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Helixer: cross-species gene annotation of large eukaryotic genomes using deep learning2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access cited by 1 patent
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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
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CrossTalkeR: analysis and visualization of ligand–receptorne tworks2021 Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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RAINFOREST: a random forest approach to predict treatment benefit in data from (failed) clinical drug trials2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
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PMIpred: a physics-informed web server for quantitative protein–membrane interaction prediction2024 Bioinformatics article Biochemistry, Genetics and Molecular Biology Machine Learning in Bioinformatics Open access
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Converting networks to predictive logic models from perturbation signalling data with CellNOpt2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Gene Regulatory Network Analysis Open access
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DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations2021 Bioinformatics article Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
Almut Heinken, Stefanía Magnúsdóttir, Ronan M. T. Fleming, Ines Thiele
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The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Vasundra Touré, Steven Vercruysse, Márcio Luís Acencio, Ruth C. Lovering, Sandra E. Orchard, Glyn Bradley, +20 more
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MiMIR: R-shiny application to infer risk factors and endpoints from Nightingale Health’s 1H-NMR metabolomics data2022 Bioinformatics article Biochemistry, Genetics and Molecular Biology Metabolomics and Mass Spectrometry Studies Open access
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LAMPA, LArge Multidomain Protein Annotator, and its application to RNA virus polyproteins2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Genomics and Phylogenetic Studies Open access
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Adjustment of spurious correlations in co-expression measurements from RNA-Sequencing data2023 Bioinformatics article Biochemistry, Genetics and Molecular Biology Gene expression and cancer classification Open access
Ping‐Han Hsieh, Camila M. Lopes‐Ramos, Manuela Zucknick, Geir Kjetil Sandve, Kimberly Glass, Marieke L. Kuijjer
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Cardinality optimization in constraint-based modelling: application to human metabolism2023 Bioinformatics article Biochemistry, Genetics and Molecular Biology Microbial Metabolic Engineering and Bioproduction Open access
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A database of flavivirus RNA structures with a search algorithm for pseudoknots and triple base interactions2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology RNA and protein synthesis mechanisms Open access
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SECEDO: SNV-based subclone detection using ultra-low coverage single-cell DNA sequencing2022 Bioinformatics article Biochemistry, Genetics and Molecular Biology Cancer Genomics and Diagnostics Open access cited by 1 patent
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SCHNEL: scalable clustering of high dimensional single-cell data2020 Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
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