Microbial Systems Technology

Laukens Kris

  • ​A machine-learning based model for automated recommendation of individualized treatment of rifampicin-resistant tuberculosis Verboven Lennert, Callens Steven, Black John, Maartens Gary, Dooley Kelly E., Potgieter Samantha, Cartuyvels Ruben, Laukens Kris, Warren Robin M., Van Rie AnneliesPLoS ONE - ISSN 1932-6203 - 19:9(2024), e0306101Full text (DOI uitgever): https://doi.org/10.1371/JOURNAL.PONE.0306101Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:25095[c:irua:206275]
  • A preliminary indication that HLA-A*03:01 may be associated with visceral leishmaniasis development in people living with HIV in Ethiopia de Vrij Nicky, Vandoren Romi, Ramadan Kadrie, Van Hul Anke, Ceulemans Ann, Kassa Mekibib, Melkamu Roma, Yeshanew Arega, Bogale Tadfe, Beyene Hailemariam, Sisay Kasaye, Kibret Aderajew, Mersha Dagnew, Cuypers Wim, Vogt Florian, van Henten Saskia, Ritmeijer Koert, Pham Thao-Thy, Meysman Pieter, Laukens Kris, ...PLoS neglected tropical diseases - ISSN 1935-2735 - 18:9(2024), e0012000Full text (DOI uitgever): https://doi.org/10.1371/JOURNAL.PNTD.0012000Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:26009[c:irua:208934]
  • Analysis of Wilms' tumor protein 1 specific TCR repertoire in AML patients uncovers higher diversity in patients in remission than in relapsed Gielis Sofie, Flumens Donovan, van der Heijden Sanne, Versteven Maarten, De Reu Hans, Bartholomeus Esther, Schippers Jolien, Campillo Davó Diana, Berneman Zwi Nisan, Anguille Sébastien, Smits Evelien, Ogunjimi Benson, Lion Eva, Laukens Kris, Meysman PieterAnnals of hematology - ISSN 1432-0584 - New york, Springer, (2024)17 p.Full text (DOI uitgever): https://doi.org/10.1007/S00277-024-05919-1Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:25456[c:irua:208548]
  • Benchmarking of small molecule feature representations for hERG, Nav1.5, and Cav1.2 cardiotoxicity prediction Arab Issar, Egghe Kristof, Laukens Kris, Chen Ke, Barakat Khaled, Bittremieux WoutJournal of Chemical Information and Modeling - ISSN 1549-960X - 64:7(2024), p. 2515-2527Full text (DOI uitgever): https://doi.org/10.1021/ACS.JCIM.3C01301Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:19931[c:irua:200034]
  • Clinical decision support for improved neonatal care : the development of a machine learning model for the prediction of late-onset sepsis and necrotizing enterocolitis Meeus Marisse, Beirnaert Charlie, Mahieu Ludo, Laukens Kris, Meysman Pieter, Mulder Antonius, Van Laere DavidThe journal of pediatrics - ISSN 1097-6833 - 266(2024), 113869Full text (DOI uitgever): https://doi.org/10.1016/J.JPEDS.2023.113869[c:irua:201724]
  • Diagnosing viral infections through T cell receptor sequencing of activated CD8+ T cells Vujkovic Alexandra, Ha My, de Block Tessa, van Petersen Lida, Brosius Isabel, Theunissen Caroline, Van Ierssel Sabrina, Bartholomeus Esther, Adriaensen Wim, Vanham Guido, Elias George, van Damme Pierre, Van Tendeloo Vigor, Beutels Philippe, van Frankenhuijsen Maartje, Vlieghe Erika, Ogunjimi Benson, Laukens Kris, Meysman Pieter, Vercauteren KoenThe journal of infectious diseases - ISSN 1537-6613 - 229:2(2024), p. 507-516Full text (DOI uitgever): https://doi.org/10.1093/INFDIS/JIAD430Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:22127[c:irua:199415]
  • Fragment ion intensity prediction improves the identification rate of non-tryptic peptides in timsTOF Adams Charlotte, Gabriel Wassim, Laukens Kris, Picciani Mario, Wilhelm Mathias, Bittremieux Wout, Boonen KurtNature communications - ISSN 2041-1723 - 15:1(2024), 3956Full text (DOI uitgever): https://doi.org/10.1038/S41467-024-48322-0Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:23515[c:irua:205724]
  • Immune-based machine learning prediction of diagnosis and illness state in schizophrenia and bipolar disorder Skorobogatov Katrien, De Picker Livia, Wu Ching-Lien, Foiselle Marianne, Richard Jean-Romain, Boukouaci Wahid, Bouassida Jihene, Laukens Kris, Meysman Pieter, le Corvoisier Philippe, Barau Caroline, Morrens Manuel, Tamouza Ryad, Leboyer MarionBrain, behavior, and immunity - ISSN 1090-2139 - 122(2024), p. 422-432Full text (DOI uitgever): https://doi.org/10.1016/J.BBI.2024.08.013Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:25602[c:irua:208696]
  • Lack of functional TCR-epitope interaction is associated with herpes zoster through reduced downstream T cell activation Boeren Marlies, de Vrij Nicky, Ha My, Valkiers Sebastiaan, Souquette Aisha, Gielis Sofie, Kuznetsova Mariia, Schippers Jolien, Bartholomeus Esther, Van den Bergh Johan, Michels Nele, Aerts Olivier, Leysen Julie, Bervoets An, Lambert Julien, Leuridan Elke, Wens Johan, Peeters Karin, Emonds Marie-Paule, Elias George, ...Cell reports - ISSN 2211-1247 - 43:4(2024), 114062Full text (DOI uitgever): https://doi.org/10.1016/J.CELREP.2024.114062Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:22936[c:irua:205106]
  • Machine learning strategies to tackle data challenges in mass spectrometry-based proteomics Dens Ceder, Adams Charlotte, Laukens Kris, Bittremieux WoutJournal of the American Society for Mass Spectrometry / American Society for Mass Spectrometry - ISSN 1879-1123 - Washington, Amer chemical soc, 35:9(2024), p. 2143-2155Full text (DOI uitgever): https://doi.org/10.1021/JASMS.4C00180Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:24787[c:irua:207458]
