The dwarf & pale leaf mutation reduces chloroplast numbers, resulting in sugar depletion that inhibits leaf growth of maize seedlings

Authors: Hamada AbdElgawad, Katrien Sprangers, Sofie Thys, Isabel Pintelon, Bart Cuypers, Mohamed A. El-Tayeb, Clifford Weil, Kris Laukens, Gerrit T.S. Beemster

Source: Current Plant Biology, Vol 40, Iss , Pp 100409- (2024)

Subject Terms: Cell division, Chlorophyll, Chloroplast, dpl, Dwarf, Growth, Botany, QK1-989

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2214662824000914; https://doaj.org/toc/2214-6628

Access URL: https://doaj.org/article/553e527782ae43c1b98bd317c99e073d

Persistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patients

Authors: Nicky de Vrij, Julia Pollmann, Antonio M. Rezende, Ana V. Ibarra-Meneses, Thao-Thy Pham, Wasihun Hailemichael, Mekibib Kassa, Tadfe Bogale, Roma Melkamu, Arega Yeshanew, Rezika Mohammed, Ermias Diro, Ilse Maes, Malgorzata A. Domagalska, Hanne Landuyt, Florian Vogt, Saskia van Henten, Kris Laukens, Bart Cuypers, Pieter Meysman, Hailemariam Beyene, Kasaye Sisay, Aderajew Kibret, Dagnew Mersha, Koert Ritmeijer, Johan van Griensven, Wim Adriaensen

Source: Communications Biology, Vol 7, Iss 1, Pp 1-13 (2024)

Subject Terms: Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://doaj.org/toc/2399-3642

Access URL: https://doaj.org/article/ce92172046b54dc88656899554e562df

Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF

Authors: Charlotte Adams, Wassim Gabriel, Kris Laukens, Mario Picciani, Mathias Wilhelm, Wout Bittremieux, Kurt Boonen

Source: Nature Communications, Vol 15, Iss 1, Pp 1-11 (2024)

Subject Terms: Science

File Description: electronic resource

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

Access URL: https://doaj.org/article/a40d30a2d0b94b5f98ca6b246be6cccf

TransExION: a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry

Authors: Danh Bui-Thi, Youzhong Liu, Jennifer L. Lippens, Kris Laukens, Thomas De Vijlder

Source: Journal of Cheminformatics, Vol 16, Iss 1, Pp 1-14 (2024)

Subject Terms: Tandem mass spectrometry, Small molecule identification, Spectral similarity, Structural similarity, Explainable deep neural network, Information technology, T58.5-58.64, Chemistry, QD1-999

File Description: electronic resource

Relation: https://doaj.org/toc/1758-2946

Access URL: https://doaj.org/article/73ad185aefad4f4d9acc13963584d7e1

A new Plasmodium vivax reference genome for South American isolates

Authors: Katlijn De Meulenaere, Bart Cuypers, Dionicia Gamboa, Kris Laukens, Anna Rosanas-Urgell

Source: BMC Genomics, Vol 24, Iss 1, Pp 1-14 (2023)

Subject Terms: Plasmodium vivax, Genome assembly, PacBio sequencing, Reference genome, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/e56cb9ddd92c4603b70a2ef69627a48a

Lack of functional TCR-epitope interaction is associated with herpes zoster through reduced downstream T cell activation

Authors: Marlies Boeren, Nicky de Vrij, My K. Ha, Sebastiaan Valkiers, Aisha Souquette, Sofie Gielis, Mariia Kuznetsova, Jolien Schippers, Esther Bartholomeus, Johan Van den Bergh, Nele Michels, Olivier Aerts, Julie Leysen, An Bervoets, Julien Lambert, Elke Leuridan, Johan Wens, Karin Peeters, Marie-Paule Emonds, George Elias, Niels Vandamme, Hilde Jansens, Wim Adriaensen, Arvid Suls, Stijn Vanhee, Niel Hens, Evelien Smits, Pierre Van Damme, Paul G. Thomas, Philippe Beutels, Peter Ponsaerts, Viggo Van Tendeloo, Peter Delputte, Kris Laukens, Pieter Meysman, Benson Ogunjimi

