Publications

Ramiro Martinez, Chiara Finocchiaro, Louis Delhaye, Fien Gysens, Jasper Anckaert, Wim Trypsteen, Maarten Versteven, Eva Lion, Sandra Van Lint, Karim Vermaelen, Eric James de Bony, Pieter Mestdagh (2024). A co-culture model to study modulators of tumor immune evasion through scalable arrayed CRISPR-interference screens. Frontiers in Immunology.

Tinus Schynkel, Willem van Snippenberg, Kimberly Verniers, Gwendolyn M Jang, Nevan J Krogan, Pieter Mestdagh, Linos Vandekerckhove, Wim Trypsteen (2024). Interactome of the HIV-1 proteome and human host RNA. EMBO Reports.

Louis Delhaye, George D. Moschonas, Daria Fijalkowska, Annick Verhee, Delphine De Sutter, Tessa Van de Steene, Margaux De Meyer, Hanna Grzesik, Laura Van Moortel, Karolien De Bosscher, Thomas Jacobs, Sven Eyckerman (2024). Leveraging a self-cleaving peptide for tailored control in proximity labeling proteomics. Cell Reports Methods.

Céleste Van Der Schueren, Philippe Decruyenaere, Francisco Avila Cobos, Johanna Bult, Jill Deleu, Laudonia Lidia Dipalo, Hetty Hilde Helsmoortel, Eva Hulstaert, Annelien Morlion, Elena Ramos Varas, Kathleen Schoofs, Wim Trypsteen, Eveline Vanden Eynde, Hanne Van Droogenbroeck, Kimberly Verniers, Jo Vandesompele, Anneleen Decock (2024). Subpar reporting of pre‐analytical variables in RNA‐focused blood plasma studies. Molecular Oncology.

Philippe Decruyenaere, Edoardo Giuili, Kimberly Verniers, Jasper Anckaert, Katrien De Grove, Malaïka Van der Linden, Dries Deeren, Jo Van Dorpe, Fritz Offner, Jo Vandesompele (2023). 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. Frontiers in Oncology.

Marieke Vromman, Jasper Anckaert, Stefania Bortoluzzi, Alessia Buratin, Chia-Ying Chen, Qinjie Chu, Trees-Juen Chuang, Roozbeh Dehghannasiri, Christoph Dieterich, Xin Dong, Paul Flicek, Enrico Gaffo, Wanjun Gu, Chunjiang He, Steve Hoffmann, Osagie Izuogu, Michael S. Jackson, Tobias Jakobi, Eric C. Lai, Justine Nuytens, Julia Salzman, Mauro Santibanez-Koref, Peter Stadler, Olivier Thas, Eveline Vanden Eynde, Kimberly Verniers, Guoxia Wen, Jakub Westholm, Li Yang, Chu-Yu Ye, Nurten Yigit, Guo-Hua Yuan, Jinyang Zhang, Fangqing Zhao, Jo Vandesompele, Pieter-Jan Volders (2023). Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision. Nature Methods.

Shanna Dewaele, Louis Delhaye, Boel De Paepe, Bram Bogaert, Ramiro Martinez, Jasper Anckaert, Nurten Yigit, Justine Nuytens, Rudy Van Coster, Sven Eyckerman, Koen Raemdonck, Pieter Mestdagh (2023). mTOR Inhibition Enhances Delivery and Activity of Antisense Oligonucleotides in Uveal Melanoma Cells. Nucleic Acid Therapeutics.

Annelien Morlion, Philippe Decruyenaere, Kathleen Schoofs, Jasper Anckaert, Justine Nuytens, Eveline Vanden Eynde, Kimberly Verniers, Celine Everaert, Fritz Offner, Jo Van Dorpe, Jo Vandesompele, Pieter Mestdagh (2023). Patient-specific alterations in blood plasma cfRNA profiles enable accurate classification of cancer patients and controls. medRxiv.

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 (2023). Benchmarking blood collection tubes and processing intervals for extracellular vesicle performance metrics. Journal of Extracellular Vesicles.

Jasper Verwilt, Pieter Mestdagh, Jo Vandesompele (2023). Artifacts and biases of the reverse transcription reaction in RNA sequencing. RNA.

Celine Everaert, Jasper Verwilt, Kimberly Verniers, Niels Vandamme, Alvaro Marcos Rubio, Jo Vandesompele, Pieter Mestdagh (2023). Blocking Abundant RNA Transcripts by High-Affinity Oligonucleotides during Transcriptome Library Preparation. Biological Procedures Online.

Alan Van Goethem, Jill Deleu, Nurten Yigit, Celine Everaert, Myrthala Moreno-Smith, Sanjeev A Vasudevan, Fjoralba Zeka, Fleur Demuynck, Eveline Barbieri, Frank Speleman, Pieter Mestdagh, Jason Shohet, Jo Vandesompele, Tom Van Maerken (2023). Longitudinal evaluation of serum microRNAs as biomarkers for neuroblastoma burden and therapeutic p53 reactivation. NAR Cancer.

Philippe Decruyenaere, Kimberly Verniers, Franco Poma-Soto, Jo Van Dorped, Fritz Offner, JoVandesompele (2023). RNA Extraction Method Impacts Quality Metrics and Sequencing Results in Formalin-Fixed, Paraffin-Embedded Tissue Samples. Laboratory Investigation.

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 (2022). Digital PCR-based evaluation of nucleic acid extraction kit performance for the co-purification of cell-free DNA and RNA. Human Genomics.

The exRNAQC Consortium, Jasper Anckaert, Francisco Avila Cobos, Anneleen Decock, Philippe Decruyenaere, Jill Deleu, Katleen De Preter, Olivier De Wever, Jilke De Wilde, Bert Dhondt, Thibaut D’huyvetter, Celine Everaert, Carolina Fierro, Hetty Hilde Helsmoortel, An Hendrix, Eva Hulstaert, Jan Koster, Scott Kuersten, Tim R Mercer, Pieter Mestdagh, Annelien Morlion, Nele Nijs, Justine Nuytens, Annouck Philippron, Thomas Piofczyk, Franco Poma-Soto, Kathleen Schoofs, Gary P. Schroth, Olivier Thas, Eveline Vanden Eynde, Jo Vandesompele, Tom Van Maerken, Ruben Van Paemel, Kimberly Verniers, Jasper Verwilt, Nurten Yigit (2022). Performance evaluation of RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control (exRNAQC) study. bioRxiv.

Vanessa Vermeirssen, Jill Deleu, Annelien Morlion, Celine Everaert, Jilke De Wilde, Jasper Anckaert, Kaat Durinck, Justine Nuytens, Muhammad Rishfi, Frank Speleman, Hanne Van Droogenbroeck, Kimberly Verniers, Maria Francesca Baietti, Maarten Albersen, Eleonora Leucci, Edward Post, Myron G Best, Tom Van Maerken, Bram De Wilde, Jo Vandesompele, Anneleen Decock (2022). Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA. NAR Cancer.

Anneleen Decock, David Creytens, Steve Lefever, Joni Van der Meulen, Jasper Anckaert, Ariane De Ganck, Jill Deleu, Bram De Wilde, Carolina Fierro, Scott Kuersten, Manuel Luypaert, Isabelle Rottiers, Gary P. Schroth, Sandra Steyaert, Katrien Vanderheyden, Eveline Vanden Eynde, Kimberly Verniers, Joke Verreth, Jo Van Dorpe, Jo Vandesompele (2022). mRNA capture sequencing and RT-qPCR for the detection of pathognomonic, novel, and secondary fusion transcripts in FFPE tissue: a sarcoma showcase. International Journal of Molecular Sciences.

Eric de Bony, Fien Gysens, Nurten Yigit, Jasper Anckaert, Celine Everaert, Eveline Vanden Eynde, Kimberly Verniers, Willem van Snippenberg, Wim Trypsteen, Pieter Mestdagh (2022). A 3′‐end capture sequencing method for high‐throughput targeted gene expression profiling. Biotechnology Journal.

Jasper Verwilt, Jan Hellemans, Tom Sante, Pieter Mestdagh, Jo Vandesompele (2022). Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for SARS-CoV-2 RT-qPCR screening purposes. Scientific reports.

Fien Gysens, Pieter Mestdagh, Eric de Bony de Lavergne, Tania Maes (2022). Unlocking the secrets of long non-coding RNAs in asthma. Thorax.

Marieke Vromman, Jasper Anckaert, Jo Vandesompele, Pieter-Jan Volders (2022). CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification. Frontiers in Bioinformatics.

Annelien Morlion, Eva Hulstaert, Marieke Vromman, Jasper Anckaert, Celine Everaert, Jo Vandesompele, Pieter Mestdagh (2022). CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin. frontiers in Bioinformatics.

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 (2022). RNA biomarkers from proximal liquid biopsy for diagnosis of ovarian cancer. Neoplasia.

Daniel Evans, Simon Cowen, Martin Kammel, Denise M O’Sullivan, Graham Stewart, Hans-Peter Grunert, Jacob Moran-Gilad, Jasper Verwilt, Jiwon In, Jo Vandesompele, Kathryn Harris, Ki Ho Hong, Nathaniel Storey, Suzie Hingley-Wilson, Ulf Dühring, Young-Kyung Bae, Carole A Foy, Julian Braybrook, Heinz Zeichhardt, Jim F Huggett (2021). The Dangers of Using Cq to Quantify Nucleic Acid in Biological Samples: A Lesson From COVID-19. Clinical Chemistry.

Annelien Morlion, Celine Everaert, Justine Nuytens, Eva Hulstaert, Jo Vandesompele, Pieter Mestdagh (2021). Custom long non-coding RNA capture enhances detection sensitivity in different human sample types. RNA Biology.

Marieke Vromman, Nurten Yigit, Kimberly Verniers, Steve Lefever, Jo Vandesompele, Pieter‐Jan Volders (2021). Validation of Circular RNAs Using RT‐qPCR After Effective Removal of Linear RNAs by Ribonuclease R. Current Protocols.

Eva Hulstaert, Anneleen Decock, Annelien Morlion, Celine Everaert, Kimberly Verniers, Justine Nuytens, Nele Nijs, Gary P. Schroth, Scott Kuersten, Stephen M. Gross, Pieter Mestdagh, Jo Vandesompele (2021). Messenger RNA capture sequencing of extracellular RNA from human biofluids using a comprehensive set of spike-in controls. Star Protocols.

Lucia Lorenzi, Hua-Sheng Chiu, Francisco Avila Cobos, Stephen Gross, Pieter-Jan Volders, Robrecht Cannoodt, Justine Nuytens, Katrien Vanderheyden, Jasper Anckaert, Steve Lefever, Aidan P. Tay, Eric J. de Bony, Wim Trypsteen, Fien Gysens, Marieke Vromman, Tine Goovaerts, Thomas Birkballe Hansen, Scott Kuersten, Nele Nijs, Tom Taghon, Karim Vermaelen, Ken R. Bracke, Yvan Saeys, Tim De Meyer, Nandan P. Deshpande, Govardhan Anande, Ting-Wen Chen, Marc R. Wilkins, Ashwin Unnikrishnan, Katleen De Preter, Jørgen Kjems, Jan Koster, Gary P. Schroth, Jo Vandesompele, Pavel Sumazin, Pieter Mestdagh (2021). The RNA Atlas expands the catalog of human non-coding RNAs. Nature Biotechnology.

Eva Hulstaert, Annelien Morlion, Francisco Avila Cobos, Kimberly Verniers, Justine Nuytens, Eveline Vanden Eynde, Nurten Yigit, Jasper Anckaert, Anja Geerts, Pieter Hindryckx, Peggy Jacques, Guy Brusselle, Ken R. Bracke, Tania Maes, Thomas Malfait, Thierry Derveaux, Virginie Ninclaus, Caroline Van Cauwenbergh, Kristien Roelens, Ellen Roets, Dimitri Hemelsoet, Kelly Tilleman, Lieve Brochez, Scott Kuersten, Lukas M. Simon, Sebastian Karg, Alexandra Kautzky-Willers, Michael Leutner, Christa Nöhammer, Ondrej Slaby, Roméo Willinge Prins, Jan Koster, Steve Lefever, Gary P. Schroth, Jo Vandesompele, Pieter Mestdagh (2020). Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas. Cell Reports.

Eva Hulstaert *, Annelien Morlion *, Keren Levanon, Jo Vandesompele, Pieter Mestdagh, (* joint first authors) (2020). Candidate RNA biomarkers in biofluids for early diagnosis of ovarian cancer: A systematic review. Gynecologic Oncology.

Francisco Avila Cobos, José Alquicira-Hernandez, Joseph E. Powell, Pieter Mestdagh, Katleen De Preter (2020). Benchmarking of cell type deconvolution pipelines for transcriptomics data. Nature Communications.

Jim F Huggett, Vladimir Benes, Stephen A Bustin, Jeremy A Garson, Karthyn Harris, Martin Kammel, Mikael Kubista, Timothy D McHugh, Jacob Moran-Gilad, Tania Nolan, Michael W Pfaffl, Marc Salit, Greg Shipley, Peter M Vallone, Jo Vandesompele, Carl Wittwer, Heinz Zeichhardt (2020). Cautionary Note on Contamination of Reagents Used for Molecular Detection of SARS-CoV-2. Clinical Chemistry.

Jasper Verwilt, Wim Trypsteen, Ruben Van Paemel, Katleen De Preter, Maria D. Giraldez, Pieter Mestdagh, Jo Vandesompele (2020). When DNA gets in the way: A cautionary note for DNA contamination in extracellular RNA-seq studies. PNAS.