  • Machine learning‐based peptide‐spectrum match rescoring opens up the immunopeptidome Adams Charlotte, Laukens Kris, Bittremieux Wout, Boonen KurtProteomics - ISSN 1615-9861 - 24:8(2024), 2300336Full text (DOI uitgever): https://doi.org/10.1002/PMIC.202300336Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:20487[c:irua:201029]
  • Malate production, sugar metabolism, and redox homeostasis in the leaf growth zone of Rye (Secale cereale) increase stress tolerance to aluminum stress : a biochemical and genome-wide transcriptional study Donnelly Chase, De Sousa Alexandra, Cuypers Bart, Laukens Kris, Al-Huqail Asma A., Asard Han, Beemster Gerrit, Abd Elgawad HamadaJournal of hazardous materials - ISSN 1873-3336 - 464(2024), 132956Full text (DOI uitgever): https://doi.org/10.1016/J.JHAZMAT.2023.132956[c:irua:202116]
  • Modeling antigen-specific T cell dynamics following Hepatitis B Vaccination indicates differences between conventional and regulatory T cell dynamics Besbassi Hajar, Elias George, Meysman Pieter, Jansens Hilde, Laukens Kris, van Damme Pierre, Hens Niel, Beutels Philippe, Ogunjimi BensonVaccine / International Society for Vaccines - ISSN 1873-2518 - 42:21(2024), 126148Full text (DOI uitgever): https://doi.org/10.1016/J.VACCINE.2024.07.049Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:26661[c:irua:207552]
  • Persistent T cell unresponsiveness associated with chronic visceral leishmaniasis in HIV-coinfected patients de Vrij Nicky, Pollmann Julia, Rezende Antonio M., Ibarra-Meneses Ana V., Pham Thao-Thy, Hailemichael Wasihun, Kassa Mekibib, Bogale Tadfe, Melkamu Roma, Yeshanew Arega, Mohammed Rezika, Diro Ermias, Maes Ilse, Domagalska Malgorzata, Landuyt Hanne, Vogt Florian, van Henten Saskia, Laukens Kris, Cuypers Bart, Meysman Pieter, ...Communications Biology - ISSN 2399-3642 - 7:1(2024), 524Full text (DOI uitgever): https://doi.org/10.1038/S42003-024-06225-2Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:23655[c:irua:206035]
  • Selective whole-genome sequencing of Plasmodium parasites directly from blood samples by nanopore adaptive sampling De Meulenaere Katlijn, Cuypers Wim, Gauglitz Julia, Guetens Pieter, Rosanas-Urgell Anna, Laukens Kris, Cuypers BartmBio / American Society for Microbiology - ISSN 2150-7511 - 15:1(2024), e01967-23Full text (DOI uitgever): https://doi.org/10.1128/MBIO.01967-23Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:20733[c:irua:201415]
  • Semisupervised learning to boost hERG, Nav1.5, and Cav1.2 cardiac ion channel toxicity prediction by mining a large unlabeled small molecule data set Arab Issar, Laukens Kris, Bittremieux WoutJournal of Chemical Information and Modeling - ISSN 1549-960X - 64:16(2024), p. 6410-6420Full text (DOI uitgever): https://doi.org/10.1021/ACS.JCIM.4C01102Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:24649[c:irua:207331]
  • Spiny dogfish, Squalus suckleyi, shows a good tolerance for hypoxia but need long recovery times De Boeck Gudrun, Lardon Isabelle, Eyckmans Marleen, Vu Trung N., Laukens Kris, Dommisse Roger, Wood Chris M.Conservation physiology - ISSN 2051-1434 - 12:1(2024), coae054Full text (DOI uitgever): https://doi.org/10.1093/CONPHYS/COAE054Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:24873[c:irua:207595]
  • T cell receptor–centric perspective to multimodal single-cell data analysis Mullan Kerry, Ha My, Valkiers Sebastiaan, de Vrij Nicky, Ogunjimi Benson, Laukens Kris, Meysman PieterScience Advances - ISSN 2375-2548 - 10:48(2024), eadr3196Full text (DOI uitgever): https://doi.org/10.1126/SCIADV.ADR3196Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:26634[c:irua:210509]
  • The dwarf & pale leaf mutation reduces chloroplast numbers, resulting in sugar depletion that inhibits leaf growth of maize seedlings Abd Elgawad Hamada, Sprangers Katrien, Thys Sofie, Pintelon Isabel, Cuypers Bart, El-Tayeb Mohamed A., Weil Clifford, Laukens Kris, Beemster GerritCurrent Plant Biology - ISSN 2214-6628 - 40(2024), 100409Full text (DOI uitgever): https://doi.org/10.1016/J.CPB.2024.100409Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:26871[c:irua:210436]
  • TransExION : a transformer based explainable similarity metric for comparing IONS in tandem mass spectrometry Bui Thi Danh, Liu Youzhong, Lippens Jennifer L., Laukens Kris, De Vijlder ThomasJournal of Cheminformatics - ISSN 1758-2946 - 16:1(2024), 61Full text (DOI uitgever): https://doi.org/10.1186/S13321-024-00858-5Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:23599[c:irua:206073]
  • Unraveling the immune signature of herpes zoster : insights into the pathophysiology and human leukocyte antigen risk profile Vandoren Romi, Boeren Marlies, Schippers Jolien, Bartholomeus Esther, Mullan Kerry, Michels Nele, Aerts Olivier, Leysen Julie, Bervoets An, Lambert Julien, Leuridan Elke, Wens Johan, Peeters Karin, Emonds Marie-Paule, Jansens Hilde, Casanova Jean-Laurent, Bastard Paul, Suls Arvid, Van Tendeloo Vigor, Ponsaerts Peter, ...The journal of infectious diseases - ISSN 0022-1899 - (2024), jiad609Full text (DOI uitgever): https://doi.org/10.1093/INFDIS/JIAD609Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:23514[c:irua:204370]
  • tcrBLOSUM : an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs Postovskaya Anna, Vercauteren Koen, Meysman Pieter, Laukens KrisBriefings in bioinformatics - ISSN 1477-4054 - 26:1(2025), bbae602Full text (DOI uitgever): https://doi.org/10.1093/BIB/BBAE602Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:26547[c:irua:210117]

