Marcel J T Reinders

Marcel J T Reinders

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Marcel J T Reinders

Publications by authors named "Marcel J T Reinders"

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ImSpectR - R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data.

Bioinformatics 2019 Oct 30. Epub 2019 Oct 30.

Leiden Computational Biology Center, Leiden University Medical Center, Leiden, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btz804DOI Listing
October 2019

A comparison of automatic cell identification methods for single-cell RNA sequencing data.

Genome Biol 2019 09 9;20(1):194. Epub 2019 Sep 9.

Leiden Computational Biology Center, Leiden University Medical Center, Einthovenweg 20, 2333 ZC, Leiden, The Netherlands.

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https://genomebiology.biomedcentral.com/articles/10.1186/s13
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http://dx.doi.org/10.1186/s13059-019-1795-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6734286PMC
September 2019

Metric Learning on Expression Data for Gene Function Prediction.

Bioinformatics 2019 Sep 28. Epub 2019 Sep 28.

Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, the Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btz731DOI Listing
September 2019

A nonsynonymous mutation in PLCG2 reduces the risk of Alzheimer's disease, dementia with Lewy bodies and frontotemporal dementia, and increases the likelihood of longevity.

Authors:
Sven J van der Lee Olivia J Conway Iris Jansen Minerva M Carrasquillo Luca Kleineidam Erik van den Akker Isabel Hernández Kristel R van Eijk Najada Stringa Jason A Chen Anna Zettergren Till F M Andlauer Monica Diez-Fairen Javier Simon-Sanchez Alberto Lleó Henrik Zetterberg Marianne Nygaard Cornelis Blauwendraat Jeanne E Savage Jonas Mengel-From Sonia Moreno-Grau Michael Wagner Juan Fortea Michael J Keogh Kaj Blennow Ingmar Skoog Manuel A Friese Olga Pletnikova Miren Zulaica Carmen Lage Itziar de Rojas Steffi Riedel-Heller Ignacio Illán-Gala Wei Wei Bernard Jeune Adelina Orellana Florian Then Bergh Xue Wang Marc Hulsman Nina Beker Niccolo Tesi Christopher M Morris Begoña Indakoetxea Lyduine E Collij Martin Scherer Estrella Morenas-Rodríguez James W Ironside Bart N M van Berckel Daniel Alcolea Heinz Wiendl Samantha L Strickland Pau Pastor Eloy Rodríguez Rodríguez Bradley F Boeve Ronald C Petersen Tanis J Ferman Jay A van Gerpen Marcel J T Reinders Ryan J Uitti Lluís Tárraga Wolfgang Maier Oriol Dols-Icardo Amit Kawalia Maria Carolina Dalmasso Mercè Boada Uwe K Zettl Natasja M van Schoor Marian Beekman Mariet Allen Eliezer Masliah Adolfo López de Munain Alexander Pantelyat Zbigniew K Wszolek Owen A Ross Dennis W Dickson Neill R Graff-Radford David Knopman Rosa Rademakers Afina W Lemstra Yolande A L Pijnenburg Philip Scheltens Thomas Gasser Patrick F Chinnery Bernhard Hemmer Martijn A Huisman Juan Troncoso Fermin Moreno Ellen A Nohr Thorkild I A Sørensen Peter Heutink Pascual Sánchez-Juan Danielle Posthuma Jordi Clarimón Kaare Christensen Nilüfer Ertekin-Taner Sonja W Scholz Alfredo Ramirez Agustín Ruiz Eline Slagboom Wiesje M van der Flier Henne Holstege

Acta Neuropathol 2019 Aug 27;138(2):237-250. Epub 2019 May 27.

Alzheimer Center Amsterdam, Department of Neurology, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1007/s00401-019-02026-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6660501PMC
August 2019

A meta-analysis of genome-wide association studies identifies multiple longevity genes.

Nat Commun 2019 08 14;10(1):3669. Epub 2019 Aug 14.

NHLBI's and Boston University's Framingham Heart Study, Framingham, MA, 01702, USA.

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http://dx.doi.org/10.1038/s41467-019-11558-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694136PMC
August 2019

Predicting Cell Populations in Single Cell Mass Cytometry Data.

Cytometry A 2019 Jul 12;95(7):769-781. Epub 2019 Mar 12.

