Castrense Savojardo

发表

eDGAR: a database of Disease-Gene Associations with annotated Relationships among genes

Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, 2017, BMC Genomics.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

Are machine learning based methods suited to address complex biological problems? Lessons from CAGI‐5 challenges

E. Capriotti, R. Casadio, P. Martelli, 2019, Human mutation.

Performance of computational methods for the evaluation of pericentriolar material 1 missense variants in CAGI‐5

Olivier Lichtarge, Emidio Capriotti, Kivilcim Ozturk, 2019, Human mutation.

Solvent Accessibility of Residues Undergoing Pathogenic Variations in Humans: From Protein Structures to Protein Sequences

R. Casadio, P. Martelli, Castrense Savojardo, 2021, Frontiers in Molecular Biosciences.

Assessment of blind predictions of the clinical significance of BRCA1 and BRCA2 variants

P. Radivojac, R. Casadio, O. Lichtarge, 2019, Human mutation.

Computer-based prediction of mitochondria-targeting peptides.

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2015, Methods in molecular biology.

Large-scale prediction and analysis of protein sub-mitochondrial localization with DeepMito

Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, 2020, BMC Bioinformatics.

Assessing predictions of the impact of variants on splicing in CAGI5

Stephen M. Mount, R. Casadio, J. Gagneur, 2019, Human Mutation.

Predicting venous thromboembolism risk from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Lipika R. Pal, R. Altman, S. Brenner, 2019, Human mutation.

Integrating ELIXIR Italy with ELIXIR Interoperability platform activities

Castrense Savojardo, Rita Casadio, Giuseppe Profiti, 2018 .

Assessment of methods for predicting the effects of PTEN and TPMT protein variants

Lipika R. Pal, Yaoqi Zhou, P. Radivojac, 2019, Human mutation.

On the biases in predictions of protein stability changes upon variations: the INPS test case

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2018, Bioinform..

Human Mutation

E. Capriotti, R. Casadio, P. Martelli, 2019 .

SVMyr: A Web Server Detecting Co- and Post-translational Myristoylation in Proteins.

R. Casadio, P. Martelli, Castrense Savojardo, 2022, Journal of molecular biology.

E-SNPs&GO: embedding of protein sequence and function improves the annotation of human pathogenic variants

R. Casadio, P. Martelli, Castrense Savojardo, 2022, bioRxiv.

Pathogenic variation types in human genes relate to diseases through Pfam and InterPro mapping

R. Casadio, P. Martelli, Giulia Babbi, 2022, Frontiers in Molecular Biosciences.

ISPRED-SEQ: Deep neural networks and embeddings for predicting interaction sites in protein sequences

R. Casadio, P. Martelli, Castrense Savojardo, 2022, bioRxiv.

Mapping human disease-associated enzymes into Reactome allows characterization of disease groups and their interactions

R. Casadio, P. Martelli, Giulia Babbi, 2022, Scientific Reports.

Machine-learning methods for structure prediction of β-barrel membrane proteins

Castrense Savojardo, Castrense Savojardo, 2013 .

Assessing the performance of in silico methods for predicting the pathogenicity of variants in the gene CHEK2, among Hispanic females with breast cancer

Olivier Lichtarge, Predrag Radivojac, Emidio Capriotti, 2019, Human mutation.

Comparative genomics of Hox and ParaHox genes among major lineages of Branchiopoda with emphasis on tadpole shrimps

Castrense Savojardo, A. Luchetti, B. Mantovani, 2023, Frontiers in Ecology and Evolution.

SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2016, Bioinform..

INPS: predicting the impact of non-synonymous variations on protein stability from sequence

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2015, Bioinform..

DeepSig: deep learning improves signal peptide detection in proteins

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2017, Bioinform..

Ancient DNA SNP-panel data suggests stability in bluefin tuna genetic diversity despite centuries of fluctuating catches in the eastern Atlantic and Mediterranean

R. Casadio, P. Martelli, Castrense Savojardo, 2021, Scientific Reports.

Assessment of predicted enzymatic activity of α‐N‐acetylglucosaminidase variants of unknown significance for CAGI 2016

Roland L. Dunbrack, Colby T. Ford, David T. Jones, 2019, Human mutation.

Assessing computational predictions of the phenotypic effect of cystathionine‐beta‐synthase variants

Silvio C. E. Tosatto, Predrag Radivojac, Mauno Vihinen, 2019, Human mutation.

Assessing predictions on fitness effects of missense variants in calmodulin

N. Grishin, E. Capriotti, R. Casadio, 2019, Human mutation.

Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge

Philip M. Kim, S. Brenner, E. Capriotti, 2019, Human mutation.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks

Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, 2019, Bioinform..

Machine learning solutions for predicting protein–protein interactions

R. Casadio, P. Martelli, Castrense Savojardo, 2022, WIREs Computational Molecular Science.

ISPRED4: interaction sites PREDiction in protein structures with a refining grammar model

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2017, Bioinform..

Protein–Protein Interaction Methods and Protein Phase Separation

R. Casadio, P. Martelli, Castrense Savojardo, 2020 .

BUSCA: an integrative web server to predict subcellular localization of proteins

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2018, Nucleic Acids Res..

Cloning the barley nec3 disease lesion mimic mutant using complementation by sequencing

S. Salvi, M. Moscou, Castrense Savojardo, 2022, The plant genome.

INPS-MD: a web server to predict stability of protein variants from sequence and structure

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2016, Bioinform..