Jasper Verwilt, Pieter Mestdagh, Jo Vandesompele (2020). Evaluation of efficiency and sensitivity of 1D and 2D sample pooling strategies for diagnostic screening purposes. medRxiv.

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 (2020). Minimally invasive classification of paediatric solid tumours using reduced representation bisulphite sequencing of cell-free DNA: a proof-of-principle study. Epigenetics.

Jim F Huggett, NA NA, Alexandra S Whale, Ward De Spiegelaere, Wim Trypsteen, Afif Abdel Nour, Young-Kyung Bae, Vladimir Benes, Daniel Burke, Megan Cleveland, Philippe Corbisier, Alison S Devonshire, Lianhua Dong, Daniela Drandi, Carole A Foy, Jeremy A Garson, Hua-Jun He, Jan Hellemans, Mikael Kubista, Antoon Lievens, Mike G Makrigiorgos, Mojca Milavec, Reinhold D Mueller, Tania Nolan, Denise M O’Sullivan, Michael W Pfaffl, Stefan Rödiger, Erica L Romsos, Gregory L Shipley, Valerie Taly, Andreas Untergasser, Carl T Wittwer, Stephen A Bustin, Jo Vandesompele (2020). The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020. Clinical Chemistry.

Srinath Govindarajan, Eveline Verheugen, Koen Venken, Djoere Gaublomme, Margaux Maelegheer, Eva Cloots, Fien Gysens, Bruno G De Geest, Tan‐Yun Cheng, D Branch Moody, Sophie Janssens, Michael Drennan, Dirk Elewaut (2020). ER stress in antigen‐presenting cells promotes NKT cell activation through endogenous neutral lipids. EMBO reports.

Ruben Van Paemel, Andries De Koker, Christa Caggiano, Annelien Morlion, Pieter Mestdagh, Bram De Wilde, Jo Vandesompele, Katleen De Preter (2020). Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome. bioRxiv.

Anne‐Catherine Dolens, Kaat Durinck, Marieke Lavaert, Joni Van der Meulen, Imke Velghe, Jelle De Medts, Karin Weening, Juliette Roels, Katrien De Mulder, Pieter‐Jan Volders, Katleen De Preter, Tessa Kerre, Bart Vandekerckhove, Georges Leclercq, Jo Vandesompele, Pieter Mestdagh, Pieter Van Vlierberghe, Frank Speleman, Tom Taghon (2020). Distinct Notch1 and BCL11B requirements mediate human γδ/αβ T cell development. EMBO reports.

Alemu Takele Assefa, Jo Vandesompele, Olivier Thas (2020). On the utility of RNA sample pooling to optimize cost and statistical power in RNA sequencing experiments. BMC Genomics.

Alemu Takele Assefa, Jo Vandesompele, Olivier Thas (2020). SPsimSeq: semi-parametric simulation of bulk and single-cell RNA-sequencing data. Bioinformatics.

Ruben Van Paemel, Roos Vlug, Katleen De Preter, Nadine Van Roy, Frank Speleman, Leen Willems, Tim Lammens, Geneviève Laureys, Gudrun Schleiermacher, Godelieve A. M. Tytgat, Kathy Astrahantseff, Hedwig Deubzer, Bram De Wilde (2020). The pitfalls and promise of liquid biopsies for diagnosing and treating solid tumors in children: a review. European Journal of Pediatrics.

Juan C. Fraire, Gaëlle Houthaeve, Jing Liu, Laurens Raes, Lotte Vermeulen, Stephan Stremersch, Toon Brans, Gerardo García-Díaz Barriga, Sarah De Keulenaer, Filip Van Nieuwerburgh, Riet De Rycke, Jo Vandesompele, Pieter Mestdagh, Koen Raemdonck, Winnok H. De Vos, Stefaan De Smedt, Kevin Braeckmans (2020). Vapor nanobubble is the more reliable photothermal mechanism for inducing endosomal escape of siRNA without disturbing cell homeostasis. Journal of Controlled Release.

Marieke Vromman, Jo Vandesompele, Pieter-Jan Volders (2020). Closing the circle: current state and perspectives of circular RNA databases. Briefings in Bioinformatics.

Celine Everaert, Hetty Helsmoortel, Anneleen Decock, Eva Hulstaert, Ruben Van Paemel, Kimberly Verniers, Justine Nuytens, Jasper Anckaert, Nele Nijs, Joeri Tulkens, Bert Dhondt, An Hendrix, Pieter Mestdagh, Jo Vandesompele (2019). Performance assessment of total RNA sequencing of human biofluids and extracellular vesicles. Scientific Reports.

Eva Hulstaert, Annelien Morlion, Francisco Avila Cobos, Kimberly Verniers, Justine Nuytens, Eveline Vanden Eynde, Nurten Yigit, Jasper Anckaert, Anja Geerts, Pieter Hindryckx, Peggy Jacques, Guy Brusselle, Ken R. Bracke, Tania Maes, Thomas Malfait, Thierry Derveaux, Virginie Ninclaus, Caroline Van Cauwenbergh, Kristien Roelens, Ellen Roets, Dimitri Hemelsoet, Kelly Tilleman, Lieve Brochez, Scott Kuersten, Lukas Simon, Sebastian Karg, Alexandra Kautzky-Willers, Michael Leutner, Christa Nöhammer, Ondrej Slaby, Roméo Willinge Prins, Jan Koster, Steve Lefever, Gary P. Schroth, Jo Vandesompele, Pieter Mestdagh (2019). Charting extracellular transcriptomes in The Human Biofluid RNA Atlas. bioRxiv.

Pei Y. Liu, Andrew E. Tee, Giorgio Milazzo, Katherine M. Hannan, Jesper Maag, Sujanna Mondal, Bernard Atmadibrata, Nenad Bartonicek, Hui Peng, Nicholas Ho, Chelsea Mayoh, Roberto Ciaccio, Yuting Sun, Michelle J. Henderson, Jixuan Gao, Celine Everaert, Amy J. Hulme, Matthew Wong, Qing Lan, Belamy B. Cheung, Leming Shi, Jenny Y. Wang, Thorsten Simon, Matthias Fischer, Xu D. Zhang, Glenn M. Marshall, Murray D. Norris, Michelle Haber, Jo Vandesompele, Jinyan Li, Pieter Mestdagh, Ross D. Hannan, Marcel E. Dinger, Giovanni Perini, Tao Liu (2019). The long noncoding RNA lncNB1 promotes tumorigenesis by interacting with ribosomal protein RPL35. Nature Communications.

Lucia Lorenzi, Hua-Sheng Chiu, Francisco Avila Cobos, Stephen Gross, Pieter-Jan Volders, Robrecht Cannoodt, Justine Nuytens, Katrien Vanderheyden, Jasper Anckaert, Steve Lefever, Tine Goovaerts, Thomas Birkballe Hansen, Scott Kuersten, Nele Nijs, Tom Taghon, Karim Vermaelen, Ken R. Bracke, Yvan Saeys, Tim De Meyer, Nandan Deshpande, Govardhan Anande, Ting-Wen Chen, Marc R. Wilkins, Ashwin Unnikrishnan, Katleen De Preter, Jørgen Kjems, Jan Koster, Gary P. Schroth, Jo Vandesompele, Pavel Sumazin, Pieter Mestdagh (2019). The RNA Atlas, a single nucleotide resolution map of the human transcriptome. bioRxiv.

Alemu Takele Assefa, Jo Vandesompele, Olivier Thas (2019). Probabilistic index models for testing differential expression in single cell RNA sequencing data. bioRxiv.

Edward Geeurickx, Joeri Tulkens, Bert Dhondt, Jan Van Deun, Lien Lippens, Glenn Vergauwen, Elisa Heyrman, Delphine De Sutter, Kris Gevaert, Francis Impens, Ilkka Miinalainen, Pieter-Jan Van Bockstal, Thomas De Beer, Marca H. M. Wauben, Esther N. M. Nolte-‘t-Hoen, Katarzyna Bloch, Johannes V. Swinnen, Edwin van der Pol, Rienk Nieuwland, Geert Braems, Nico Callewaert, Pieter Mestdagh, Jo Vandesompele, Hannelore Denys, Sven Eyckerman, Olivier De Wever, An Hendrix (2019). The generation and use of recombinant extracellular vesicles as biological reference material. Nature Communications.

Karen Verboom, Wouter Van Loocke, Emmanuelle Clappier, Jean Soulier, Jo Vandesompele, Frank Speleman, Kaat Durinck (2019). A comprehensive dataset of TLX1 positive ALL-SIL lymphoblasts and primary T-cell acute lymphoblastic leukemias. bioRxiv.

Karen Verboom, Celine Everaert, Nathalie Bolduc, Kenneth J Livak, Nurten Yigit, Dries Rombaut, Jasper Anckaert, Simon Lee, Morten T Venø, Jørgen Kjems, Frank Speleman, Pieter Mestdagh, Jo Vandesompele (2019). SMARTer single cell total RNA sequencing. Nucleic Acids Research.

Dries Rombaut, Hua-Sheng Chiu, Bieke Decaesteker, Celine Everaert, Nurten Yigit, Agathe Peltier, Isabelle Janoueix-Lerosey, Christoph Bartenhagen, Matthias Fischer, Stephen Roberts, Nicky D’Haene, Katleen De Preter, Frank Speleman, Geertrui Denecker, Pavel Sumazin, Jo Vandesompele, Steve Lefever, Pieter Mestdagh (2019). Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes. Scientific Reports.

Siebe Loontiens, Lisa Depestel, Suzanne Vanhauwaert, Givani Dewyn, Charlotte Gistelinck, Karen Verboom, Wouter Van Loocke, Filip Matthijssens, Andy Willaert, Jo Vandesompele, Frank Speleman, Kaat Durinck (2019). Purification of high-quality RNA from a small number of fluorescence activated cell sorted zebrafish cells for RNA sequencing purposes. BMC Genomics.

Jana Janssens, René A.J. Crans, Kathleen Van Craenenbroeck, Jo Vandesompele, Christophe P. Stove, Debby Van Dam, Peter P. De Deyn (2019). Evaluating the applicability of mouse SINEs as an alternative normalization approach for RT-qPCR in brain tissue of the APP23 model for Alzheimer’s disease. Journal of Neuroscience Methods.

Steve Lefever, Ali Rihani, Joni Van der Meulen, Filip Pattyn, Tom Van Maerken, Jo Van Dorpe, Jan Hellemans, Jo Vandesompele (2019). Cost-effective and robust genotyping using double-mismatch allele-specific quantitative PCR. Scientific Reports.

Bert Dhondt, Elise De Bleser, Tom Claeys, Sarah Buelens, Nicolaas Lumen, Jo Vandesompele, Anneleen Beckers, Valerie Fonteyne, Kim Van der Eecken, Aurélie De Bruycker, Jérôme Paul, Pierre Gramme, Piet Ost (2018). Discovery and validation of a serum microRNA signature to characterize oligo- and polymetastatic prostate cancer: not ready for prime time. World Journal of Urology.

Sandra Ackermann, Maria Cartolano, Barbara Hero, Anne Welte, Yvonne Kahlert, Andrea Roderwieser, Christoph Bartenhagen, Esther Walter, Judith Gecht, Laura Kerschke, Ruth Volland, Roopika Menon, Johannes M. Heuckmann, Moritz Gartlgruber, Sabine Hartlieb, Kai-Oliver Henrich, Konstantin Okonechnikov, Janine Altmüller, Peter Nürnberg, Steve Lefever, Bram de Wilde, Frederik Sand, Fakhera Ikram, Carolina Rosswog, Janina Fischer, Jessica Theissen, Falk Hertwig, Aatur D. Singhi, Thorsten Simon, Wenzel Vogel, Sven Perner, Barbara Krug, Matthias Schmidt, Sven Rahmann, Viktor Achter, Ulrich Lang, Christian Vokuhl, Monika Ortmann, Reinhard Büttner, Angelika Eggert, Frank Speleman, Roderick J. O’Sullivan, Roman K. Thomas, Frank Berthold, Jo Vandesompele, Alexander Schramm, Frank Westermann, Johannes H. Schulte, Martin Peifer, Matthias Fischer (2018). A mechanistic classification of clinical phenotypes in neuroblastoma. Science.

Joeri Tulkens, Glenn Vergauwen, Jan Van Deun, Edward Geeurickx, Bert Dhondt, Lien Lippens, Marie-Angélique De Scheerder, Ilkka Miinalainen, Pekka Rappu, Bruno G De Geest, Katrien Vandecasteele, Debby Laukens, Linos Vandekerckhove, Hannelore Denys, Jo Vandesompele, Olivier De Wever, An Hendrix (2018). Increased levels of systemic LPS-positive bacterial extracellular vesicles in patients with intestinal barrier dysfunction. Gut.

Fjoralba Zeka, Anneleen Decock, Alan Van Goethem, Katrien Vanderheyden, Fleur Demuynck, Tim Lammens, Hetty H. Helsmoortel, Joëlle Vermeulen, Rosa Noguera, Ana P. Berbegall, Valérie Combaret, Gudrun Schleiermacher, Geneviève Laureys, Alexander Schramm, Johannes H. Schulte, Sven Rahmann, Julie Bienertová-Vašků, Pavel Mazánek, Marta Jeison, Shifra Ash, Michael D. Hogarty, Mirthala Moreno-Smith, Eveline Barbieri, Jason Shohet, Frank Berthold, Tom Van Maerken, Frank Speleman, Matthias Fischer, Katleen De Preter, Pieter Mestdagh, Jo Vandesompele (2018). Circulating microRNA biomarkers for metastatic disease in neuroblastoma patients. JCI Insight.

