Human skeletal muscle fiber heterogeneity beyond myosin heavy chains

Authors: Roger Moreno-Justicia, Thibaux Van der Stede, Ben Stocks, Jenni Laitila, Robert A. Seaborne, Alexia Van de Loock, Eline Lievens, Diana Samodova, Leyre Marín-Arraiza, Oksana Dmytriyeva, Robin Browaeys, Kim Van Vossel, Lukas Moesgaard, Nurten Yigit, Jasper Anckaert, Anneleen Weyns, Ruud Van Thienen, Ronni E. Sahl, Edmar Zanoteli, Michael W. Lawlor, Michael Wierer, Pieter Mestdagh, Jo Vandesompele, Julien Ochala, Morten Hostrup, Wim Derave, Atul S. Deshmukh

Source: Nature Communications, Vol 16, Iss 1, Pp 1-18 (2025)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/11b7769c84094140ae8d2cbc1b31d098

Therapy response monitoring in blood plasma from esophageal adenocarcinoma patients using cell-free DNA methylation profiling

Authors: Kathleen Schoofs, Maísa R. Ferro Dos Santos, Jilke De Wilde, Sofie Roelandt, Sofie Van de Velde, Philippe Decruyenaere, Leander Meuris, Olivier Thas, Annouck Philippron, Lieven Depypere, Philippe Nafteux, Hanne Vanommeslaeghe, Elke Van Daele, Piet Pattyn, Jo Vandesompele, Katleen De Preter

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-11 (2024)

Subject Terms: Esophageal adenocarcinoma, cfDNA, Liquid biopsy, DNA methylation, Blood plasma, Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/00ff7189cb934594b537eaf34af77134

Flexible methods for uncertainty estimation of digital PCR data

Authors: Yao Chen, Ward De Spiegelaere, Matthijs Vynck, Wim Trypsteen, David Gleerup, Jo Vandesompele, Olivier Thas

Source: iScience, Vol 28, Iss 3, Pp 111772- (2025)

Subject Terms: Bioinformatics, Bioinformatic numerical analysis, Methodology in biological sciences, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004225000318; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/e511a5a767d742dfb518128f690c9382

Nationwide quality assurance of high-throughput diagnostic molecular testing during the SARS-CoV-2 pandemic: role of the Belgian National Reference Centre

Authors: Reile Janssen, Lize Cuypers, Lies Laenen, Els Keyaerts, Kurt Beuselinck, Sunita Janssenswillen, Bram Slechten, Jannes Bode, Elke Wollants, Kristel Van Laethem, Annabel Rector, Mandy Bloemen, Anke Sijmons, Nathalie de Schaetzen, Arnaud Capron, Kurt Van Baelen, Thierry Pascal, Céline Vermeiren, Fabrice Bureau, Jo Vandesompele, Pieter De Smet, Wouter Uten, Hugues Malonne, Pierre Kerkhofs, Jo De Cock, Veerle Matheeussen, Bruno Verhasselt, Laurent Gillet, Gautier Detry, Bertrand Bearzatto, Jonathan Degosserie, Coralie Henin, Gregor Pairoux, COVID-19 Genomics Belgium Consortium, Piet Maes, Marc Van Ranst, Katrien Lagrou, Elisabeth Dequeker, Emmanuel André

Source: Virology Journal, Vol 21, Iss 1, Pp 1-17 (2024)

Subject Terms: SARS-CoV-2, COVID-19, Belgium, Quality assurance, High-throughput testing, National reference centre, Infectious and parasitic diseases, RC109-216

File Description: electronic resource

Relation: https://doaj.org/toc/1743-422X

Access URL: https://doaj.org/article/9c2e68e9c67a4a0499475f6f4e2cdd5d

Identification and validation of extracellular vesicle reference genes for the normalization of RT‐qPCR data

Authors: Cláudio Pinheiro, Niké Guilbert, Lien Lippens, Quentin Roux, Robin Boiy, Suzanne Fischer, Sofie Van Dorpe, Bram De Craene, Geert Berx, Tom Boterberg, Gwen Sys, Hannelore Denys, Ilkka Miinalainen, Pieter Mestdagh, Jo Vandesompele, Olivier De Wever, An Hendrix

Source: Journal of Extracellular Vesicles, Vol 13, Iss 4, Pp n/a-n/a (2024)

Subject Terms: blood, conditioned medium, exosomes, extracellular vesicles, microvesicles, mRNA, Cytology, QH573-671

File Description: electronic resource

Relation: https://doaj.org/toc/2001-3078

Access URL: https://doaj.org/article/5495443dd1164b7f83e192f541975d2c

HTSplotter: An end-to-end data processing, analysis and visualisation tool for chemical and genetic in vitro perturbation screening.