Source: Cell Reports, Vol 43, Iss 4, Pp 114062- (2024)

Subject Terms: CP: Immunology, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2211124724003905; https://doaj.org/toc/2211-1247

Access URL: https://doaj.org/article/0b4efad8a12a42feb58eab2d4fa7e411

Selective whole-genome sequencing of Plasmodium parasites directly from blood samples by nanopore adaptive sampling

Authors: Katlijn De Meulenaere, Wim L. Cuypers, Julia M. Gauglitz, Pieter Guetens, Anna Rosanas-Urgell, Kris Laukens, Bart Cuypers

Source: mBio, Vol 15, Iss 1 (2024)

Subject Terms: Plasmodium falciparum, nanopore sequencing, adaptive sampling, Microbiology, QR1-502

File Description: electronic resource

Relation: https://doaj.org/toc/2150-7511

Access URL: https://doaj.org/article/01ae47e2750449539a0c46dd5f0c7a87

A machine-learning based model for automated recommendation of individualized treatment of rifampicin-resistant tuberculosis.

Authors: Lennert Verboven, Steven Callens, John Black, Gary Maartens, Kelly E Dooley, Samantha Potgieter, Ruben Cartuyvels, SMARTT team, Kris Laukens, Robin M Warren, Annelies Van Rie

Source: PLoS ONE, Vol 19, Iss 9, p e0306101 (2024)

Subject Terms: Medicine, Science

File Description: electronic resource

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

Access URL: https://doaj.org/article/1179cd02ccde4d34ba148e7d1cd3bf69

A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia

Authors: Wim L. Cuypers, Pieter Meysman, François-Xavier Weill, Rene S. Hendriksen, Getenet Beyene, John Wain, Satheesh Nair, Marie A. Chattaway, Blanca M. Perez-Sepulveda, Pieter-Jan Ceyssens, Tessa de Block, Winnie W. Y. Lee, Maria Pardos de la Gandara, Christian Kornschober, Jacob Moran-Gilad, Kees T. Veldman, Martin Cormican, Mia Torpdahl, Patricia I. Fields, Tomáš Černý, Liselotte Hardy, Bieke Tack, Kate C. Mellor, Nicholas Thomson, Gordon Dougan, Stijn Deborggraeve, Jan Jacobs, Kris Laukens, Sandra Van Puyvelde

Source: Nature Communications, Vol 14, Iss 1, Pp 1-12 (2023)

Subject Terms: Science

File Description: electronic resource

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

Access URL: https://doaj.org/article/59517a087b904537b95142633e90211a

Fractionated irradiation of MCF7 breast cancer cells rewires a gene regulatory circuit towards a treatment‐resistant stemness phenotype

Authors: Auchi Inalegwu, Bart Cuypers, Jürgen Claesen, Ann Janssen, Amelie Coolkens, Sarah Baatout, Kris Laukens, Winnok H. De Vos, Roel Quintens

Source: Molecular Oncology, Vol 16, Iss 19, Pp 3410-3435 (2022)

Subject Terms: breast cancer, circular RNA, radioresistance, relapse‐free survival, stemness, tamoxifen resistance, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282

File Description: electronic resource

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

Access URL: https://doaj.org/article/65577c9f7e304b9b8713ac0344f9c9d7

Blood transcriptomics to facilitate diagnosis and stratification in pediatric rheumatic diseases – a proof of concept study

Authors: My Kieu Ha, Esther Bartholomeus, Luc Van Os, Julie Dandelooy, Julie Leysen, Olivier Aerts, Vasiliki Siozopoulou, Eline De Smet, Jan Gielen, Khadija Guerti, Michel De Maeseneer, Nele Herregods, Bouchra Lechkar, Ruth Wittoek, Elke Geens, Laura Claes, Mahmoud Zaqout, Wendy Dewals, Annelies Lemay, David Tuerlinckx, David Weynants, Koen Vanlede, Gerlant van Berlaer, Marc Raes, Helene Verhelst, Tine Boiy, Pierre Van Damme, Anna C. Jansen, Marije Meuwissen, Vito Sabato, Guy Van Camp, Arvid Suls, Jutte Van der Werff ten Bosch, Joke Dehoorne, Rik Joos, Kris Laukens, Pieter Meysman, Benson Ogunjimi

