. 814-825 http://dx.doi.org/doi:10.1109/TCBB.2014.2311795 
  • Palagani Ajay, op de Beeck Ken, Naulaerts Stefan, Diddens Jolien, Chirumamilla Chandra Sekhar, van Camp Guy, Laukens Kris, Vanden Berghe Wim, et al..- Ectopic microRNA-150-5p transcription sensitizes glucocorticoid therapy response in MM1S multiple myeloma cells but fails to overcome hormone therapy resistance in MM1R cells. PLoS ONE 9:12(2014), e113842 http://dx.doi.org/doi:10.1371/journal.pone.0113842 
  • Vu Trung N., Bittremieux Wout, Valkenborg Dirk, Goethals Bart, Lemière Filip, Laukens Kris.- Efficient reduction of candidate matches in peptide spectrum library searching using the top k most intense peaks. Journal of proteome research - ISSN 1535-3893 - 13:9(2014), p. 4175-4183 http://dx.doi.org/doi:10.1021/pr401269z 
  • Kelchtermans Pieter, Bittremieux Wout, De Grave Kurt, Degroeve Sven, Ramon Jan, Laukens Kris, Valkenborg Dirk, Barsnes Harald, Martens Lennart.- Machine learning applications in proteomics research : how the past can boost the future. Proteomics - ISSN 1615-9853 - 14:4-5(2014), p. 353-366 http://dx.doi.org/doi:10.1002/pmic.201300289 
  • Meysman Pieter, Collado-Vides Julio, Morrett Enrique, Viola Roberto, Engelen Kristof, Laukens Kris.- Structural properties of prokaryotic promoter regions correlate with functional features. PLoS ONE 9:2(2014), e88717 http://dx.doi.org/doi:10.1371/journal.pone.0088717 
  • Wouters An, Pauwels Bea, Burrows Nathalie, Baay Marc, Deschoolmeester Vanessa, Vu Trung N., Laukens Kris, Meijnders Paul, Van Gestel Dirk, Williams Kaye J., van den Weyngaert Danielle, Vermorken Jan Baptist, Pauwels Patrick, Peeters Marc, Lardon Filip.- The radiosensitising effect of gemcitabine and its main metabolite dFdU under low oxygen conditions is in vitro not dependent on functional HIF-1 protein. BMC cancer 14(2014), 594 http://dx.doi.org/doi:10.1186/1471-2407-14-594 
  • Tran Huyen Thi Thanh, Van den Bergh Rafael, Vu Trung N., Laukens Kris, Worodria William, Massinga Loembé Marguerite, Colebunders Robert, Kestens Luc, De Baetselier Patrick, Raes Geert.- The role of monocytes in the development of tuberculosis-associated immune reconstitution inflammatory syndrome. Immunobiology 219:1(2014), p. 37-44 http://dx.doi.org/doi:10.1016/j.imbio.2013.07.004 
  • Ghavidel Fatemeh Zamanzad, Mertens Inge, Baggerman Geert, Laukens Kris, Burzykowski Tomasz, Valkenborg Dirk.- The use of the isotopic distribution as a complementary quality metric to assess tandem mass spectra results. Journal of proteomics - 98(2014), p. 150-158 http://dx.doi.org/doi:10.1016/j.jprot.2013.12.013 
  • Vu Trung N., Mrzic Aida, Valkenborg Dirk, Maes Evelyne, Lemière Filip, Goethals Bart, Laukens Kris.- Unravelling associations between unassigned mass spectrometry peaks with frequent itemset mining techniques. Proteome science 12(2014), 54 http://dx.doi.org/doi:10.1186/s12953-014-0054-1 
  • Bittremieux Wout, Kelchtermans Pieter, Valkenborg Dirk, Martens Lennart, Laukens Kris.- jqcML : an open-source Java API for mass spectrometry quality control data in the qcML format. Journal of proteome research 13:7(2014), p. 3484-3487 http://dx.doi.org/doi:10.1021/pr401274z 
  • Walzer Mathias, Espona Pernas Lucia, Nasso Sara, Bittremieux Wout, Valkenborg Dirk, Laukens Kris, et al..- qcML : an exchange format for quality control metrics from mass spectrometry experiments. Molecular and cellular proteomics  13:8(2014), p. 1905-1913 http://dx.doi.org/doi:10.1074/mcp.M113.035907 
  • Dittwald Piotr, Nghia Vu Trung, Harris Glenn A., Caprioli Richard M., Van de Plas Raf, Laukens Kris, Gambin Anna, Valkenborg Dirk.- Towards automated discrimination of lipids versus peptides from full scan mass spectra. EuPA open proteomics  (2014) http://dx.doi.org/doi:10.1016/j.euprot.2014.05.002 
  • Sonego Paolo, Meysman Pieter, Moretto Marco, Viola Robert, Laukens Kris, Cavalieri Duccio, Engelen Kristof.- Comparative analysis of gene expression : uncovering expression conservation and divergence between salmonella enterica serovar Typhimurium strains LT2 and 14028S. Bacterial pangenomics / Mengoni, Alessio [edit.]; e.a. - ISBN 978-1-4939-1719-8 - S.l., Humana Press, 2014, p. 1-17 