Delft Bioinformatics Lab, Delft University of Technology, Delft 2628 XE, The Netherlands.

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http://doi.wiley.com/10.1002/cyto.a.23738
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http://dx.doi.org/10.1002/cyto.a.23738DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6767556PMC
July 2019

PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors.

Bioinformatics 2019 Jul;35(14):i510-i519

Computational Cancer Biology, Division of Molecular Carcinogenesis, Oncode Institute, the Netherlands Cancer Institute, Amsterdam CX, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btz372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6612899PMC
July 2019

Improving protein function prediction using protein sequence and GO-term similarities.

Bioinformatics 2019 Apr;35(7):1116-1124

Department of Intelligent Systems, Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bty751DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6449755PMC
April 2019

How Metabolic State May Regulate Fear: Presence of Metabolic Receptors in the Fear Circuitry.

Front Neurosci 2018 27;12:594. Epub 2018 Aug 27.

Leiden Computational Biology Center, Leiden University Medical Center, Leiden University, Leiden, Netherlands.

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https://www.frontiersin.org/article/10.3389/fnins.2018.00594
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http://dx.doi.org/10.3389/fnins.2018.00594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6119828PMC
August 2018

Nucleus-specific expression in the multinuclear mushroom-forming fungus reveals different nuclear regulatory programs.

Proc Natl Acad Sci U S A 2018 04 11;115(17):4429-4434. Epub 2018 Apr 11.

Delft Bioinformatics Lab, Delft University of Technology, 2628XE Delft, The Netherlands;

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http://dx.doi.org/10.1073/pnas.1721381115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5924919PMC
April 2018

A survey of functional genomic variation in domesticated chickens.

Genet Sel Evol 2018 04 16;50(1):17. Epub 2018 Apr 16.

Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/s12711-018-0390-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902831PMC
April 2018

WISExome: a within-sample comparison approach to detect copy number variations in whole exome sequencing data.

Eur J Hum Genet 2017 12 8;25(12):1354-1363. Epub 2017 Nov 8.

Clinical Genetics, VU University Medical Center Amsterdam, van der Boechorststraat 7 (BS7/J377), 1081 BT, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/s41431-017-0005-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5865163PMC
December 2017

Visual analysis of mass cytometry data by hierarchical stochastic neighbour embedding reveals rare cell types.

Nat Commun 2017 11 23;8(1):1740. Epub 2017 Nov 23.

Pattern Recognition and Bioinformatics Group, Delft University of Technology, Mekelweg 4, 2628, CD, Delft, The Netherlands.

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http://dx.doi.org/10.1038/s41467-017-01689-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700955PMC
November 2017

Comparing methods for fetal fraction determination and quality control of NIPT samples.

Prenat Diagn 2017 Aug 10;37(8):769-773. Epub 2017 Jul 10.

Department of Clinical Genetics, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/pd.5079DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5599991PMC
August 2017

Brain transcriptome atlases: a computational perspective.

Brain Struct Funct 2017 May 1;222(4):1557-1580. Epub 2016 Dec 1.

Delft Bioinformatics Laboratory, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1007/s00429-016-1338-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5406417PMC
May 2017

Transcription factors of Schizophyllum commune involved in mushroom formation and modulation of vegetative growth.

Sci Rep 2017 03 22;7(1):310. Epub 2017 Mar 22.

Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584, CH, Utrecht, The Netherlands.

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http://dx.doi.org/10.1038/s41598-017-00483-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5428507PMC
March 2017

Continuous infusion of manganese improves contrast and reduces side effects in manganese-enhanced magnetic resonance imaging studies.

Neuroimage 2017 02 21;147:1-9. Epub 2016 Oct 21.

Department of Radiology, Leiden University Medical Centre, Leiden, Netherlands; Department of Human Genetics, Leiden University Medical Centre, Leiden, Netherlands.

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http://dx.doi.org/10.1016/j.neuroimage.2016.09.030DOI Listing
February 2017

Data-driven identification of prognostic tumor subpopulations using spatially mapped t-SNE of mass spectrometry imaging data.

Proc Natl Acad Sci U S A 2016 10 10;113(43):12244-12249. Epub 2016 Oct 10.