Authors: Carolina Nunes, Jasper Anckaert, Fanny De Vloed, Jolien De Wyn, Kaat Durinck, Jo Vandesompele, Frank Speleman, Vanessa Vermeirssen

Source: PLoS ONE, Vol 19, Iss 1, p e0296322 (2024)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0296322&type=printable; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/00b55034d5574d7f8c2b20ce3905bf90

Disclosing quantitative RT‐PCR raw data during manuscript submission: a call for action

Authors: Andreas Untergasser, Jan Hellemans, Michael W. Pfaffl, Jan M. Ruijter, Maurice J. B. van denHoff, Mihnea P. Dragomir, Douglas Adamoski, Sandra Martha Gomes Dias, Rui Manuel Reis, Manuela Ferracin, Emmanuel Dias‐Neto, Ian Marsh, Mikael Kubista, Muller Fabbri, Ajay Goel, Ondřej Slabý, Erik Knutsen, Baoqing Chen, Massimo Negrini, Koshi Mimori, Martin Pichler, Maria Papatriantafyllou, Simone Anfossi, Thomas D. Schmittgen, Jim Huggett, Stephen Bustin, Jo Vandesompele, George A. Calin, for the HEROIC (tHe initiativE gRoup On qRT dIsClosure) Consortium

Source: Molecular Oncology, Vol 17, Iss 5, Pp 713-717 (2023)

Subject Terms: accuracy, quantification, RNA, RT‐qPCR, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/1574-7891; https://doaj.org/toc/1878-0261

Access URL: https://doaj.org/article/fc57157ea1114752966f2e759b70680f

Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation

Authors: Celine Everaert, Jasper Verwilt, Kimberly Verniers, Niels Vandamme, Alvaro Marcos Rubio, Jo Vandesompele, Pieter Mestdagh

Source: Biological Procedures Online, Vol 25, Iss 1, Pp 1-19 (2023)

Subject Terms: RNA sequencing, Oxford nanopore technologies, Single-cell RNA sequencing, Depletion, Medicine (General), R5-920, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1480-9222

Access URL: https://doaj.org/article/72d160ee571d4042a249a3fb72af33c7

Exploring the cell-free total RNA transcriptome in diffuse large B-cell lymphoma and primary mediastinal B-cell lymphoma patients as biomarker source in blood plasma liquid biopsies

Authors: Philippe Decruyenaere, Edoardo Giuili, Kimberly Verniers, Jasper Anckaert, Katrien De Grove, Malaïka Van der Linden, Dries Deeren, Jo Van Dorpe, Fritz Offner, Jo Vandesompele

Source: Frontiers in Oncology, Vol 13 (2023)

Subject Terms: cell-free RNA, liquid biopsy, blood plasma, biomarkers, DLBCL, diffuse large B-cell lymphoma, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fonc.2023.1221471/full; https://doaj.org/toc/2234-943X

Access URL: https://doaj.org/article/2c87a35fc9414d3b8bd1a3f9d2605b45

Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA

Authors: Jill Deleu, Kathleen Schoofs, Anneleen Decock, Kimberly Verniers, Sofie Roelandt, Angie Denolf, Joke Verreth, Bram De Wilde, Tom Van Maerken, Katleen De Preter, Jo Vandesompele

Source: Human Genomics, Vol 16, Iss 1, Pp 1-14 (2022)

Subject Terms: Liquid biopsies, Co-purification, Cell-free RNA, Extracellular RNA, Cell-free DNA, Mutation detection, Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1479-7364

Access URL: https://doaj.org/article/ef68bffeabae4ba1a11a505e8f590a7c

Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for SARS-CoV-2 RT-qPCR screening purposes

Authors: Jasper Verwilt, Jan Hellemans, Tom Sante, Pieter Mestdagh, Jo Vandesompele

Source: Scientific Reports, Vol 12, Iss 1, Pp 1-10 (2022)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/c363eea6eff446b8a403c2a30d2cf9d7

Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics

Authors: Bert Dhondt, Cláudio Pinheiro, Edward Geeurickx, Joeri Tulkens, Glenn Vergauwen, Edwin Van Der Pol, Rienk Nieuwland, Anneleen Decock, Ilkka Miinalainen, Pekka Rappu, Gary Schroth, Scott Kuersten, Jo Vandesompele, Pieter Mestdagh, Nicolaas Lumen, Olivier De Wever, An Hendrix

Source: Journal of Extracellular Vesicles, Vol 12, Iss 5, Pp n/a-n/a (2023)

Subject Terms: anticoagulants, biomarkers, cancer, exosomes, extracellular vesicles, plasma, Cytology, QH573-671

File Description: electronic resource

Relation: https://doaj.org/toc/2001-3078

Access URL: https://doaj.org/article/88cf6c37fc744c8b910af6ec08d4058f

Comprehensive RNA dataset of tissue and plasma from patients with esophageal cancer or precursor lesions

