Works by Reinders, Marcel J T

Results: 93

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

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

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

Published in:

Genome Biology, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s13059-019-1795-z

By:

Abdelaal, Tamim;
Michielsen, Lieke;
Cats, Davy;
Hoogduin, Dylan;
Mei, Hailiang;
Reinders, Marcel J. T.;
Mahfouz, Ahmed

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

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

Published in:

Nature, 2006, v. 443, n. 7109, p. E5, doi. 10.1038/nature05218

By:

Pike-Overzet, Karin;
de Ridder, Dick;
Weerkamp, Floor;
Baert, Miranda R. M.;
Verstegen, Monique M.;
Brugman, Martijn H.;
Howe, Steven J.;
Reinders, Marcel J. T.;
Thrasher, Adrian J.;
Wagemaker, Gerard;
van Dongen, Jacques J. M.;
Staal, Frank J. T.

Publication type:

Article

Gene therapy: Is IL2RG oncogenic in T-cell development?: X-SCID transgene leukaemogenicity (reply).

Published in:

Nature, 2006, v. 443, n. 7109, p. E6, doi. 10.1038/nature05220

By:

Pike-Overzet, Karin;
de Ridder, Dick;
Weerkamp, Floor;
Baert, Miranda R. M.;
Verstegen, Monique M.;
Brugman, Martijn H.;
Howe, Steven J.;
Reinders, Marcel J. T.;
Thrasher^4, Adrian J.;
Wagemaker, Gerard;
van Dongen, Jacques J. M.;
Staal, Frank 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

Single-Cell Transcriptomics Links Loss of Human Pancreatic β-Cell Identity to ER Stress.

Published in:

Cells (2073-4409), 2021, v. 10, n. 12, p. 3585, doi. 10.3390/cells10123585

By:

Groen, Nathalie;
Leenders, Floris;
Mahfouz, Ahmed;
Munoz-Garcia, Amadeo;
Muraro, Mauro J.;
de Graaf, Natascha;
Rabelink, Ton. J.;
Hoeben, Rob;
van Oudenaarden, Alexander;
Zaldumbide, Arnaud;
Reinders, Marcel J. T.;
Koning, Eelco J. P. de;
Carlotti, Françoise

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

KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data.

Published in:

BMC Research Notes, 2010, v. 3, p. 298, doi. 10.1186/1756-0500-3-298

By:

de Ronde, Jorma J.;
Klijn, Christiaan;
Velds, Arno;
Holstege, Henne;
Reinders, Marcel J. T.;
Jonkers, Jos;
Wessels, Lodewyk F. A.

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

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

Transcriptomic signatures of brain regional vulnerability to Parkinson's disease.

Published in:

Communications Biology, 2020, v. 3, n. 1, p. 1, doi. 10.1038/s42003-020-0804-9

By:

Keo, Arlin;
Mahfouz, Ahmed;
Ingrassia, Angela M. T.;
Meneboo, Jean-Pascal;
Villenet, Celine;
Mutez, Eugénie;
Comptdaer, Thomas;
Lelieveldt, Boudewijn P. F.;
Figeac, Martin;
Chartier-Harlin, Marie-Christine;
van de Berg, Wilma D. J.;
van Hilten, Jacobus J.;
Reinders, Marcel J. T.

Publication type:

Article

Longitudinal Dynamics of Human B-Cell Response at the Single-Cell Level in Response to Tdap Vaccination.

Published in:

Vaccines, 2021, v. 9, n. 11, p. 1352, doi. 10.3390/vaccines9111352

By:

Khatri, Indu;
Diks, Annieck M.;
van den Akker, Erik B.;
Oosten, Liesbeth E. M.;
Zwaginga, Jaap Jan;
Reinders, Marcel J. T.;
van Dongen, Jacques J. M.;
Berkowska, Magdalena A.

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

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

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

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

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

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

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

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

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

Co-expression Patterns between ATN1 and ATXN2 Coincide with Brain Regions Affected in Huntington's Disease.

Published in:

Frontiers in Molecular Neuroscience, 2017, p. 1, doi. 10.3389/fnmol.2017.00399

By:

Keo, Arlin;
Aziz, N. Ahmad;
Dzyubachyk, Oleh;
van der Grond, Jeroen;
van Roon-Mom, Willeke M. C.;
Lelieveldt, Boudewijn P. F.;
Reinders, Marcel J. T.;
Mahfouz, Ahmed

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

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

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

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

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

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

Published in:

Nature Communications, 2016, v. 7, n. 7, p. 12159, doi. 10.1038/ncomms12159

By:

van Dyk, Ewald;
Hoogstraat, Marlous;
ten Hoeve, Jelle;
Reinders, Marcel J. T.;
Wessels, Lodewyk F. A.

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