Division of Image Processing, Department of Radiology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands; Pattern Recognition and Bioinformatics Group, Faculty of Electrical Engineering, Mathematics, and Computer Science, Delft University of Technology, 2600 AA Delft, The Netherlands.

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http://dx.doi.org/10.1073/pnas.1510227113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5087072PMC
October 2016

Schizophyllum commune has an extensive and functional alternative splicing repertoire.

Sci Rep 2016 Sep 23;6:33640. Epub 2016 Sep 23.

Delft Bioinformatics Lab, Delft University of Technology, Delft, Zuid-Holland 2628 CD, The Netherlands.

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http://dx.doi.org/10.1038/srep33640DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5034255PMC
September 2016

The transcriptional regulator c2h2 accelerates mushroom formation in Agaricus bisporus.

Appl Microbiol Biotechnol 2016 Aug 21;100(16):7151-9. Epub 2016 May 21.

Microbiology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.

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http://dx.doi.org/10.1007/s00253-016-7574-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4947489PMC
August 2016

2D Representation of Transcriptomes by t-SNE Exposes Relatedness between Human Tissues.

PLoS One 2016 23;11(2):e0149853. Epub 2016 Feb 23.

Delft Bioinformatics Lab (DBL), Delft University of Technology, Delft, 2628CD, the Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0149853PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4764374PMC
July 2016

Calculating the fetal fraction for noninvasive prenatal testing based on genome-wide nucleosome profiles.

Prenat Diagn 2016 Jul 20;36(7):614-21. Epub 2016 May 20.

Department of Clinical Genetics, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1002/pd.4816DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111749PMC
July 2016

RUBIC identifies driver genes by detecting recurrent DNA copy number breaks.

Nat Commun 2016 07 11;7:12159. Epub 2016 Jul 11.

Department of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1038/ncomms12159DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4942583PMC
July 2016

Erratum to: Breast cancer subtype predictors revisited: from consensus to concordance?

BMC Med Genomics 2016 07 14;9(1):39. Epub 2016 Jul 14.

Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.

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http://dx.doi.org/10.1186/s12920-016-0209-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4944428PMC
July 2016

Breast cancer subtype predictors revisited: from consensus to concordance?

BMC Med Genomics 2016 06 3;9(1):26. Epub 2016 Jun 3.

Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, Amsterdam, 1105 AZ, The Netherlands.

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http://dx.doi.org/10.1186/s12920-016-0185-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4893290PMC
June 2016

Improved intra-array and interarray normalization of peptide microarray phosphorylation for phosphorylome and kinome profiling by rational selection of relevant spots.

Sci Rep 2016 05 26;6:26695. Epub 2016 May 26.

Department of Developmental BioEngineering, MIRA institute for biomedical technology and technical medicine, University of Twente, P.O. Box 217, NL-7500 AE Enschede, The Netherlands.

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http://dx.doi.org/10.1038/srep26695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4881024PMC
May 2016

Insight into neutral and disease-associated human genetic variants through interpretable predictors.

PLoS One 2015 31;10(3):e0120729. Epub 2015 Mar 31.

European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, United Kingdom; Biozentrum, University of Basel, Basel 4056, Switzerland; SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0120729PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4380319PMC
March 2016

Shared Pathways Among Autism Candidate Genes Determined by Co-expression Network Analysis of the Developing Human Brain Transcriptome.

J Mol Neurosci 2015 Dec 23;57(4):580-94. Epub 2015 Sep 23.

Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1007/s12031-015-0641-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4644211PMC
December 2015

Proteny: discovering and visualizing statistically significant syntenic clusters at the proteome level.

Bioinformatics 2015 Nov 27;31(21):3437-44. Epub 2015 Jun 27.

Delft Bioinformatics Lab, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btv389DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4612220PMC
November 2015

Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data.

PLoS Comput Biol 2015 Aug 14;11(8):e1004336. Epub 2015 Aug 14.

The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands; Platform Green Synthetic Biology, Delft, The Netherlands; Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands; Bioinformatics Group, Wageningen University, Wageningen, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1004336DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537299PMC
August 2015

Analysis of high-throughput screening reveals the effect of surface topographies on cellular morphology.

Acta Biomater 2015 Mar 30;15:29-38. Epub 2014 Dec 30.

