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Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Matthias A. Schmitz, Nicholas J Dimonaco, Thomas Clavel, Thomas C. A. Hitch
1citations -
A hybrid model combining evolutionary probability and machine learning leverages data-driven protein engineering2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Protein Structure and Dynamics Open access
Alexander-Maurice Illig, Niklas E. Siedhoff, Ulrich Schwaneberg, Mehdi D. Davari
11citations -
Phyletic distribution and diversification of the Phage Shock Protein stress response system in bacteria and archaea2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bacterial Genetics and Biotechnology Open access
Philipp F. Popp, Vadim M. Gumerov, Ekaterina P. Andrianova, Lisa Bewersdorf, Thorsten Mascher, Igor B. Zhulin, +1 more
5citations -
Ten numbers from the Laplace–Beltrami spectrum facilitate training-free classification of protein structures based on surface shape2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Protein Structure and Dynamics Open access
Miriam Fernández-Giro Muñoz, Jessica Emonts, Benjamin Berkels, Johannes F. Buyel
0citations -
PMIpred: A physics-informed web server for quantitative Protein-Membrane Interaction prediction2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
Niek van Hilten, Nino Verwei, Jeroen Methorst, Carsten Nase, Andrius Bernatavicius, Herre Jelger Risselada
4citations -
Cell type matching across species using protein embeddings and transfer learning2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Kirti Biharie, Lieke Michielsen, Marcel J. T. Reinders, Ahmed Essam Mahfouz
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 -
Modeling the Orthosteric Binding Site of the G Protein-Coupled Odorant Receptor OR5K12022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Receptor Mechanisms and Signaling Open access
Alessandro Nicoli, Franziska Haag, Patrick Marcinek, Ruiming He, Johanna Kreißl, Jörg Stein, +5 more
2citations -
A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics2020 bioRxiv (Cold Spring Harbor Laboratory) preprint Computer Science Computational Drug Discovery Methods Open access
Jonas Goßen, Simone Albani, Anton Hanke, Benjamin Philipp Joseph, Cathrine C. Bergh, Maria Kuzikov, +14 more
5citations -
Intronization enhances expression of S-protein and other transgenes challenged by cryptic splicing2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology RNA Research and Splicing Open access cited by 2 patents
Kärt Tomberg, Liliana Antunes, Yangyang Pan, Jacob Hepkema, Dimitrios A. Garyfallos, Ahmed Essam Mahfouz, +1 more
1citations -
Fasciola hepatica Fatty Acid Binding Protein 1 modulates T cell polarization by promoting dendritic cell thrombospondin-1 secretion without affecting metabolic homeostasis in obese mice2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Immunology and Microbiology Parasites and Host Interactions Open access
Anna Zawistowska‐Deniziak, Joost M. Lambooij, Alicja Kalinowska, Thiago A. Patente, Maciej Łapiński, Hendrik J.P. van der Zande, +9 more
0citations -
A single-nucleotide change in the Kozak sequence enhances protein expression2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology RNA and protein synthesis mechanisms Open access
Renzo A. Knol, Tahmina Fariaby, Eveline A. de Vlieger, Alexander Kros, Bram Slütter
0citations -
A β-Hairpin Epitope as Novel Structural Requirement for Protein Arginine Rhamnosylation2020 ChemRxiv preprint Biochemistry, Genetics and Molecular Biology Glycosylation and Glycoproteins Research Open access
Nathaniel I. Martin, Marthe T. C. Walvoort, Liubov Yakovlieva, Thomas Keith Wood, Johan Kemmink, Franziska Koller, +2 more
0citations -
Systems-wide analysis of the GATC-binding nucleoid-associated protein Gbn and its impact on Streptomyces development2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Bacterial Genetics and Biotechnology Open access
Chao Du, Joost J. Willemse, Amanda M. Erkelens, Víctor J. Carrión, Remus Thei Dame, Gilles P. van Wezel
0citations -
Gene and protein sequence features augment HLA class I ligand predictions2023 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology vaccines and immunoinformatics approaches Open access
Kaspar Bresser, Benoît P. Nicolet, Anita Jekő, Wei Wu, Fabricio Loayza‐Puch, Reuven Agami, +3 more
0citations -
Fold first, ask later: structure-informed function annotation of Pseudomonas phage proteins2025 bioRxiv (Cold Spring Harbor Laboratory) preprint Environmental Science Bacteriophages and microbial interactions Open access
Hannelore Longin, George Spyro Bouras, Susanna R. Grigson, Robert Alan Edwards, Hanne Hendrix, Rob Lavigne, +1 more
0citations -
BRCA2 and RAD54B FxPP motifs Bind DMC1 Filaments through Persistent and Transient Interfaces2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology DNA Repair Mechanisms Open access
Dupaigne Pauline, Simona M. Miron, Sonia Baconnais, Pierre Legrand, Sari E. van Rossum-Fikkert, Koichi Sato, +7 more
0citations -
Structural and functional characterization of SARS-CoV-2 RBD domains produced in mammalian cells2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine SARS-CoV-2 and COVID-19 Research Open access
Christoph Gstöttner, Tao Zhang, Anja Resemann, Sophia Ruben, Stuart Pengelley, Detlev Suckau, +3 more
5citations -
Human TRMT2A methylates tRNA and contributes to translation fidelity2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology RNA modifications and cancer Open access
Monika Witzenberger, Sandra Burczyk, David Settele, Wieland Mayer, Luisa M. Welp, Matthias Heiß, +8 more
4citations -
Investigating Enzyme Function by Geometric Matching of Catalytic Motifs2026 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Protein Structure and Dynamics Open access
Ioannis G. Riziotis, Martin F. Larralde, António J. M. Ribeiro, Georg Zeller, Janet M. Thornton
2citations -
Physics-based inverse design of cholesterol attracting transmembrane helices reveals a paradoxical role of hydrophobic length2021 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Lipid Membrane Structure and Behavior Open access
Jeroen Methorst, Nino Verwei, Christian Hoffmann, Paweł Chodnicki, Roberto Sansevrino, Han Wang, +7 more
7citations