Publications databank
Databank
Everything the lab has published or released: papers, software, datasets and protocols. Each entry links to the paper and to the code, data and preprints behind it.
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LiraSearch-ultrafast ligand shape and electrostatic matching server
Montalvao RW, Bray S, Verissimo-Alves M, Cubero E, Gruning B, Pinheiro VB. Bioinformatics Advances (2026).
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Beyond CEN.PK – parallel engineering of selected S. cerevisiae strains reveals that superior chassis strains require different engineering approaches for limonene production
Zhu Y, Yogiswara S, Willekens A, Gérardin A, Lavigne R, Goossens A, Pinheiro V, Dai Z, Verstrepen K. Metabolic Engineering (2025).
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A versatile platform for combinatorial antibody library cloning and NGS-based quality control with high accuracy
Zhang Z, D’Hondt S, Van der Kant R, Hermans G, Geukens N, Pinheiro VB, Schymkowitz J, Rousseau F, Dewilde M. Nucleic Acids Research (2025).
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Structural insights into the morpholino nucleic acid/RNA duplex using the new XNA builder Ducque in a molecular modeling pipeline
Rihon J, Mattelaer CA, Montalvao RW, Froeyen M, Pinheiro VB, Lescrinier E. Nucleic Acids Research (2024).
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Rational evolution for altering the ligand preference of estrogen receptor alpha
Eerlings R, Gupta P, Lee XJ, Nguyen T, El Kharraz S, Handle F, Smeets E, Moris L, Devlies W, Vandewinkel B, Thiry I, Ta DT, Gorkovskiy A, Voordeckers K, Henckaerts E, Pinheiro VB, Claessens F, Verstrepen K, Voet A, Helsen C. Protein Science (2024).
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From competition to cure: the development of live biotherapeutic products for anticancer therapy in the iGEM competition
Van den Berghe L, Masschelein J, Bernardes Pinheiro V. Frontiers in Bioengineering and Biotechnology (2024).
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Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification
van de Velde C, Joseph C, Biclot A, Huys G, Bernardes Pinheiro V, Bernaerts K, Raes J, Faust K. ISME Communications (2022).
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Antha-Guided Automation of Darwin Assembly for the Construction of Bespoke Gene Libraries
Handal-Marquez P, Koch M, Kestemont D, Arangundy-Franklin S, Pinheiro VB. Methods in Molecular Biology (2022).
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Directed evolution of colE1 plasmid replication compatibility: a fast tractable tunable model for investigating biological orthogonality
Chaillou S, Stamou PE, Torres LL, Riesco AB, Hazelton W, Pinheiro VB. Nucleic Acids Research (2022).
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Structural Studies of HNA Substrate Specificity in Mutants of an Archaeal DNA Polymerase Obtained by Directed Evolution
Samson C, Legrand P, Tekpinar M, Rozenski J, Abramov M, Holliger P, Pinheiro VB, Herdewijn P, Delarue M. Biomolecules (2020).
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Beneath the XNA world: Tools and targets to build novel biology
Handal-Marquez P, Anupama A, Pezo V, Marlière P, Herdewijn P, Pinheiro VB. Current Opinion in Systems Biology (2020).
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Two New Plasmid Post-segregational Killing Mechanisms for the Implementation of Synthetic Gene Networks in Escherichia coli
Fedorec AJH, Ozdemir T, Doshi A, Ho YK, Rosa L, Rutter J, Velazquez O, Pinheiro VB, Danino T, Barnes CP. iScience (2019).
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Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins
Vanmeert M, Razzokov J, Mirza MU, Weeks SD, Schepers G, Bogaerts A, Rozenski J, Froeyen M, Herdewijn P, Pinheiro V, Lescrinier E. Nucleic Acids Research (2019).
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Kinetic analysis of N-alkylaryl carboxamide hexitol nucleotides as substrates for evolved polymerases
Renders M, Dumbre S, Abramov M, Kestemont D, Margamuljana L, Largy E, Cozens C, Vandenameele J, Bernardes Pinheiro V, Toye D, Frère JM, Herdewijn P. Nucleic Acids Research (2019).
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Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology
Vecchioni S, Capece MC, Toomey E, Le N, Ray A, Greenberg A, Fujishima K, Urbina J, Paulino-Lima IG, Pinheiro V, Shih J, Wessel G, Wind SJ, Rothschild L. Scientific Reports (2019).
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XNA ligation using T4 DNA ligase in crowding conditions
Kestemont D, Renders M, Leonczak P, Abramov M, Schepers G, Pinheiro VB, Rozenski J, Herdewijn P. Chemical Communications (2018).
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Phosphonomethyl Oligonucleotides as Backbone-Modified Artificial Genetic Polymers
Liu C, Cozens C, Jaziri F, Rozenski J, Marechal A, Dumbre S, Pezo V, Marliere P, Pinheiro VB, Groaz E, Herdewijn P. Journal of the American Chemical Society (2018).
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Methylated Nucleobases: Synthesis and Evaluation for Base Pairing In Vitro and In Vivo
Jabgunde AM, Jaziri F, Bande O, Froeyen M, Abramov M, Hoai N, Schepers G, Lescrinier E, Pinheiro VB, Pezo V, Marliere P, Herdewijn P. Chemistry – A European Journal (2018).
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E. coli surface display of streptavidin for directed evolution of an allylic deallylase
Heinisch T, Schwizer F, Garabedian B, Csibra E, Jeschek M, Vallapurackal J, Pinheiro VB, Marliere P, Panke S, Ward TR. Chemical Science (2018).
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Isoguanine and 5-Methyl-Isocytosine Bases, In Vitro and In Vivo
Bande O, Abou El Asrar R, Braddick D, Dumbre S, Pezo V, Schepers G, Pinheiro VB, Lescrinier E, Holliger P, Marlière P, Herdewijn P. Chemistry – A European Journal (2015).
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Catalysts from synthetic genetic polymers
Taylor AI, Pinheiro VB, Smola MJ, Morgunov AS, Peak-Chew S, Cozens C, Weeks KM, Herdewijn P, Holliger P. Nature (2015).
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Synthetic genetic polymers capable of heredity and evolution
Pinheiro VB, Taylor AI, Cozens C, Abramov M, Renders M, Zhang S, Chaput JC, Wengel J, Peak-Chew SY, McLaughlin SH, Herdewijn P, Holliger P. Science (2012).
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Evolving a Polymerase for Hydrophobic Base Analogues
Loakes D, Gallego J, Pinheiro VB, Kool ET, Holliger P. Journal of the American Chemical Society (2009).