Delft Bioinformatics Lab, Delft University of Technology, Mekelweg 4, Delft 2628 CD, The Netherlands.

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http://dx.doi.org/10.1016/j.actbio.2014.12.019DOI Listing
March 2015

Protein redesign by learning from data.

Protein Eng Des Sel 2014 Sep 30;27(9):281-8. Epub 2014 Jul 30.

Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628CD, Delft, The Netherlands Netherlands Bioinformatics Centre, Nijmegen, The Netherlands Kluyver Centre for Genomics of Industrial Fermentation, Delft, The Netherlands Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands

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http://dx.doi.org/10.1093/protein/gzu031DOI Listing
September 2014

Introducing WISECONDOR for noninvasive prenatal diagnostics.

Expert Rev Mol Diagn 2014 Jun 16;14(5):513-5. Epub 2014 May 16.

Delft Bioinformatics Lab, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://www.tandfonline.com/doi/full/10.1586/14737159.2014.91
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http://dx.doi.org/10.1586/14737159.2014.919855DOI Listing
June 2014

Meta-analysis on blood transcriptomic studies identifies consistently coexpressed protein-protein interaction modules as robust markers of human aging.

Aging Cell 2014 Apr 19;13(2):216-25. Epub 2013 Nov 19.

Department of Molecular Epidemiology, Leiden University Medical Center, PO Box 9600, 2300 RC, Leiden, The Netherlands; The Delft Bioinformatics Lab, Delft University of Technology, PO Box 5031, 2600 GA, Delft, The Netherlands.

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http://dx.doi.org/10.1111/acel.12160DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4331790PMC
April 2014

Efficient calculation of compound similarity based on maximum common subgraphs and its application to prediction of gene transcript levels.

Int J Bioinform Res Appl 2013 ;9(4):407-32

The Delft Bioinformatics Lab/Kluyver Centre for Genomics of Industrial Fermentation, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1504/IJBRA.2013.054688DOI Listing
March 2014

WISECONDOR: detection of fetal aberrations from shallow sequencing maternal plasma based on a within-sample comparison scheme.

Nucleic Acids Res 2014 Mar 28;42(5):e31. Epub 2013 Oct 28.

Delft Bioinformatics Lab, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands, Department of Clinical Genetics, VU University Medical Center Amsterdam, van der Boechorststraat 7 (BS7/J377), 1081 BT Amsterdam, The Netherlands and Department of Clinical Chemistry, VU University Medical Center Amsterdam, van der Boechorststraat 7 (BS7/J377), 1081 BT Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkt992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950725PMC
March 2014

SPiCE: a web-based tool for sequence-based protein classification and exploration.

BMC Bioinformatics 2014 Mar 31;15:93. Epub 2014 Mar 31.

Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628CD, Delft, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-15-93DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021553PMC
March 2014

Exploring variation-aware contig graphs for (comparative) metagenomics using MaryGold.

Bioinformatics 2013 Nov 20;29(22):2826-34. Epub 2013 Sep 20.

Department of Intelligent Systems, The Delft Bioinformatics Lab, Delft University of Technology, 2628 CD Delft, The Netherlands, Kluyver Centre for Genomics of Industrial Fermentation, 2600 GA Delft, The Netherlands and Department of Computer Science, Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt502DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3916741PMC
November 2013

Pattern recognition in bioinformatics.

Brief Bioinform 2013 Sep 4;14(5):633-47. Epub 2013 Apr 4.

Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty of Electrical Engineering, Mathematics & Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands. Tel.: +31 15 2785114; Fax: +31 15 2787022;

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http://dx.doi.org/10.1093/bib/bbt020DOI Listing
September 2013

Predicting the therapeutic efficacy of MSC in bone tissue engineering using the molecular marker CADM1.

Biomaterials 2013 Jun 26;34(19):4592-601. Epub 2013 Mar 26.

University of Twente, MIRA Institute for Biomedical Technology and Technical Medicine, Department of Tissue Regeneration, Drienerlolaan 5, 7522 NB Enschede, The Netherlands.

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http://dx.doi.org/10.1016/j.biomaterials.2013.03.001DOI Listing
June 2013

A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control.

Nucleic Acids Res 2013 May 8;41(9):e100. Epub 2013 Mar 8.

Bioinformatics and Statistics group, Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.

