Publications

2021

Schorn, Michelle A; Verhoeven, Stefan; Ridder, Lars; Huber, Florian; Acharya, Deepa D; Aksenov, Alexander A; Aleti, Gajender; Moghaddam, Jamshid Amiri; Aron, Allegra T; Aziz, Saefuddin; Bauermeister, Anelize; Bauman, Katherine D; Baunach, Martin; Beemelmanns, Christine; Beman, Michael J; Berlanga-Clavero, María Victoria; Blacutt, Alex A; Bode, Helge B; Boullie, Anne; Brejnrod, Asker; Bugni, Tim S; Calteau, Alexandra; Cao, Liu; Carrión, Víctor J; Castelo-Branco, Raquel; Chanana, Shaurya; Chase, Alexander B; Chevrette, Marc G; Costa-Lotufo, Leticia V; Crawford, Jason M; Currie, Cameron R; Cuypers, Bart; Dang, Tam; de Rond, Tristan; Demko, Alyssa M; Dittmann, Elke; Du, Chao; Drozd, Christopher; Dujardin, Jean-Claude; Dutton, Rachel J; Edlund, Anna; Fewer, David P; Garg, Neha; Gauglitz, Julia M; Gentry, Emily C; Gerwick, Lena; Glukhov, Evgenia; Gross, Harald; Gugger, Muriel; Matus, Dulce G Guillén; Helfrich, Eric J N; Hempel, Benjamin-Florian; Hur, Jae-Seoun; Iorio, Marianna; Jensen, Paul R; Kang, Kyo Bin; Kaysser, Leonard; Kelleher, Neil L; Kim, Chung Sub; Kim, Ki Hyun; Koester, Irina; König, Gabriele M; Leao, Tiago; Lee, Seoung Rak; Lee, Yi-Yuan; Li, Xuanji; Little, Jessica C; Maloney, Katherine N; Männle, Daniel; H., Christian Martin; McAvoy, Andrew C; Metcalf, Willam W; Mohimani, Hosein; Molina-Santiago, Carlos; Moore, Bradley S; Mullowney, Michael W; Muskat, Mitchell; Nothias, Louis-Félix; O'Neill, Ellis C; Parkinson, Elizabeth I; Petras, Daniel; Piel, Jörn; Pierce, Emily C; Pires, Karine; Reher, Raphael; Romero, Diego; Roper, Caroline M; Rust, Michael; Saad, Hamada; Saenz, Carmen; Sanchez, Laura M; Sørensen, Søren Johannes; Sosio, Margherita; Süssmuth, Roderich D; Sweeney, Douglas; Tahlan, Kapil; Thomson, Regan J; Tobias, Nicholas J; Trindade-Silva, Amaro E; van Wezel, Gilles P; Wang, Mingxun; Weldon, Kelly C; Zhang, Fan; Ziemert, Nadine; Duncan, Katherine R; Crüsemann, Max; Rogers, Simon; Dorrestein, Pieter C; Medema, Marnix H; van der Hooft, Justin J J

A community resource for paired genomic and metabolomic data mining Journal Article

In: Nature Chemical Biology, 2021, ISSN: 1552-4469.

Abstract | Links | BibTeX | Altmetric | Tags: genomics, metabolomics, multi-omics

de Vrij, Nicky; Meysman, Pieter; Gielis, Sofie; Adriaensen, Wim; Laukens, Kris; Cuypers, Bart

HLA-DRB1 Alleles Associated with Lower Leishmaniasis Susceptibility Share Common Amino Acid Polymorphisms and Epitope Binding Repertoires Journal Article

In: Vaccines, 9 (3), 2021, ISSN: 2076-393X.

Abstract | Links | BibTeX | Altmetric | Tags: immunology, leishmania, leishmaniasis

Hees, Stijn Van; Cuypers, Bart; Bourgeois, Stefan; Groothuismink, Zwier M A; Meysman, Pieter; der Vlies, Pieter Van; de Knegt, Rob; Vonghia, Luisa; Michielsen, Peter; Francque, Sven; Laukens, Kris; Boonstra, Andre; Vanwolleghem, Thomas

Sorted B cell transcriptomes point towards actively regulated B cell responses during ongoing chronic hepatitis B infections Journal Article

In: Cellular Immunology, 362 , pp. 104283, 2021, ISSN: 0008-8749.

