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

A co-culture model to study modulators of tumor immune evasion through scalable arrayed CRISPR-interference screens

Authors: 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

Source: Frontiers in Immunology, Vol 15 (2024)

Subject Terms: immuno-oncology, long non-coding RNAs, arrayed screens, CRISPRi, co-culture, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2024.1444886/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/49b655d42ec24ce69326b7dd266ba321

People with HIV have higher percentages of circulating CCR5+ CD8+ T cells and lower percentages of CCR5+ regulatory T cells

Authors: Louise E. van Eekeren, Vasiliki Matzaraki, Zhenhua Zhang, Lisa van de Wijer, Marc J. T. Blaauw, Marien I. de Jonge, Linos Vandekerckhove, Wim Trypsteen, Leo A. B. Joosten, Mihai G. Netea, Quirijn de Mast, Hans J. P. M. Koenen, Yang Li, André J. A. M. van der Ven

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

Subject Terms: Medicine, Science

File Description: electronic resource

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

Access URL: https://doaj.org/article/9d9df5a0e9dc4f38a2e4af830557c8ab

Targeted plasma proteomics identifies MICA and IL1R1 proteins associated with HIV-1 reservoir size

Authors: Marc J.T. Blaauw, Jéssica Cristina dos Santos, Nadira Vadaq, Wim Trypsteen, Wouter van der Heijden, Albert Groenendijk, Zhenhua Zhang, Yang Li, Quirijn de Mast, Mihai G. Netea, Leo A.B. Joosten, Linos Vandekerckhove, Andre van der Ven, Vasiliki Matzaraki

Source: iScience, Vol 26, Iss 4, Pp 106486- (2023)

Subject Terms: Health sciences, Proteomics, Virology, Science

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2589004223005631; https://doaj.org/toc/2589-0042

Access URL: https://doaj.org/article/dc2d7fc16e594419bf81a364b03db50e

Organ-specific genome diversity of replication-competent SARS-CoV-2

Authors: Jolien Van Cleemput, Willem van Snippenberg, Laurens Lambrechts, Amélie Dendooven, Valentino D’Onofrio, Liesbeth Couck, Wim Trypsteen, Jan Vanrusselt, Sebastiaan Theuns, Nick Vereecke, Thierry P. P. van den Bosch, Martin Lammens, Ann Driessen, Ruth Achten, Ken R. Bracke, Wim Van den Broeck, Jan Von der Thüsen, Hans Nauwynck, Jo Van Dorpe, Sarah Gerlo, Piet Maes, Janneke Cox, Linos Vandekerckhove

Source: Nature Communications, Vol 12, Iss 1, Pp 1-11 (2021)

Subject Terms: Science

File Description: electronic resource

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

Access URL: https://doaj.org/article/d7ddc26aed524990a6ce3aa009110d7b

IRF7 and RNH1 are modifying factors of HIV-1 reservoirs: a genome-wide association analysis

Authors: Zhenhua Zhang, Wim Trypsteen, Marc Blaauw, Xiaojing Chu, Sofie Rutsaert, Linos Vandekerckhove, Wouter van der Heijden, Jéssica Cristina dos Santos, Cheng-Jian Xu, Morris A. Swertz, Andre van der Ven, Yang Li

Source: BMC Medicine, Vol 19, Iss 1, Pp 1-17 (2021)

Subject Terms: HIV, Cell-associated HIV-1 RNA, Cell-associated HIV-1 DNA, Genetic variants, Quantitative trait locus, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/1741-7015

Access URL: https://doaj.org/article/9d335b9fadb540eeb1f023c64679c30e

A specific microRNA profile as predictive biomarker for systemic treatment in patients with metastatic colorectal cancer

Authors: Dennis Poel, Elske C. Gootjes, Lotte Bakkerus, Wim Trypsteen, Henk Dekker, Hans J. van derVliet, Nicole C. T. vanGrieken, Cornelis Verhoef, Tineke E. Buffart, Henk M. W. Verheul

Source: Cancer Medicine, Vol 9, Iss 20, Pp 7558-7571 (2020)

Subject Terms: chemotherapy, colorectal cancer, metastases, miRNA, response prediction, serum, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

Relation: https://doaj.org/toc/2045-7634

Access URL: https://doaj.org/article/2ede2aac37804a52ab03c1a26358e7e8

Author Correction: Organ-specific genome diversity of replication-competent SARS-CoV-2