2013

  • Thanh Hai Dang ; Koen Smets ; Walter Verbrugghe ; Philippe G. Jorens ; Tim Van den Bulcke. - Improving SAPS3-based Mortality Risk Prediction for ICU Patients using Random Forest Models: A Single-center Study. Proceedings of AMIA 2013 annual symposium, 2013 (in press).
  • D. Damen, K. Luyckx, G. Hellebaut,T. Van den Bulcke. PASTEL: A Semantic Platform for Assisted Clinical Trial Patient Recruitment. IEEE International Conference on Healthcare Informatics 2013.
  • Scheurwegs, E., Luyckx, K., Van der Schueren, F., Van den Bulcke, T. De-Identification of Clinical Free Text in Dutch with Limited Training Data: A Case Study. In: Workshop on NLP for Medicine and Biology. 2013. p. 18-23.
  • Meyer Pablo, Siwo Geoffrey, Zeevi Danny, Meysman Pieter [collab.], et al.. - Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. Genome research - ISSN 1088-9051 - 23:11(2013), p. 1928-1937 
  • Lardon Isabelle, Eyckmans Marleen, Vu Trung N., Laukens Kris , de Boeck Gudrun, Dommisse Roger.- 1H-NMR study of the metabolome of a moderately hypoxia-tolerant fish, the common carp (**Cyprinus carpio**). Metabolomics - ISSN 1573-3882 - (2013) 
  • Lardon Isabelle, Nilsson Göran E., Steyck Jonathan A.W., Vu Trung N., Laukens Kris , Dommisse Roger, de Boeck Gudrun.- 1H-NMR study of the metabolome of an exceptionally anoxia tolerant vertebrate, the crucian carp (**Carassius carassius**). Metabolomics - ISSN 1573-3882 - 9:2(2013), p. 311-323 
  • Hagenaars An, Vergauwen Lucia, Benoot Donald, Laukens Kris , Knapen Dries.- Mechanistic toxicity study of perfluorooctanoic acid in zebrafish suggests mitochondrial dysfunction to play a key role in PFOA toxicity. Chemosphere - ISSN 0045-6535 - 91:6(2013), p. 844-856 
  • Vu Trung N., Laukens Kris .- Getting your peaks in line : a review of alignment methods for NMR spectral data. Metabolites - ISSN 2218-1989 - 3:2(2013), p. 259-276 
  • Zhou Cheng, Meysman Pieter, Cule Boris, Laukens Kris , Goethals Bart.- Mining spatially cohesive itemsets in protein molecular structures. BioKDD13: 12th International Workshop on Data Mining in Bioinformatics proceedings, 2013 - S.l., 2013, p. 1-9 

2012 and earlier

  • D. Damen, T. Van den Bulcke. - Towards a Flexible Semantic Framework for Clinical Trial Eligibility using Topic Maps. In Proceedings of the ACM SIGKDD Workshop on Health Informatics, HI-KDD ’12, NY, USA, (2012).
  • Vu Trung N., Valkenborg Dirk, Smets Koen, Verwaest Kim, Dommisse Roger, Lemière Filip, Verschoren Alain, Goethals Bart, Laukens Kris: An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. BMC bioinformatics -12(2011), p. 405
  • Duc Dong Do, Dinh Huy Q., Dang Thanh Hai, Laukens Kris , Hoang Xuan Huan.- AcoSeeD : an ant colony optimization for finding optimal spaced seeds in biological sequence search. Lecture notes in computer science - ISSN 0302-9743 - 7461(2012), p. 204-211 
  • Verwaest Kim, Vu Trung N., Laukens Kris, Clemens Laura E., Nguyen Huu P., van Gasse Bjorn, Martins José C., van der Linden Anne-Marie, Dommisse Roger: 1H NMR based metabolomics of CSF and blood serum: a metabolic profile for a transgenic rat model of Huntington disease. Biochimica et biophysica acta: molecular basis of disease - 1812:11(2011), p. 1371-1379
  • Remmerie N, De Vijlder T, Valkenborg D, Laukens K, Smets K, Vreeken J, Mertens I, Carpentier S, Panis B, De Jaeger G, Blust R, Prinsen E, Witters E: Unraveling tobacco BY-2 protein complexes with BN PAGE/LC–MS/MS and clustering methods. Journal of Proteomics, 74:8(2011), p. 1201-1217
  • Van den Bulcke T, Broucke PV, Hoof VV, Wouters K, Broucke SV, Smits G, Smits E, Proesmans S, Genechten TV, Eyskens F: Data mining methods for classification of Medium-Chain Acyl-CoA dehydrogenase deficiency (MCADD) using non-derivatized tandem MS neonatal screening dataJ Biomed Inform 2011, 44:319-325.
  • Remmerie N, De Vijlder T, Laukens K, Dang TH, Lemière F, Mertens I, Valkenborg D, Blust R, Witters E: Next generation functional proteomics in non-model plants: A survey on techniques and applications for the analysis of protein complexes and post-translational modifications. Phytochemistry, 72:10(2011), p. 1192-1218.
  • Meysman P, Dang TH, Laukens K, De Smet R, Wu Y, Marchal K, Engelen K: Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coli. Nucleic Acids Research 2011, 39:e6-e6.
  • Zhao H, Cloots L, Van den Bulcke T, Wu Y, De Smet R, Storms V, Meysman P, Engelen K, Marchal K: Query-based biclustering of gene expression data using Probabilistic Relational Models. BMC Bioinformatics 2011, 12 Suppl 1:S37.

