Microbial Systems Technology

Laukens Kris

  • A global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia Cuypers Wim, Meysman Pieter, Weill François-Xavier, Hendriksen Rene S., Beyene Getenet, Wain John, Nair Satheesh, Chattaway Marie A., Perez-Sepulveda Blanca M., Ceyssens Pieter-Jan, de Block Tessa, Lee Winnie W.Y., Pardos de la Gandara Maria, Kornschober Christian, Moran-Gilad Jacob, Veldman Kees T., Cormican Martin, Torpdahl Mia, Fields Patricia I., Černý Tomáš, ...Nature communications - ISSN 2041-1723 - 14:1(2023), 3517Full text (DOI uitgever): https://doi.org/10.1038/S41467-023-38902-XFull text (open access): https://repository.uantwerpen.be/docstore/d:irua:17977[c:irua:197029]
  • A new Plasmodium vivax reference genome for South American isolates De Meulenaere Katlijn, Cuypers Bart, Gamboa Dionicia, Laukens Kris, Rosanas-Urgell AnnaBMC genomics - ISSN 1471-2164 - 24:1(2023), 606Full text (DOI uitgever): https://doi.org/10.1186/S12864-023-09707-5Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:19878[c:irua:199945]
  • Acquired non-thermal plasma resistance mediates a shift towards aerobic glycolysis and ferroptotic cell death in melanoma Lin Abraham, Sahun Maxime, Biscop Eline, Verswyvel Hanne, De Waele Jorrit, De Backer Joey, Theys Claudia, Cuypers Bart, Laukens Kris, Vanden Berghe Wim, Smits Evelien, Bogaerts AnnemieDrug resistance updates - ISSN 1532-2084 - 67(2023), 100914Full text (DOI uitgever): https://doi.org/10.1016/J.DRUP.2022.100914Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:15864[c:irua:193167]
  • How deep learning influences workflows and roles in virtual surgical planning Hofer Beat, Kittler Markus, Laukens KrisDiscover Health Systems - ISSN 2731-7501 - 2:1(2023), 26Full text (DOI uitgever): https://doi.org/10.1007/S44250-023-00041-XFull text (open access): https://repository.uantwerpen.be/docstore/d:irua:20360[c:irua:199416]
  • IL-22-activated MUC13 impacts on colonic barrier function through JAK1/STAT3, SNAI1/ZEB1 and ROCK2/MAPK signaling Breugelmans Tom, Arras Wout, Oosterlinck Baptiste, Jauregui Aranzazu, Somers Michaël, Cuypers Bart, Laukens Kris, de Man Joris, de Schepper Heiko, De Winter Benedicte, Smet AnnemiekeCells - ISSN 2073-4409 - 12:9(2023), 1224Full text (DOI uitgever): https://doi.org/10.3390/CELLS12091224Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:17501[c:irua:196439]
  • Kynurenine pathway abnormalities are state-specific but not diagnosis-specific in schizophrenia and bipolar disorder Skorobogatov Katrien, Autier Valérie, Foiselle Marianne, Richard Jean-Romain, Boukouaci Wahid, Wu Ching-Lien, Raynal Sophie, Carbonne Christel, Laukens Kris, Meysman Pieter, Coppens Violette, le Corvoisier Philippe, Barau Caroline, De Picker Livia, Morrens Manuel, Tamouza Ryad, Leboyer MarionBrain, behavior, & immunity : health - ISSN 2666-3546 - 27(2023), 100584Full text (DOI uitgever): https://doi.org/10.1016/J.BBIH.2022.100584Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:19375[c:irua:199019]
  • 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 Van Breedam Elise, Buyle-Huybrecht Tamariche, Govaerts Jonas, Meysman Pieter, Bours Andrea, Boeren Marlies, Di Stefano Julia, Caers Thalissa, De Reu Hans, Dirkx Laura, Schippers Jolien, Bartholomeus Esther, Lebrun Marielle, Sadzot-Delvaux Catherine, Rybakowska Paulina, Alarcón-Riquelme Marta E., Marañón Concepción, Laukens Kris, Delputte Peter, Ogunjimi Benson, ...Frontiers in immunology - ISSN 1664-3224 - 14(2023), 1177245Full text (DOI uitgever): https://doi.org/10.3389/FIMMU.2023.1177245Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:17839[c:irua:196881]
  • 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 Postovskaya Anna, Vujkovic Alexandra, de Block Tessa, van Petersen Lida, van Frankenhuijsen Maartje, Brosius Isabel, Bottieau Emmanuel, Van Dijck Christophe, Theunissen Caroline, Van Ierssel Sabrina, Vlieghe Erika, Bartholomeus Esther, Mullan Kerry, Adriaensen Wim, Vanham Guido, Ogunjimi Benson, Laukens Kris, Vercauteren Koen, Meysman PieterFrontiers in immunology - ISSN 1664-3224 - 14(2023), 1130876Full text (DOI uitgever): https://doi.org/10.3389/FIMMU.2023.1130876Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:17838[c:irua:196880]
  • MeRgeION : a multifunctional R pipeline for small molecule LC-MS/MS data processing, searching, and organizing Liu Youzhong, Zhang Yingjie, Vennekens Tom, Lippens Jennifer L., Duijsens Luc, Bui Thi Danh, Laukens Kris, de Vijlder ThomasAnalytical chemistry - ISSN 1520-6882 - 95:22(2023), p. 8433-8442Full text (DOI uitgever): https://doi.org/10.1021/ACS.ANALCHEM.2C04343Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:17836[c:irua:196822]
  • Multi-view learning to unravel the different levels underlying hepatitis B vaccine response Affaticati Fabio, Bartholomeus Esther, Mullan Kerry, van Damme Pierre, Beutels Philippe, Ogunjimi Benson, Laukens Kris, Meysman PieterVaccines - ISSN 2076-393X - 11:7(2023), 1236Full text (DOI uitgever): https://doi.org/10.3390/VACCINES11071236Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:18344[c:irua:197619]
  • Semisupervised machine learning for sensitive open modification spectral library searching Arab Issar, Fondrie William Ee, Laukens Kris, Bittremieux WoutJournal of proteome research - ISSN 1535-3907 - 22:2(2023), p. 585-593Full text (DOI uitgever): https://doi.org/10.1021/ACS.JPROTEOME.2C00616Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:15922[c:irua:193533]
  • T cell immunity in HSV-1- and VZV-infected neural ganglia Boeren Marlies, Meysman Pieter, Laukens Kris, Ponsaerts Peter, Ogunjimi Benson, Delputte PeterTrends in microbiology - ISSN 1878-4380 - 31:1(2023), p. 51-61Full text (DOI uitgever): https://doi.org/10.1016/J.TIM.2022.07.008Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:13472[c:irua:189842]

