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QSP Designer: Quantitative systems pharmacology modeling with modular biological process map notation and multiple language code generation2023 CPT Pharmacometrics & Systems Pharmacology article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
David M. Hollinshead, Piet H. van der Graaf, Andrzej M. Kierzek
14citations -
Hybrid Chains: A Collaboration of Ubiquitin and Ubiquitin-Like Modifiers Introducing Cross-Functionality to the Ubiquitin Code2020 Frontiers in Chemistry article Biochemistry, Genetics and Molecular Biology Ubiquitin and proteasome pathways Open access
David A. Pérez Berrocal, Katharina F. Witting, Huib Ovaa, Monique P. C. Mulder
58citations -
Editorial: Protecting the code: DNA double-strand break repair pathway choice2022 Frontiers in Genetics editorial Biochemistry, Genetics and Molecular Biology DNA Repair Mechanisms Open access
Jenny Kaur Singh, Sylvie M. Noordermeer, Judit Jiménez-Sáinz, David G. Maranon, Matthias Altmeyer
2citations -
How bacterial pathogens of the gastrointestinal tract use the mucosal glyco-code to harness mucus and microbiota: New ways to study an ancient bag of tricks2020 International Journal of Medical Microbiology article Biochemistry, Genetics and Molecular Biology Gut microbiota and health Open access
Christine Josenhans, Johannes Müthing, Lothar Elling, Sina Bartfeld, Herbert Schmidt
40citations -
SPARKI: a tool for the statistical analysis of pathogen identification results2025 Bioinformatics article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Jacqueline Marcia Boccacino, Martin Del Castillo Velasco‐Herrera, Mathew A. Beale, Jamie Billington, Ian Vermes, Sofia Obolenski, +8 more
2citations -
LncRNA-BERT: An RNA Language Model for Classifying Coding and Long Non-Coding RNA2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Luuk Romeijn, Davy Cats, Katherine Wolstencroft, Hailiang Mei
4citations -
A perspective on causality assessment in epigenetic research on neurodegenerative disorders2022 Neural Regeneration Research article Biochemistry, Genetics and Molecular Biology Epigenetics and DNA Methylation Open access
Philippos Koulousakis, Assia Tiane, Niels Hellings, Jos Prickaerts, Daniël van den Hove, Tim Vanmierlo
8citations -
Identifying signs and symptoms of AL amyloidosis in electronic health records using natural language processing, diagnosis codes, and manually abstracted registry data2023 American Journal of Hematology article Biochemistry, Genetics and Molecular Biology Amyloidosis: Diagnosis, Treatment, Outcomes Open access
Eli Silvert, Laura Hester, Eshwan Ramudu, Colin Pawlowski, Britte Kranenburg, Francis K. Buadi, +7 more
5citations -
Comprehensive lincRNA Transcriptome in Acute Myeloid Leukemia: Integrating Known and Newly Identified lincRNAs Across Pediatric and Adult Cohorts2026 Non-Coding RNA article Biochemistry, Genetics and Molecular Biology Cancer-related molecular mechanisms research Open access
Saioa Arza-Apalategi, Daan Gilissen, Anne van der Grinten, Seline N. van den Oever, Erik B. van den Akker, Marieke Griffioen, +4 more
0citations -
Multi-omics approach dissects cis-regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy2022 The American Journal of Human Genetics article Biochemistry, Genetics and Molecular Biology Retinal Development and Disorders Open access cited by 1 patent
Stijn Van de Sompele, Kent W. Small, Munevver Burcu Cicekdal, Víctor López-Soriano, Eva D’haene, Fadi S. Shaya, +23 more
33citations -
Artificial Intelligence Approach for the Discovery of Autoantigen Recognition By B-Cell Lymphomas2023 Blood conference-abstract Biochemistry, Genetics and Molecular Biology vaccines and immunoinformatics approaches
David Medina, Julieta Sepúlveda-Yáñez, Diego Álvarez-Saravia, Roberto Uribe-Paredes, Hendrik Veelken, Marcelo A. Navarrete
3citations -
Multi-omics profiling, in vitro and in vivo enhancer assays dissect the cis -regulatory mechanisms underlying North Carolina macular dystrophy, a retinal enhanceropathy2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Retinal Development and Disorders Open access
Stijn Van de Sompele, Kent W. Small, Munevver Burcu Cicekdal, Víctor López-Soriano, Eva D’haene, Fadi S. Shaya, +23 more
3citations -
Handling of spurious sequences affects the outcome of high-throughput 16S rRNA gene amplicon profiling2021 Zenodo (CERN European Organization for Nuclear Research) article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Sandra Reitmeier, Thomas C. A. Hitch, Nicole Simone Treichel, Nikolaos Fikas, Bela Hausmann, Amanda E. Ramer‐Tait, +5 more
0citations -
FIGURE 2 in Consideration of range-wide variation is critical when splitting widely distributed species: the case of the proposed Iguana melanoderma2026 Zenodo (CERN European Organization for Nuclear Research) other Biochemistry, Genetics and Molecular Biology Genetic diversity and population structure Open access
Matthijs P. van den Burg, Kevin De Queiroz, MARINA VENTAYOL, Adolphe O. Debrot, Catherine L. Malone
0citations -
Genolator: A Multimodal Large Language Model Fusing Natural Language, Genomic, and Structural Tokens for Protein Function Interpretation2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
Martin Danner, Tanhim Islam, Matthias Begemann, Florian Kraft, Miriam Elbracht, Ingo Kurth, +1 more
0citations -
Genolator enables protein function interpretation using a multimodal large language model fusing genomic and structural interpretation with natural language interaction2026 Genome biology article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
Martin Danner, Tanhim Islam, Matthias Begemann, Florian Kraft, Miriam Elbracht, Ingo Kurth, +1 more
0citations -
Towards complete and error-free genome assemblies of all vertebrate species2021 Nature article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access cited by 1 patent
Arang Rhie, Shane McCarthy, Olivier D. Fedrigo, Joana Damas, Giulio Formenti, Sergey Koren, +93 more
3,333citations