Abstract | Links | BibTeX | Altmetric | Tags: immunology, RNA-seq, transcriptomics, virology

Boullosa, Laurie Freire; Loenhout, Jinthe Van; Flieswasser, Tal; Waele, Jorrit De; Hermans, Christophe; Lambrechts, Hilde; Cuypers, Bart; Laukens, Kris; Bartholomeus, Esther; Siozopoulou, Vasiliki; Vos, Winnok H De; Peeters, Marc; Smits, Evelien L J; Deben, Christophe

Auranofin reveals therapeutic anticancer potential by triggering distinct molecular cell death mechanisms and innate immunity in mutant p53 non-small cell lung cancer Journal Article

In: Redox Biology, pp. 101949, 2021, ISSN: 2213-2317.

Abstract | Links | BibTeX | Altmetric | Tags: cancer, genomics, RNA-seq, transcriptomics

Houtven, Joris Van; Cuypers, Bart; Meysman, Pieter; Hooyberghs, Jef; Laukens, Kris; Valkenborg, Dirk

Constrained Standardization of Count Data from Massive Parallel Sequencing Journal Article

In: Journal of Molecular Biology, pp. 166966, 2021, ISSN: 0022-2836.

Abstract | Links | BibTeX | Altmetric | Tags: multi-omics, normalization, proteomics, RNA-seq, transcriptomics

Logie, Emilie; Chirumamilla, Chandra S; Perez-Novo, Claudina; Shaw, Priyanka; Declerck, Ken; Palagani, Ajay; Rangarajan, Savithri; Cuypers, Bart; Neuter, Nicolas De; Turabe, Fazil Mobashar Hussain Urf; Verma, Navin Kumar; Bogaerts, Annemie; Laukens, Kris; Offner, Fritz; Vlierberghe, Pieter Van; Ostade, Xaveer Van; Berghe, Wim Vanden

Covalent Cysteine Targeting of Bruton’s Tyrosine Kinase (BTK) Family by Withaferin-A Reduces Survival of Glucocorticoid-Resistant Multiple Myeloma MM1 Cells Journal Article

In: Cancers, 13 (7), 2021, ISSN: 2072-6694.

Abstract | Links | BibTeX | Altmetric | Tags: cancer, transcriptomics

Hefnawy, Aya; Negreira, Gabriel; Jara, Marlene; Cotton, James A; Maes, Ilse; Haenens, Erika Dtextquoteright; Imamura, Hideo; Cuypers, Bart; Monsieurs, Pieter; Mouchtoglou, Christina; Winter, Hans De; Berriman, Matt; Sanders, Mandy; Martin, Julio; de Muylder, Geraldine; Dujardin, Jean-Claude; Sterckx, Yann G -J; Domagalska, Malgorzata Anna

Genomic and phenotypic characterization of experimentally selected resistant Leishmania donovani reveals a role for dynamin-1 like protein in the mechanism of resistance to a novel anti-leishmanial compound Journal Article

In: bioRxiv, 2021.

Abstract | Links | BibTeX | Altmetric | Tags: drug-resistance, genomics, leishmania

2020

Adriaensen, Wim; Cuypers, Bart; Cordero, Carlota F; Mengasha, Bewketu; Blesson, Séverine; Cnops, Lieselotte; Kaye, Paul M; Alves, Fabiana; Diro, Ermias; van Griensven, Johan

Host transcriptomic signature as alternative test-of-cure in visceral leishmaniasis patients co-infected with HIV Journal Article

In: EBioMedicine, 55 , 2020, ISSN: 2352-3964.