Authors: Jolien Van Cleemput, Willem van Snippenberg, Laurens Lambrechts, Amélie Dendooven, Valentino D’Onofrio, Liesbeth Couck, Wim Trypsteen, Jan Vanrusselt, Sebastiaan Theuns, Nick Vereecke, Thierry P. P. van den Bosch, Martin Lammens, Ann Driessen, Ruth Achten, Ken R. Bracke, Wim Van den Broeck, Jan Von der Thüsen, Hans Nauwynck, Jo Van Dorpe, Sarah Gerlo, Piet Maes, Janneke Cox, Linos Vandekerckhove

Source: Nature Communications, Vol 13, Iss 1, Pp 1-1 (2022)

Subject Terms: Science

File Description: electronic resource

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

Access URL: https://doaj.org/article/9f77ef830b194c9b9a8e8fd6596e4eaf

Chronic HIV infection induces transcriptional and functional reprogramming of innate immune cells

Authors: Wouter A. van der Heijden, Lisa Van de Wijer, Farid Keramati, Wim Trypsteen, Sofie Rutsaert, Rob ter Horst, Martin Jaeger, Hans J.P.M. Koenen, Hendrik G. Stunnenberg, Irma Joosten, Paul E. Verweij, Jan van Lunzen, Charles A. Dinarello, Leo A.B. Joosten, Linos Vandekerckhove, Mihai G. Netea, André J.A.M. van der Ven, Quirijn de Mast

Source: JCI Insight, Vol 6, Iss 7 (2021)

Subject Terms: AIDS/HIV, Immunology, Medicine

File Description: electronic resource

Relation: https://doaj.org/toc/2379-3708

Access URL: https://doaj.org/article/b2994f3dd9f54fcfa5fbfca638fec075

The Architecture of Circulating Immune Cells Is Dysregulated in People Living With HIV on Long Term Antiretroviral Treatment and Relates With Markers of the HIV-1 Reservoir, Cytomegalovirus, and Microbial Translocation

Authors: Lisa Van de Wijer, Wouter A. van der Heijden, Rob ter Horst, Martin Jaeger, Wim Trypsteen, Sofie Rutsaert, Bram van Cranenbroek, Esther van Rijssen, Irma Joosten, Leo Joosten, Linos Vandekerckhove, Till Schoofs, Jan van Lunzen, Mihai G. Netea, Hans J.P.M. Koenen, André J.A.M. van der Ven, Quirijn de Mast

Source: Frontiers in Immunology, Vol 12 (2021)

Subject Terms: HIV, Th17 & Tregs cells, CD4+/CD8+ lymphocytes, B cell, HIV reservoir, CMV, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2021.661990/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/e9c41e13fb5e4b64bc9b68de40eb9eb4

On the whereabouts of SARS-CoV-2 in the human body: A systematic review.

Authors: Wim Trypsteen, Jolien Van Cleemput, Willem van Snippenberg, Sarah Gerlo, Linos Vandekerckhove

Source: PLoS Pathogens, Vol 16, Iss 10, p e1009037 (2020)

Subject Terms: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/1553-7366; https://doaj.org/toc/1553-7374

Access URL: https://doaj.org/article/a2b9d6cd545944ca9a875b0518c93592

Early treated HIV-1 positive individuals demonstrate similar restriction factor expression profile as long-term non-progressorsResearch in context

Authors: Clarissa Van Hecke, Wim Trypsteen, Eva Malatinkova, Ward De Spiegelaere, Karen Vervisch, Sofie Rutsaert, Sabine Kinloch-de Loes, Magdalena Sips, Linos Vandekerckhove

Source: EBioMedicine, Vol 41, Iss , Pp 443-454 (2019)

Subject Terms: Medicine, Medicine (General), R5-920

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352396419300787; https://doaj.org/toc/2352-3964

Access URL: https://doaj.org/article/1136f58e76a74e148cdf17df17ae635c

Digital PCR as a tool to measure HIV persistence

Authors: Sofie Rutsaert, Kobus Bosman, Wim Trypsteen, Monique Nijhuis, Linos Vandekerckhove

Source: Retrovirology, Vol 15, Iss 1, Pp 1-8 (2018)

Subject Terms: Digital PCR, HIV, ddPCR, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12977-018-0399-0; https://doaj.org/toc/1742-4690

Access URL: https://doaj.org/article/cafddd08815343ae9e3bd0ef5c1b5f0d

Highlights from the 24th Conference on Retroviruses and Opportunistic Infections

Authors: Trevor A. Crowell, Hermione Lyall, Eva Malatinkova, Sanjay Bhagani, Denise Hsu, Donn J. Colby, Christina Polyak, Christina Psomas, Andrew Hill, Esther N. Gathogo, Wim Trypsteen, Linos Vandekerckhove, Sabie Kinloch