Source: Pediatric Rheumatology Online Journal, Vol 20, Iss 1, Pp 1-10 (2022)

Subject Terms: Pediatric rheumatic diseases, RNA sequencing, Blood transcriptomics, Classification model, Pediatrics, RJ1-570, Diseases of the musculoskeletal system, RC925-935

File Description: electronic resource

Relation: https://doaj.org/toc/1546-0096

Access URL: https://doaj.org/article/ae24e919db6f48029c4bfddf7ebc815c

Interpretable deep learning to uncover the molecular binding patterns determining TCR–epitope interaction predictions

Authors: Ceder Dens, Wout Bittremieux, Fabio Affaticati, Kris Laukens, Pieter Meysman

Source: ImmunoInformatics, Vol 11, Iss , Pp 100027- (2023)

Subject Terms: T-cell epitope prediction, Interpretable deep learning, Immunoinformatics, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2667119023000071; https://doaj.org/toc/2667-1190

Access URL: https://doaj.org/article/dcf887033abf472a950627027aa0fb79

Lack of strong innate immune reactivity renders macrophages alone unable to control productive Varicella-Zoster Virus infection in an isogenic human iPSC-derived neuronal co-culture model

Authors: Elise Van Breedam, Tamariche Buyle-Huybrecht, Jonas Govaerts, Pieter Meysman, Andrea Bours, Marlies Boeren, Julia Di Stefano, Thalissa Caers, Hans De Reu, Laura Dirkx, Jolien Schippers, Esther Bartholomeus, Marielle Lebrun, Catherine Sadzot-Delvaux, Paulina Rybakowska, Marta E. Alarcón-Riquelme, Concepción Marañón, Kris Laukens, Peter Delputte, Benson Ogunjimi, Peter Ponsaerts

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: varicella zoster virus, iPSC, neurons, macrophages, neuronal models, axonal infection, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1177245/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/7df04dec848e456790f8cd9bda1ae948

Leveraging T-cell receptor – epitope recognition models to disentangle unique and cross-reactive T-cell response to SARS-CoV-2 during COVID-19 progression/resolution

Authors: Anna Postovskaya, Alexandra Vujkovic, Tessa de Block, Lida van Petersen, Maartje van Frankenhuijsen, Isabel Brosius, Emmanuel Bottieau, Christophe Van Dijck, Caroline Theunissen, Sabrina H. van Ierssel, Erika Vlieghe, Esther Bartholomeus, Kerry Mullan, Wim Adriaensen, Guido Vanham, Benson Ogunjimi, Kris Laukens, Koen Vercauteren, Pieter Meysman

Source: Frontiers in Immunology, Vol 14 (2023)

Subject Terms: TCR repertoire analysis, CD8+ T-cell response, COVID-19, SARS-CoV-2 epitopes, immunoinformatics, cross-reactive T-cell response, Immunologic diseases. Allergy, RC581-607

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fimmu.2023.1130876/full; https://doaj.org/toc/1664-3224

Access URL: https://doaj.org/article/ba2fc2c6e4b2476896a2379ad77d5b6f

A treatment recommender clinical decision support system for personalized medicine: method development and proof-of-concept for drug resistant tuberculosis

Authors: Lennert Verboven, Toon Calders, Steven Callens, John Black, Gary Maartens, Kelly E. Dooley, Samantha Potgieter, Robin M. Warren, Kris Laukens, Annelies Van Rie

Source: BMC Medical Informatics and Decision Making, Vol 22, Iss 1, Pp 1-11 (2022)

Subject Terms: Clinical decision support system, Treatment individualisation, Machine learning, Computer applications to medicine. Medical informatics, R858-859.7