Abstract | Links | BibTeX | Altmetric | Tags: immunology, leishmania, machine-learning, RNA-seq, transcriptomics

Uzureau, Sophie; Lecordier, Laurence; Uzureau, Pierrick; Hennig, Dorle; Graversen, Jonas H; Homblé, Fabrice; Mfutu, Pepe Ekulu; Arcolino], Fanny [Oliveira; Ramos, Ana Raquel; Rovere], Rita [La M; Luyten, Tomas; Vermeersch, Marjorie; Tebabi, Patricia; Dieu, Marc; Cuypers, Bart; Deborggraeve, Stijn; Rabant, Marion; Legendre, Christophe; Moestrup, Søren K; Levtchenko, Elena; Bultynck, Geert; Erneux, Christophe; Pérez-Morga, David; Pays, Etienne

APOL1 C-Terminal Variants May Trigger Kidney Disease through Interference with APOL3 Control of Actomyosin Journal Article

In: Cell Reports, 30 (11), pp. 3821 - 3836.e13, 2020, ISSN: 2211-1247.

Abstract | Links | BibTeX | Altmetric | Tags: genomics

Cuypers, Bart; Dumetz, Franck; Meysman, Pieter; Laukens, Kris; Muylder, Géraldine De; Dujardin, Jean-Claude; Domagalska, Malgorzata Anna

The Absence of C-5 DNA Methylation in Leishmania donovani Allows DNA Enrichment from Complex Samples Journal Article

In: Microorganisms, 8 (8), 2020, ISSN: 2076-2607.

Abstract | Links | BibTeX | Altmetric | Tags: bisulfite-sequencing, genomics, leishmania

Deben, Christophe; Boullosa, Laurie Freire; Domen, Andreas; Wouters, An; Cuypers, Bart; Laukens, Kris; Lardon, Filip; Pauwels, Patrick

Characterization of acquired nutlin-3 resistant non-small cell lung cancer cells Journal Article

In: Cancer Drug Resistance, 3 , pp. [Online First], 2020, ISSN: 2578-532X.

Abstract | Links | BibTeX | Altmetric | Tags: cancer, drug-resistance, transcriptomics

2019

Shome, S; Parra, RG; Fatima, N; Monzon, AM; Cuypers, B; Moosa, Y; Coimbra, NDR; Assis, J; Giner-Delgado, C; Dönerta?, HM; Cuesta-Astroz, Y; Saarunya, G; Allali, I; Gupta, S; Srivastava, A; Kalsan, M; Valdivia, C; Olguin-Orellana, G J.; Papadimitriou, S; Parisi, D; Kristensen, NP; Rib, L; Guebila, MB; Bauer, E; Zaffaroni, G; Bekkar, A; Ashano, E; Paladin, L; Necci, M; Moreyra, NN; Rydén, M; Villalobos-Solís, J; Papadopoulos, N; Rafael, C; Karakulak, T; Kaya, Y; Gladbach, Y; Dhanda, SK; ?o?tari?, N; Alex, A; DeBlasio, D; Rahman, F

Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers Journal Article

In: F1000Research, 8 (1574), 2019.

Links | BibTeX | Altmetric | Tags:

2018

Hassan, Mehedi; Namasivayam, Aishwarya Alex; DeBlasio, Dan; Fatima, Nazeefa; Siranosian, Benjamin; Parra, Gonzalo R; Cuypers, Bart; Shome, Sayane; Monzon, Alexander Miguel; Fumey, Julien; Rahman, Farzana

Reflections on a journey: a retrospective of the ISCB Student Council symposium series Journal Article

In: BMC Bioinformatics, 19 (12), pp. 347, 2018, ISSN: 1471-2105.

Abstract | Links | BibTeX | Altmetric | Tags:

Krivoshiev, Boris V; Beemster, Gerrit T S; Sprangers, Katrien; Cuypers, Bart; Laukens, Kris; Blust, Ronny; Husson, Steven J

Transcriptome profiling of HepG2 cells exposed to the flame retardant 9,10-dihydro-9-oxa-10-phosphaphenanthrene 10-oxide (DOPO) Journal Article

In: Toxicology research, 7 (3), pp. 492-502, 2018, ISSN: 2045-452X, (c8tx00006a[PII]).

Abstract | Links | BibTeX | Altmetric | Tags: transcriptomics

Neuter, Nicolas De; Bittremieux, Wout; Beirnaert, Charlie; Cuypers, Bart; Mrzic, Aida; Moris, Pieter; Suls, Arvid; Tendeloo, Viggo Van; Ogunjimi, Benson; Laukens, Kris; Meysman, Pieter

On the feasibility of mining CD8+ T cell receptor patterns underlying immunogenic peptide recognition Journal Article

In: Immunogenetics, 70 (3), pp. 159-168, 2018, ISSN: 1432-1211.