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http://dx.doi.org/10.1093/nar/gkt155DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3643574PMC
May 2013

Understanding regulation of metabolism through feasibility analysis.

PLoS One 2012 9;7(7):e39396. Epub 2012 Jul 9.

The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, Delft, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0039396PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3392259PMC
March 2013

Integration of clinical and gene expression data has a synergetic effect on predicting breast cancer outcome.

PLoS One 2012 11;7(7):e40358. Epub 2012 Jul 11.

Delft Bioinformatics Laboratory, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg, Delft, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040358PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3394805PMC
March 2013

Exploring sequence characteristics related to high-level production of secreted proteins in Aspergillus niger.

PLoS One 2012 1;7(10):e45869. Epub 2012 Oct 1.

Delft Bioinformatics Lab, Department of Intelligent Systems, Faculty Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0045869PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462195PMC
February 2013

De novo detection of copy number variation by co-assembly.

Bioinformatics 2012 Dec 9;28(24):3195-202. Epub 2012 Oct 9.

The Delft Bioinformatics Lab, Department of Intelligent Systems, Delft University of Technology, 2628 CD Delft, The Netherlands.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bts601DOI Listing
December 2012

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.

Bioinformatics 2012 Jun 6;28(11):1429-37. Epub 2012 Apr 6.

The Delft Bioinformatics Lab, Department of Mediamatics, Delft University of Technology, Mekelweg 4, Delft.

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http://dx.doi.org/10.1093/bioinformatics/bts175DOI Listing
June 2012

An evaluation protocol for subtype-specific breast cancer event prediction.

PLoS One 2011 8;6(7):e21681. Epub 2011 Jul 8.

Molecular Diagnostics Department, Philips Research, Eindhoven, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021681PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3132736PMC
October 2011

An algorithm-based topographical biomaterials library to instruct cell fate.

Proc Natl Acad Sci U S A 2011 Oct 26;108(40):16565-70. Epub 2011 Sep 26.

Department of Tissue Regeneration, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, 7500AE, Enschede, The Netherlands.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1109861108
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http://dx.doi.org/10.1073/pnas.1109861108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3189082PMC
October 2011

CytoscapeRPC: a plugin to create, modify and query Cytoscape networks from scripting languages.

Bioinformatics 2011 Sep 27;27(17):2451-2. Epub 2011 Jun 27.

Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/btr388DOI Listing
September 2011

Predicting metabolic fluxes using gene expression differences as constraints.

IEEE/ACM Trans Comput Biol Bioinform 2011 Jan-Mar;8(1):206-16

Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1109/TCBB.2009.55DOI Listing
February 2011

HAT: hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data.

BMC Bioinformatics 2010 May 21;11:275. Epub 2010 May 21.

Department of Hematology, Erasmus University Medical Center, Rotterdam, 3015 GE, the Netherlands.

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http://dx.doi.org/10.1186/1471-2105-11-275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892465PMC
May 2010

Evolutionary optimization of kernel weights improves protein complex comembership prediction.

IEEE/ACM Trans Comput Biol Bioinform 2009 Jul-Sep;6(3):427-37

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1109/TCBB.2008.137DOI Listing
November 2009

Fewer permutations, more accurate P-values.

Bioinformatics 2009 Jun;25(12):i161-8

Institute for Systems Biology, Seattle, WA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687965PMC
June 2009

Knowledge driven decomposition of tumor expression profiles.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S20. Epub 2009 Jan 30.

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648763PMC
January 2009

Analysis of mass spectrometry data using sub-spectra.

BMC Bioinformatics 2009 Jan 30;10 Suppl 1:S51. Epub 2009 Jan 30.

Bioinformatics and Statistics, Department of Molecular Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-10-S1-S51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2648731PMC
January 2009

Metabolic pathway alignment between species using a comprehensive and flexible similarity measure.

BMC Syst Biol 2008 Dec 24;2:111. Epub 2008 Dec 24.

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, the Netherlands.

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http://dx.doi.org/10.1186/1752-0509-2-111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2677397PMC
December 2008

Sign language recognition by combining statistical DTW and independent classification.

