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 Guillén G; 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 Open Access

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 Open Access

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

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 De H; 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

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 Open Access

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 Open Access

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; textquoteright, Erika D; 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 Preprint

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 Open Access

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 Open Access

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 Open Access

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 Open Access

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 Open AccessEditorial

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 Open AccessEditorial

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 Open Access

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

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; textquoteright, E D; Maes, I; Domagalska, M A; Clos, J; Dujardin, J -C; Muylder, De G

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

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

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 Open Access

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 Open Access

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 Open Access

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 Open Access

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, De G; 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 Open Access

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 De P; 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 Open Access

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; ł, Przemys{ł}aw Sza; 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 Open AccessEditorial

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 Open Access

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 Open Access

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 Open AccessEditorial

F1000Research, 5 (2852), 2016.

Links | BibTeX | Altmetric | Tags:

2015

Berg, Maya; 'i, Raquel Garc; 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 Open Access

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 Open Access

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 Open Access

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 Open Access

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 Open Access

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

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