Suzanne Vanhauwaert, Bieke Decaesteker, Sara De Brouwer, Carina Leonelli, Kaat Durinck, Pieter Mestdagh, Jo Vandesompele, Karen Sermon, Geertrui Denecker, Christophe Van Neste, Frank Speleman, Katleen De Preter (2018). In silico discovery of a FOXM1 driven embryonal signaling pathway in therapy resistant neuroblastoma tumors. Scientific Reports.

Lucía Lorenzi, Francisco Avila Cobos, Anneleen Decock, Celine Everaert, Hetty Helsmoortel, Steve Lefever, Karen Verboom, Pieter-Jan Volders, Frank Speleman, Jo Vandesompele, Pieter Mestdagh (2018). Long noncoding RNA expression profiling in cancer: Challenges and opportunities. Genes, Chromosomes and Cancer.

Pieter-Jan Volders, Jasper Anckaert, Kenneth Verheggen, Justine Nuytens, Lennart Martens, Pieter Mestdagh, Jo Vandesompele (2018). LNCipedia 5: towards a reference set of human long non-coding RNAs. Nucleic Acids Research.

PDF Project DOI

Pieter-Jan Volders, Steve Lefever, Shalina Baute, Justine Nuytens, Katrien Vanderheyden, Björn Menten, Pieter Mestdagh, Jo Vandesompele (2018). Targeted Genomic Screen Reveals Focal Long Non-Coding RNA Copy Number Alterations in Cancer Cell Lines. Non-Coding RNA.

Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele (2018). Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data. Genome Biology.

Matthijs Vynck, Jo Vandesompele, Olivier Thas (2018). On determining the power of digital PCR experiments. Analytical and Bioanalytical Chemistry.

Karen Verboom, Wouter Van Loocke, Pieter-Jan Volders, Bieke Decaesteker, Francisco Avila Cobos, Simon Bornschein, Charles E. de Bock, Zeynep Kalender Atak, Emmanuelle Clappier, Stein Aerts, Jan Cools, Jean Soulier, Tom Taghon, Pieter Van Vlierberghe, Jo Vandesompele, Frank Speleman, Kaat Durinck (2018). A comprehensive inventory of TLX1 controlled long non-coding RNAs in T-cell acute lymphoblastic leukemia through polyA+ and total RNA sequencing. Haematologica.

Hetty Helsmoortel, Celine Everaert, Nicolaas Lumen, Piet Ost, Jo Vandesompele (2018). Detecting long non-coding RNA biomarkers in prostate cancer liquid biopsies: Hype or hope?. Non-coding RNA Research.

Maria Polycarpou-Schwarz, Matthias Groß, Pieter Mestdagh, Johanna Schott, Stefanie E. Grund, Catherina Hildenbrand, Joachim Rom, Sebastian Aulmann, Hans-Peter Sinn, Jo Vandesompele, Sven Diederichs (2018). The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation. Oncogene.

Marjolijn Renard, Suzanne Vanhauwaert, Marine Vanhomwegen, Ali Rihani, Niels Vandamme, Steven Goossens, Geert Berx, Pieter Van Vlierberghe, Jody J. Haigh, Bieke Decaesteker, Jolien Van Laere, Irina Lambertz, Frank Speleman, Jo Vandesompele, Andy Willaert (2018). Expressed repetitive elements are broadly applicable reference targets for normalization of reverse transcription-qPCR data in mice. Scientific Reports.

Sabitri Ghimire, Margot Van der Jeught, Jitesh Neupane, Matthias S. Roost, Jasper Anckaert, Mina Popovic, Filip Van Nieuwerburgh, Pieter Mestdagh, Jo Vandesompele, Dieter Deforce, Björn Menten, Susana Chuva de Sousa Lopes, Petra De Sutter, Björn Heindryckx (2018). Comparative analysis of naive, primed and ground state pluripotency in mouse embryonic stem cells originating from the same genetic background. Scientific Reports.

Gert Van Peer, Evelien Mets, Shana Claeys, Ines De Punt, Steve Lefever, Maté Ongenaert, Pieter Rondou, Frank Speleman, Pieter Mestdagh, Jo Vandesompele (2018). A high-throughput 3’ UTR reporter screening identifies microRNA interactomes of cancer genes. PLOS ONE.

Presha Rajbhandari, Gonzalo Lopez, Claudia Capdevila, Beatrice Salvatori, Jiyang Yu, Ruth Rodriguez-Barrueco, Daniel Martinez, Mark Yarmarkovich, Nina Weichert-Leahey, Brian J. Abraham, Mariano J. Alvarez, Archana Iyer, Jo Lynne Harenza, Derek Oldridge, Katleen De Preter, Jan Koster, Shahab Asgharzadeh, Robert C. Seeger, Jun S. Wei, Javed Khan, Jo Vandesompele, Pieter Mestdagh, Rogier Versteeg, A. Thomas Look, Richard A. Young, Antonio Iavarone, Anna Lasorella, Jose M. Silva, John M. Maris, Andrea Califano (2018). Cross-Cohort Analysis Identifies a TEAD4–MYCN Positive Feedback Loop as the Core Regulatory Element of High-Risk Neuroblastoma. Cancer Discovery.

Sandrine Herbelet, Elly De Vlieghere, Amanda Gonçalves, Boel De Paepe, Karsten Schmidt, Eline Nys, Laurens Weynants, Joachim Weis, Gert Van Peer, Jo Vandesompele, Jens Schmidt, Olivier De Wever, Jan L. De Bleecker (2018). Localization and Expression of Nuclear Factor of Activated T-Cells 5 in Myoblasts Exposed to Pro-inflammatory Cytokines or Hyperosmolar Stress and in Biopsies from Myositis Patients. Frontiers in Physiology.

Francisco Avila Cobos, Jo Vandesompele, Pieter Mestdagh, Katleen De Preter (2018). Computational deconvolution of transcriptomics data from mixed cell populations. Bioinformatics.

Sarah Buelens, Tom Claeys, Bert Dhondt, Filip Poelaert, Matthijs Vynck, Nurten Yigit, Olivier Thas, Piet Ost, Jo Vandesompele, Nicolaas Lumen, Candy Kumps (2017). Prognostic and Therapeutic Implications of Circulating Androgen Receptor Gene Copy Number in Prostate Cancer Patients Using Droplet Digital Polymerase Chain Reaction. Clinical Genitourinary Cancer.

Bram De Wilde, Anneleen Beckers, Sven Lindner, Althoff Kristina, Katleen De Preter, Pauline Depuydt, Pieter Mestdagh, Tom Sante, Steve Lefever, Falk Hertwig, Zhiyu Peng, Le-Ming Shi, Sangkyun Lee, Elien Vandermarliere, Lennart Martens, Björn Menten, Alexander Schramm, Matthias Fischer, Johannes Schulte, Jo Vandesompele, Frank Speleman (2017). The mutational landscape of MYCN, Lin28b and ALKF1174L driven murine neuroblastoma mimics human disease. Oncotarget.

Bram De Wilde, Anneleen Beckers, Sven Lindner, Althoff Kristina, Katleen De Preter, Pauline Depuydt, Pieter Mestdagh, Tom Sante, Steve Lefever, Falk Hertwig, Zhiyu Peng, Le-ming Shi, Sangkyun Lee, Elien Vandermarliere, Lennart Martens, Björn Menten, Alexander Schramm, Matthias Fischer, Johannes Schulte, Jo Vandesompele, Frank Speleman (2017). The mutational landscape of <i>MYCN, Lin28b</i> and <i>ALK<sup>F1174L</sup></i> driven murine neuroblastoma mimics human disease. Oncotarget.

Mattias Van Heetvelde, Wouter Van Loocke, Wim Trypsteen, Annelot Baert, Katrien Vanderheyden, Brecht Crombez, Jo Vandesompele, Kim De Leeneer, Kathleen B.M. Claes (2017). Evaluation of relative quantification of alternatively spliced transcripts using droplet digital PCR. Biomolecular Detection and Quantification.

Alan Van Goethem, Pieter Mestdagh, Tom Van Maerken, Jo Vandesompele (2017). MicroRNA Expression Analysis Using Small RNA Sequencing Discovery and RT-qPCR-Based Validation. Methods in Molecular Biology,Functional Genomics.

Steve Lefever, Filip Pattyn, Bram De Wilde, Frauke Coppieters, Sarah De Keulenaer, Jan Hellemans, Jo Vandesompele (2017). High-throughput PCR assay design for targeted resequencing using primerXL. BMC Bioinformatics.

Dhruvitkumar Sutaria, Jinmai Jiang, Ana Azevedo-Pouly, Eun Lee, Megan Lerner, Daniel Brackett, Jo Vandesompele, Pieter Mestdagh, Thomas Schmittgen (2017). Expression Profiling Identifies the Noncoding Processed Transcript of HNRNPU with Proliferative Properties in Pancreatic Ductal Adenocarcinoma. Non-Coding RNA.

Peter Pipelers, Lieven Clement, Matthijs Vynck, Jan Hellemans, Jo Vandesompele, Olivier Thas (2017). A unified censored normal regression model for qPCR differential gene expression analysis. PLOS ONE.

Matthijs Vynck, Jo Vandesompele, Olivier Thas (2017). Quality control of digital PCR assays and platforms. Analytical and Bioanalytical Chemistry.

Alan Van Goethem, Nurten Yigit, Myrthala Moreno-Smith, Sanjeev A. Vasudevan, Eveline Barbieri, Frank Speleman, Jason Shohet, Jo Vandesompele, Tom Van Maerken (2017). Dual targeting of MDM2 and BCL2 as a therapeutic strategy in neuroblastoma. Oncotarget.

Hanny Willems, An Jacobs, Wahyu Wijaya Hadiwikarta, Tom Venken, Dirk Valkenborg, Nadine Van Roy, Jo Vandesompele, Jef Hooyberghs (2017). Thermodynamic framework to assess low abundance DNA mutation detection by hybridization. PLOS ONE.

Kenneth Verheggen, Pieter-Jan Volders, Pieter Mestdagh, Gerben Menschaert, Petra Van Damme, Kris Gevaert, Lennart Martens, Jo Vandesompele (2017). Noncoding after All: Biases in Proteomics Data Do Not Explain Observed Absence of lncRNA Translation Products. Journal of Proteome Research.

Steve Lefever, Jasper Anckaert, Pieter-Jan Volders, Manuel Luypaert, Jo Vandesompele, Pieter Mestdagh (2017). decodeRNA— predicting non-coding RNA functions using guilt-by-association. Database.

Lapeire Lore, Hendrix An, Lecoutere Evelyne, Van Bockstal Mieke, Vandesompele Jo, Maynard Dawn, Braems Geert, Van Den Broecke Rudy, Müller Cathérine, Bracke Marc, Cocquyt Véronique, Denys Hannelore, De Wever Olivier (2017). Secretome analysis of breast cancer-associated adipose tissue to identify paracrine regulators of breast cancer growth. Oncotarget.

Francisco Avila Cobos, Jasper Anckaert, Pieter-Jan Volders, Celine Everaert, Dries Rombaut, Jo Vandesompele, Katleen De Preter, Pieter Mestdagh (2017). Zipper plot: visualizing transcriptional activity of genomic regions. BMC Bioinformatics.

Cristina Zanchi, Daniela Macconi, Piera Trionfini, Susanna Tomasoni, Daniela Rottoli, Monica Locatelli, Michael Rudnicki, Jo Vandesompele, Pieter Mestdagh, Giuseppe Remuzzi, Ariela Benigni, Carlamaria Zoja (2017). MicroRNA-184 is a downstream effector of albuminuria driving renal fibrosis in rats with diabetic nephropathy. Diabetologia.

Eva Hulstaert, Lieve Brochez, Pieter-Jan Volders, Jo Vandesompele, Pieter Mestdagh (2017). Long non-coding RNAs in cutaneous melanoma: clinical perspectives. Oncotarget.

Bart K. M. Jacobs, Els Goetghebeur, Jo Vandesompele, Ariane De Ganck, Nele Nijs, Anneleen Beckers, Nina Papazova, Nancy H. Roosens, Lieven Clement (2017). Model-Based Classification for Digital PCR: Your Umbrella for Rain. Analytical Chemistry.

Griet Conickx, Pieter Mestdagh, Jo Vandesompele, Guy G. Brusselle, Ken R. Bracke (2017). Reply: Direct Detection of Circulating MicroRNAs Unveiled the Absence of MicroRNA-218-5p in Smoker Subjects. American Journal of Respiratory and Critical Care Medicine.

Duncan Ayers, Jo Vandesompele (2017). Influence of microRNAs and Long Non-Coding RNAs in Cancer Chemoresistance. Genes.