Abstract | Links | BibTeX | Altmetric | Tags: immunology, machine-learning, virology

Cuypers, Bart

A systems biology approach for a comprehensive understanding of molecular adaptation in** Leishmania donovani PhD Thesis

University of Antwerp, 2018.

BibTeX | Tags: genomics, LC-MS, leishmania, multi-omics, proteomics, RNA-seq, transcriptomics

Dumetz, F; Cuypers, B; Imamura, H; Zander, D; DtextquoterightHaenens, E; Maes, I; Domagalska, M A; Clos, J; Dujardin, J -C; Muylder, G De

Molecular Preadaptation to Antimony Resistance in Leishmania donovani on the Indian Subcontinent Journal Article

In: mSphere, 3 (2), 2018.

Abstract | Links | BibTeX | Altmetric | Tags: LC-MS, leishmania, metabolomics, multi-omics, RNA-seq, transcriptomics

Krivoshiev, Boris V; Beemster, Gerrit T S; Sprangers, Katrien; Cuypers, Bart; Laukens, Kris; Blust, Ronny; Husson, Steven J

Toxicogenomics of the flame retardant tris (2-butoxyethyl) phosphate in HepG2 cells using RNA-seq Journal Article

In: Toxicology in Vitro, 46 , pp. 178 - 188, 2018, ISSN: 0887-2333.

Abstract | Links | BibTeX | Altmetric | Tags: RNA-seq, transcriptomics

Cuypers, Bart; Berg, Maya; Imamura, Hideo; Dumetz, Franck; Muylder], Géraldine [De; Domagalska, Malgorzata A; Rijal, Suman; Bhattarai, Narayan Raj; Maes, Ilse; Sanders, Mandy; Cotton, James A; Meysman, Pieter; Laukens, Kris; Dujardin, Jean-Claude

Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent Journal Article

In: Infection, Genetics and Evolution, 62 , pp. 170 - 178, 2018, ISSN: 1567-1348.

Abstract | Links | BibTeX | Altmetric | Tags: genomics, LC-MS, metabolomics, multi-omics

2017

Cuypers, Bart; Domagalska, Malgorzata A; Meysman, Pieter; de Muylder, Géraldine; Vanaerschot, Manu; Imamura, Hideo; Dumetz, Franck; Verdonckt, Thomas Wolf; Myler, Peter J; Ramasamy, Gowthaman; Laukens, Kris; Dujardin, Jean-Claude

Multiplexed Spliced-Leader Sequencing: A high-throughput, selective method for RNA-seq in Trypanosomatids Journal Article

In: Scientific Reports, 7 (1), pp. 3725, 2017, ISSN: 2045-2322.

Abstract | Links | BibTeX | Altmetric | Tags: leishmania, RNA-seq, transcriptomics

Cuypers, Bart; den Broeck, Frederik Van; Reet, Nick Van; Meehan, Conor J; Cauchard, Julien; Wilkes, Jonathan M; Claes, Filip; Goddeeris, Bruno; Birhanu, Hadush; Dujardin, Jean-Claude; Laukens, Kris; Büscher, Philippe; Deborggraeve, Stijn

Genome-Wide SNP Analysis Reveals Distinct Origins of Trypanosoma evansi and Trypanosoma equiperdum Journal Article

In: Genome Biology and Evolution, 9 (8), pp. 1990-1997, 2017, ISSN: 1759-6653.

Abstract | Links | BibTeX | Altmetric | Tags: evolution, genomics

Jara, Marlene; Berg, Maya; Caljon, Guy; de Muylder, Geraldine; Cuypers, Bart; Castillo, Denis; Maes, Ilse; del Orozco, María Carmen; Vanaerschot, Manu; Dujardin, Jean-Claude; Arevalo, Jorge

Macromolecular biosynthetic parameters and metabolic profile in different life stages of Leishmania braziliensis: Amastigotes as a functionally less active stage Journal Article

In: PLOS ONE, 12 (7), pp. 1-22, 2017.

