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List of works by Rita Casadio

3D structure of Sulfolobus solfataricus carboxypeptidase developed by molecular modeling is confirmed by site-directed mutagenesis and small angle X-ray scattering

scientific article

A 3D model of the voltage-dependent anion channel (VDAC).

scientific article

A New Protein Representation Based on Fragment Contacts: Towards an Improvement of Contact Maps Predictions

A Shannon entropy-based filter detects high- quality profile-profile alignments in searches for remote homologues

scientific article published in February 2004

A combined approach of mass spectrometry, molecular modeling, and site-directed mutagenesis highlights key structural features responsible for the thermostability of Sulfolobus solfataricus carboxypeptidase

scientific article published in June 2008

A computational approach for detecting peptidases and their specific inhibitors at the genome level

scientific article

A genome wide association study for backfat thickness in Italian Large White pigs highlights new regions affecting fat deposition including neuronal genes

scientific article

A graph theoretic approach to protein structure selection.

scientific article

A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding.

scientific article

A large-scale evaluation of computational protein function prediction

scientific article

A low-resolution 3D model of the tetrameric alcohol dehydrogenase from Sulfolobus solfataricus

scientific article published in March 2002

A mathematical model relating diffusion of hydrophobic ions to their adsorption on biological membranes as detected with a microdialyzer

scholarly article by Piero Fariselli published in September 1993

A neural-network-based method for predicting protein stability changes upon single point mutations.

scientific article

A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins

scientific article

A novel subfamily of mitochondrial dicarboxylate carriers from Drosophila melanogaster: biochemical and computational studies

scientific article published on 3 December 2010

A protein structure prediction service in the ProGenGrid system.

scientific article

A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins

scientific article

A three-state prediction of single point mutations on protein stability changes.

scientific article

ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

scientific article

AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints

scientific article published on 30 July 2015

An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins

scientific article

An expanded evaluation of protein function prediction methods shows an improvement in accuracy ⬇️

scientific article

An initial comparative map of copy number variations in the goat (Capra hircus) genome

scientific article

Analysis of all subunits, SDHA, SDHB, SDHC, SDHD, of the succinate dehydrogenase complex in KIT/PDGFRA wild-type GIST.

scientific article published on 24 April 2013

Ancient pathogen-driven adaptation triggers increased susceptibility to non-celiac wheat sensitivity in present-day European populations.

scientific article published on 23 May 2016

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

scientific article published on 18 June 2019

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

scientific article published on 03 September 2019

Assessing predictions of the impact of variants on splicing in CAGI5

scientific article published on 19 August 2019

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

scientific article published on 23 August 2019

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

scientific article published on 01 September 2019

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences

scientific article

BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming.

scientific article

BETAWARE: a machine-learning tool to detect and predict transmembrane beta-barrel proteins in prokaryotes ⬇️

scientific article published on January 6, 2013

BRCA1 p.His1673del is a pathogenic mutation associated with a predominant ovarian cancer phenotype.

scientific article

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

scientific article published in July 2018

BaCelLo: a balanced subcellular localization predictor

scientific article

Benchmarking predictions of allostery in liver pyruvate kinase in CAGI4.

scientific article published on 29 March 2017

Blind prediction of deleterious amino acid variations with SNPs&GO.

scientific article published on 19 January 2017

Blurring contact maps of thousands of proteins: what we can learn by reconstructing 3D structure

scientific article

CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases

scientific article published on 03 September 2019

CBFA2T3-GLIS2 fusion transcript is a novel common feature in pediatric, cytogenetically normal AML, not restricted to FAB M7 subtype

scientific article published on 13 February 2013

CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information.

scientific article

Cloning, functional identification and structural modelling of Vitis vinifera S-adenosylmethionine decarboxylase

scientific article published on 18 September 2006

Computer-based prediction of mitochondria-targeting peptides

scientific article published on January 2015

ConSeq: the identification of functionally and structurally important residues in protein sequences

scientific article published on 10 February 2004

Correlating disease-related mutations to their effect on protein stability: a large-scale analysis of the human proteome

scientific article

DeepSig: deep learning improves signal peptide detection in proteins

scientific article

Divide and Conquer Strategies for Protein Structure Prediction

Draft genomes and genomic divergence of two Lepidurus tadpole shrimp species (Crustacea, Branchiopoda, Notostraca)

article published in 2018

EX-HOM (EXome HOMozygosity): a proof of principle

scientific article published on 18 August 2011

Effect of molecular confinement on internal enzyme dynamics: frequency domain fluorometry and molecular dynamics simulation studies.