Jan Van Deun, NA NA, Pieter Mestdagh, Patrizia Agostinis, Özden Akay, Sushma Anand, Jasper Anckaert, Zoraida Andreu Martinez, Tine Baetens, Els Beghein, Laurence Bertier, Geert Berx, Janneke Boere, Stephanie Boukouris, Michel Bremer, Dominik Buschmann, James B Byrd, Clara Casert, Lesley Cheng, Anna Cmoch, Delphine Daveloose, Eva De Smedt, Seyma Demirsoy, Victoria Depoorter, Bert Dhondt, Tom A P Driedonks, Aleksandra Dudek, Abdou Elsharawy, Ilaria Floris, Andrew D Foers, Kathrin Gärtner, Abhishek D Garg, Edward Geeurickx, Jan Gettemans, Farzaneh Ghazavi, Bernd Giebel, Tom Groot Kormelink, Grace Hancock, Hetty Helsmoortel, Andrew F Hill, Vincent Hyenne, Hina Kalra, David Kim, Joanna Kowal, Sandra Kraemer, Petra Leidinger, Carina Leonelli, Yaxuan Liang, Lien Lippens, Shu Liu, Alessandra Lo Cicero, Shaun Martin, Suresh Mathivanan, Prabhu Mathiyalagan, Támas Matusek, Gloria Milani, Marta Monguió-Tortajada, Liselot M Mus, Dillon C Muth, Andrea Németh, Esther N M Nolte-'t Hoen, Lorraine O'Driscoll, Roberta Palmulli, Michael W Pfaffl, Bjarke Primdal-Bengtson, Erminia Romano, Quentin Rousseau, Susmita Sahoo, Natalia Sampaio, Monisha Samuel, Benjamin Scicluna, Bieke Soen, Anneleen Steels, Johannes V Swinnen, Maarit Takatalo, Safia Thaminy, Clotilde Théry, Joeri Tulkens, Isabel Van Audenhove, Susanne van der Grein, Alan Van Goethem, Martijn J van Herwijnen, Guillaume Van Niel, Nadine Van Roy, Alexander R Van Vliet, Niels Vandamme, Suzanne Vanhauwaert, Glenn Vergauwen, Frederik Verweij, Annelynn Wallaert, Marca Wauben, Kenneth W Witwer, Marijke I Zonneveld, Olivier De Wever, Jo Vandesompele, An Hendrix (2017). EV-TRACK: transparent reporting and centralizing knowledge in extracellular vesicle research. Nature Methods.

Wim Trypsteen, Pejman Mohammadi, Clarissa Van Hecke, Pieter Mestdagh, Steve Lefever, Yvan Saeys, Pieter De Bleser, Jo Vandesompele, Angela Ciuffi, Linos Vandekerckhove, Ward De Spiegelaere (2017). Erratum: Corrigendum: Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay. Scientific Reports.

Gert Van Peer, Ayla De Paepe, Michiel Stock, Jasper Anckaert, Pieter-Jan Volders, Jo Vandesompele, Bernard De Baets, Willem Waegeman (2016). miSTAR: miRNA target prediction through modeling quantitative and qualitative miRNA binding site information in a stacked model structure. Nucleic Acids Research.

Alan Van Goethem, Nurten Yigit, Celine Everaert, Myrthala Moreno-Smith, Liselot M. Mus, Eveline Barbieri, Frank Speleman, Pieter Mestdagh, Jason Shohet, Tom Van Maerken, Jo Vandesompele (2016). Depletion of tRNA-halves enables effective small RNA sequencing of low-input murine serum samples. Scientific Reports.

Lotte Pyfferoen, Elisabeth Brabants, Celine Everaert, Nancy De Cabooter, Kelly Heyns, Kim Deswarte, Manon Vanheerswynghels, Sofie De Prijck, Glenn Waegemans, Melissa Dullaers, Hamida Hammad, Olivier De Wever, Pieter Mestdagh, Jo Vandesompele, Bart N. Lambrecht, Karim Y. Vermaelen (2016). The transcriptome of lung tumor-infiltrating dendritic cells reveals a tumor-supporting phenotype and a microRNA signature with negative impact on clinical outcome. OncoImmunology.

Wim Trypsteen, Pejman Mohammadi, Clarissa Van Hecke, Pieter Mestdagh, Steve Lefever, Yvan Saeys, Pieter De Bleser, Jo Vandesompele, Angela Ciuffi, Linos Vandekerckhove, Ward De Spiegelaere (2016). Differential expression of lncRNAs during the HIV replication cycle: an underestimated layer in the HIV-host interplay. Scientific Reports.

Anneleen Decock, Maté Ongenaert, Bram De Wilde, Bénédicte Brichard, Rosa Noguera, Frank Speleman, Jo Vandesompele (2016). Stage 4S neuroblastoma tumors show a characteristic DNA methylation portrait. Epigenetics.

Johannes Fabian, Desirée Opitz, Kristina Althoff, Marco Lodrini, Barbara Hero, Ruth Volland, Anneleen Beckers, Katleen de Preter, Anneleen Decock, Nitin Patil, Mohammed Abba, Annette Kopp-Schneider, Kathy Astrahantseff, Jasmin Wünschel, Sebastian Pfeil, Maria Ercu, Annette Künkele, Jamie Hu, Theresa Thole, Leonille Schweizer, Gunhild Mechtersheimer, Daniel Carter, Belamy B. Cheung, Odilia Popanda, Andreas von Deimling, Jan Koster, Rogier Versteeg, Manfred Schwab, Glenn M. Marshall, Frank Speleman, Ulrike Erb, Margot Zoeller, Heike Allgayer, Thorsten Simon, Matthias Fischer, Andreas E. Kulozik, Angelika Eggert, Olaf Witt, Johannes H. Schulte, Hedwig E. Deubzer (2016). MYCN and HDAC5 transcriptionally repress CD9 to trigger invasion and metastasis in neuroblastoma. Oncotarget.

Griet Conickx, Pieter Mestdagh, Francisco Avila Cobos, Fien M. Verhamme, Tania Maes, Bart M. Vanaudenaerde, Leen J. M. Seys, Lies Lahousse, Richard Y. Kim, Alan C. Hsu, Peter A. Wark, Philip M. Hansbro, Guy F. Joos, Jo Vandesompele, Ken R. Bracke, Guy G. Brusselle (2016). MicroRNA Profiling Reveals a Role for MicroRNA-218-5p in the Pathogenesis of Chronic Obstructive Pulmonary Disease. American Journal of Respiratory and Critical Care Medicine.

Pieter Mestdagh, Steve Lefever, Pieter-Jan Volders, Stefaan Derveaux, Jan Hellemans, Jo Vandesompele (2016). Long non-coding RNA expression profiling in the NCI60 cancer cell line panel using high-throughput RT-qPCR. Scientific Data.

Matthijs Vynck, Jo Vandesompele, Nele Nijs, Björn Menten, Ariane De Ganck, Olivier Thas (2016). Flexible analysis of digital PCR experiments using generalized linear mixed models. Biomolecular Detection and Quantification.

Tania Maes, Francisco Avila Cobos, Florence Schleich, Valentina Sorbello, Monique Henket, Katleen De Preter, Ken R. Bracke, Griet Conickx, Claire Mesnil, Jo Vandesompele, Lies Lahousse, Fabrice Bureau, Pieter Mestdagh, Guy F. Joos, Fabio L.M. Ricciardolo, Guy G. Brusselle, Renaud Louis (2016). Asthma inflammatory phenotypes show differential microRNA expression in sputum. Journal of Allergy and Clinical Immunology.

A Wallaert, K Durinck, W Van Loocke, I Van de Walle, F Matthijssens, P J Volders, F Avila Cobos, D Rombaut, P Rondou, P Mestdagh, J Vandesompele, B Poppe, T Taghon, J Soulier, P Van Vlierberghe, F Speleman (2016). Long noncoding RNA signatures define oncogenic subtypes in T-cell acute lymphoblastic leukemia. Leukemia.

Eleonora Leucci, Roberto Vendramin, Marco Spinazzi, Patrick Laurette, Mark Fiers, Jasper Wouters, Enrico Radaelli, Sven Eyckerman, Carina Leonelli, Katrien Vanderheyden, Aljosja Rogiers, Els Hermans, Pieter Baatsen, Stein Aerts, Frederic Amant, Stefan Van Aelst, Joost van den Oord, Bart de Strooper, Irwin Davidson, Denis L. J. Lafontaine, Kris Gevaert, Jo Vandesompele, Pieter Mestdagh, Jean-Christophe Marine (2016). Melanoma addiction to the long non-coding RNA SAMMSON. Nature.

S. Vanhauwaert, S. Lefever, P. Coucke, F. Speleman, A. De Paepe, J. Vandesompele, A. Willaert (2016). RT-qPCR gene expression analysis in zebrafish. Methods in Cell Biology,The Zebrafish - Genetics, Genomics, and Transcriptomics.

Fjoralba Zeka, Katrien Vanderheyden, Els De Smet, Claude A. Cuvelier, Pieter Mestdagh, Jo Vandesompele (2016). Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples. Scientific Reports.

Anneleen Decock, Maté Ongenaert, Wim Van Criekinge, Frank Speleman, Jo Vandesompele (2016). DNA methylation profiling of primary neuroblastoma tumors using methyl-CpG-binding domain sequencing. Scientific Data.

Michael Rudnicki, Paul Perco, Barbara D′haene, Johannes Leierer, Andreas Heinzel, Irmgard Mühlberger, Ninella Schweibert, Judith Sunzenauer, Heinz Regele, Andreas Kronbichler, Pieter Mestdagh, Jo Vandesompele, Bernd Mayer, Gert Mayer (2015). Renal microRNA- and RNA-profiles in progressive chronic kidney disease. European Journal of Clinical Investigation.

Anneleen Decock, Maté Ongenaert, Robrecht Cannoodt, Kimberly Verniers, Bram De Wilde, Geneviève Laureys, Nadine Van Roy, Ana P. Berbegall, Julie Bienertova-Vasku, Nick Bown, Nathalie Clément, Valérie Combaret, Michelle Haber, Claire Hoyoux, Jayne Murray, Rosa Noguera, Gaelle Pierron, Gudrun Schleiermacher, Johannes H. Schulte, Ray L. Stallings, Deborah A. Tweddle, for the Children’s Cancer and Leukaemi Group, Katleen De Preter, Frank Speleman, Jo Vandesompele (2015). Methyl-CpG-binding domain sequencing reveals a prognostic methylation signature in neuroblastoma. Oncotarget.

Frauke Coppieters, Kimberly Verniers, Kim De Leeneer, Jo Vandesompele, Steve Lefever (2015). Targeted resequencing and variant validation using pxlence PCR assays. Biomolecular Detection and Quantification.

Ali Rihani, Jo Vandesompele, Frank Speleman, Tom Van Maerken (2015). Inhibition of CDK4/6 as a novel therapeutic option for neuroblastoma. Cancer Cell International.

Michael Rudnicki, Anneleen Beckers, Hannes Neuwirt, Jo Vandesompele (2015). RNA expression signatures and posttranscriptional regulation in diabetic nephropathy. Nephrology Dialysis Transplantation.

Anneleen Beckers, Gert Van Peer, Daniel R. Carter, Moritz Gartlgruber, Carl Herrmann, Saurabh Agarwal, Hetty H. Helsmoortel, Kristina Althoff, Jan J. Molenaar, Belamy B. Cheung, Johannes H. Schulte, Yves Benoit, Jason M. Shohet, Frank Westermann, Glenn M. Marshall, Jo Vandesompele, Katleen De Preter, Frank Speleman (2015). MYCN-driven regulatory mechanisms controlling LIN28B in neuroblastoma. Cancer Letters.

Galbha Duggal, Sharat Warrier, Sabitri Ghimire, Dorien Broekaert, Margot Van der Jeught, Sylvie Lierman, Tom Deroo, Luc Peelman, Ann Van Soom, Ria Cornelissen, Björn Menten, Pieter Mestdagh, Jo Vandesompele, Matthias Roost, Roderick C. Slieker, Bastiaan T. Heijmans, Dieter Deforce, Petra De Sutter, Susana Chuva De Sousa Lopes, Björn Heindryckx (2015). Alternative Routes to Induce Naïve Pluripotency in Human Embryonic Stem Cells. STEM CELLS.

Wenqian Zhang, Ying Yu, Falk Hertwig, Jean Thierry-Mieg, Wenwei Zhang, Danielle Thierry-Mieg, Jian Wang, Cesare Furlanello, Viswanath Devanarayan, Jie Cheng, Youping Deng, Barbara Hero, Huixiao Hong, Meiwen Jia, Li Li, Simon M Lin, Yuri Nikolsky, André Oberthuer, Tao Qing, Zhenqiang Su, Ruth Volland, Charles Wang, May D. Wang, Junmei Ai, Davide Albanese, Shahab Asgharzadeh, Smadar Avigad, Wenjun Bao, Marina Bessarabova, Murray H. Brilliant, Benedikt Brors, Marco Chierici, Tzu-Ming Chu, Jibin Zhang, Richard G. Grundy, Min Max He, Scott Hebbring, Howard L. Kaufman, Samir Lababidi, Lee J. Lancashire, Yan Li, Xin X. Lu, Heng Luo, Xiwen Ma, Baitang Ning, Rosa Noguera, Martin Peifer, John H. Phan, Frederik Roels, Carolina Rosswog, Susan Shao, Jie Shen, Jessica Theissen, Gian Paolo Tonini, Jo Vandesompele, Po-Yen Wu, Wenzhong Xiao, Joshua Xu, Weihong Xu, Jiekun Xuan, Yong Yang, Zhan Ye, Zirui Dong, Ke K. Zhang, Ye Yin, Chen Zhao, Yuanting Zheng, Russell D. Wolfinger, Tieliu Shi, Linda H. Malkas, Frank Berthold, Jun Wang, Weida Tong, Leming Shi, Zhiyu Peng, Matthias Fischer (2015). Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. Genome Biology.

Jan M. Ruijter, NA NA, Steve Lefever, Jasper Anckaert, Jan Hellemans, Michael W. Pfaffl, Vladimir Benes, Stephen A. Bustin, Jo Vandesompele, Andreas Untergasser (2015). RDML-Ninja and RDMLdb for standardized exchange of qPCR data. BMC Bioinformatics.

Elise G De Smet, Pieter Mestdagh, Jo Vandesompele, Guy G Brusselle, Ken R Bracke (2015). Non-coding RNAs in the pathogenesis of COPD. Thorax.

Duncan Ayers, Pieter Mestdagh, Tom Van Maerken, Jo Vandesompele (2015). Identification of miRNAs contributing to neuroblastoma chemoresistance. Computational and Structural Biotechnology Journal.