Dataset

  • Library of Two Million Unique Small Molecules with Precalculated Fingerprints, Descriptors, and Cardiotoxicity Inhibition Data Arab Issar, Laukens Kris, Bittremieux WoutZenodo, 2024Full text (DOI uitgever): https://doi.org/10.5281/ZENODO.11066707[c:irua:208064]
  • Machine learning strategies to tackle data challenges in mass spectrometry-based proteomics Dens Ceder, Adams Charlotte, Laukens Kris, Bittremieux WoutZenodo, 2024Full text (DOI uitgever): https://doi.org/10.5281/ZENODO.12748803[c:irua:208079]

PhD thesis

  • A multi-omics approach to study the effect of increasingly persistent precipitation patterns on grassland plant species in Northern Europe Donnelly Chase, Laukens Kris [Promotor], Beemster Gerrit [Promotor], Asard Han [Promotor]Antwerp, University of Antwerp, Faculty of Science, 2024, 243 p.Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:25122[c:irua:207909]
  • Artificial intelligence to decode the peptide sequences driving the immune response Dens Ceder, Laukens Kris [Promotor], Bittremieux Wout [Promotor]Antwerp, University of Antwerp, Faculty of Science, Department of Computer Science, 2024, 161 p.Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:25111[c:irua:207897]
  • Bioinformatics approaches to unravel hidden knowledge from mass spectrometry-based proteomics data Adams Charlotte, Bittremieux Wout [Promotor], Boonen Kurt [Promotor], Laukens Kris [Promotor]Antwerp, University of Antwerp, Faculty of Science, Department of Computer Science, 2024, 117 p.Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:26388[c:irua:209963]
  • Elucidating the molecular mechanisms underlying grassland species in response to more persistent precipitation regimes Zi Lin, Asard Han [Promotor], Abd Elgawad Hamada [Promotor], Laukens Kris [Promotor]Antwerp, University of Antwerp, Faculty of Science, Department of Biology, 2024, 267 p.Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:21266[c:irua:202298]
  • Unlocking the T cell receptor repertoire for personalized cancer immunotherapies Gielis Sofie, Laukens Kris [Promotor], Meysman Pieter [Promotor]Antwerp, University of Antwerp, Faculty of Science, Department of Computer Science, 2024, 145 p.Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:26859[c:irua:210620]

Book Chapter

  • Training of epitope-TCR prediction models with healthy donor-derived cancer-specific T cells Flumens Donovan, Gielis Sofie, Bartholomeus Esther, Campillo Davó Diana, van der Heijden Sanne, Versteven Maarten, De Reu Hans, Smits Evelien, Ogunjimi Benson, Laukens Kris, Meysman Pieter, Lion EvaMethods in cell biology - ISSN 0091-679X - Elsevier, 183(2024), p. 143-160Full text (DOI uitgever): https://doi.org/10.1016/BS.MCB.2023.08.001