Works matching AU Reinders, Marcel J T

Results: 93

Comparative validation of handheld fractional exhaled nitric oxide measurements.

Published in:

Expert Review of Medical Devices, 2025, v. 22, n. 6, p. 643, doi. 10.1080/17434440.2025.2499652

By:

van Deelen, Sanne;
Tramper-Stranders, Gerdien A.;
Hendriks, Rudi W.;
Reinders, Marcel J. T.;
Braunstahl, Gert-Jan

Publication type:

Article

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

Published in:

Bioinformatics, 2015, v. 31, n. 21, p. 3437, doi. 10.1093/bioinformatics/btv389

By:

Gehrmann, Thies;
Reinders, Marcel J. T.

Publication type:

Article

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

Published in:

Bioinformatics, 2013, v. 29, n. 22, p. 2826, doi. 10.1093/bioinformatics/btt502

By:

Nijkamp, Jurgen F.;
Pop, Mihai;
Reinders, Marcel J. T.;
de Ridder, Dick

Publication type:

Article

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

Published in:

Bioinformatics, 2012, v. 28, n. 24, p. 3195, doi. 10.1093/bioinformatics/bts601

By:

Nijkamp, Jurgen F.;
van den Broek, Marcel A.;
Geertman, Jan-Maarten A.;
Reinders, Marcel J. T.;
Daran, Jean-Marc G.;
de Ridder, Dick

Publication type:

Article

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

Published in:

Bioinformatics, 2011, v. 27, n. 17, p. 2451, doi. 10.1093/bioinformatics/btr388

By:

Bot, Jan J.;
Reinders, Marcel J. T.

Publication type:

Article

Fewer permutations, more accurate P-values.

Published in:

Bioinformatics, 2009, v. 25, n. 12, p. i161, doi. 10.1093/bioinformatics/btp211

By:

Theo A. Knijnenburg;
Lodewyk F. A. Wessels;
Marcel J. T. Reinders;
Ilya Shmulevich

Publication type:

Article

Maximum significance clustering of oligonucleotide microarrays.

Published in:

Bioinformatics, 2006, v. 22, n. 3, p. 326, doi. 10.1093/bioinformatics/bti788

By:

Dick de Ridder;
Frank J. T. Staal;
Jacques J. M. van Dongen;
Marcel J. T. Reinders

Publication type:

Article

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

Published in:

Bioinformatics, 2005, v. 21, n. 19, p. 3755

By:

Lodewyk F. A. Wessels;
Marcel J. T. Reinders;
Augustinus A. M. Hart;
Cor J. Veenman;
Hongyue Dai;
Yudong D. He;
Laura J. van't Veer

Publication type:

Article

A transcriptomic based deconvolution framework for assessing differentiation stages and drug responses of AML.

Published in:

NPJ Precision Oncology, 2024, v. 8, n. 1, p. 1, doi. 10.1038/s41698-024-00596-9

By:

Karakaslar, E. Onur;
Severens, Jeppe F.;
Sánchez-López, Elena;
van Veelen, Peter A.;
Zlei, Mihaela;
van Dongen, Jacques J. M.;
Otte, Annemarie M.;
Halkes, Constantijn J. M.;
van Balen, Peter;
Veelken, Hendrik;
Reinders, Marcel J. T.;
Griffioen, Marieke;
van den Akker, Erik B.

Publication type:

Article

Author Correction: Pan-cancer subtyping in a 2D-map shows substructures that are driven by specific combinations of molecular characteristics.

Published in:

Scientific Reports, 2018, v. 8, n. 1, p. 1, doi. 10.1038/s41598-018-35518-w

By:

Taskesen, Erdogan;
Huisman, Sjoerd M. H.;
Mahfouz, Ahmed;
Krijthe, Jesse H.;
de Ridder, Jeroen;
van de Stolpe, Anja;
van den Akker, Erik;
Verhaegh, Wim;
Reinders, Marcel J. T.

Publication type:

Article

Technical Report: A Comprehensive Comparison between Different Quantification Versions of Nightingale Health's 1 H-NMR Metabolomics Platform.

