Works by Reinders, Marcel J T

Results: 92

PROTEIN COMPLEX PREDICTION USING AN INTEGRATIVE BIOINFORMATICS APPROACH.

Published in:

Journal of Bioinformatics & Computational Biology, 2007, v. 5, n. 4, p. 839, doi. 10.1142/S0219720007002953

By:

VAN BERLO, ROGIER J. P.;
WESSELS, LODEWYK F. A.;
DE RIDDER, DICK;
REINDERS, MARCEL J. T.

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

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

Benchmarking variational AutoEncoders on cancer transcriptomics data.

Published in:

PLoS ONE, 2023, v. 18, n. 10, p. 1, doi. 10.1371/journal.pone.0292126

By:

Eltager, Mostafa;
Abdelaal, Tamim;
Charrout, Mohammed;
Mahfouz, Ahmed;
Reinders, Marcel J. T.;
Makrodimitris, Stavros

Publication type:

Article

SIRV: spatial inference of RNA velocity at the single-cell resolution.

Published in:

NAR Genomics & Bioinformatics, 2024, v. 6, n. 3, p. 1, doi. 10.1093/nargab/lqae100

By:

Abdelaal, Tamim;
Grossouw, Laurens M;
Pasterkamp, R Jeroen;
Lelieveldt, Boudewijn P F;
Reinders, Marcel J T;
Mahfouz, Ahmed

Publication type:

Article

Single-cell reference mapping to construct and extend cell-type hierarchies.

Published in:

NAR Genomics & Bioinformatics, 2023, v. 5, n. 3, p. 1, doi. 10.1093/nargab/lqad070

By:

Michielsen, Lieke;
Lotfollahi, Mohammad;
Strobl, Daniel;
Sikkema, Lisa;
Reinders, Marcel J T;
Theis, Fabian J;
Mahfouz, Ahmed

Publication type:

Article

Differential analysis of binarized single-cell RNA sequencing data captures biological variation.

Published in:

NAR Genomics & Bioinformatics, 2021, v. 3, n. 4, p. 1, doi. 10.1093/nargab/lqab118

By:

Bouland, Gerard A;
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

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

Published in:

Nature Communications, 2017, v. 8, n. 1, p. 1, doi. 10.1038/s41467-017-01689-9

By:

van Unen, Vincent;
Höllt, Thomas;
Pezzotti, Nicola;
Li, Na;
Reinders, Marcel J. T.;
Eisemann, Elmar;
Koning, Frits;
Vilanova, Anna;
Lelieveldt, Boudewijn P. F.

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

A survey of functional genomic variation in domesticated chickens.

Published in:

Genetics Selection Evolution, 2018, v. 50, n. 1, p. N.PAG, doi. 10.1186/s12711-018-0390-1

By:

Derks, Martijn F. L.;
Megens, Hendrik-Jan;
Bosse, Mirte;
Visscher, Jeroen;
Peeters, Katrijn;
Bink, Marco C. A. M.;
Vereijken, Addie;
Gross, Christian;
de Ridder, Dick;
Reinders, Marcel J. T.;
Groenen, Martien A. M.

Publication type:

Article

Predicting cell population-specific gene expression from genomic sequence.

Published in:

Frontiers in Bioinformatics, 2024, p. 1, doi. 10.3389/fbinf.2024.1347276

By:

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

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

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

Published in:

PLoS ONE, 2016, v. 11, n. 2, p. 1, doi. 10.1371/journal.pone.0149853

By:

Taskesen, Erdogan;
Reinders, Marcel J. T.

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

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

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

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

Published in:

Frontiers in Neuroscience, 2018, p. N.PAG, doi. 10.3389/fnins.2018.00594

By:

Koorneef, Lisa L.;
Bogaards, Marit;
Reinders, Marcel J. T.;
Meijer, Onno C.;
Mahfouz, Ahmed

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

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

Published in:

2016

By:

Straver, Roy;
Oudejans, Cees B. M.;
Sistermans, Erik A.;
Reinders, Marcel J. T.

Publication type:

journal article

Cover Image, Volume 36, Issue 7.

Published in:

Prenatal Diagnosis, 2016, v. 36, n. 7, p. i, doi. 10.1002/pd.4738

By:

Straver, Roy;
Oudejans, Cees B. M.;
Sistermans, Erik A.;
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

Single-cell immune profiling reveals thymus-seeding populations, T cell commitment, and multilineage development in the human thymus.

Published in:

Science Immunology, 2022, v. 7, n. 77, p. 1, doi. 10.1126/sciimmunol.ade0182

By:

Cordes, Martijn;
Canté-Barrett, Kirsten;
van den Akker, Erik B.;
Moretti, Federico A.;
Kiełbasa, Szymon M.;
Vloemans, Sandra A.;
Garcia-Perez, Laura;
Teodosio, Cristina;
van Dongen, Jacques J. M.;
Pike-Overzet, Karin;
Reinders, Marcel J. T.;
Staal, Frank J. T.

Publication type:

Article

Extreme enrichment of VNTR-associated polymorphicity in human subtelomeres: genes with most VNTRs are predominantly expressed in the brain.

Published in:

Translational Psychiatry, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41398-020-01060-5

By:

Linthorst, Jasper;
Meert, Wim;
Hestand, Matthew S.;
Korlach, Jonas;
Vermeesch, Joris Robert;
Reinders, Marcel J. T.;
Holstege, Henne

Publication type:

Article

Immune response and endocytosis pathways are associated with the resilience against Alzheimer's disease.