Fjoralba Zeka, Pieter Mestdagh, Jo Vandesompele (2015). RT-qPCR-Based Quantification of Small Non-Coding RNAs. Methods in Molecular Biology,Small Non-Coding RNAs.

Ali Rihani, Alan Van Goethem, Maté Ongenaert, Sara De Brouwer, Pieter-Jan Volders, Saurabh Agarwal, Katleen De Preter, Pieter Mestdagh, Jason Shohet, Frank Speleman, Jo Vandesompele, Tom Van Maerken (2015). Genome wide expression profiling of p53 regulated miRNAs in neuroblastoma. Scientific Reports.

Kristoffer von Stedingk, Katleen De Preter, Jo Vandesompele, Rosa Noguera, Ingrid Øra, Jan Koster, Rogier Versteeg, Sven Påhlman, David Lindgren, Håkan Axelson (2015). Individual patient risk stratification of high-risk neuroblastomas using a two-gene score suited for clinical use. International Journal of Cancer.

Kim De Leeneer, Jan Hellemans, Wouter Steyaert, Steve Lefever, Inge Vereecke, Eveline Debals, Brecht Crombez, Machteld Baetens, Mattias Van Heetvelde, Frauke Coppieters, Jo Vandesompele, Annelies De Jaegher, Elfride De Baere, Paul Coucke, Kathleen Claes (2014). Flexible, Scalable, and Efficient Targeted Resequencing on a Benchtop Sequencer for Variant Detection in Clinical Practice. Human Mutation.

Ali Rihani, Bram De Wilde, Fjoralba Zeka, Geneviève Laureys, Nadine Francotte, Gian Paolo Tonini, Simona Coco, Rogier Versteeg, Rosa Noguera, Johannes H. Schulte, Angelika Eggert, Raymond L. Stallings, Frank Speleman, Jo Vandesompele, Tom Van Maerken (2014). CASP8 SNP D302H (rs1045485) Is Associated with Worse Survival in MYCN-Amplified Neuroblastoma Patients. PLoS ONE.

Ajay Palagani, Ken Op de Beeck, Stefan Naulaerts, Jolien Diddens, Chandra Sekhar Chirumamilla, Guy Van Camp, Kris Laukens, Karen Heyninck, Sarah Gerlo, Pieter Mestdagh, Joke Vandesompele, Wim Vanden Berghe (2014). Ectopic MicroRNA-150-5p Transcription Sensitizes Glucocorticoid Therapy Response in MM1S Multiple Myeloma Cells but Fails to Overcome Hormone Therapy Resistance in MM1R Cells. PLoS ONE.

P. Mestdagh, J. Vandesompele, G. Brusselle, K. Vermaelen (2014). Non-coding RNAs and respiratory disease. Thorax.

Pieter-Jan Volders, Kenneth Verheggen, Gerben Menschaert, Klaas Vandepoele, Lennart Martens, Jo Vandesompele, Pieter Mestdagh (2014). An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Research.

Theresa Thor, Annette Künkele, Kristian W. Pajtler, Annika K. Wefers, Harald Stephan, Pieter Mestdagh, Lukas Heukamp, Wolfgang Hartmann, Jo Vandesompele, Natalie Sadowski, Lore Becker, Lillian Garrett, Sabine M. Hölter, Marion Horsch, Julia Calzada-Wack, Tanja Klein-Rodewald, Ildiko Racz, Andreas Zimmer, Johannes Beckers, Frauke Neff, Thomas Klopstock, Pasqualino De Antonellis, Massimo Zollo, Wolfgang Wurst, Helmut Fuchs, Valérie Gailus-Durner, Ulrich Schüller, Martin Hrabě de Angelis, Angelika Eggert, Alexander Schramm, Johannes H. Schulte (2014). MiR-34a deficiency accelerates medulloblastoma formationin vivo. International Journal of Cancer.

K. Durinck, A. Wallaert, I. Van de Walle, W. Van Loocke, P.-J. Volders, S. Vanhauwaert, E. Geerdens, Y. Benoit, N. Van Roy, B. Poppe, J. Soulier, J. Cools, P. Mestdagh, J. Vandesompele, P. Rondou, P. Van Vlierberghe, T. Taghon, F. Speleman (2014). The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia. Haematologica.

Suzanne Vanhauwaert, Gert Van Peer, Ali Rihani, Els Janssens, Pieter Rondou, Steve Lefever, Anne De Paepe, Paul J. Coucke, Frank Speleman, Jo Vandesompele, Andy Willaert (2014). Expressed Repeat Elements Improve RT-qPCR Normalization across a Wide Range of Zebrafish Gene Expression Studies. PLoS ONE.

L. Lapeire, A. Hendrix, K. Lambein, M. Van Bockstal, G. Braems, R. Van Den Broecke, R. Limame, P. Mestdagh, J. Vandesompele, C. Vanhove, D. Maynard, C. Lehuede, C. Muller, P. Valet, C. P. Gespach, M. Bracke, V. Cocquyt, H. Denys, O. De Wever (2014). Cancer-Associated Adipose Tissue Promotes Breast Cancer Progression by Paracrine Oncostatin M and Jak/STAT3 Signaling. Cancer Research.

Jan Van Deun, Pieter Mestdagh, Raija Sormunen, Veronique Cocquyt, Karim Vermaelen, Jo Vandesompele, Marc Bracke, Olivier De Wever, An Hendrix (2014). The impact of disparate isolation methods for extracellular vesicles on downstream RNA profiling. Journal of Extracellular Vesicles.

A. Oberthuer, D. Juraeva, B. Hero, R. Volland, C. Sterz, R. Schmidt, A. Faldum, Y. Kahlert, A. Engesser, S. Asgharzadeh, R. Seeger, M. Ohira, A. Nakagawara, P. Scaruffi, G. P. Tonini, I. Janoueix-Lerosey, O. Delattre, G. Schleiermacher, J. Vandesompele, F. Speleman, R. Noguera, M. Piqueras, J. Benard, A. Valent, S. Avigad, I. Yaniv, R. G. Grundy, M. Ortmann, C. Shao, M. Schwab, R. Eils, T. Simon, J. Theissen, F. Berthold, F. Westermann, B. Brors, M. Fischer (2014). Revised Risk Estimation and Treatment Stratification of Low- and Intermediate-Risk Neuroblastoma Patients by Integrating Clinical and Molecular Prognostic Markers. Clinical Cancer Research.

E Mets, J Van der Meulen, G Van Peer, M Boice, P Mestdagh, I Van de Walle, T Lammens, S Goossens, B De Moerloose, Y Benoit, N Van Roy, E Clappier, B Poppe, J Vandesompele, H-G Wendel, T Taghon, P Rondou, J Soulier, P Van Vlierberghe, F Speleman (2014). MicroRNA-193b-3p acts as a tumor suppressor by targeting the MYB oncogene in T-cell acute lymphoblastic leukemia. Leukemia.

Gert Van Peer, Steve Lefever, Jasper Anckaert, Anneleen Beckers, Ali Rihani, Alan Van Goethem, Pieter-Jan Volders, Fjoralba Zeka, Maté Ongenaert, Pieter Mestdagh, Jo Vandesompele (2014). miRBase Tracker: keeping track of microRNA annotation changes. Database.

Filip Van Nieuwerburgh, Sarah De Keulenaer, Joachim De Schrijver, Jo Vandesompele, Wim Van Criekinge, Paul J Coucke, Dieter Deforce (2014). Illumina sequencing of 15 deafness genes using fragmented amplicons. BMC Research Notes.

Kristina Althoff, Sven Lindner, Andrea Odersky, Pieter Mestdagh, Anneleen Beckers, Sarah Karczewski, Jan J. Molenaar, Anna Bohrer, Shirley Knauer, Frank Speleman, Matthias Epple, Diana Kozlova, Sena Yoon, Kwanghee Baek, Jo Vandesompele, Angelika Eggert, Alexander Schramm, Johannes H. Schulte (2014). miR-542-3p exerts tumor suppressive functions in neuroblastoma by downregulating Survivin. International Journal of Cancer.

Pieter Mestdagh, Nicole Hartmann, Lukas Baeriswyl, Ditte Andreasen, Nathalie Bernard, Caifu Chen, David Cheo, Petula D'Andrade, Mike DeMayo, Lucas Dennis, Stefaan Derveaux, Yun Feng, Stephanie Fulmer-Smentek, Bernhard Gerstmayer, Julia Gouffon, Chris Grimley, Eric Lader, Kathy Y Lee, Shujun Luo, Peter Mouritzen, Aishwarya Narayanan, Sunali Patel, Sabine Peiffer, Silvia Rüberg, Gary Schroth, Dave Schuster, Jonathan M Shaffer, Elliot J Shelton, Scott Silveria, Umberto Ulmanella, Vamsi Veeramachaneni, Frank Staedtler, Thomas Peters, Toumy Guettouche, Linda Wong, Jo Vandesompele (2014). Evaluation of quantitative miRNA expression platforms in the microRNA quality control (miRQC) study. Nature Methods.

Pasqualino De Antonellis, Marianeve Carotenuto, Jonathan Vandenbussche, Gennaro De Vita, Veronica Ferrucci, Chiara Medaglia, Iolanda Boffa, Alessandra Galiero, Sarah Di Somma, Daniela Magliulo, Nadia Aiese, Alessandro Alonzi, Daniela Spano, Lucia Liguori, Cristina Chiarolla, Antonio Verrico, Johannes H. Schulte, Pieter Mestdagh, Jo Vandesompele, Kris Gevaert, Massimo Zollo (2014). Early Targets of miR-34a in Neuroblastoma. Molecular & Cellular Proteomics.

E. Mets, G. Van Peer, J. Van der Meulen, M. Boice, T. Taghon, S. Goossens, P. Mestdagh, Y. Benoit, B. De Moerloose, N. Van Roy, B. Poppe, J. Vandesompele, H.-G. Wendel, P. Van Vlierberghe, F. Speleman, P. Rondou (2014). MicroRNA-128-3p is a novel oncomiR targeting PHF6 in T-cell acute lymphoblastic leukemia. Haematologica.

Lotte Pyfferoen, Pieter Mestdagh, Karl Vergote, Nancy De Cabooter, Jo Vandesompele, Bart N. Lambrecht, Karim Y. Vermaelen (2014). Lung tumours reprogram pulmonary dendritic cell immunogenicity at the microRNA level. International Journal of Cancer.

Jan Hellemans, Jo Vandesompele (2014). Selection of Reliable Reference Genes for RT-qPCR Analysis. Methods in Molecular Biology,Quantitative Real-Time PCR.

Bram De Wilde, Steve Lefever, Wes Dong, Jude Dunne, Syed Husain, Stefaan Derveaux, Jan Hellemans, Jo Vandesompele (2014). Target enrichment using parallel nanoliter quantitative PCR amplification. BMC Genomics.

J. Vandesompele, P. Mestdagh (2014). Some cautionary notes on the petite "Holy Grail" of molecular diagnostics. Haematologica.

Ali Rihani, Tom Van Maerken, Bram De Wilde, Fjoralba Zeka, Geneviève Laureys, Koen Norga, Gian Paolo Tonini, Simona Coco, Rogier Versteeg, Rosa Noguera, Johannes H. Schulte, Angelika Eggert, Raymond L. Stallings, Frank Speleman, Jo Vandesompele (2014). Lack of association betweenMDM2promoter SNP309 and clinical outcome in patients with neuroblastoma. Pediatric Blood & Cancer.

Tom Van Maerken, Ali Rihani, Alan Van Goethem, Anne De Paepe, Frank Speleman, Jo Vandesompele (2013). Pharmacologic activation of wild-type p53 by nutlin therapy in childhood cancer. Cancer Letters.

Stephen A Bustin, Vladimir Benes, Jeremy Garson, Jan Hellemans, Jim Huggett, Mikael Kubista, Reinhold Mueller, Tania Nolan, Michael W Pfaffl, Gregory Shipley, Carl T Wittwer, Peter Schjerling, Philip J Day, Mónica Abreu, Begoña Aguado, Jean-François Beaulieu, Anneleen Beckers, Sara Bogaert, John A Browne, Fernando Carrasco-Ramiro, Liesbeth Ceelen, Kate Ciborowski, Pieter Cornillie, Stephanie Coulon, Ann Cuypers, Sara De Brouwer, Leentje De Ceuninck, Jurgen De Craene, Hélène De Naeyer, Ward De Spiegelaere, Kato Deckers, Annelies Dheedene, Kaat Durinck, Margarida Ferreira-Teixeira, Annelies Fieuw, Jack M Gallup, Sandra Gonzalo-Flores, Karen Goossens, Femke Heindryckx, Elizabeth Herring, Hans Hoenicka, Laura Icardi, Rolf Jaggi, Farzad Javad, Michael Karampelias, Frederick Kibenge, Molly Kibenge, Candy Kumps, Irina Lambertz, Tim Lammens, Amelia Markey, Peter Messiaen, Evelien Mets, Sofia Morais, Alberto Mudarra-Rubio, Justine Nakiwala, Hilde Nelis, Pal A Olsvik, Claudina Pérez-Novo, Michelle Plusquin, Tony Remans, Ali Rihani, Paulo Rodrigues-Santos, Pieter Rondou, Rebecca Sanders, Katharina Schmidt-Bleek, Kerstin Skovgaard, Karen Smeets, Laura Tabera, Stefan Toegel, Tim Van Acker, Wim Van den Broeck, Joni Van der Meulen, Mireille Van Gele, Gert Van Peer, Mario Van Poucke, Nadine Van Roy, Sarah Vergult, Joris Wauman, Marina Tshuikina-Wiklander, Erik Willems, Sara Zaccara, Fjoralba Zeka, Jo Vandesompele (2013). The need for transparency and good practices in the qPCR literature. Nature Methods.