Published in:

Metabolites (2218-1989), 2023, v. 13, n. 12, p. 1181, doi. 10.3390/metabo13121181

By:

Bizzarri, Daniele;
Reinders, Marcel J. T.;
Beekman, Marian;
Slagboom, P. Eline;
van den Akker, Erik B.

Publication type:

Article

Benchmarking Outlier Detection Methods for Detecting IEM Patients in Untargeted Metabolomics Data.

Published in:

Metabolites (2218-1989), 2023, v. 13, n. 1, p. 97, doi. 10.3390/metabo13010097

By:

Bongaerts, Michiel;
Kulkarni, Purva;
Zammit, Alan;
Bonte, Ramon;
Kluijtmans, Leo A. J.;
Blom, Henk J.;
Engelke, Udo F. H.;
Tax, David M. J.;
Ruijter, George J. G.;
Reinders, Marcel J. T.

Publication type:

Article

Using Out-of-Batch Reference Populations to Improve Untargeted Metabolomics for Screening Inborn Errors of Metabolism.

Published in:

Metabolites (2218-1989), 2021, v. 11, n. 1, p. 8, doi. 10.3390/metabo11010008

By:

Bongaerts, Michiel;
Bonte, Ramon;
Demirdas, Serwet;
Jacobs, Edwin H.;
Oussoren, Esmee;
van der Ploeg, Ans T.;
Wagenmakers, Margreet A. E. M.;
Hofstra, Robert M. W.;
Blom, Henk J.;
Reinders, Marcel J. T.;
Ruijter, George J. G.

Publication type:

Article

Automatic Gene Function Prediction in the 2020's.

Published in:

Genes, 2020, v. 11, n. 11, p. 1264, doi. 10.3390/genes11111264

By:

Makrodimitris, Stavros;
van Ham, Roeland C. H. J.;
Reinders, Marcel J. T.

Publication type:

Article

Breast cancer subtype predictors revisited: from consensus to concordance?

Published in:

BMC Medical Genomics, 2016, v. 9, p. 1, doi. 10.1186/s12920-016-0185-6

By:

Sontrop, Herman M. J.;
Reinders, Marcel J. T.;
Moerland, Perry D.

Publication type:

Article

An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas.

Published in:

Nature Genetics, 2005, v. 37, n. 2, p. 182, doi. 10.1038/ng1502

By:

Roepman, Paul;
Wessels, Lodewyk F. A.;
Kettelarij, Nienke;
Kemmeren, Patrick;
Miles, Antony J.;
Lijnzaad, Philip;
Tilanus, Marcel G. J.;
Koole, Ronald;
Hordijk, Gert-Jan;
van der Vliet, Peter C.;
Reinders, Marcel J. T.;
Slootweg, Piet J.;
Holstege, Frank C. P.

Publication type:

Article

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

Published in:

BMC Genomics, 2008, v. 9, p. 1, doi. 10.1186/1471-2164-9-375

By:

van Vliet, Martin H.;
Reyal, Fabien;
Horlings, Hugo M.;
van de Vijver, Marc J.;
Reinders, Marcel J. T.;
Wessels, Lodewyk F. A.

Publication type:

Article

Genome-wide association study of frontotemporal dementia identifies a C9ORF72 haplotype with a median of 12-G4C2 repeats that predisposes to pathological repeat expansions.

Published in:

Translational Psychiatry, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41398-021-01577-3

By:

Reus, Lianne M.;
Jansen, Iris E.;
Mol, Merel O.;
van Ruissen, Fred;
van Rooij, Jeroen;
van Schoor, Natasja M.;
Tesi, Niccolò;
Reinders, Marcel J. T.;
Huisman, Martijn A.;
Holstege, Henne;
Visser, Pieter Jelle;
de Boer, Sterre C. M.;
Hulsman, Marc;
Ahmad, Shahzad;
Amin, Najaf;
Uitterlinden, Andre G.;
Ikram, Arfan;
van Duijn, Cornelia M.;
Seelaar, Harro;
Ramakers, Inez H. G. B.

Publication type:

Article

Hypergeometric analysis of tiling-array and sequence data: detection and interpretation of peaks.