Wood feeding and social living: Draft genome of the subterranean termite Reticulitermes lucifugus (Blattodea; Termitoidae)

R. Casadio, P. Martelli, Castrense Savojardo, 2022, Insect molecular biology.

Large scale analysis of protein stability in OMIM disease related human protein variants

R. Casadio, P. Fariselli, P. Martelli, 2016, BMC Genomics.

TPpred3 detects and discriminates mitochondrial and chloroplastic targeting peptides in eukaryotic proteins

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2015, Bioinform..

On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2019, Briefings Bioinform..

Transmembrane Domain Prediction

Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, 2019, Encyclopedia of Bioinformatics and Computational Biology.

Large scale analysis of protein stability in OMIM disease related human protein variants

R. Casadio, P. Fariselli, P. Martelli, 2016, BMC Genomics.

Huntingtin: A Protein with a Peculiar Solvent Accessible Surface

R. Casadio, P. Martelli, Castrense Savojardo, 2021, International journal of molecular sciences.

Resources and tools for rare disease variant interpretation

E. Capriotti, R. Casadio, S. Pascarella, 2023, Frontiers in Molecular Biosciences.

BetAware-Deep: An Accurate Web Server for Discrimination and Topology Prediction of Prokaryotic Transmembrane β-barrel Proteins.

Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, 2020, Journal of molecular biology.

Discriminating physiological from non‐physiological interfaces in structures of protein complexes: A community‐wide study

Charles W Christoffer, H. Wolfson, O. Schueler‐Furman, 2023, Proteomics.

Mapping OMIM Disease–Related Variations on Protein Domains Reveals an Association Among Variation Type, Pfam Models, and Disease Classes

R. Casadio, P. Martelli, Castrense Savojardo, 2021, Frontiers in Molecular Biosciences.

Finding functional motifs in protein sequences with deep learning and natural language models.

R. Casadio, P. Martelli, Castrense Savojardo, 2023, Current opinion in structural biology.

MemPype: a pipeline for the annotation of eukaryotic membrane proteins

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2011, Nucleic Acids Res..

Improving the detection of transmembrane β-barrel chains with N-to-1 extreme learning machines

Piero Fariselli, Castrense Savojardo, Rita Casadio, 2011, Bioinform..

Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project

Julius O. B. Jacobsen, Fullerton, Azza, 2023, medRxiv.

CoCoNat: a novel method based on deep learning for coiled-coil prediction

R. Casadio, P. Martelli, Castrense Savojardo, 2023, bioRxiv.

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2009, Algorithms for Molecular Biology.

Human Mutation

Guillermo del Angel, Lipika R. Pal, P. Radivojac, 2019 .

Machine-Learning Methods to Predict Protein Interaction Sites in Folded Proteins

Piero Fariselli, Damiano Piovesan, Castrense Savojardo, 2011, CIBB.

TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2014, Bioinform..

DeepREx-WS: A web server for characterising protein–solvent interaction starting from sequence

R. Casadio, P. Martelli, Castrense Savojardo, 2021, Computational and structural biotechnology journal.

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

R. Casadio, Castrense Savojardo, D. Baldazzi, 2020, Biomedicines.

Assessing predictions on fitness effects of missense variants in calmodulin

N. Grishin, E. Capriotti, R. Casadio, 2019, Human mutation.

Human Mutation

Colby T. Ford, Lipika R. Pal, Meng Wang, 2019 .

Disulfide Connectivity Prediction with Extreme Learning Machines

Piero Fariselli, Monther Alhamdoosh, Castrense Savojardo, 2011, BIOINFORMATICS.

BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation

R. Casadio, P. Martelli, Castrense Savojardo, 2021, Nucleic Acids Res..

A Glance into MTHFR Deficiency at a Molecular Level

R. Casadio, P. Martelli, Castrense Savojardo, 2021, International journal of molecular sciences.

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Silvio C. E. Tosatto, Julius O. B. Jacobsen, Nicholas A. Sinnott-Armstrong, 2024, Genome biology.

E-pRSA: Embeddings improve the prediction of residue Relative Solvent Accessibility in protein sequence

R. Casadio, Castrense Savojardo, Matteo Manfredi, 2024, Journal of Molecular Biology.

Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment

C. Laczny, S. Rampelli, S. Turroni, 2024, Animal Microbiome.

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Nicholas A. Sinnott-Armstrong, Jonathan M. Mudge, Hui Ting Grace Yeo, 2022, Genome biology.

TPpred2: improving the prediction of mitochondrial targeting peptide cleavage sites by exploiting sequence motifs

R. Casadio, P. Fariselli, P. Martelli, 2014, Bioinform..

Computer-Aided Prediction of Protein Mitochondrial Localization.

R. Casadio, P. Fariselli, P. Martelli, 2021, Methods in molecular biology.

Evaluation of enzyme activity predictions for variants of unknown significance in Arylsulfatase A

P. Radivojac, W. Clark, R. Casadio, 2024, bioRxiv.

The prediction of organelle-targeting peptides in eukaryotic proteins with Grammatical-Restrained Hidden Conditional Random Fields

Piero Fariselli, Castrense Savojardo, Pier Luigi Martelli, 2013, Bioinform..

A multidisciplinary approach to describe population structure of Solea solea in the Mediterranean Sea

Castrense Savojardo, A. Cariani, E. Armelloni, 2024, Frontiers in Marine Science.

Evaluating predictors of kinase activity of STK11 variants identified in primary human non-small cell lung cancers

P. Radivojac, R. Casadio, A. O’Donnell-Luria, 2024, Research square.