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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 -
Analytic pipelines to assess the relationship between immune response and germline genetics in human tumors2022 STAR Protocols article Biochemistry, Genetics and Molecular Biology Genetic Associations and Epidemiology Open access
Rosalyn W. Sayaman, Mohamad Saad, Carolina Heimann, Donglei Hu, Khalid B. Kunji, Jessica P Roelands, +6 more
3citations -
bio.tools: an expanded web service for research software in the life sciences2026 Nucleic Acids Research article Decision Sciences Scientific Computing and Data Management Open access
Ana Mendes, Hans Ienasescu, Christian A T Andersen, Erin Calhoun, Piotr Jaroslaw Chmura, Kathleen Collier, +17 more
0citations -
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 -
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
23citations -
Integrative analysis of multi-omics data reveals importance of collagen and the PI3K AKT signalling pathway in CAKUT2024 Scientific Reports article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Jumamurat R. Bayjanov, Cenna Doornbos, Ozan Özışık, Woosub Shin, Núria Queralt-Rosiñach, Daphne Wijnbergen, +9 more
2citations -
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
Felix Stiehler, Marvin Steinborn, Daniela Dey, Andreas P.M. Weber, Alisandra K. Denton
179citations -
CrossTalkeR: analysis and visualization of ligand–receptorne tworks2021 Bioinformatics article Biochemistry, Genetics and Molecular Biology Single-cell and spatial transcriptomics Open access
James Shiniti Nagai, Nils B. Leimkühler, Michael T. Schaub, Rebekka K. Schneider, Ivan G. Costa
58citations -
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
Joske Ubels, Tilman Schaefers, Cornelis J.A. Punt, Henk‐Jan Guchelaar, Jeroen de Ridder
43citations -
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
Enio Gjerga, Panuwat Trairatphisan, Attila Gábor, Hermann Koch, Franceco Ceccarelli, Aurélien J. F. Dugourd, +2 more
37citations -
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
32citations -
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
Daniele Bizzarri, Marcel J. T. Reinders, Marian Beekman, P. Eline Slagboom, Erik B. van den Akker
17citations -
Recommendations for the analysis of gene expression data to identify intrinsic differences between similar tissues2020 Genomics article Biochemistry, Genetics and Molecular Biology Bioinformatics and Genomic Networks Open access
Tooba Abbassi‐Daloii, Hermien E. Kan, Vered Raz, Peter A.C. ’t Hoen
16citations -
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
Anastasia A. Gulyaeva, Andrey I Sigorskih, Elena S Ocheredko, Dmitry V. Samborskiy, Alexander E. Gorbalenya
14citations -
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
Alan Zammit, Leon Helwerda, René C. L. Olsthoorn, Fons J. Verbeek, Alexander P. Gultyaev
10citations