Published in:

Advances & Applications in Bioinformatics & Chemistry, 2013, v. 6, p. 55, doi. 10.2147/AABC.S51271

By:

Taskesen, Erdogan;
Hoogeboezem, Remco;
Delwel, Ruud;
Reinders, Marcel J. T.

Publication type:

Article

Consequences and opportunities arising due to sparser single-cell RNA-seq datasets.

Published in:

Genome Biology, 2023, v. 24, n. 1, p. 1, doi. 10.1186/s13059-023-02933-w

By:

Bouland, Gerard A.;
Mahfouz, Ahmed;
Reinders, Marcel J. T.

Publication type:

Article

Insight into Neutral and Disease-Associated Human Genetic Variants through Interpretable Predictors.

Published in:

PLoS ONE, 2015, v. 10, n. 3, p. 1, doi. 10.1371/journal.pone.0120729

By:

van den Berg, Bastiaan A.;
Reinders, Marcel J. T.;
de Ridder, Dick;
de Beer, Tjaart A. P.

Publication type:

Article

Analysis of Tumor Heterogeneity and Cancer Gene Networks Using Deep Sequencing of MMTV-Induced Mouse Mammary Tumors

Published in:

PLoS ONE, 2013, v. 8, n. 5, p. 1, doi. 10.1371/journal.pone.0062113

By:

Klijn, Christiaan;
Koudijs, Marco J.;
Kool, Jaap;
ten Hoeve, Jelle;
Boer, Mandy;
de Moes, Joost;
Akhtar, Waseem;
van Miltenburg, Martine;
Vendel-Zwaagstra, Annabel;
Reinders, Marcel J. T.;
Adams, David J.;
van Lohuizen, Maarten;
Hilkens, John;
Wessels, Lodewyk F. A.;
Jonkers, Jos

Publication type:

Article

Exploring Sequence Characteristics Related to High-Level Production of Secreted Proteins in Aspergillus niger.

Published in:

PLoS ONE, 2012, v. 7, n. 10, p. 1, doi. 10.1371/journal.pone.0045869

By:

den Berg, Bastiaan A. van;
Reinders, Marcel J. T.;
Hulsman, Marc;
Liang Wu;
Pel, Herman J.;
Roubos, Johannes A.;
de Ridder, Dick

Publication type:

Article

Integration of Clinical and Gene Expression Data Has a Synergetic Effect on Predicting Breast Cancer Outcome.

Published in:

PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0040358

By:

van Vliet, Martin H.;
Horlings, Hugo M.;
van de Vijver, Marc J.;
Reinders, Marcel J. T.;
Wessels, Lodewyk F. A.

Publication type:

Article

Understanding Regulation of Metabolism through Feasibility Analysis.

Published in:

PLoS ONE, 2012, v. 7, n. 7, p. 1, doi. 10.1371/journal.pone.0039396

By:

Nikerel, Emrah;
Berkhout, Jan;
Fengyuan Hu;
Teusink, Bas;
Reinders, Marcel J. T.;
De Ridder, Dick

Publication type:

Article

An Evaluation Protocol for Subtype-Specific Breast Cancer Event Prediction.

Published in:

PLoS ONE, 2011, v. 6, n. 7, p. 1, doi. 10.1371/journal.pone.0021681

By:

Sontrop, Herman M. J.;
Verhaegh, Wim F. J.;
Reinders, Marcel J. T.;
Moerland, Perry D.

Publication type:

Article

PLIS: A metabolomic response monitor to a lifestyle intervention study in older adults.

Published in:

FASEB Journal, 2022, v. 36, n. 11, p. 1, doi. 10.1096/fj.202201037R

By:

Bogaards, Fatih A.;
Gehrmann, Thies;
Beekman, Marian;
van den Akker, Erik Ben;
van de Rest, Ondine;
Hangelbroek, Roland W. J.;
Noordam, Raymond;
Mooijaart, Simon P.;
de Groot, Lisette C. P. G. M.;
Reinders, Marcel J. T.;
Slagboom, P. Eline

Publication type:

Article

A data‐driven methodology reveals novel myofiber clusters in older human muscles.