File Description: electronic resource

Relation: https://doaj.org/toc/1472-6947

Access URL: https://doaj.org/article/e9c5a705a93944bba7b196480038f145

Kynurenine pathway abnormalities are state-specific but not diagnosis-specific in schizophrenia and bipolar disorder

Authors: Katrien Skorobogatov, Valérie Autier, Marianne Foiselle, Jean-Romain Richard, Wahid Boukouaci, Ching-Lien Wu, Sophie Raynal, Christel Carbonne, Kris Laukens, Pieter Meysman, Violette Coppens, Philippe le Corvoisier, Caroline Barau, Livia De Picker, Manuel Morrens, Ryad Tamouza, Marion Leboyer

Source: Brain, Behavior, & Immunity - Health, Vol 27, Iss , Pp 100584- (2023)

Subject Terms: Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666354622001740; https://doaj.org/toc/2666-3546

Access URL: https://doaj.org/article/fa0b123252a24b13a54f64fcc6943d9b

Multi-View Learning to Unravel the Different Levels Underlying Hepatitis B Vaccine Response

Authors: Fabio Affaticati, Esther Bartholomeus, Kerry Mullan, Pierre Van Damme, Philippe Beutels, Benson Ogunjimi, Kris Laukens, Pieter Meysman

Source: Vaccines, Vol 11, Iss 7, p 1236 (2023)

Subject Terms: immunoinformatics, integrative algorithms, predictive framework, interpretable framework, systems vaccinology, Medicine

File Description: electronic resource

Relation: https://www.mdpi.com/2076-393X/11/7/1236; https://doaj.org/toc/2076-393X

Access URL: https://doaj.org/article/3772ab768c93496bb0ca1d551898cec9

Band 3–mediated Plasmodium vivax invasion is associated with transcriptional variation in PvTRAg genes

Authors: Katlijn De Meulenaere, Surendra Kumar Prajapati, Elizabeth Villasis, Bart Cuypers, Johanna Helena Kattenberg, Bernadine Kasian, Moses Laman, Leanne J. Robinson, Dionicia Gamboa, Kris Laukens, Anna Rosanas-Urgell

Source: Frontiers in Cellular and Infection Microbiology, Vol 12 (2022)

Subject Terms: P. vivax (Plasmodium vivax), Southeast Asian Ovalocytosis (SAO), transcriptome, differential expression analysis, malaria, band 3, Microbiology, QR1-502

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fcimb.2022.1011692/full; https://doaj.org/toc/2235-2988

Access URL: https://doaj.org/article/0f47f859507147cdb71e2ce712462d94

The effect of local non‐thermal plasma therapy on the cancer‐immunity cycle in a melanoma mouse model

Authors: Abraham Lin, Joey De Backer, Delphine Quatannens, Bart Cuypers, Hanne Verswyvel, Edgar Cardenas De La Hoz, Bart Ribbens, Vasiliki Siozopoulou, Jonas Van Audenaerde, Elly Marcq, Filip Lardon, Kris Laukens, Steve Vanlanduit, Evelien Smits, Annemie Bogaerts

Source: Bioengineering & Translational Medicine, Vol 7, Iss 3, Pp n/a-n/a (2022)

Subject Terms: cancer‐immunity cycle, cancer therapy, cold atmospheric plasma, melanoma, non‐thermal plasma, plasma oncology, Chemical engineering, TP155-156, Biotechnology, TP248.13-248.65, Therapeutics. Pharmacology, RM1-950

File Description: electronic resource

Relation: https://doaj.org/toc/2380-6761

Access URL: https://doaj.org/article/17eb6880cebd4836b899d3e52353311c

Four layer multi-omics reveals molecular responses to aneuploidy in Leishmania.

Authors: Bart Cuypers, Pieter Meysman, Ionas Erb, Wout Bittremieux, Dirk Valkenborg, Geert Baggerman, Inge Mertens, Shyam Sundar, Basudha Khanal, Cedric Notredame, Jean-Claude Dujardin, Malgorzata A Domagalska, Kris Laukens

Source: PLoS Pathogens, Vol 18, Iss 9, p e1010848 (2022)

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/971c52a3e6d5441a9d50b4cdeadf69e1