A3 Article

  • Interpretable deep learning to uncover the molecular binding patterns determining TCR–epitope interaction predictions Dens Ceder, Bittremieux Wout, Affaticati Fabio, Laukens Kris, Meysman PieterImmunoInformatics - ISSN 2667-1190 - 11(2023), 100027Full text (DOI uitgever): https://doi.org/10.1016/J.IMMUNO.2023.100027Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:18760[c:irua:197045]

Dataset

  • A large comprehensive curated dataset of small molecules and their activities covering three cardiac ion channels: hERG, Cav1.2, and Nav1.5 Arab Issar, Egghe Kristof, Laukens Kris, Chen Ke, Barakat Khaled, Bittremieux WoutZenodo, 2023Full text (DOI uitgever): https://doi.org/10.5281/ZENODO.8359714[c:irua:208065]
  • Data for "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 PieterZenodo, 2023Full text (DOI uitgever): https://doi.org/10.5281/ZENODO.8129250[c:irua:209040]
  • TransExtION: Transformer based Explainable similarity metric for IONS Bui Thi Danh, Youzhong Liu, Jennifer Lippens, Laukens Kris, de Vijlder ThomasZenodo, 2023GNPS model + dataFull text (DOI uitgever): https://doi.org/10.5281/ZENODO.8175528[c:irua:206202]

PhD thesis

  • Computational methods for whole genome sequence guided individualized treatment of drug resistant tuberculosis Verboven Lennert, Van Rie Annelies [Promotor], Laukens Kris [Promotor]Antwerp, University of Antwerp, Faculty of Sciences, Department of Computer Science, 2023, 200 p.Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:18716[c:irua:198038]
  • Genomic adaptation of Salmonella to antimicrobials and the human host Cuypers Wim, Laukens Kris [Promotor], Van Puyvelde Sandra [Promotor]Antwerp, University of Antwerp, 2023, 169 p.[c:irua:197184]
  • Investigation of the Plasmodium vivax reticulocyte invasion process : a combination of wet and dry lab approaches De Meulenaere Katlijn, Rosanas-Urgell Anna [Promotor], Laukens Kris [Promotor]Antwerp, University of Antwerp, 2023, xxiii, 225 p.Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:18103[c:irua:197181]
  • Towards an improved understanding of rare variants in Mycobacterium tuberculosis candidate resistance genes Rivière Emmanuel, Van Rie Annelies [Promotor], Laukens Kris [Promotor]Antwerp, University of Antwerp, Faculty of Medicine and Health Sciences, 2023, 230 p.Full text (open access): https://repository.uantwerpen.be/docstore/d:irua:15950[c:irua:193570]

Book Chapter

  • Clustering and annotation of T cell receptor repertoires Valkiers Sebastiaan, Gielis Sofie, Van Deuren Vincent, Laukens Kris, Meysman PieterComputational vaccine design - ISBN 978-1-0716-3238-3 - New York, N.Y., Humana, 2023, p. 33-51Full text (DOI uitgever): https://doi.org/10.1007/978-1-0716-3239-0_3