Published in:

FASEB Journal, 2020, v. 34, n. 4, p. 5525, doi. 10.1096/fj.201902350R

By:

Raz, Yotam;
Akker, Erik B.;
Roest, Tijmen;
Riaz, Muhammad;
Rest, Ondine;
Suchiman, H. Eka D.;
Lakenberg, Nico;
Stassen, Stefanie A.;
Putten, Maaike;
Feskens, Edith J. M.;
Reinders, Marcel J. T.;
Goeman, Jelle;
Beekman, Marian;
Raz, Vered;
Slagboom, Pieternella Eline

Publication type:

Article

A framework for employing longitudinally collected multicenter electronic health records to stratify heterogeneous patient populations on disease history.

Published in:

2022

By:

Maurits, Marc P;
Korsunsky, Ilya;
Raychaudhuri, Soumya;
Murphy, Shawn N;
Smoller, Jordan W;
Weiss, Scott T;
Huizinga, Thomas W J;
Reinders, Marcel J T;
Karlson, Elizabeth W;
Akker, Erik B van den;
Knevel, Rachel;
van den Akker, Erik B

Publication type:

journal article

Machine learning-based somatic variant calling in cell-free DNA of metastatic breast cancer patients using large NGS panels.

Published in:

Scientific Reports, 2023, v. 13, n. 1, p. 1, doi. 10.1038/s41598-023-37409-1

By:

Jongbloed, Elisabeth M.;
Jansen, Maurice P. H. M.;
de Weerd, Vanja;
Helmijr, Jean A.;
Beaufort, Corine M.;
Reinders, Marcel J. T.;
van Marion, Ronald;
van IJcken, Wilfred F. J.;
Sonke, Gabe S.;
Konings, Inge R.;
Jager, Agnes;
Martens, John W. M.;
Wilting, Saskia M.;
Makrodimitris, Stavros

Publication type:

Article

Transcriptomic Signatures Associated With Regional Cortical Thickness Changes in Parkinson's Disease.

Published in:

Frontiers in Neuroscience, 2021, p. 1, doi. 10.3389/fnins.2021.733501

By:

Keo, Arlin;
Dzyubachyk, Oleh;
van der Grond, Jeroen;
van Hilten, Jacobus J.;
Reinders, Marcel J. T.;
Mahfouz, Ahmed

Publication type:

Article

TREM2 Burden associates solely with Alzheimer's Disease, and decreases the Chance to become a Centenarian.

Published in:

Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2023, v. 19, p. 1, doi. 10.1002/alz.078234

By:

Dijkstra, Janna I.R.;
Vermunt, Lisa;
Biessels, Geert Jan;
Braber, Anouk;
Claassen, Jurgen A.H.R.;
De Deyn, Peter Paul;
Ghanbari, Mohsen;
Huisman, Martijn;
Hulsman, Marc;
Ramakers, Inez H.G.B.;
Reinders, Marcel J. T.;
Seelaar, Harro;
Tesi, Niccoló;
Visser, Pieter Jelle;
van der Flier, Wiesje M.;
Teunissen, Charlotte E.;
Holstege, Henne;
Van Der Lee, Sven J

Publication type:

Article

TREM2 Burden associates solely with Alzheimer's Disease, and decreases the Chance to become a Centenarian.

Published in:

Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2023, v. 19, p. 1, doi. 10.1002/alz.078234

By:

Dijkstra, Janna I.R.;
Vermunt, Lisa;
Biessels, Geert Jan;
Braber, Anouk;
Claassen, Jurgen A.H.R.;
De Deyn, Peter Paul;
Ghanbari, Mohsen;
Huisman, Martijn;
Hulsman, Marc;
Ramakers, Inez H.G.B.;
Reinders, Marcel J. T.;
Seelaar, Harro;
Tesi, Niccoló;
Visser, Pieter Jelle;
van der Flier, Wiesje M.;
Teunissen, Charlotte E.;
Holstege, Henne;
Van Der Lee, Sven J

Publication type:

Article

The correlation between neuropathology levels and cognitive performance in centenarians.