Liesbeth Vossaert, Thomas O’Leary, Christophe Van Neste, Björn Heindryckx, Jo Vandesompele, Petra De Sutter, Dieter Deforce (2013). Reference loci for RT-qPCR analysis of differentiating human embryonic stem cells. BMC Molecular Biology.

Steve Lefever, Filip Pattyn, Jan Hellemans, Jo Vandesompele (2013). Single-Nucleotide Polymorphisms and Other Mismatches Reduce Performance of Quantitative PCR Assays. Clinical Chemistry.

Ali Rihani, Tom Van Maerken, Filip Pattyn, Gert Van Peer, Anneleen Beckers, Sara De Brouwer, Candy Kumps, Evelien Mets, Joni Van der Meulen, Pieter Rondou, Carina Leonelli, Pieter Mestdagh, Frank Speleman, Jo Vandesompele (2013). Effective Alu Repeat Based RT-Qpcr Normalization in Cancer Cell Perturbation Experiments. PLoS ONE.

Jim F Huggett, Carole A Foy, Vladimir Benes, Kerry Emslie, Jeremy A Garson, Ross Haynes, Jan Hellemans, Mikael Kubista, Reinhold D Mueller, Tania Nolan, Michael W Pfaffl, Gregory L Shipley, Jo Vandesompele, Carl T Wittwer, Stephen A Bustin (2013). The Digital MIQE Guidelines: Minimum Information for Publication of Quantitative Digital PCR Experiments. Clinical Chemistry.

Valerie Pede, Ans Rombout, Jolien Vermeire, Evelien Naessens, Pieter Mestdagh, Nore Robberecht, Hanne Vanderstraeten, Nadine Van Roy, Jo Vandesompele, Frank Speleman, Jan Philippé, Bruno Verhasselt (2013). CLL Cells Respond to B-Cell Receptor Stimulation with a MicroRNA/mRNA Signature Associated with MYC Activation and Cell Cycle Progression. PLoS ONE.

Karen Goossens, Pieter Mestdagh, Steve Lefever, Mario Van Poucke, Alex Van Zeveren, Ann Van Soom, Jo Vandesompele, Luc Peelman (2013). Regulatory microRNA Network Identification in Bovine Blastocyst Development. Stem Cells and Development.

Kristina Althoff, Anneleen Beckers, Andrea Odersky, Pieter Mestdagh, Johannes Köster, Isabella M. Bray, Kenneth Bryan, Jo Vandesompele, Frank Speleman, Raymond L. Stallings, Alexander Schramm, Angelika Eggert, Annika Sprüssel, Johannes H. Schulte (2013). MiR-137 functions as a tumor suppressor in neuroblastoma by downregulating KDM1A. International Journal of Cancer.

Candy Kumps, Annelies Fieuw, Pieter Mestdagh, Björn Menten, Steve Lefever, Filip Pattyn, Sara De Brouwer, Tom Sante, Johannes Hubertus Schulte, Alexander Schramm, Nadine Van Roy, Tom Van Maerken, Rosa Noguera, Valérie Combaret, Christine Devalck, Frank Westermann, Geneviève Laureys, Angelika Eggert, Jo Vandesompele, Katleen De Preter, Frank Speleman (2013). Focal DNA Copy Number Changes in Neuroblastoma Target MYCN Regulated Genes. PLoS ONE.

A Schramm, B Schowe, K Fielitz, M Heilmann, M Martin, T Marschall, J Köster, J Vandesompele, J Vermeulen, K de Preter, J Koster, R Versteeg, R Noguera, F Speleman, S Rahmann, A Eggert, K Morik, J H Schulte (2012). Exon-level expression analyses identify MYCN and NTRK1 as major determinants of alternative exon usage and robustly predict primary neuroblastoma outcome. British Journal of Cancer.

Pieter-Jan Volders, Kenny Helsens, Xiaowei Wang, Björn Menten, Lennart Martens, Kris Gevaert, Jo Vandesompele, Pieter Mestdagh (2012). LNCipedia: a database for annotated human lncRNA transcript sequences and structures. Nucleic Acids Research.

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Jan J Molenaar, Raquel Domingo-Fernández, Marli E Ebus, Sven Lindner, Jan Koster, Ksenija Drabek, Pieter Mestdagh, Peter van Sluis, Linda J Valentijn, Johan van Nes, Marloes Broekmans, Franciska Haneveld, Richard Volckmann, Isabella Bray, Lukas Heukamp, Annika Sprüssel, Theresa Thor, Kristina Kieckbusch, Ludger Klein-Hitpass, Matthias Fischer, Jo Vandesompele, Alexander Schramm, Max M van Noesel, Luigi Varesio, Frank Speleman, Angelika Eggert, Raymond L Stallings, Huib N Caron, Rogier Versteeg, Johannes H Schulte (2012). LIN28B induces neuroblastoma and enhances MYCN levels via let-7 suppression. Nature Genetics.

Anneleen Decock, Maté Ongenaert, Jasmien Hoebeeck, Katleen De Preter, Gert Van Peer, Wim Van Criekinge, Ruth Ladenstein, Johannes H Schulte, Rosa Noguera, Raymond L Stallings, An Van Damme, Geneviève Laureys, Joëlle Vermeulen, Tom Van Maerken, Frank Speleman, Jo Vandesompele (2012). Genome-wide promoter methylation analysis in neuroblastoma identifies prognostic methylation biomarkers. Genome Biology.

Jan M. Ruijter, Michael W. Pfaffl, Sheng Zhao, Andrej N. Spiess, Gregory Boggy, Jochen Blom, Robert G. Rutledge, Davide Sisti, Antoon Lievens, Katleen De Preter, Stefaan Derveaux, Jan Hellemans, Jo Vandesompele (2012). Evaluation of qPCR curve analysis methods for reliable biomarker discovery: Bias, resolution, precision, and implications. Methods.

Martin Peifer, Lynnette Fernández-Cuesta, Martin L Sos, Julie George, Danila Seidel, Lawryn H Kasper, Dennis Plenker, Frauke Leenders, Ruping Sun, Thomas Zander, Roopika Menon, Mirjam Koker, Ilona Dahmen, Christian Müller, Vincenzo Di Cerbo, Hans-Ulrich Schildhaus, Janine Altmüller, Ingelore Baessmann, Christian Becker, Bram de Wilde, Jo Vandesompele, Diana Böhm, Sascha Ansén, Franziska Gabler, Ines Wilkening, Stefanie Heynck, Johannes M Heuckmann, Xin Lu, Scott L Carter, Kristian Cibulskis, Shantanu Banerji, Gad Getz, Kwon-Sik Park, Daniel Rauh, Christian Grütter, Matthias Fischer, Laura Pasqualucci, Gavin Wright, Zoe Wainer, Prudence Russell, Iver Petersen, Yuan Chen, Erich Stoelben, Corinna Ludwig, Philipp Schnabel, Hans Hoffmann, Thomas Muley, Michael Brockmann, Walburga Engel-Riedel, Lucia A Muscarella, Vito M Fazio, Harry Groen, Wim Timens, Hannie Sietsma, Erik Thunnissen, Egbert Smit, Daniëlle A M Heideman, Peter J F Snijders, Federico Cappuzzo, Claudia Ligorio, Stefania Damiani, John Field, Steinar Solberg, Odd Terje Brustugun, Marius Lund-Iversen, Jörg Sänger, Joachim H Clement, Alex Soltermann, Holger Moch, Walter Weder, Benjamin Solomon, Jean-Charles Soria, Pierre Validire, Benjamin Besse, Elisabeth Brambilla, Christian Brambilla, Sylvie Lantuejoul, Philippe Lorimier, Peter M Schneider, Michael Hallek, William Pao, Matthew Meyerson, Julien Sage, Jay Shendure, Robert Schneider, Reinhard Büttner, Jürgen Wolf, Peter Nürnberg, Sven Perner, Lukas C Heukamp, Paul K Brindle, Stefan Haas, Roman K Thomas (2012). Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer. Nature Genetics.

Peter Dynoodt, Pieter Mestdagh, Gert Van Peer, Jo Vandesompele, Karen Goossens, Luc J. Peelman, Barbara Geusens, Reinhart M. Speeckaert, Jo L.W. Lambert, Mireille J.L. Van Gele (2012). Identification of miR-145 as a Key Regulator of the Pigmentary Process. Journal of Investigative Dermatology.

David Nittner, Irina Lambertz, Frederic Clermont, Pieter Mestdagh, Corinna Köhler, Søren Jensby Nielsen, Aart Jochemsen, Frank Speleman, Jo Vandesompele, Michael A. Dyer, Alexander Schramm, Johannes H. Schulte, Jean-Christophe Marine (2012). Synthetic lethality between Rb, p53 and Dicer or miR-17–92 in retinal progenitors suppresses retinoblastoma formation. Nature Cell Biology.

S Das, K Bryan, P G Buckley, O Piskareva, I M Bray, N Foley, J Ryan, J Lynch, L Creevey, J Fay, S Prenter, J Koster, P van Sluis, R Versteeg, A Eggert, J H Schulte, A Schramm, P Mestdagh, J Vandesompele, F Speleman, R L Stallings (2012). Modulation of neuroblastoma disease pathogenesis by an extensive network of epigenetically regulated microRNAs. Oncogene.

Susanne Krauss-Etschmann, Andrew Bush, Saverio Bellusci, Guy G Brusselle, Sven Erik K Dahlén, Stefan Dehmel, Oliver Eickelberg, Greg Gibson, Machteld N Hylkema, Petra Knaus, Melanie Königshoff, Clare M Lloyd, Paolo Macciarini, Arnaud Mailleux, Benjamin J Marsland, Dirkje S Postma, Graham Roberts, Christos Samakovlis, Janet Stocks, Joke Vandesompele, Matthias Wjst, John Holloway (2012). Of flies, mice and men: a systematic approach to understanding the early life origins of chronic lung disease. Thorax.

L. C. Heukamp, T. Thor, A. Schramm, K. De Preter, C. Kumps, B. De Wilde, A. Odersky, M. Peifer, S. Lindner, A. Spruessel, F. Pattyn, P. Mestdagh, B. Menten, S. Kuhfittig-Kulle, A. Kunkele, K. Konig, L. Meder, S. Chatterjee, R. T. Ullrich, S. Schulte, J. Vandesompele, F. Speleman, R. Buttner, A. Eggert, J. H. Schulte (2012). Targeted Expression of Mutated ALK Induces Neuroblastoma in Transgenic Mice. Science Translational Medicine.

A Sprüssel, J H Schulte, S Weber, M Necke, K Händschke, T Thor, K W Pajtler, A Schramm, K König, L Diehl, P Mestdagh, J Vandesompele, F Speleman, H Jastrow, L C Heukamp, R Schüle, U Dührsen, R Buettner, A Eggert, J R Göthert (2012). Lysine-specific demethylase 1 restricts hematopoietic progenitor proliferation and is essential for terminal differentiation. Leukemia.

Sarah De Keulenaer, Jan Hellemans, Steve Lefever, Jean-Pierre Renard, Joachim De Schrijver, Hendrik Van de Voorde, Mohammad Amin Tabatabaiefar, Filip Van Nieuwerburgh, Daisy Flamez, Filip Pattyn, Bieke Scharlaken, Dieter Deforce, Sofie Bekaert, Wim Van Criekinge, Jo Vandesompele, Guy Van Camp, Paul Coucke (2012). Molecular diagnostics for congenital hearing loss including 15 deafness genes using a next generation sequencing platform. BMC Medical Genomics.

J H Schulte, S Lindner, A Bohrer, J Maurer, K De Preter, S Lefever, L Heukamp, S Schulte, J Molenaar, R Versteeg, T Thor, A Künkele, J Vandesompele, F Speleman, H Schorle, A Eggert, A Schramm (2012). MYCN and ALKF1174L are sufficient to drive neuroblastoma development from neural crest progenitor cells. Oncogene.

Annelies Fieuw, Bram De Wilde, Frank Speleman, Jo Vandesompele, Katleen De Preter (2012). Cancer Gene Prioritization for Targeted Resequencing Using FitSNP Scores. PLoS ONE.

Tim Lammens, Katrien Swerts, Lara Derycke, Annemie De Craemer, Sara De Brouwer, Katleen De Preter, Nadine Van Roy, Jo Vandesompele, Frank Speleman, Jan Philippé, Yves Benoit, Klaus Beiske, Marc Bracke, Geneviève Laureys (2012). N-Cadherin in Neuroblastoma Disease: Expression and Clinical Significance. PLoS ONE.

A Formosa, A M Lena, E K Markert, S Cortelli, R Miano, A Mauriello, N Croce, J Vandesompele, P Mestdagh, E Finazzi-Agrò, A J Levine, G Melino, S Bernardini, E Candi (2012). DNA methylation silences miR-132 in prostate cancer. Oncogene.

Frauke Coppieters, Bram De Wilde, Steve Lefever, Ellen De Meester, Nina De Rocker, Caroline Van Cauwenbergh, Filip Pattyn, Françoise Meire, Bart P. Leroy, Jan Hellemans, Jo Vandesompele, Elfride De Baere (2012). Massively parallel sequencing for early molecular diagnosis in Leber congenital amaurosis. Genetics in Medicine.

Gert Van Peer, Pieter Mestdagh, Jo Vandesompele (2012). Accurate RT-qPCR gene expression analysis on cell culture lysates. Scientific Reports.

