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R. Casadio · SciRah

Researcher profile · Semantic Scholar

R. Casadio

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R. Casadio — researcher profile on SciRah

h-index: 65
Works: 467
Citations: 20K

Most-cited papers

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens
Nai-Hui Zhou, Yuxiang Jiang, T. Bergquist, Alexandra J. Lee +163 more
2019Genome Biology451 citations Open access
Semantic Scholar
DOME: recommendations for supervised machine learning validation in biology
Ian Walsh, D. Fishman, D. García-Gasulla, Tiina Titma +32 more
2021Nature Methods248 citations Open access
Semantic Scholar
Solvent Accessibility of Residues Undergoing Pathogenic Variations in Humans: From Protein Structures to Protein Sequences
Castrense Savojardo, Matteo Manfredi, P. Martelli, R. Casadio
2021Frontiers in Molecular Biosciences150 citations Open access
Semantic Scholar
DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks
Castrense Savojardo, Niccolò Bruciaferri, G. Tartari, P. Martelli +1 more
2019Bioinform.100 citations Open access
Semantic Scholar
Faculty Opinions recommendation of A framework for understanding the functions of biomolecular condensates across scales.
R. Casadio
2021Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature87 citations
Semantic Scholar
Machine learning solutions for predicting protein–protein interactions
R. Casadio, P. Martelli, Castrense Savojardo
2022WIREs Computational Molecular Science67 citations Open access
Semantic Scholar
E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants
Matteo Manfredi, Castrense Savojardo, P. Martelli, R. Casadio
2022bioRxiv45 citations Open access
Semantic Scholar
Biallelic variants in LIG3 cause a novel mitochondrial neurogastrointestinal encephalomyopathy.
E. Bonora, Sanjiban Chakrabarty, Georgios Kellaris, M. Tsutsumi +63 more
2021Brain : a journal of neurology40 citations Open access
Semantic Scholar
CoCoNat: a novel method based on deep learning for coiled-coil prediction
G. Madeo, Castrense Savojardo, Matteo Manfredi, P. Martelli +1 more
2023bioRxiv30 citations Open access
Semantic Scholar
Finding functional motifs in protein sequences with deep learning and natural language models.
Castrense Savojardo, P. Martelli, R. Casadio
2023Current Opinion in Structural Biology27 citations Open access
Semantic Scholar
DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning
Castrense Savojardo, Matteo Manfredi, P. Martelli, R. Casadio
2024bioRxiv25 citations
Semantic Scholar
Critical assessment of missense variant effect predictors on disease-relevant variant data
Ruchir Rastogi, Ryan Chung, Sindy Li, Chang Li +32 more
2024bioRxiv22 citations Open access
Semantic Scholar
Protein–Protein Interaction Methods and Protein Phase Separation
Castrense Savojardo, P. Martelli, R. Casadio
202022 citations Open access
Semantic Scholar
DeepREx-WS: A web server for characterising protein–solvent interaction starting from sequence
Matteo Manfredi, Castrense Savojardo, P. Martelli, R. Casadio
2021Computational and Structural Biotechnology Journal20 citations Open access
Semantic Scholar
Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study
Hugo Schweke, Qifang Xu, G. Tauriello, L. Pantolini +42 more
2023Proteomics19 citations Open access
Semantic Scholar
Assessment of predicted enzymatic activity of alpha-N-acetylglucosaminidase (NAGLU) variants of unknown significance for CAGI 2016
W. Clark, Laura Kasak, C. Bakolitsa, Zhi-Qiang Hu +29 more
2019Human Mutation19 citations Open access
Semantic Scholar
Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project
S. L. Stenton, M. O’Leary, G. Lemire, G. VanNoy +70 more
2023Human Genomics18 citations Open access
Semantic Scholar
ISPRED-SEQ: Deep neural networks and embeddings for predicting interaction sites in protein sequences
Matteo Manfredi, Castrense Savojardo, P. Martelli, R. Casadio
2022bioRxiv18 citations Open access
Semantic Scholar
Assessing predictions of the impact of variants on splicing in CAGI5
Stephen M. Mount, Žiga Avsec, L. Carmel, R. Casadio +18 more
2019Human Mutation18 citations Open access
Semantic Scholar
Alpha&ESMhFolds: a web server for comparing AlphaFold2 and ESMFold models of the human reference proteome.
Matteo Manfredi, Castrense Savojardo, Georgii Iardukhin, D. Salomoni +3 more
2024Journal of Molecular Biology17 citations Open access
Semantic Scholar
Resources and tools for rare disease variant interpretation
L. Licata, Allegra Via, P. Turina, G. Babbi +18 more
2023Frontiers in Molecular Biosciences17 citations Open access
Semantic Scholar
Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge
Castrense Savojardo, M. Petrosino, G. Babbi, Samuele Bovo +21 more
2019Human Mutation17 citations Open access
Semantic Scholar
Whole Genome Sequence Analysis of Brucella abortus Isolates from Various Regions of South Africa
M. B. Ledwaba, B. Glover, I. Matle, Giuseppe Profiti +7 more
2021Microorganisms16 citations Open access
Semantic Scholar
Assessment of methods for predicting the effects of PTEN and TPMT protein variants
V. Pejaver, G. Babbi, R. Casadio, Lukas Folkman +12 more
2019Human Mutation16 citations Open access
Semantic Scholar
Functional and Structural Features of Disease-Related Protein Variants
Castrense Savojardo, G. Babbi, P. Martelli, R. Casadio
2019International Journal of Molecular Sciences15 citations Open access
Semantic Scholar
Critical assessment of missense variant effect predictors on disease-relevant variant data