Relevant former publications of biomina members: 

  • Engelen K, Sifrim A, Van de Plas B, Laukens K, Arckens L, Marchal K: Alternative experimental design with an applied normalization scheme can improve statistical power in 2D-DIGE experimentsJ. Proteome Res 2010, 9:4919-4926.
  • Meysman P, Dang TH, Laukens K, De Smet R, Wu Y, Marchal K, Engelen K: Use of structural DNA properties for the prediction of transcription-factor binding sites in Escherichia coliNucleic Acids Res 2010.
  • Van Damme E, Laukens K, Dang TH, Van Ostade X: A manually curated network of the PML nuclear body interactome reveals an important role for PML-NBs in SUMOylation dynamicsInt. J. Biol. Sci 2010, 6:51-67.
  • Van Leene J, Hollunder J, Eeckhout D, Persiau G, Van De Slijke E, Stals H, Van Isterdael G, Verkest A, Neirynck S, Buffel Y, De Bodt S, Maere S, Laukens K, Pharazyn A, Ferreira PCG, Eloy N, Renne C, Meyer C, Faure J-D, Steinbrenner J, Beynon J, Larkin JC, Van de Peer Y, Hilson P, Kuiper M, De Veylder L, Van Onckelen H, Inze D, Witters E, De Jaeger G: Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thalianaMol Syst Biol 2010, 6.
  • Laukens K, Hollunder J, Dang TH, De Jaeger G, Kuiper M, Witters E, Verschoren A, Van Leemput K: Flexible network reconstruction from relational databases with Cytoscape and CytoSQLBMC Bioinformatics 2010, 11:360.
  • Sun H, Lemmens K, Van den Bulcke T, Engelen K, De Moor B, Marchal K: ViTraM: visualization of transcriptional modulesBioinformatics 2009, 25:2450-2451.
  • Knapen D, Vergauwen L, Laukens K, Blust R: Best practices for hybridization design in two-colour microarray analysisTrends Biotechnol 2009.
  • Dang TH, Engelen K, Meysman P, Marchal K, Verschoren A, Laukens K: Conditional random fields feature subset selection based on genetic algorithms for phosphorylation site prediction. First International Conference on Knowledge and Systems Engineering, October 13-17 2009, Hanoi, Vietnam. In S.l. 2009:7-12.
  • Van Leemput K, Van den Bulcke T, Dhollander T, De Moor B, Marchal K, van Remortel P: Exploring the operational characteristics of inference algorithms for transcriptional networks by means of synthetic data. Artif. Life 2008, 14:49-63.
  • Dang TH, Van Leemput K, Verschoren A, Laukens K: Prediction of kinase-specific phosphorylation sites using conditional random fieldsBioinformatics 2008, 24:2857-2864.
  • Michoel T, Maere S, Bonnet E, Joshi A, Saeys Y, Van den Bulcke T, Van Leemput K, van Remortel P, Kuiper M, Marchal K, Van de Peer Y: Validating module network learning algorithms using simulated data. BMC Bioinformatics 2007, 8 Suppl 2:S5.
  • Thomsen AL, Laukens K, Matthiesen R, Jensen ON: Organization of proteomics data with YassDB. Methods Mol. Biol 2007, 367:271-287.
  • Van den Bulcke T, Van Leemput K, Naudts B, van Remortel P, Ma H, Verschoren A, De Moor B, Marchal K: SynTReN: a generator of synthetic gene expression data for design and analysis of structure learning algorithmsBMC Bioinformatics 2006, 7:43.
  • Laukens K, Matthiesen R, Lemière F, Esmans E, Onckelen HV, Jensen ON, Witters E: Integration of gel-based proteome data with pProRepBioinformatics 2006, 22:2838-2840.
  • Laukens K, Deckers P, Esmans E, Van Onckelen H, Witters E: Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension cultureProteomics 2004, 4:720-727.