Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment by Mohammed El-Kebir, Jaap Heringa, Gunnar W. Klau

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CLUB-MARTINI: Selecting Favourable Interactions amongst Available Candidates, a Coarse-Grained Simulation Approach to Scoring Docking Decoys. by Qingzhen Hou, Marc F Lensink, Jaap Heringa, K Anton Feenstra

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Quantifying the displacement of mismatches in multiple sequence alignment benchmarks. by Punto Bawono, Arjan van der Velde, Sanne Abeln, Jaap Heringa

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Towards a knowledge graph for pre-/probiotics and microbiota–gut–brain axis diseases by Ting Liu, Gongjin Lan, K. Anton Feenstra, Zhisheng Huang, Jaap Heringa

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Motif-Aware PRALINE: Improving the alignment of motif regions. by Maurits Dijkstra, Punto Bawono, Sanne Abeln, K Anton Feenstra, Wan Fokkink, Jaap Heringa

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Construction and Experimental Validation of a Petri Net Model of Wnt/β-Catenin Signaling. by Annika Jacobsen, Nika Heijmans, Folkert Verkaar, Martine J Smit, Jaap Heringa, Renée van Amerongen, K Anton Feenstra

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HIV-1 replication fitness of HLA-B*57/58:01 CTL escape variants is restored by the accumulation of compensatory mutations in gag. by Esther F Gijsbers, K Anton Feenstra, Ad C van Nuenen, Marjon Navis, Jaap Heringa, Hanneke Schuitemaker, Neeltje A Kootstra

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The ability of transcription factors to differentially regulate gene expression is a crucial component of the mechanism underlying inversion, a frequently observed genetic interact... by Saman Amini, Annika Jacobsen, Olga Ivanova, Philip Lijnzaad, Jaap Heringa, Frank C P Holstege, K Anton Feenstra, Patrick Kemmeren

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FluxSimulator: An R Package to Simulate Isotopomer Distributions in Metabolic Networks by Thomas W. Binsl, Katharine M. Mullen, Ivo H. M. van Stokkum, Jaap Heringa, Johannes H. G. M. van Beek

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A protein prioritization approach tailored for the FA/BRCA pathway. by Anneke Haitjema, Bernd W Brandt, Najim Ameziane, Patrick May, Jaap Heringa, Johan P de Winter, Hans Joenje, Josephine C Dorsman

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Correction: A Protein Prioritization Approach Tailored for the FA/BRCA Pathway. by Anneke Haitjema, Bernd W. Brandt, Najim Ameziane, Patrick May, Jaap Heringa, Johan P. de Winter, Hans Joenje, Josephine C. Dorsman

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Author Correction: Applying federated learning to combat food fraud in food supply chains by Anand Gavai, Yamine Bouzembrak, Wenjuan Mu, Frank Martin, Rajaram Kaliyaperumal, Johan van Soest, Ananya Choudhury, Jaap Heringa, Andre Dekker, Hans J. P. Marvin

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Applying federated learning to combat food fraud in food supply chains by Anand Gavai, Yamine Bouzembrak, Wenjuan Mu, Frank Martin, Rajaram Kaliyaperumal, Johan van Soest, Ananya Choudhury, Jaap Heringa, Andre Dekker, Hans J. P. Marvin

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Integration of EGA secure data access into Galaxy [version 1; referees: 2 approved] by Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J.A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer, Andrew Stubbs, Jordi Rambla, Dylan Spalding, Sanne Abeln

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Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data [version 1; referees: 2 approved] by Chao Zhang, Jochem Bijlard, Christine Staiger, Serena Scollen, David van Enckevort, Youri Hoogstrate, Alexander Senf, Saskia Hiltemann, Susanna Repo, Wibo Pipping, Mariska Bierkens, Stefan Payralbe, Bas Stringer, Jaap Heringa, Andrew Stubbs, Luiz Olavo Bonino Da Silva Santos, Jeroen Belien, Ward Weistra, Rita Azevedo, Kees van Bochove, Gerrit Meijer, Jan-Willem Boiten, Jordi Rambla, Remond Fijneman, J. Dylan Spalding, Sanne Abeln

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