Source: Journal of Virus Eradication, Vol 3, Iss 2, Pp 101-108 (2017)

Subject Terms: HIV, eradication, reservoirs, T cells, opportunistic infections, hepatitis C, Microbiology, QR1-502, Public aspects of medicine, RA1-1270

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2055664020302910; https://doaj.org/toc/2055-6640

Access URL: https://doaj.org/article/5c8a84b850be4929ad4c268978d5f9b9

Diagnostic utility of droplet digital PCR for HIV reservoir quantification

Authors: Wim Trypsteen, Maja Kiselinova, Linos Vandekerckhove, Ward De Spiegelaere

Source: Journal of Virus Eradication, Vol 2, Iss 3, Pp 162-169 (2016)

Subject Terms: droplet digital PCR, digital PCR, quantitative real-time PCR, HIV quantification, virus detection, Microbiology, QR1-502, Public aspects of medicine, RA1-1270

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S205566402030460X; https://doaj.org/toc/2055-6640

Access URL: https://doaj.org/article/39130b7e6a0f47e2b57437d558f1fe2d

Long non-coding RNAs and latent HIV - A search for novel targets for latency reversal.

Authors: Wim Trypsteen, Cory H White, Amey Mukim, Celsa A Spina, Ward De Spiegelaere, Steve Lefever, Vicente Planelles, Alberto Bosque, Christopher H Woelk, Linos Vandekerckhove, Nadejda Beliakova-Bethell

Source: PLoS ONE, Vol 14, Iss 11, p e0224879 (2019)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/d0e1f770761a4faf935a8f6d6d2cba20

P1 Contribution of lncRNAs in the establishment of HIV latency in central memory CD4 T Cells

Authors: Wim Trypsteen, Cory White, Alberto Bosque, Steve Lefever, Pieter Mestdagh, Linos Vandekerckhove, Christopher Woelk

Source: Journal of Virus Eradication, Vol 3, Iss , Pp 4- (2017)

Subject Terms: Microbiology, QR1-502, Public aspects of medicine, RA1-1270

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2055664020308268; https://doaj.org/toc/2055-6640

Access URL: https://doaj.org/article/21d8a7346e5c423e94698867a0b4a2d5

Emerging PCR-Based Techniques to Study HIV-1 Reservoir Persistence

Authors: Laurens Lambrechts, Basiel Cole, Sofie Rutsaert, Wim Trypsteen, Linos Vandekerckhove

Source: Viruses, Vol 12, Iss 2, p 149 (2020)

Subject Terms: hiv-1, hiv-1 reservoir, pcr, sequencing, ngs, replication-competent, integration site, hiv-1 genome, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.mdpi.com/1999-4915/12/2/149; https://doaj.org/toc/1999-4915

Access URL: https://doaj.org/article/997910568c97491eb66f48c221560858

Impact of a decade of successful antiretroviral therapy initiated at HIV-1 seroconversion on blood and rectal reservoirs

Authors: Eva Malatinkova, Ward De Spiegelaere, Pawel Bonczkowski, Maja Kiselinova, Karen Vervisch, Wim Trypsteen, Margaret Johnson, Chris Verhofstede, Danny de Looze, Charles Murray, Sabine Kinloch-de Loes, Linos Vandekerckhove

Source: eLife, Vol 4 (2015)

Subject Terms: HIV-1 reservoir, early long-term ART, seroconversion, long-term non-progressors, Medicine, Science, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://elifesciences.org/articles/09115; https://doaj.org/toc/2050-084X

Access URL: https://doaj.org/article/36943e574147408383d7ca3d3e4e7a23

Comparison of methods for in-house screening of HLA-B*57:01 to prevent abacavir hypersensitivity in HIV-1 care.

Authors: Ward De Spiegelaere, Jan Philippé, Karen Vervisch, Chris Verhofstede, Eva Malatinkova, Maja Kiselinova, Wim Trypsteen, Pawel Bonczkowski, Dirk Vogelaers, Steven Callens, Jean Ruelle, Kabamba Kabeya, Stephane De Wit, Petra Van Acker, Vicky Van Sandt, Marie-Paule Emonds, Paul Coucke, Erica Sermijn, Linos Vandekerckhove

Source: PLoS ONE, Vol 10, Iss 4, p e0123525 (2015)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: http://europepmc.org/articles/PMC4398410?pdf=render; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/e34e992d508a4e7ca2e338a8729d4f0b