Ruchir Rastogi, Ryan Chung, Sindy Li, Chang Li +32 more
2025Human Genetics14 citations Open access
Semantic Scholar
Wood feeding and social living: Draft genome of the subterranean termite Reticulitermes lucifugus (Blattodea; Termitoidae)
J. Martelossi, G. Forni, M. Iannello, Castrense Savojardo +5 more
2022Insect molecular biology (Print)14 citations Open access
Semantic Scholar
BetAware-Deep: An Accurate Web Server for Discrimination and Topology Prediction of Prokaryotic Transmembrane β-barrel Proteins.
G. Madeo, Castrense Savojardo, P. Martelli, R. Casadio
2020Journal of Molecular Biology14 citations Open access
Semantic Scholar
Mapping OMIM Disease–Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes
Castrense Savojardo, G. Babbi, P. Martelli, R. Casadio
2021Frontiers in Molecular Biosciences13 citations Open access
Semantic Scholar
Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean
A. J. Andrews, G. N. Puncher, D. Bernal-Casasola, A. Di Natale +13 more
2021Scientific Reports13 citations Open access
Semantic Scholar
Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges
G. McInnes, Roxana Daneshjou, Panagiostis Katsonis, O. Lichtarge +18 more
2019Human Mutation13 citations Open access
Semantic Scholar
Merging metabolomics and genomics provides a catalog of genetic factors that influence molecular phenotypes in pigs linking relevant metabolic pathways
Samuele Bovo, A. Ribani, F. Fanelli, G. Galimberti +15 more
2025Genetics Selection Evolution12 citations Open access
Semantic Scholar
Assessing predictions on fitness effects of missense variants in calmodulin
Jing Zhang, Lisa N. Kinch, Qian Cong, Panagiotis Katsonis +13 more
2019Human Mutation12 citations Open access
Semantic Scholar
PhenPath: a tool for characterizing biological functions underlying different phenotypes
G. Babbi, P. Martelli, R. Casadio
2019BMC Genomics12 citations Open access
Semantic Scholar
AlphaFold2 and ESMFold: A large-scale pairwise model comparison of human enzymes upon Pfam functional annotation
Matteo Manfredi, Gabriele Vazzana, Castrense Savojardo, P. Martelli +1 more
2025Computational and Structural Biotechnology Journal11 citations Open access
Semantic Scholar
E-pRSA: Embeddings Improve the Prediction of Residue Relative Solvent Accessibility in Protein Sequence.
Matteo Manfredi, Castrense Savojardo, P. Martelli, R. Casadio
2024Journal of Molecular Biology11 citations Open access
Semantic Scholar
MultifacetedProtDB: a database of human proteins with multiple functions
Elisa Bertolini, G. Babbi, Castrense Savojardo, P. Martelli +1 more
2023Nucleic Acids Research11 citations Open access
Semantic Scholar
SVMyr: A Web Server Detecting Co- and Post-translational Myristoylation in Proteins.
G. Madeo, Castrense Savojardo, P. Martelli, R. Casadio
2022Journal of Molecular Biology11 citations Open access
Semantic Scholar
Genomic tools for durum wheat breeding: de novo assembly of Svevo transcriptome and SNP discovery in elite germplasm
Vera Vendramin, D. Ormanbekova, S. Scalabrin, D. Scaglione +9 more
2019BMC Genomics11 citations Open access
Semantic Scholar
On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation
Castrense Savojardo, P. Martelli, R. Casadio, P. Fariselli
2019Briefings Bioinform.11 citations Open access
Semantic Scholar
Gravitational decoupling and aerodynamics: black holes and analog gravity in a jet propulsion lab
R. Casadio, C. N. Souza, R. da Rocha
2024The European Physical Journal C10 citations Open access
Semantic Scholar
Comparative genomics of tadpole shrimps (Crustacea, Branchiopoda, Notostraca): Dynamic genome evolution against the backdrop of morphological stasis.
A. Luchetti, G. Forni, J. Martelossi, Castrense Savojardo +5 more
2021Genomics10 citations Open access
Semantic Scholar
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation
D. Baldazzi, Castrense Savojardo, P. Martelli, R. Casadio
2021Nucleic Acids Res.10 citations Open access
Semantic Scholar
Highlighting Human Enzymes Active in Different Metabolic Pathways and Diseases: The Case Study of EC 1.2.3.1 and EC 2.3.1.9
G. Babbi, D. Baldazzi, Castrense Savojardo, P. Martelli +1 more
2020Biomedicines9 citations Open access
Semantic Scholar
Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito
Castrense Savojardo, P. Martelli, G. Tartari, R. Casadio
2020BMC Bioinformatics8 citations Open access
Semantic Scholar
Mapping human disease-associated enzymes into Reactome allows characterization of disease groups and their interactions
Castrense Savojardo, D. Baldazzi, G. Babbi, P. Martelli +1 more
2022Scientific Reports7 citations Open access
Semantic Scholar
Author Correction: DOME: recommendations for supervised machine learning validation in biology
Ian Walsh, D. Fishman, D. García-Gasulla, Tiina Titma +32 more
2021Nature Methods7 citations Open access
Semantic Scholar
Assessing the performance of in-silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer
A. Voskanian, Panagiotis Katsonis, O. Lichtarge, V. Pejaver +25 more
2019Human Mutation7 citations Open access
Semantic Scholar
Whole Genome Sequence Analysis of Brucella spp. from Human, Livestock, and Wildlife in South Africa
K. D. Mazwi, K. Lekota, B. A. Glover, F. Kolo +12 more
2024Journal of Microbiology6 citations Open access
Semantic Scholar
Assessing Computational Predictions of the Phenotypic Effect of Cystathionine-beta-Synthase Variants
Laura Kasak, C. Bakolitsa, Zhi-Qiang Hu, Changhua Yu +31 more
2019Human Mutation6 citations Open access
Semantic Scholar

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