Barbara D’haene, Pieter Mestdagh, Jan Hellemans, Jo Vandesompele (2011). miRNA Expression Profiling: From Reference Genes to Global Mean Normalization. Methods in Molecular Biology,Next-Generation MicroRNA Expression Profiling Technology.

Pieter Mestdagh, Stefaan Derveaux, Jo Vandesompele (2011). Whole-Genome RT-qPCR MicroRNA Expression Profiling. Methods in Molecular Biology,Functional Genomics.

K. De Preter, P. Mestdagh, J. Vermeulen, F. Zeka, A. Naranjo, I. Bray, V. Castel, C. Chen, E. Drozynska, A. Eggert, M. D. Hogarty, E. Izycka-Swieszewska, W. B. London, R. Noguera, M. Piqueras, K. Bryan, B. Schowe, P. van Sluis, J. J. Molenaar, A. Schramm, J. H. Schulte, R. L. Stallings, R. Versteeg, G. Laureys, N. Van Roy, F. Speleman, J. Vandesompele (2011). miRNA Expression Profiling Enables Risk Stratification in Archived and Fresh Neuroblastoma Tumor Samples. Clinical Cancer Research.

Anneleen Decock, Maté Ongenaert, Jo Vandesompele, Frank Speleman (2011). Neuroblastoma epigenetics: From candidate gene approaches to genome-wide screenings. Epigenetics.

Kim De Leeneer, Joachim De Schrijver, Lieven Clement, Machteld Baetens, Steve Lefever, Sarah De Keulenaer, Wim Van Criekinge, Dieter Deforce, Filip Van Nieuwerburgh, Sofie Bekaert, Filip Pattyn, Bram De Wilde, Paul Coucke, Jo Vandesompele, Kathleen Claes, Jan Hellemans (2011). Practical Tools to Implement Massive Parallel Pyrosequencing of PCR Products in Next Generation Molecular Diagnostics. PLoS ONE.

E E Santo, M E Ebus, J Koster, J H Schulte, A Lakeman, P van Sluis, J Vermeulen, D Gisselsson, I Øra, S Lindner, P G Buckley, R L Stallings, J Vandesompele, A Eggert, H N Caron, R Versteeg, J J Molenaar (2011). Oncogenic activation of FOXR1 by 11q23 intrachromosomal deletion-fusions in neuroblastoma. Oncogene.

Pieter Mestdagh, Steve Lefever, Filip Pattyn, Dana Ridzon, Erik Fredlund, Annelies Fieuw, Maté Ongenaert, Joëlle Vermeulen, Anne De Paepe, Linda Wong, Frank Speleman, Caifu Chen, Jo Vandesompele (2011). The microRNA body map: dissecting microRNA function through integrative genomics. Nucleic Acids Research.

Frank Speleman, Katleen De Preter, Jo Vandesompele (2011). Neuroblastoma genetics and phenotype: A tale of heterogeneity. Seminars in Cancer Biology.

Annelies Fieuw, Candy Kumps, Alexander Schramm, Filip Pattyn, Björn Menten, Francesca Antonacci, Peter Sudmant, Johannes H. Schulte, N Van Roy, Sarah Vergult, Patrick G. Buckley, A De Paepe, Rosa Noguera, Rogier Versteeg, Raymond Stallings, Angelika Eggert, Jo Vandesompele, K De Preter, Frank Speleman (2011). Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas. International Journal of Cancer.

Sara De Brouwer, Pieter Mestdagh, Irina Lambertz, Filip Pattyn, Anne De Paepe, Frank Westermann, Christina Schroeder, Johannes H. Schulte, Alexander Schramm, Katleen De Preter, Jo Vandesompele, Frank Speleman (2011). Dickkopf-3 is regulated by the MYCN-induced miR-17-92 cluster in neuroblastoma. International Journal of Cancer.

J. H. Schulte, H. S. Bachmann, B. Brockmeyer, K. DePreter, A. Oberthur, S. Ackermann, Y. Kahlert, K. Pajtler, J. Theissen, F. Westermann, J. Vandesompele, F. Speleman, F. Berthold, A. Eggert, B. Brors, B. Hero, A. Schramm, M. Fischer (2011). High ALK Receptor Tyrosine Kinase Expression Supersedes ALK Mutation as a Determining Factor of an Unfavorable Phenotype in Primary Neuroblastoma. Clinical Cancer Research.

An De Weer, Joni Van der Meulen, Pieter Rondou, Tom Taghon, Torsten A. Konrad, Katleen De Preter, Pieter Mestdagh, Tom Van Maerken, Nadine Van Roy, Marta Jeison, Isaac Yaniv, Barbara Cauwelier, Lucien Noens, Hélène-Antoine Poirel, Peter Vandenberghe, Frédéric Lambert, Anne De Paepe, Maria García Sánchez, Maria Odero, Bruno Verhasselt, Jan Philippé, Joke Vandesompele, Rotraud Wieser, Nicole Dastugue, Pieter Van Vlierberghe, Bruce Poppe, Frank Speleman (2011). EVI1-mediated down regulation of MIR449A is essential for the survival of EVI1 positive leukaemic cells. British Journal of Haematology.

T. Van Maerken, A. Rihani, D. Dreidax, S. De Clercq, N. Yigit, J.-C. Marine, F. Westermann, A. De Paepe, J. Vandesompele, F. Speleman (2011). Functional Analysis of the p53 Pathway in Neuroblastoma Cells Using the Small-Molecule MDM2 Antagonist Nutlin-3. Molecular Cancer Therapeutics.

Stephen A Bustin, Vladimir Benes, Jeremy A Garson, Jan Hellemans, Jim Huggett, Mikael Kubista, Reinhold Mueller, Tania Nolan, Michael W Pfaffl, Gregory L Shipley, Jo Vandesompele, Carl T Wittwer (2011). Primer Sequence Disclosure: A Clarification of the MIQE Guidelines. Clinical Chemistry.

Joëlle Vermeulen, Katleen De Preter, Steve Lefever, Justine Nuytens, Fanny De Vloed, Stefaan Derveaux, Jan Hellemans, Frank Speleman, Jo Vandesompele (2011). Measurable impact of RNA quality on gene expression results from quantitative PCR. Nucleic Acids Research.

E A Afanasyeva, P Mestdagh, C Kumps, J Vandesompele, V Ehemann, J Theissen, M Fischer, M Zapatka, B Brors, L Savelyeva, V Sagulenko, F Speleman, M Schwab, F Westermann (2011). MicroRNA miR-885-5p targets CDK2 and MCM5, activates p53 and inhibits proliferation and survival. Cell Death & Differentiation.

J Ban, G Jug, P Mestdagh, R Schwentner, M Kauer, D N T Aryee, K-L Schaefer, F Nakatani, K Scotlandi, M Reiter, D Strunk, F Speleman, J Vandesompele, H Kovar (2011). Hsa-mir-145 is the top EWS-FLI1-repressed microRNA involved in a positive feedback loop in Ewing's sarcoma. Oncogene.

Sara Bogaert, Debby Laukens, Harald Peeters, Lode Melis, Kim Olievier, Nico Boon, Gust Verbruggen, Jo Vandesompele, Dirk Elewaut, Martine De Vos (2011). Differential mucosal expression of Th17-related genes between the inflamed colon and ileum of patients with inflammatory bowel disease. BMC Immunology.

Pieter Mestdagh, Anna-Karin Boström, Francis Impens, Erik Fredlund, Gert Van Peer, Pasqualino De Antonellis, Kristoffer von Stedingk, Bart Ghesquière, Stefanie Schulte, Michael Dews, Andrei Thomas-Tikhonenko, Johannes H. Schulte, Massimo Zollo, Alexander Schramm, Kris Gevaert, Håkan Axelson, Frank Speleman, Jo Vandesompele (2010). The miR-17-92 MicroRNA Cluster Regulates Multiple Components of the TGF-β Pathway in Neuroblastoma. Molecular Cell.

T. Erkens, J. Vandesompele, A. Van Zeveren, L. J. Peelman (2010). Correlation between porcinePPARGC1A mRNA expression and its downstream target genes in backfat andlongissimus dorsi muscle. Journal of Applied Genetics.

Geert R. Van Pottelberge, Pieter Mestdagh, Ken R. Bracke, Olivier Thas, Yannick M. T. A. van Durme, Guy F. Joos, Jo Vandesompele, Guy G. Brusselle (2010). MicroRNA Expression in Induced Sputum of Smokers and Patients with Chronic Obstructive Pulmonary Disease. American Journal of Respiratory and Critical Care Medicine.

S. De Brouwer, K. De Preter, C. Kumps, P. Zabrocki, M. Porcu, E. M. Westerhout, A. Lakeman, J. Vandesompele, J. Hoebeeck, T. Van Maerken, A. De Paepe, G. Laureys, J. H. Schulte, A. Schramm, C. Van Den Broecke, J. Vermeulen, N. Van Roy, K. Beiske, M. Renard, R. Noguera, O. Delattre, I. Janoueix-Lerosey, P. Kogner, T. Martinsson, A. Nakagawara, M. Ohira, H. Caron, A. Eggert, J. Cools, R. Versteeg, F. Speleman (2010). Meta-analysis of Neuroblastomas Reveals a Skewed ALK Mutation Spectrum in Tumors with MYCN Amplification. Clinical Cancer Research.

André Oberthuer, Barbara Hero, Frank Berthold, Dilafruz Juraeva, Andreas Faldum, Yvonne Kahlert, Shahab Asgharzadeh, Robert Seeger, Paola Scaruffi, Gian Paolo Tonini, Isabelle Janoueix-Lerosey, Olivier Delattre, Gudrun Schleiermacher, Jo Vandesompele, Joëlle Vermeulen, Frank Speleman, Rosa Noguera, Marta Piqueras, Jean Bénard, Alexander Valent, Smadar Avigad, Isaac Yaniv, Axel Weber, Holger Christiansen, Richard G. Grundy, Katharina Schardt, Manfred Schwab, Roland Eils, Patrick Warnat, Lars Kaderali, Thorsten Simon, Boris DeCarolis, Jessica Theissen, Frank Westermann, Benedikt Brors, Matthias Fischer (2010). Prognostic Impact of Gene Expression–Based Classification for Neuroblastoma. Journal of Clinical Oncology.

Joachim M De Schrijver, Kim De Leeneer, Steve Lefever, Nick Sabbe, Filip Pattyn, Filip Van Nieuwerburgh, Paul Coucke, Dieter Deforce, Jo Vandesompele, Sofie Bekaert, Jan Hellemans, Wim Van Criekinge (2010). Analysing 454 amplicon resequencing experiments using the modular and database oriented Variant Identification Pipeline. BMC Bioinformatics.

Johannes H. Schulte, Tobias Marschall, Marcel Martin, Philipp Rosenstiel, Pieter Mestdagh, Stefanie Schlierf, Theresa Thor, Jo Vandesompele, Angelika Eggert, Stefan Schreiber, Sven Rahmann, Alexander Schramm (2010). Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma. Nucleic Acids Research.

Candy Kumps, Nadine Van Roy, Lien Heyrman, Dirk Goossens, Jurgen Del-Favero, Rosa Noguera, Jo Vandesompele, Frank Speleman, Katleen De Preter (2010). Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma.. BMC Genomics.

Johannes H. Schulte, Benjamin Schowe, Pieter Mestdagh, Lars Kaderali, Prabhav Kalaghatgi, Stefanie Schlierf, Joelle Vermeulen, Bent Brockmeyer, Kristian Pajtler, Theresa Thor, Katleen de Preter, Frank Speleman, Katharina Morik, Angelika Eggert, Jo Vandesompele, Alexander Schramm (2010). Accurate prediction of neuroblastoma outcome based on miRNA expression profiles. International Journal of Cancer.

Kah Hoong Chang, Pieter Mestdagh, Jo Vandesompele, Michael J Kerin, Nicola Miller (2010). MicroRNA expression profiling to identify and validate reference genes for relative quantification in colorectal cancer. BMC Cancer.

P. G. Buckley, L. Alcock, K. Bryan, I. Bray, J. H. Schulte, A. Schramm, A. Eggert, P. Mestdagh, K. De Preter, J. Vandesompele, F. Speleman, R. L. Stallings (2010). Chromosomal and MicroRNA Expression Patterns Reveal Biologically Distinct Subgroups of 11q- Neuroblastoma. Clinical Cancer Research.

P Mestdagh, E Fredlund, F Pattyn, A Rihani, T Van Maerken, J Vermeulen, C Kumps, B Menten, K De Preter, A Schramm, J Schulte, R Noguera, G Schleiermacher, I Janoueix-Lerosey, G Laureys, R Powel, D Nittner, J-C Marine, M Ringnér, F Speleman, J Vandesompele (2010). An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours. Oncogene.

Barbara D'haene, Jan Hellemans, Margarita Craen, Jean De Schepper, Koen Devriendt, Jean-Pierre Fryns, Kathelijn Keymolen, Eveline Debals, Annelies de Klein, Elisabeth M. de Jong, Karin Segers, Anne De Paepe, Geert Mortier, Jo Vandesompele, Elfride De Baere (2010). Improved Molecular Diagnostics of Idiopathic Short Stature and Allied Disorders: Quantitative Polymerase Chain Reaction-Based Copy Number Profiling ofSHOXand Pseudoautosomal Region 1. The Journal of Clinical Endocrinology & Metabolism.

K. De Preter, J. Vermeulen, B. Brors, O. Delattre, A. Eggert, M. Fischer, I. Janoueix-Lerosey, C. Lavarino, J. M. Maris, J. Mora, A. Nakagawara, A. Oberthuer, M. Ohira, G. Schleiermacher, A. Schramm, J. H. Schulte, Q. Wang, F. Westermann, F. Speleman, J. Vandesompele (2010). Accurate Outcome Prediction in Neuroblastoma across Independent Data Sets Using a Multigene Signature. Clinical Cancer Research.