Abstract | Links | BibTeX | Altmetric | Tags: LC-MS, leishmania, metabolomics

Dumetz, F; Imamura, H; Sanders, M; Seblova, V; Myskova, J; Pescher, P; Vanaerschot, M; Meehan, C J; Cuypers, B; Muylder, G De; Späth, G F; Bussotti, G; Vermeesch, J R; Berriman, M; Cotton, J A; Volf, P; Dujardin, J C; Domagalska, M A

Modulation of Aneuploidy in Leishmania donovani during Adaptation to Different In Vitro and In Vivo Environments and Its Impact on Gene Expression Journal Article

In: mBio, 8 (3), 2017.

Abstract | Links | BibTeX | Altmetric | Tags: genomics, leishmania, multi-omics, RNA-seq, transcriptomics

2016

Imamura, Hideo; Downing, Tim; den Broeck, Frederik Van; Sanders, Mandy J; Rijal, Suman; Sundar, Shyam; Mannaert, An; Vanaerschot, Manu; Berg, Maya; Muylder, Géraldine De; Dumetz, Franck; Cuypers, Bart; Maes, Ilse; Domagalska, Malgorzata; Decuypere, Saskia; Rai, Keshav; Uranw, Surendra; Bhattarai, Narayan Raj; Khanal, Basudha; Prajapati, Vijay Kumar; Sharma, Smriti; Stark, Olivia; Schönian, Gabriele; Koning, Harry P De; Settimo, Luca; Vanhollebeke, Benoit; Roy, Syamal; Ostyn, Bart; Boelaert, Marleen; Maes, Louis; Berriman, Matthew; Dujardin, Jean-Claude; Cotton, James A

Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent Journal Article

In: eLife, 5 , pp. e12613, 2016, ISSN: 2050-084X.

Abstract | Links | BibTeX | Altmetric | Tags: drug-resistance, evolution, genomics

Wilkins, Katie; Hassan, Mehedi; Francescatto, Margherita; Jespersen, Jakob; Parra, Gonzalo R; Cuypers, Bart; DeBlasio, Dan; Junge, Alexander; Jigisha, Anupama; Rahman, Farzana; Laenen, Griet; Willems, Sander; Thorrez, Lieven; Moreau, Yves; Raju, Nagarajan; Chothani, Sonia Pankaj; Ramakrishnan, C; Sekijima, Masakazu; Gromiha, Michael M; Slator, Paddy J; Burroughs, Nigel J; Szałaj, Przemysław; Tang, Zhonghui; Michalski, Paul; Luo, Oskar; Li, Xingwang; Ruan, Yijun; Plewczynski, Dariusz; Fiscon, Giulia; Weitschek, Emanuel; Ciccozzi, Massimo; Bertolazzi, Paola; Felici, Giovanni; Meysman, Pieter; Vanaerschot, Manu; Berg, Maya; Imamura, Hideo; Dujardin, Jean-Claude; Laukens, Kris; Domanova, Westa; Krycer, James R; Chaudhuri, Rima; Yang, Pengyi; Vafaee, Fatemeh; Fazakerley, Daniel J; Humphrey, Sean J; James, David E; Kuncic, Zdenka

Highlights from the 11th ISCB Student Council Symposium 2015 Journal Article

In: BMC Bioinformatics, 17 (3), pp. 95, 2016, ISSN: 1471-2105.

Abstract | Links | BibTeX | Altmetric | Tags:

Mondelaers, Annelies; Sanchez-Cañete, Maria P; Hendrickx, Sarah; Eberhardt, Eline; Garcia-Hernandez, Raquel; Lachaud, Laurence; Cotton, James; Sanders, Mandy; Cuypers, Bart; Imamura, Hideo; Dujardin, Jean-Claude; Delputte, Peter; Cos, Paul; Caljon, Guy; Gamarro, Francisco; Castanys, Santiago; Maes, Louis

Genomic and Molecular Characterization of Miltefosine Resistance in Leishmania infantum Strains with Either Natural or Acquired Resistance through Experimental Selection of Intracellular Amastigotes Journal Article

In: PLOS ONE, 11 (4), pp. 1-15, 2016.