Published in:

Alzheimer's & Dementia: The Journal of the Alzheimer's Association, 2023, v. 19, n. 11, p. 5036, doi. 10.1002/alz.13087

By:

Zhang, Meng;
Ganz, Andrea B.;
Rohde, Susan;
Lorenz, Linda;
Rozemuller, Annemieke J. M.;
van Vliet, Kimberley;
Graat, Marieke;
Sikkes, Sietske A. M.;
Reinders, Marcel J. T.;
Scheltens, Philip;
Hulsman, Marc;
Hoozemans, Jeroen J. M.;
Holstege, Henne

Publication type:

Article

An integrated approach of gene expression and DNA-methylation profiles of WNT signaling genes uncovers novel prognostic markers in Acute Myeloid Leukemia.

Published in:

BMC Bioinformatics, 2015, v. 16, p. 1, doi. 10.1186/1471-2105-16-S4-S4.3d

By:

Taskesen, Erdogan;
Staal, Frank J. T.;
Reinders, Marcel J. T.

Publication type:

Article

Epigenetic and Metabolomic Biomarkers for Biological Age: A Comparative Analysis of Mortality and Frailty Risk.

Published in:

Journals of Gerontology Series A: Biological Sciences & Medical Sciences, 2023, v. 78, n. 10, p. 1753, doi. 10.1093/gerona/glad137

By:

Kuiper, Lieke M;
Polinder-Bos, Harmke A;
Bizzarri, Daniele;
Vojinovic, Dina;
Vallerga, Costanza L;
Beekman, Marian;
Dollé, E T;
Ghanbari, Mohsen;
Voortman, Trudy;
Reinders, Marcel J T;
Verschuren, W M Monique;
Slagboom, P Eline;
Akker, Erik B van den;
Meurs, Joyce B J van

Publication type:

Article

Polygenic Risk Score of Longevity Predicts Longer Survival Across an Age Continuum.

Published in:

Journals of Gerontology Series A: Biological Sciences & Medical Sciences, 2021, v. 76, n. 5, p. 750, doi. 10.1093/gerona/glaa289

By:

Tesi, Niccoló;
van der Lee, Sven J.;
Hulsman, Marc;
Jansen, Iris E.;
Stringa, Najada;
van Schoor, Natasja M.;
Scheltens, Philip;
van der Flier, Wiesje M.;
Huisman, Martijn;
Reinders, Marcel J. T.;
Holstege, Henne

Publication type:

Article

Schizophyllum commune has an extensive and functional alternative splicing repertoire.

Published in:

Scientific Reports, 2016, p. 33640, doi. 10.1038/srep33640

By:

Gehrmann, Thies;
Pelkmans, Jordi F.;
Lugones, Luis G.;
Wösten, Han A. B.;
Abeel, Thomas;
Reinders, Marcel J. T.

Publication type:

Article

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

Published in:

Scientific Reports, 2016, p. 26695, doi. 10.1038/srep26695

By:

Scholma, Jetse;
Fuhler, Gwenny M.;
Joore, Jos;
Hulsman, Marc;
Schivo, Stefano;
List, Alan F.;
Reinders, Marcel J. T.;
Peppelenbosch, Maikel P.;
Post, Janine N.

Publication type:

Article

Pan-cancer subtyping in a 2D-map shows substructures that are driven by specific combinations of molecular characteristics.

Published in:

Scientific Reports, 2016, p. 24949, doi. 10.1038/srep24949

By:

Taskesen, Erdogan;
Huisman, Sjoerd M. H.;
Mahfouz, Ahmed;
Krijthe, Jesse H.;
de Ridder, Jeroen;
van de Stolpe, Anja;
van den Akker, Erik;
Verheagh, Wim;
Reinders, Marcel J. T.

Publication type:

Article

scTopoGAN: unsupervised manifold alignment of single-cell data.

Published in:

Bioinformatics Advances, 2023, v. 3, n. 1, p. 1, doi. 10.1093/bioadv/vbad171

By:

Singh, Akash;
Biharie, Kirti;
Reinders, Marcel J T;
Mahfouz, Ahmed;
Abdelaal, Tamim

Publication type:

Article

scMoC: single-cell multi-omics clustering.