scientific article

Erratum to: Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human

scientific article published on 5 October 2016

Expression of IGF-1 receptor in KIT/PDGF receptor-α wild-type gastrointestinal stromal tumors with succinate dehydrogenase complex dysfunction

scientific article

Expression of different forms of transglutaminases by immature cells of Helianthus tuberosus sprout apices.

scientific article published on 18 October 2012

Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters

FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps

scientific article published in April 2008

Fast overlapping of protein contact maps by alignment of eigenvectors

scientific article

Fishing new proteins in the twilight zone of genomes: the test case of outer membrane proteins in Escherichia coli K12, Escherichia coli O157:H7, and other Gram-negative bacteria

scientific article published on June 2003

Frataxin mRNA isoforms in FRDA patients and normal subjects: effect of tocotrienol supplementation

scientific article published on 23 September 2013

From protein sequence to function and structure with BAR+

Functional annotations improve the predictive score of human disease-related mutations in proteins

scientific article

Functional characterization of a second porin isoform in Drosophila melanogaster. DmPorin2 forms voltage-independent cation-selective pores.

scientific article

Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human

scientific article

Grammatical-Restrained Hidden Conditional Random Fields for Bioinformatics applications

scientific article published on 22 October 2009

Haplotype of single nucleotide polymorphisms in exon 6 of the MZF-1 gene and Alzheimer's disease

scientific article

Hierarchical mechanochemical switches in angiostatin

scientific article

High Throughput Comparison of Prokaryotic Genomes

High-throughput SNP discovery in the rabbit (Oryctolagus cuniculus) genome by next-generation semiconductor-based sequencing

scientific article published on 21 January 2014

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.

scientific article published on 29 July 2020

Histone deacetylase 1: a target of 9-hydroxystearic acid in the inhibition of cell growth in human colon cancer.

scientific article published on 16 February 2005

How to inherit statistically validated annotation within BAR+ protein clusters

scientific article published on 28 February 2013

I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure

scientific article

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

scientific article published on 10 April 2016

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

scientific article

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

scientific article published on 27 January 2017

Improving Coiled-Coil Prediction with Evolutionary Information

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

scientific article published on October 3, 2011

Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization.

scientific article published on 29 June 2011

In silico prediction of the structure of membrane proteins: is it feasible?

scientific article published on 01 December 2003

Is there an optimal substitution matrix for contact prediction with correlated mutations?

scientific article published in July 2011

LGANN: a parallel system combining a local genetic algorithm and neural networks for the prediction of secondary structure of proteins

scientific article published in 1995

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

scientific article

MIMO: an efficient tool for molecular interaction maps overlap

scientific article published on 15 May 2013

Machine learning and the prediction of protein structure: the state of the art

scholarly article published 2006

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

scholarly article by Castrense Savojardo et al published 2012 in Lecture Notes in Computer Science

Mapping and annotating obesity-related genes in pig and human genomes

scientific article published on January 2014

MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments

scientific article published in March 2003

MemLoci: predicting subcellular localization of membrane proteins in eukaryotes

scientific article published on 2 March 2011

MemPype: a pipeline for the annotation of eukaryotic membrane proteins

scientific article

Modulating the thermostability of Endoglucanase I from Trichoderma reesei using computational approaches.

scientific article

Molecular mechanism of thioredoxin regulation in photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase

scientific article

NET-GE: a novel NETwork-based Gene Enrichment for detecting biological processes associated to Mendelian diseases

scientific article published on 18 June 2015

NET-GE: a web-server for NETwork-based human gene enrichment

scientific article published on 02 August 2016

New Escherichia coli outer membrane proteins identified through prediction and experimental verification

scientific article

New functions of an old protein: the eukaryotic porin or voltage dependent anion selective channel (VDAC).

scientific article

Oligomerization of Sulfolobus solfataricus signature amidase is promoted by acidic pH and high temperature

scientific article published on December 2005

On the Reconstruction of Three-dimensional Protein Structures from Contact Maps

On the Upper Bound of the Prediction Accuracy of Residue Contacts in Proteins with Correlated Mutations: The Case Study of the Similarity Matrices

On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions

scientific article

PONGO: a web server for multiple predictions of all-alpha transmembrane proteins

scientific article published on July 2006

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.

scientific article

Phospholipid composition of photosynthetic membranes of Rhodopseudomonas capsulata

scientific article published on May 1, 1979

Plant and animal transglutaminases: do similar functions imply similar structures?

scientific article published on 12 July 2008

PredGPI: a GPI-anchor predictor

scientific article

Predicting cancer-associated germline variations in proteins

scientific article

Predicting protein stability changes from sequences using support vector machines

scientific article published in September 2005

Predicting protein thermostability changes from sequence upon multiple mutations

scientific article

Prediction of Protein-Protein Interacting Sites: How to Bridge Molecular Events to Large Scale Protein Interaction Networks

