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EchoGO: Traceable Functional Interpretation Across Annotation Contexts2026 Zenodo (CERN European Organization for Nuclear Research) software Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Camilo Escobar-Sierra, Felix Langschied, Angelina Miller, Pedro A. Inostroza
0citations -
GeneSurfer Enables Transcriptome-wide Exploration and Functional Annotation of Gene Co-expression Modules in 3D Spatial Transcriptomics Data2024 bioRxiv (Cold Spring Harbor Laboratory) preprint Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
0citations -
A thorough analysis of the contribution of experimental, derived and sequence-based predicted protein-protein interactions for functional annotation of proteins2020 PLoS ONE article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Stavros Makrodimitris, Marcel J. T. Reinders, Roeland C. H. J. van Ham
4citations -
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 -
Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element2021 The American Journal of Human Genetics article Biochemistry, Genetics and Molecular Biology Genomics and Chromatin Dynamics Open access
Joseph S. Baxter, Nichola Johnson, Katarzyna Tomczyk, Andrea Gillespie, Sarah L. Maguire, Rachel Brough, +93 more
9citations -
Variants of uncertain clinical significance in hereditary breast and ovarian cancer genes: best practices in functional analysis for clinical annotation2020 Journal of Medical Genetics article Biochemistry, Genetics and Molecular Biology BRCA gene mutations in cancer Open access
Álvaro N.A. Monteiro, Arne Nedergaard Kousholt, Diana Eccles, Gaël A. Millot, Jean‐Yves Masson, Marjanka K. Schmidt, +5 more
48citations -
Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access cited by 2 patents
Amelia Villegas-Morcillo, Stavros Makrodimitris, Roeland C. H. J. van Ham, Angel Manuel Gomez, Marcel J. T. Reinders
137citations -
Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing2022 Applied and Environmental Microbiology article Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
Matthias Schmidt, Allison N. Pearson, Matthew R. Incha, Mitchell G. Thompson, Edward E. K. Baidoo, Ramu D. Kakumanu, +5 more
27citations -
mOTUs annotation database (v4)2026 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Hans-Joachim Ruscheweyh, Marija Dmitrijeva, Lilith Feer, Samuel Miravet‐Verde, Anna Sintsova, Daniel R. Mende, +2 more
0citations -
mOTUs annotation database (v4)2025 Zenodo (CERN European Organization for Nuclear Research) dataset Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Hans‐Joachim Ruscheweyh, Marija Dmitrijeva, Lilith Feer, Samuel Miravet‐Verde, Anna Sintsova, Daniel R. Mende, +1 more
0citations -
Precision Activity‐Based α‐Amylase Probes for Dissection and Annotation of Linear and Branched‐Chain Starch‐Degrading Enzymes2024 Angewandte Chemie International Edition article Biochemistry, Genetics and Molecular Biology Enzyme Catalysis and Immobilization Open access
Isabelle B. Pickles, Yurong Chen, Olga V. Moroz, Haley A. Brown, Casper de Boer, Zachary Armstrong, +6 more
10citations -
Precision Activity‐Based α‐Amylase Probes for Dissection and Annotation of Linear and Branched‐Chain Starch‐Degrading Enzymes2024 Angewandte Chemie article Biochemistry, Genetics and Molecular Biology Enzyme Catalysis and Immobilization Open access
Isabelle B. Pickles, Yurong Chen, Olga V. Moroz, Haley A. Brown, Casper de Boer, Zachary Armstrong, +6 more
0citations -
De novo transcriptome assembly and annotation of the common freshwater amphipod (Gammarus pulex) a valuable resource for ecotoxicogenomics2025 Scientific Data data-paper Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
Camilo Escobar-Sierra, Sameer Hassan, Fabian G. Weichert, Henrik Aronsson, Kathrin P. Lampert, Henner Hollert, +2 more
1citations -
GeneSurfer enables transcriptome-wide exploration and annotation of gene co-expression modules in 3D spatial transcriptomics data2025 iScience article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
Chang Li, Julian Thijssen, Thomas Kroes, Ximaine R. van der Burg, Louise van der Weerd, Thomas Höllt, +1 more
0citations -
EukFunc : A Holistic Eukaryotic Functional Reference for Automated Profiling of Soil Eukaryotes2025 Molecular Ecology Resources article Agricultural and Biological Sciences Mycorrhizal Fungi and Plant Interactions Open access
Guillaume Lentendu, David Singer, Sabine Agatha, Mohammad Bahram, S. Emilia Hannula, Johannes Helder, +4 more
17citations -
Analysis of pre-symptomatic Drosophila models for ALS and SMA reveals convergent impact on functional protein complexes linked to neuro-muscular degeneration2022 bioRxiv (Cold Spring Harbor Laboratory) preprint Medicine Amyotrophic Lateral Sclerosis Research Open access
Marina L. García‐Vaquero, Barbara Flix, Marcelo Henrique Neves Pereira, Lucile Palin, Tânia Monteiro Marques, Francisco Rodrigues Pinto, +4 more
0citations -
Investigating enzyme function by geometric matching of catalytic motifs2026 Protein Science article Biochemistry, Genetics and Molecular Biology Protein Structure and Dynamics Open access
R. Hackett, Ioannis G. Riziotis, Martin F. Larralde, António J. M. Ribeiro, Georg Zeller, Janet M. Thornton
0citations