Li Ma, Jennifer Young, Harsha Prabhala, Elizabeth Pan, Pieter Mestdagh, Daniel Muth, Julie Teruya-Feldstein, Ferenc Reinhardt, Tamer T. Onder, Scott Valastyan, Frank Westermann, Frank Speleman, Jo Vandesompele, Robert A. Weinberg (2010). miR-9, a MYC/MYCN-activated microRNA, regulates E-cadherin and cancer metastasis. Nature Cell Biology.

Barbara D’haene, Jo Vandesompele, Jan Hellemans (2010). Accurate and objective copy number profiling using real-time quantitative PCR. Methods.

I Lambertz, D Nittner, P Mestdagh, G Denecker, J Vandesompele, M A Dyer, J-C Marine (2009). Monoallelic but not biallelic loss of Dicer1 promotes tumorigenesis in vivo. Cell Death & Differentiation.

Katrien Smits, Karen Goossens, Ann Van Soom, Jan Govaere, Maarten Hoogewijs, Emilie Vanhaesebrouck, Cesare Galli, Silvia Colleoni, Jo Vandesompele, Luc Peelman (2009). Selection of reference genes for quantitative real-time PCR in equine in vivo and fresh and frozen-thawed in vitro blastocysts. BMC Research Notes.

Stefaan Derveaux, Jo Vandesompele, Jan Hellemans (2009). How to do successful gene expression analysis using real-time PCR. Methods.

P Mestdagh, E Fredlund, F Pattyn, J H Schulte, D Muth, J Vermeulen, C Kumps, S Schlierf, K De Preter, N Van Roy, R Noguera, G Laureys, A Schramm, A Eggert, F Westermann, F Speleman, J Vandesompele (2009). MYCN/c-MYC-induced microRNAs repress coding gene networks associated with poor outcome in MYCN/c-MYC-activated tumors. Oncogene.

Joëlle Vermeulen, Stefaan Derveaux, Steve Lefever, Els De Smet, Katleen De Preter, Nurten Yigit, Anne De Paepe, Filip Pattyn, Frank Speleman, Jo Vandesompele (2009). RNA pre-amplification enables large-scale RT-qPCR gene-expression studies on limiting sample amounts. BMC Research Notes.

Isabella Bray, Kenneth Bryan, Suzanne Prenter, Patrick G. Buckley, Niamh H. Foley, Derek M. Murphy, Leah Alcock, Pieter Mestdagh, Jo Vandesompele, Frank Speleman, Wendy B. London, Patrick W. McGrady, Desmond G. Higgins, Anne O'Meara, Maureen O'Sullivan, Raymond L. Stallings (2009). Widespread Dysregulation of MiRNAs by MYCN Amplification and Chromosomal Imbalances in Neuroblastoma: Association of miRNA Expression with Survival. PLoS ONE.

Tom Van Maerken, Liesbeth Ferdinande, Jasmien Taildeman, Irina Lambertz, Nurten Yigit, Liesbeth Vercruysse, Ali Rihani, Martin Michaelis, Jindrich Cinatl, Claude A. Cuvelier, Jean-Christophe Marine, Anne De Paepe, Marc Bracke, Frank Speleman, Jo Vandesompele (2009). Antitumor Activity of the Selective MDM2 Antagonist Nutlin-3 Against Chemoresistant Neuroblastoma With Wild-Type p53. JNCI: Journal of the National Cancer Institute.

Joëlle Vermeulen, Katleen De Preter, Geneviève Laureys, Frank Speleman, Jo Vandesompele (2009). 59-gene prognostic signature sub-stratifies high-risk neuroblastoma patients. The Lancet Oncology.

T Van Maerken, J Vandesompele, A Rihani, A De Paepe, F Speleman (2009). Escape from p53-mediated tumor surveillance in neuroblastoma: switching off the p14ARF-MDM2-p53 axis. Cell Death & Differentiation.

Pieter Van Vlierberghe, An De Weer, Pieter Mestdagh, Tom Feys, Katleen De Preter, Pascale De Paepe, Kathleen Lambein, Jo Vandesompele, Nadine Van Roy, Bruno Verhasselt, Bruce Poppe, Frank Speleman (2009). Comparison of miRNA profiles of microdissected Hodgkin/Reed-Sternberg cells and Hodgkin cell linesversusCD77+B-cells reveals a distinct subset of differentially expressed miRNAs. British Journal of Haematology.

Bart Jacobs, Wendy De Roock, Hubert Piessevaux, Robin Van Oirbeek, Bart Biesmans, Jef De Schutter, Steffen Fieuws, Jo Vandesompele, Marc Peeters, Jean-Luc Van Laethem, Yves Humblet, Frederique Pénault-Llorca, Gert De Hertogh, Pierre Laurent-Puig, Eric Van Cutsem, Sabine Tejpar (2009). Amphiregulin and Epiregulin mRNA Expression in Primary Tumors Predicts Outcome in Metastatic Colorectal Cancer Treated With Cetuximab. Journal of Clinical Oncology.

Joëlle Vermeulen, Filip Pattyn, Katleen De Preter, Liesbeth Vercruysse, Stefaan Derveaux, Pieter Mestdagh, Steve Lefever, Jan Hellemans, Frank Speleman, Jo Vandesompele (2009). External oligonucleotide standards enable cross laboratory comparison and exchange of real-time quantitative PCR data. Nucleic Acids Research.

Joëlle Vermeulen, Filip Pattyn, Katleen De Preter, Liesbeth Vercruysse, Stefaan Derveaux, Pieter Mestdagh, Steve Lefever, Jan Hellemans, Frank Speleman, Jo Vandesompele (2009). External oligonucleotide standards enable cross laboratory comparison and exchange of real-time quantitative PCR data. Nucleic Acids Research.

Nadine Van Roy, Katleen De Preter, Jasmien Hoebeeck, Tom Van Maerken, Filip Pattyn, Pieter Mestdagh, Joëlle Vermeulen, Jo Vandesompele, Frank Speleman (2009). The emerging molecular pathogenesis of neuroblastoma: implications for improved risk assessment and targeted therapy. Genome Medicine.

Jasmien Hoebeeck, Bram De Wilde, Evi Michels, Valérie Combaret, Nurten Yigit, Els De Smet, Nadine Van Roy, Eric Stanbridge, Ning Ru, Geneviève Laureys, Anne De Paepe, Frank Speleman, Jo Vandesompele (2009). Chromosome 3p Microsatellite Allelotyping in Neuroblastoma: A Report on the Technical Hurdles. Cancer Investigation.

Pieter Mestdagh, Pieter Van Vlierberghe, An De Weer, Daniel Muth, Frank Westermann, Frank Speleman, Jo Vandesompele (2009). A novel and universal method for microRNA RT-qPCR data normalization. Genome Biology.

Joëlle Vermeulen, Katleen De Preter, Arlene Naranjo, Liesbeth Vercruysse, Nadine Van Roy, Jan Hellemans, Katrien Swerts, Sophie Bravo, Paola Scaruffi, Gian Paolo Tonini, Bruno De Bernardi, Rosa Noguera, Marta Piqueras, Adela Cañete, Victoria Castel, Isabelle Janoueix-Lerosey, Olivier Delattre, Gudrun Schleiermacher, Jean Michon, Valérie Combaret, Matthias Fischer, André Oberthuer, Peter F Ambros, Klaus Beiske, Jean Bénard, Bárbara Marques, Hervé Rubie, Janice Kohler, Ulrike Pötschger, Ruth Ladenstein, Michael D Hogarty, Patrick McGrady, Wendy B London, Geneviève Laureys, Frank Speleman, Jo Vandesompele (2009). Predicting outcomes for children with neuroblastoma using a multigene-expression signature: a retrospective SIOPEN/COG/GPOH study. The Lancet Oncology.

K. De Preter, S. De Brouwer, T. Van Maerken, F. Pattyn, A. Schramm, A. Eggert, J. Vandesompele, F. Speleman (2009). Meta-mining of Neuroblastoma and Neuroblast Gene Expression Profiles Reveals Candidate Therapeutic Compounds. Clinical Cancer Research.

Jeremy A. Garson, Jim F. Huggett, Stephen A. Bustin, Michael W. Pfaffl, Vladimir Benes, Jo Vandesompele, Gregory L. Shipley (2009). Unreliable Real-Time PCR Analysis of Human Endogenous Retrovirus-W (HERV-W) RNA Expression and DNA Copy Number in Multiple Sclerosis. AIDS Research and Human Retroviruses.

Stephen A Bustin, Vladimir Benes, Jeremy A Garson, Jan Hellemans, Jim Huggett, Mikael Kubista, Reinhold Mueller, Tania Nolan, Michael W Pfaffl, Gregory L Shipley, Jo Vandesompele, Carl T Wittwer (2009). The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments. Clinical Chemistry.

S. Lefever, J. Hellemans, F. Pattyn, D. R. Przybylski, C. Taylor, R. Geurts, A. Untergasser, J. Vandesompele, NA NA (2009). RDML: structured language and reporting guidelines for real-time quantitative PCR data. Nucleic Acids Research.

Evelyne Lampo, Mario Van Poucke, Jo Vandesompele, Tim Erkens, Alex Van Zeveren, Luc J. Peelman (2008). Positive correlation between relative mRNA expression of PRNP and SPRN in cerebral and cerebellar cortex of sheep. Molecular and Cellular Probes.

S. Lefever, J. Vandesompele, F. Speleman, F. Pattyn (2008). RTPrimerDB: the portal for real-time PCR primers and probes. Nucleic Acids Research.

Pieter Mestdagh, Tom Feys, Nathalie Bernard, Simone Guenther, Caifu Chen, Frank Speleman, Jo Vandesompele (2008). High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA. Nucleic Acids Research.

Frank Westermann, Daniel Muth, Axel Benner, Tobias Bauer, Kai-Oliver Henrich, André Oberthuer, Benedikt Brors, Tim Beissbarth, Jo Vandesompele, Filip Pattyn, Barbara Hero, Rainer König, Matthias Fischer, Manfred Schwab (2008). Distinct transcriptional MYCN/c-MYC activities are associated with spontaneous regression or malignant progression in neuroblastomas. Genome Biology.

Jasmien Hoebeeck, Evi Michels, Filip Pattyn, Valérie Combaret, Joëlle Vermeulen, Nurten Yigit, Claire Hoyoux, Geneviève Laureys, Anne De Paepe, Frank Speleman, Jo Vandesompele (2008). Aberrant methylation of candidate tumor suppressor genes in neuroblastoma. Cancer Letters.

Chris F Taylor, Dawn Field, Susanna-Assunta Sansone, Jan Aerts, Rolf Apweiler, Michael Ashburner, Catherine A Ball, Pierre-Alain Binz, Molly Bogue, Tim Booth, Alvis Brazma, Ryan R Brinkman, Adam Michael Clark, Eric W Deutsch, Oliver Fiehn, Jennifer Fostel, Peter Ghazal, Frank Gibson, Tanya Gray, Graeme Grimes, John M Hancock, Nigel W Hardy, Henning Hermjakob, Randall K Julian, Matthew Kane, Carsten Kettner, Christopher Kinsinger, Eugene Kolker, Martin Kuiper, Nicolas Le Novère, Jim Leebens-Mack, Suzanna E Lewis, Phillip Lord, Ann-Marie Mallon, Nishanth Marthandan, Hiroshi Masuya, Ruth McNally, Alexander Mehrle, Norman Morrison, Sandra Orchard, John Quackenbush, James M Reecy, Donald G Robertson, Philippe Rocca-Serra, Henry Rodriguez, Heiko Rosenfelder, Javier Santoyo-Lopez, Richard H Scheuermann, Daniel Schober, Barry Smith, Jason Snape, Christian J Stoeckert, Keith Tipton, Peter Sterk, Andreas Untergasser, Jo Vandesompele, Stefan Wiemann (2008). Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology.

Evi Michels, Jasmien Hoebeeck, Katleen De Preter, Alexander Schramm, Bénédicte Brichard, Anne De Paepe, Angelika Eggert, Geneviève Laureys, Jo Vandesompele, Frank Speleman (2008). CADM1 is a strong neuroblastoma candidate gene that maps within a 3.72 Mb critical region of loss on 11q23. BMC Cancer.

Katleen De Preter, Björn Menten, Sara De Brouwer, Candy Kumps, Evi Michels, Nadine Van Roy, Jo Vandesompele, Frank Speleman (2008). Low-cost dedicated mini-arrays for high-throughput analysis of DNA copy-number alterations in neuroblastoma. Cancer Letters.

Karl Vandepoele, Vanessa Andries, Nadine Van Roy, Katrien Staes, Jo Vandesompele, Geneviève Laureys, Els De Smet, Geert Berx, Frank Speleman, Frans van Roy (2008). A Constitutional Translocation t(1;17)(p36.2;q11.2) in a Neuroblastoma Patient Disrupts the Human NBPF1 and ACCN1 Genes. PLoS ONE.

Erik Willems, Luc Leyns, Jo Vandesompele (2008). Standardization of real-time PCR gene expression data from independent biological replicates. Analytical Biochemistry.

K. De Preter, R. Barriot, F. Speleman, J. Vandesompele, Y. Moreau (2008). Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions. Nucleic Acids Research.

David Hoogewijs, Koen Houthoofd, Filip Matthijssens, Jo Vandesompele, Jacques R Vanfleteren (2008). Selection and validation of a set of reliable reference genes for quantitative sod gene expression analysis in C. elegans. BMC Molecular Biology.