Prediction of coordination number and relative solvent accessibility in proteins.

scientific article

Prediction of disulfide connectivity in proteins with machine-learning methods and correlated mutations. ⬇️

scientific article

Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network

scientific article

Prediction of protein--protein interaction sites in heterocomplexes with neural networks

scientific article published in March 2002

Prediction of the Bonding State of Cysteine Residues in Proteins with Machine-Learning Methods

scholarly article by Castrense Savojardo et al published 2011 in Lecture Notes in Computer Science

Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks

scientific article published in December 2002

Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy

scientific article

Preprotein Translocase of the Outer Mitochondrial Membrane: Reconstituted Tom40 Forms a Characteristic TOM Pore

article

Pressure and temperature as tools for investigating the role of individual non-covalent interactions in enzymatic reactions Sulfolobus solfataricus carboxypeptidase as a model enzyme

scientific article published on 10 January 2006

Progress and challenges in predicting protein-protein interaction sites

scientific article published on 03 April 2009

Protein Sequence Annotation by Means of Community Detection

Reconstruction of 3D structures from protein contact maps

scientific article

Reduction of active elastase concentration by means of immobilized inhibitors: a novel therapeutic approach

scientific article

Robust determinants of thermostability highlighted by a codon frequency index capable of discriminating thermophilic from mesophilic genomes

scientific article published on 26 May 2007

Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins

scholarly article by Piero Fariselli published in August 1999

Role of the C-terminus of Pleurotus eryngii Ery4 laccase in determining enzyme structure, catalytic properties and stability

scientific article published on 20 September 2012

SChloro: directing Viridiplantae proteins to six chloroplastic sub-compartments

scientific article published on February 2017

SDHA loss-of-function mutations in KIT-PDGFRA wild-type gastrointestinal stromal tumors identified by massively parallel sequencing

scientific article

SPEPlip: the detection of signal peptide and lipoprotein cleavage sites

scientific article published in 2003

SUS-BAR: a database of pig proteins with statistically validated structural and functional annotation

scientific article published on 23 September 2013

Searching for signatures of cold adaptations in modern and archaic humans: hints from the brown adipose tissue genes

scientific article

Sequence-based feature prediction and annotation of proteins

scientific article (publication date: 2009)

Substitution in the murine nectin1 receptor of a single conserved amino acid at a position distal from the herpes simplex virus gD binding site confers high-affinity binding to gD.

scientific article published on June 2002

Substrate-induced conformational changes of the mitochondrial oxoglutarate carrier: a spectroscopic and molecular modelling study

scientific article published in September 2005

Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity

scientific article published in December 2005

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

scientific article

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

scientific article

TRAMPLE: the transmembrane protein labelling environment

scientific article

Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length

scientific article published in 2024

The 4th Bologna Winter School: hot topics in structural genomics

scientific article published on January 2003

The Bologna Annotation Resource (BAR 3.0): improving protein functional annotation.

scientific article published on 27 April 2017

The WWWH of remote homolog detection: the state of the art.

scientific article

The bologna annotation resource: a non hierarchical method for the functional and structural annotation of protein sequences relying on a comparative large-scale genome analysis

article

The ectodomain of herpes simplex virus glycoprotein H contains a membrane alpha-helix with attributes of an internal fusion peptide, positionally conserved in the herpesviridae family

scientific article published on March 2005

The human "magnesome": detecting magnesium binding sites on human proteins

scientific article

The implications of alternative splicing in the ENCODE protein complement

scientific article (publication date: 27 March 2007)

The prediction of membrane protein structure and genome structural annotation

scientific article

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

scientific article published on 21 February 2013

The prediction of protein subcellular localization from sequence: a shortcut to functional genome annotation

scientific article published on January 2008

The pros and cons of predicting protein contact maps.

scientific article

The side chain of glutamine 13 is the acyl-donor amino acid modified by type 2 transglutaminase in subunit T of the native rabbit skeletal muscle troponin complex

scientific article published on 16 November 2011

Thermodynamics of binding of regulatory ligands to tissue transglutaminase

scientific article published on 22 December 2009

Thinking the impossible: how to solve the protein folding problem with and without homologous structures and more.

scientific article

Tools and data services registry: a community effort to document bioinformatics resources

scientific article

Topology prediction of membrane proteins: how distantly related homologs come into play

article published in 2010

Transglutaminases: nature's biological glues

scientific article

Use of estimated evolutionary strength at the codon level improves the prediction of disease-related protein mutations in humans

scientific article published in January 2008

WS-SNPs&GO: a web server for predicting the deleterious effect of human protein variants using functional annotation

scientific article

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges.

scientific article published on 21 June 2017

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

scientific article published on 11 August 2017

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