Abstract | Links | BibTeX | Altmetric | Tags: genomics, leishmania

Cuypers, Bart; Lecordier, Laurence; Meehan, Conor J; den Broeck, Frederik Van; Imamura, Hideo; Büscher, Philippe; Dujardin, Jean-Claude; Laukens, Kris; Schnaufer, Achim; Dewar, Caroline; Lewis, Michael; Balmer, Oliver; Azurago, Thomas; Kyei-Faried, Sardick; Ohene, Sally-Ann; Duah, Boateng; Homiah, Prince; Mensah, Ebenezer Kofi; Anleah, Francis; Franco, Jose Ramon; Pays, Etienne; Deborggraeve, Stijn

Apolipoprotein L1 Variant Associated with Increased Susceptibility to Trypanosome Infection Journal Article

In: mBio, 7 (2), 2016.

Abstract | Links | BibTeX | Altmetric | Tags: evolution, genomics

Cuypers, B; Jacobsen, A; Siranosian, B; Schwahn, K; Conard, AM; Aben, N; Hassan, M; Fatima, N; Hermans, SMA; Woghiren, M; Meysman, P; Rahman, F; Jigisha, A

Highlights from the ISCB Student Council Symposia in 2016 Journal Article

In: F1000Research, 5 (2852), 2016.

Links | BibTeX | Altmetric | Tags:

2015

Berg, Maya; Garc'ia-Hernández, Raquel; Cuypers, Bart; Vanaerschot, Manu; Manzano, José I; Poveda, José A; Ferragut, José A; Castanys, Santiago; Dujardin, Jean-Claude; Gamarro, Francisco

Experimental Resistance to Drug Combinations in Leishmania donovani: Metabolic and Phenotypic Adaptations Journal Article

In: Antimicrobial Agents and Chemotherapy, 59 (4), pp. 2242–2255, 2015, ISSN: 0066-4804.

Abstract | Links | BibTeX | Altmetric | Tags: LC-MS, leishmania, leishmaniasis, metabolomics

Gryseels, Sophie; Rieger, Toni; Oestereich, Lisa; Cuypers, Bart; Borremans, Benny; Makundi, Rhodes; Leirs, Herwig; Günther, Stephan; de Bellocq], Joëlle [Goüy

Gairo virus, a novel arenavirus of the widespread Mastomys natalensis: Genetically divergent, but ecologically similar to Lassa and Morogoro viruses Journal Article

In: Virology, 476 , pp. 249 - 256, 2015, ISSN: 0042-6822.

Abstract | Links | BibTeX | Altmetric | Tags: evolution, virology

2013

Berg, Maya; Vanaerschot, Manu; Jankevics, Andris; Cuypers, Bart; Maes, Ilse; Mukherjee, Sandip; Khanal, Basudha; Rijal, Suman; Roy, Syamal; Opperdoes, Fred; Breitling, Rainer; Dujardin, Jean-Claude

Metabolic adaptations of Leishmania donovani in relation to differentiation, drug resistance, and drug pressure Journal Article

In: Molecular Microbiology, 90 (2), pp. 428-442, 2013.

Abstract | Links | BibTeX | Altmetric | Tags: drug-resistance, LC-MS, leishmania, metabolomics

Rai, Keshav; Cuypers, Bart; Bhattarai, Narayan Raj; Uranw, Surendra; Berg, Maya; Ostyn, Bart; Dujardin, Jean-Claude; Rijal, Suman; Vanaerschot, Manu

Relapse after Treatment with Miltefosine for Visceral Leishmaniasis Is Associated with Increased Infectivity of the Infecting Leishmania donovani Strain Journal Article

In: mBio, 4 (5), 2013.

Abstract | Links | BibTeX | Altmetric | Tags: drug-resistance, leishmania

Berg, Maya; Vanaerschot, Manu; Jankevics, Andris; Cuypers, Bart; Breitling, Rainer; Dujardin, Jean-Claude

LC-MS Metabolomics from study design to data-analysis – using a versatile pathogen as a test case Journal Article

In: Computational and Structural Biotechnology Journal, 4 (5), pp. e201301002, 2013, ISSN: 2001-0370.

Abstract | Links | BibTeX | Altmetric | Tags: LC-MS, leishmania, metabolomics