FM
Frederikke Isa Marin
cs.LGq-bio.GNAntibody modelingCDR3 modelingClusteringCoevolutionComplementarity Determining RegionsComputational BiologyComputational designDeepH3
On Valency
published · living versionsW_yaar2ca2·v1 · currentpublished
BEND 2.0: Benchmarking the Capabilities Needed to Design DNA
with Andreas Bjerregaard, Rachael DeVries, Dionysia Danai Brilli, Panagiotis Antoniadis +4
1 version
Preprints & journals
9 papers in the corpus · 2019–2026RAGenome: Scaling Retrieval-Based Genomic Language Models to Long Contexts2610.11761v1 · Frederikke Isa Marin, Panagiotis Antoniadis, Dionysia Danai Brilli et al.2026 · 0 citationsarXiv
Annotating the genome at single-nucleotide resolution with DNA foundation models.41162646 · de Almeida, Bernardo P, Dalla-Torre, Hugo, Richard, Guillaume et al.2025 · 30 citationsNature methods. 2025;22(11):2301-2315
Gene finding revisited: improved robustness through structured decoding from learned embeddings2505.03377v1 · Frederikke I. Marin, Dennis Pultz, Wouter Boomsma2025 · 0 citationsarXiv
BEND: Benchmarking DNA Language Models on biologically meaningful tasks2311.12570v4 · Frederikke Isa Marin, Felix Teufel, Marc Horlacher et al.2023 · 31 citationsarXiv
Computational Modeling of Antibody and T-Cell Receptor (CDR3 Loops).36346586 · Marin, Frederikke I, Marcatili, Paolo2022 · 2 citationsMethods in molecular biology (Clifton, N.J.). 2023;2552:83-100
Design of a Protein with Improved Thermal Stability by an Evolution-Based Generative Model.36259321 · Tian, Pengfei, Lemaire, Adrien, Sénéchal, Fabien et al.2022 · 13 citationsAngewandte Chemie (International ed. in English). 2022;61(50):e202202711
Computational and Experimental Assessment of Backbone Templates for Computational Redesign of the Thioredoxin Fold.34592819 · Marin, Frederikke Isa, Johansson, Kristoffer Enøe, O'Shea, Charlotte et al.2021 · 5 citationsThe journal of physical chemistry. B. 2021;125(40):11141-11149
T cell receptor sequence clustering and antigen specificity.32952933 · Vujovic, Milena, Degn, Kristine Fredlund, Marin, Frederikke Isa et al.2025 · 20 citationsComputational and structural biotechnology journal. 2020;18:2166-2173
Toward mechanistic models for genotype-phenotype correlations in phenylketonuria using protein stability calculations.30648773 · Scheller, Rasmus, Stein, Amelie, Nielsen, Sofie V et al.2020 · 59 citationsHuman mutation. 2019;40(4):444-457
Career total: 12 works. 9 are in this corpus.
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