IEEE Trans Pattern Anal Mach Intell 2008 Nov;30(11):2040-6

Delft University of Technology, Faculty ofElectrical Engineering, Mathematics, and Computer Science, Informationand Communication Theory Group, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1109/TPAMI.2008.123DOI Listing
November 2008

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability.

BMC Genomics 2008 Aug 6;9:375. Epub 2008 Aug 6.

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-9-375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527336PMC
August 2008

Physiological and transcriptional responses of Saccharomyces cerevisiae to zinc limitation in chemostat cultures.

Appl Environ Microbiol 2007 Dec 12;73(23):7680-92. Epub 2007 Oct 12.

Yeast Research Group, Division of Molecular and Life Sciences, University of Abertay, Dundee DD1 1HG, Scotland.

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http://dx.doi.org/10.1128/AEM.01445-07DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2168061PMC
December 2007

Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes.

Microbiology 2007 Nov;153(Pt 11):3864-78

Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.

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http://dx.doi.org/10.1099/mic.0.2007/009969-0DOI Listing
November 2007

Module-based outcome prediction using breast cancer compendia.

PLoS One 2007 Oct 17;2(10):e1047. Epub 2007 Oct 17.

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001047PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2002511PMC
October 2007

Generic and specific transcriptional responses to different weak organic acids in anaerobic chemostat cultures of Saccharomyces cerevisiae.

FEMS Yeast Res 2007 Sep 30;7(6):819-33. Epub 2007 Apr 30.

Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1111/j.1567-1364.2007.00242.xDOI Listing
September 2007

Protein complex prediction using an integrative bioinformatics approach.

J Bioinform Comput Biol 2007 Aug;5(4):839-64

Information and Communication Theory Group, Delft University of Technology, Mekelweg 4, Delft, Zuid-Holland, 2628 CD, The Netherlands.

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http://dx.doi.org/10.1142/s0219720007002953DOI Listing
August 2007

Integration of known transcription factor binding site information and gene expression data to advance from co-expression to co-regulation.

Genomics Proteomics Bioinformatics 2007 May;5(2):86-101

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, 2600 GA Delft, the Netherlands.

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http://linkinghub.elsevier.com/retrieve/pii/S167202290760019
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http://dx.doi.org/10.1016/S1672-0229(07)60019-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054099PMC
May 2007

Exploiting combinatorial cultivation conditions to infer transcriptional regulation.

BMC Genomics 2007 Jan 22;8:25. Epub 2007 Jan 22.

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1186/1471-2164-8-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1797021PMC
January 2007

Gene therapy: is IL2RG oncogenic in T-cell development?

Nature 2006 Sep;443(7109):E5; discussion E6-7

Department of Immunology, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands.

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http://dx.doi.org/10.1038/nature05218DOI Listing
September 2006

A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets.

BMC Bioinformatics 2006 May 2;7:235. Epub 2006 May 2.

Information and Communication Theory Group, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1186/1471-2105-7-235DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1569875PMC
May 2006

Maximum significance clustering of oligonucleotide microarrays.

Bioinformatics 2006 Feb 22;22(3):326-31. Epub 2005 Nov 22.

Information and Communication Theory Group, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, PO Box 5031, 2600 GA Delft, The Netherlands.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/bti788DOI Listing
February 2006

A protocol for building and evaluating predictors of disease state based on microarray data.

Bioinformatics 2005 Oct 7;21(19):3755-62. Epub 2005 Apr 7.

Department of Mediamatics, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology Mekelweg 4, 2628 CD Delft, The Netherlands.

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http://dx.doi.org/10.1093/bioinformatics/bti429DOI Listing
October 2005

Edge-based image restoration.

IEEE Trans Image Process 2005 Oct;14(10):1454-68

Information and Communication Theory Group, Mediamatics Department, Faculty of Electrical Engineering, Mathematics and Computer Science, Delft University of Technology, Delft, The Netherlands.

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http://dx.doi.org/10.1109/tip.2005.854466DOI Listing
October 2005

The nearest subclass classifier: a compromise between the nearest mean and nearest neighbor classifier.

IEEE Trans Pattern Anal Mach Intell 2005 Sep;27(9):1417-29

Department of Mediamatics, Delft University of Technology, P.O. Box 5031, 2600 GA Delft, The Netherlands.

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http://dx.doi.org/10.1109/TPAMI.2005.187DOI Listing
September 2005