Published in:

Translational Psychiatry, 2020, v. 10, n. 1, p. N.PAG, doi. 10.1038/s41398-020-01018-7

By:

Tesi, Niccolò;
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

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

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

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

Published in:

BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-93

By:

van den Berg, Bastiaan A.;
Reinders, Marcel J. T.;
Roubos, Johannes A.;
de Ridder, Dick

Publication type:

Article

HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 275, doi. 10.1186/1471-2105-11-275

By:

Taskesen, Erdogan;
Beekman, Renee;
de Ridder, Jeroen;
Wouters, Bas J.;
Peeters, Justine K.;
Touw, Ivo P.;
Reinders, Marcel J. T.;
Delwel, Ruud

Publication type:

Article

Delineation of amplification, hybridization andlocation effects in microarray data yieldsbetter-quality normalization.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 156, doi. 10.1186/1471-2105-11-156

By:

Hulsman, Marc;
Mentink, Anouk;
van Someren, Eugene P.;
Dechering, Koen J.;
de Boer, Jan;
Reinders, Marcel J. T.

Publication type:

Article

Analysis of mass spectrometry data using sub-spectra.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-S1-S51

By:

Meuleman, Wouter;
Engwegen, Judith Y. M. N.;
Gast, Marie-Christine W.;
Wessels, Lodewyk F. A.;
Reinders, Marcel J. T.

Publication type:

Article

Knowledge driven decomposition of tumor expression profiles.

Published in:

BMC Bioinformatics, 2009, v. 10, p. 1, doi. 10.1186/1471-2105-10-S1-S20

By:

van Vliet, Martin H.;
Wessels, Lodewyk F. A.;
Reinders, Marcel J. T.

Publication type:

Article

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-88

By:

Meuleman, Wouter;
Engwegen, Judith Y. M. N.;
Gast, Marie-Christine W.;
Beijnen, Jos H.;
Reinders, Marcel J. T.;
Wessels, Lodewyk F. A.

Publication type:

Article

SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets.

Published in:

BMC Bioinformatics, 2007, v. 8, p. 422, doi. 10.1186/1471-2105-8-422

By:

Lai, Carmen;
Horlings, Hugo M.;
van de Vijver, Marc J.;
van Beers, Eric H.;
Nederlof, Petra M.;
Wessels, Lodewyk F. A.;
Reinders, Marcel J. T.

Publication type:

Article

Determining epitope specificity of T-cell receptors with transformers.

Published in:

Bioinformatics, 2023, v. 39, n. 11, p. 1, doi. 10.1093/bioinformatics/btad632

By:

Khan, Abdul Rehman;
Reinders, Marcel J T;
Khatri, Indu

Publication type:

Article

Cell type matching across species using protein embeddings and transfer learning.

Published in:

Bioinformatics, 2023, v. 39, p. i404, doi. 10.1093/bioinformatics/btad248

By:

Biharie, Kirti;
Michielsen, Lieke;
Reinders, Marcel J T;
Mahfouz, Ahmed

Publication type:

Article

Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function.

Published in:

Bioinformatics, 2021, v. 37, n. 2, p. 162, doi. 10.1093/bioinformatics/btaa701

By:

Villegas-Morcillo, Amelia;
Makrodimitris, Stavros;
Ham, Roeland C H J van;
Gomez, Angel M;
Sanchez, Victoria;
Reinders, Marcel J T

Publication type:

Article

SCHNEL: scalable clustering of high dimensional single-cell data.

Published in:

Bioinformatics, 2020, v. 36, p. i849, doi. 10.1093/bioinformatics/btaa816

By:

Abdelaal, Tamim;
Raadt, Paul de;
Lelieveldt, Boudewijn P F;
Reinders, Marcel J T;
Mahfouz, Ahmed

Publication type:

Article

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

Published in:

Bioinformatics, 2020, v. 36, n. 6, p. 1930, doi. 10.1093/bioinformatics/btz804

By:

Cordes, Martijn;
Pike-Overzet, Karin;
Eggermond, Marja van;
Vloemans, Sandra;
Baert, Miranda R;
Garcia-Perez, Laura;
Staal, Frank J T;
Reinders, Marcel J T;
Akker, Erik B van den

Publication type:

Article

Metric learning on expression data for gene function prediction.

Published in:

Bioinformatics, 2020, v. 36, n. 4, p. 1182, doi. 10.1093/bioinformatics/btz731

By:

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

Publication type:

Article

CyTOFmerge: integrating mass cytometry data across multiple panels.

Published in:

Bioinformatics, 2019, v. 35, n. 20, p. 4063, doi. 10.1093/bioinformatics/btz180

By:

Abdelaal, Tamim;
Höllt, Thomas;
Unen, Vincent van;
Lelieveldt, Boudewijn P F;
Koning, Frits;
Reinders, Marcel J T;
Mahfouz, Ahmed

Publication type:

Article

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

Published in:

Bioinformatics, 2019, v. 35, n. 14, p. i510, doi. 10.1093/bioinformatics/btz372

By:

Mourragui, Soufiane;
Loog, Marco;
Wiel, Mark A van de;
Reinders, Marcel J T;
Wessels, Lodewyk F A

Publication type:

Article

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

Published in:

Bioinformatics, 2019, v. 35, n. 7, p. 1116, doi. 10.1093/bioinformatics/bty751

By:

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

Publication type:

Article