Authors: Kathleen Schoofs, Annouck Philippron, Francisco Avila Cobos, Jan Koster, Steve Lefever, Jasper Anckaert, Danny De Looze, Jo Vandesompele, Piet Pattyn, Katleen De Preter

Source: Scientific Data, Vol 9, Iss 1, Pp 1-12 (2022)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2052-4463

Access URL: https://doaj.org/article/d7024e6d48cf4b9f8910695c89064ea4

RNA biomarkers from proximal liquid biopsy for diagnosis of ovarian cancer

Authors: Eva Hulstaert, Keren Levanon, Annelien Morlion, Stefan Van Aelst, Anthony-Alexander Christidis, Ruben Zamar, Jasper Anckaert, Kimberly Verniers, Keren Bahar-Shany, Stav Sapoznik, Jo Vandesompele, Pieter Mestdagh

Source: Neoplasia: An International Journal for Oncology Research, Vol 24, Iss 2, Pp 155-164 (2022)

Subject Terms: Ovarian cancer, Utero-tubal lavage, Biomarker, Cell-free RNA, Liquid biopsy, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S1476558621001123; https://doaj.org/toc/1476-5586

Access URL: https://doaj.org/article/1167a7ed4eff480293361fff2bcb29f0

Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome

Authors: Ruben Van Paemel, Andries De Koker, Christa Caggiano, Annelien Morlion, Pieter Mestdagh, Bram De Wilde, Jo Vandesompele, Katleen De Preter

Source: Epigenetics, Vol 16, Iss 7, Pp 797-807 (2021)

Subject Terms: liquid biopsy, cell-free reduced representation bisulfite sequencing (cfrrbs), pre-analytical factors, methylation, cfdna, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1559-2294; https://doaj.org/toc/1559-2308

Access URL: https://doaj.org/article/80b0d5ff24a042f0839e131709be5448

Circulating RNA biomarkers in diffuse large B-cell lymphoma: a systematic review

Authors: Philippe Decruyenaere, Fritz Offner, Jo Vandesompele

Source: Experimental Hematology & Oncology, Vol 10, Iss 1, Pp 1-22 (2021)

Subject Terms: DLBCL, Diffuse large B-cell lymphoma, Biomarkers, Liquid biopsy, Extracellular RNA, Diseases of the blood and blood-forming organs, RC633-647.5, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/2162-3619

Access URL: https://doaj.org/article/86ad1389c8094391901e727c70f08396

Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study

Authors: Ruben Van Paemel, Andries De Koker, Charlotte Vandeputte, Lieke van Zogchel, Tim Lammens, Geneviève Laureys, Jo Vandesompele, Gudrun Schleiermacher, Mathieu Chicard, Nadine Van Roy, Ales Vicha, G.A.M. Tytgat, Nico Callewaert, Katleen De Preter, Bram De Wilde

Source: Epigenetics, Vol 16, Iss 2, Pp 196-208 (2021)

Subject Terms: dna methylation, cell-free dna, liquid biopsy, pediatric oncology, biomarker, diagnosis, infinium, reduced representation bisulfite sequencing, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1559-2294; https://doaj.org/toc/1559-2308

Access URL: https://doaj.org/article/153594e540924d19b722b22372f1d54c

On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments

Authors: Alemu Takele Assefa, Jo Vandesompele, Olivier Thas

Source: BMC Genomics, Vol 21, Iss 1, Pp 1-14 (2020)

Subject Terms: RNA sample pooling, RNA sequencing, Differential gene expression, Experimental design, Statistical power, Cost, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-020-6721-y; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/dfda64b19d06466b83d33df6e5d61e5d

CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification

Authors: Marieke Vromman, Jasper Anckaert, Jo Vandesompele, Pieter-Jan Volders

Source: Frontiers in Bioinformatics, Vol 2 (2022)

Subject Terms: RT-qPCR – real-time quantitative polymerase chain reaction, circular RNA (circRNA), primer design tool, back-splice junction, circRNA validation, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fbinf.2022.834655/full; https://doaj.org/toc/2673-7647

Access URL: https://doaj.org/article/affa476aa90344ebb5569e9b6da29f05

CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin

Authors: Annelien Morlion, Eva Hulstaert, Marieke Vromman, Jasper Anckaert, Celine Everaert, Jo Vandesompele, Pieter Mestdagh

Source: Frontiers in Bioinformatics, Vol 2 (2022)

Subject Terms: RNA, circular, linear, splicing, bioinformatics, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fbinf.2022.834034/full; https://doaj.org/toc/2673-7647

Access URL: https://doaj.org/article/35276272e3f646908fd1b3e4a0342fa3