Published in:

Bioinformatics Advances, 2022, v. 2, n. 1, p. 1, doi. 10.1093/bioadv/vbac011

By:

Eltager, Mostafa;
Abdelaal, Tamim;
Mahfouz, Ahmed;
Reinders, Marcel J T

Publication type:

Article

Pattern recognition in bioinformatics.

Published in:

Briefings in Bioinformatics, 2013, v. 14, n. 5, p. 633, doi. 10.1093/bib/bbt020

By:

de Ridder, Dick;
de Ridder, Jeroen;
Reinders, Marcel J. T.

Publication type:

Article

The Effect of Alzheimer's Disease-Associated Genetic Variants on Longevity.

Published in:

Frontiers in Genetics, 2021, v. 12, p. 1, doi. 10.3389/fgene.2021.748781

By:

Tesi, Niccolò;
Hulsman, Marc;
van der Lee, Sven J.;
Jansen, Iris E.;
Stringa, Najada;
van Schoor, Natasja M.;
Scheltens, Philip;
van der Flier, Wiesje M.;
Huisman, Martijn;
Reinders, Marcel J. T.;
Holstege, Henne

Publication type:

Article

CBA: Cluster-Guided Batch Alignment for Single Cell RNA-seq.

Published in:

Frontiers in Genetics, 2021, v. 11, p. N.PAG, doi. 10.3389/fgene.2021.644211

By:

Yu, Wenbo;
Mahfouz, Ahmed;
Reinders, Marcel J. T.

Publication type:

Article

Hierarchical progressive learning of cell identities in single-cell data.

Published in:

Nature Communications, 2021, v. 12, n. 1, p. 1, doi. 10.1038/s41467-021-23196-8

By:

Michielsen, Lieke;
Reinders, Marcel J. T.;
Mahfouz, Ahmed

Publication type:

Article

Effect of Phenotype and Genotype on the Plasma Proteome in Patients with Inflammatory Bowel Disease.

Published in:

Journal of Crohn's & Colitis, 2022, v. 16, n. 3, p. 414, doi. 10.1093/ecco-jcc/jjab157

By:

Bourgonje, Arno R;
Hu, Shixian;
Spekhorst, Lieke M;
Zhernakova, Daria V;
Vila, Arnau Vich;
Li, Yanni;
Voskuil, Michiel D;
Berkel, Lisette A van;
Folly, Brenda Bley;
Charrout, Mohammed;
Mahfouz, Ahmed;
Reinders, Marcel J T;
Heck, Julia I P van;
Joosten, Leo A B;
Visschedijk, Marijn C;
Dullemen, Hendrik M van;
Faber, Klaas Nico;
Samsom, Janneke N;
Festen, Eleonora A M;
Dijkstra, Gerard

Publication type:

Article

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

Published in:

PLoS Computational Biology, 2015, v. 11, n. 8, p. 1, doi. 10.1371/journal.pcbi.1004336

By:

Gritsenko, Alexey A.;
Hulsman, Marc;
Reinders, Marcel J. T.;
de Ridder, Dick

Publication type:

Article

Computational Estimation of the Composition of Fat/Oil Mixtures Containing Interesterifications from Gas and Liquid Chromatography Data.

Published in:

Journal of the American Oil Chemists' Society (JAOCS), 2005, v. 82, n. 10, p. 707, doi. 10.1007/s11746-005-1132-z

By:

Van Vliet, Martin H.;
Van Kempen, Geert M. P.;
Reinders, Marcel J. T.;
De Ridder, Dick

Publication type:

Article

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

Published in:

2017

By:

Beek, Daphne M.;
Straver, Roy;
Weiss, Marian M.;
Boon, Elles M. J.;
Huijsdens‐van Amsterdam, Karin;
Oudejans, Cees B. M.;
Reinders, Marcel J. T.;
Sistermans, Erik A.;
van Beek, Daphne M;
Huijsdens-van Amsterdam, Karin

Publication type:

journal article