List of works - Stefano Toppo

The genome of the domesticated apple (Malus × domestica Borkh.)

scientific article

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

scientific article

A large-scale evaluation of computational protein function prediction

scientific article

Catalytic mechanisms and specificities of glutathione peroxidases: variations of a basic scheme

scientific article published on 17 April 2009

Applications of next-generation sequencing technologies to diagnostic virology

scientific article published on 14 November 2011

Telethonin, a novel sarcomeric protein of heart and skeletal muscle

scientific journal article

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

scientific article

A comparison of thiol peroxidase mechanisms

scientific article

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

scientific article

Evolutionary and structural insights into the multifaceted glutathione peroxidase (Gpx) superfamily.

scientific article

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.

scientific article

Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'

scientific article published on 30 June 2020

The catalytic site of glutathione peroxidases.

scientific article published in September 2008

Next-generation sequencing technologies in diagnostic virology

scientific article published on 21 March 2013

The thioredoxin specificity of Drosophila GPx: a paradigm for a peroxiredoxin-like mechanism of many glutathione peroxidases.

scientific article published on 13 October 2006

Human papillomavirus genotyping by 454 next generation sequencing technology

scientific article

Transcriptome analysis of Medicago truncatula leaf senescence: similarities and differences in metabolic and transcriptional regulations as compared with Arabidopsis, nodule senescence and nitric oxide signalling.

scientific article

Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology

scientific article

Antimicrobial treatment and containment measures for an extremely drug-resistant Klebsiella pneumoniae ST101 isolate carrying pKPN101-IT, a novel fully sequenced bla(KPC-2) plasmid

scientific article published on 12 September 2012

Phylogenetic characterization of Central/Southern European lineage 2 West Nile virus: analysis of human outbreaks in Italy and Greece, 2013-2014.

scientific article published on 30 July 2015

Functional interaction of phospholipid hydroperoxide glutathione peroxidase with sperm mitochondrion-associated cysteine-rich protein discloses the adjacent cysteine motif as a new substrate of the selenoperoxidase.

scientific article

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications

scientific article (publication date: 2014)

Organochalcogen peroxidase mimetics as potential drugs: a long story of a promise still unfulfilled.

scientific article published on 14 March 2013

Pattern recognition in gene expression profiling using DNA array: a comparative study of different statistical methods applied to cancer classification

scientific article published in April 2003

Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak

scientific article

Glutathione peroxidase 4-catalyzed reduction of lipid hydroperoxides in membranes: The polar head of membrane phospholipids binds the enzyme and addresses the fatty acid hydroperoxide group toward the redox center.

scientific article published on 11 July 2017

Accurate human papillomavirus genotyping by 454 pyrosequencing

scientific article published on 10 April 2013

Linear motifs in the C-terminus of D. melanogaster cryptochrome

scientific article published on 9 February 2007

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data

scientific article

Reducing bias in RNA sequencing data: a novel approach to compute counts

scientific article

The SSEA server for protein secondary structure alignment.

scientific article

Protein disulfide isomerase and glutathione are alternative substrates in the one Cys catalytic cycle of glutathione peroxidase 7.

scientific article published on 27 February 2013

Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions.

scientific article published on 18 July 2017

Selenocysteine oxidation in glutathione peroxidase catalysis: an MS-supported quantum mechanics study.

scientific article published on 7 July 2015

G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide

article published in 2018

Novel West Nile virus lineage 1a full genome sequences from human cases of infection in north-eastern Italy, 2011.

scientific article published on 25 September 2012

Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server.

scientific article published on 27 August 2015

Characterization of Intra-Type Variants of Oncogenic Human Papillomaviruses by Next-Generation Deep Sequencing of the E6/E7 Region

scientific article published on 14 March 2016

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

scientific article published on 19 November 2019

Primary structure of the nuclear forms of phospholipid hydroperoxide glutathione peroxidase (PHGPx) in rat spermatozoa

scientific article published in January 2005

Reproducibility: In praise of open research measures

scientific article published in June 2013

Improving the quality of protein structure models by selecting from alignment alternatives

scientific article

Peroxiredoxin 6 from the Antarctic emerald rockcod: molecular characterization of its response to warming

scientific article published on 3 October 2015

Quantitative label-free redox proteomics of reversible cysteine oxidation in red blood cell membranes

scientific article published on 15 March 2014

Characterization of a novel complex BRAF mutation in a follicular variant papillary thyroid carcinoma

scientific article published on 21 April 2008

Human cytomegalovirus productively infects adrenocortical cells and induces an early cortisol response

scientific article

Transcriptome and Cell Physiological Analyses in Different Rice Cultivars Provide New Insights Into Adaptive and Salinity Stress Responses.

scientific article published on 5 March 2018

Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis

scientific article

Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices

scientific article published on 01 August 2002

Insight into the mechanism of ferroptosis inhibition by ferrostatin-1

scientific article published on 20 September 2019

List of works by Stefano Toppo

The genome of the domesticated apple (Malus × domestica Borkh.)

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

A large-scale evaluation of computational protein function prediction

Catalytic mechanisms and specificities of glutathione peroxidases: variations of a basic scheme

Applications of next-generation sequencing technologies to diagnostic virology

Telethonin, a novel sarcomeric protein of heart and skeletal muscle

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

A comparison of thiol peroxidase mechanisms

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

Evolutionary and structural insights into the multifaceted glutathione peroxidase (Gpx) superfamily.

Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms.

Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'

The catalytic site of glutathione peroxidases.

Next-generation sequencing technologies in diagnostic virology

The thioredoxin specificity of Drosophila GPx: a paradigm for a peroxiredoxin-like mechanism of many glutathione peroxidases.

Human papillomavirus genotyping by 454 next generation sequencing technology

Transcriptome analysis of Medicago truncatula leaf senescence: similarities and differences in metabolic and transcriptional regulations as compared with Arabidopsis, nodule senescence and nitric oxide signalling.

Rapid annotation of anonymous sequences from genome projects using semantic similarities and a weighting scheme in gene ontology

Antimicrobial treatment and containment measures for an extremely drug-resistant Klebsiella pneumoniae ST101 isolate carrying pKPN101-IT, a novel fully sequenced bla(KPC-2) plasmid

Phylogenetic characterization of Central/Southern European lineage 2 West Nile virus: analysis of human outbreaks in Italy and Greece, 2013-2014.

Functional interaction of phospholipid hydroperoxide glutathione peroxidase with sperm mitochondrion-associated cysteine-rich protein discloses the adjacent cysteine motif as a new substrate of the selenoperoxidase.

Toward more transparent and reproducible omics studies through a common metadata checklist and data publications

Organochalcogen peroxidase mimetics as potential drugs: a long story of a promise still unfulfilled.

Pattern recognition in gene expression profiling using DNA array: a comparative study of different statistical methods applied to cancer classification

Genomic comparative analysis and gene function prediction in infectious diseases: application to the investigation of a meningitis outbreak

Glutathione peroxidase 4-catalyzed reduction of lipid hydroperoxides in membranes: The polar head of membrane phospholipids binds the enzyme and addresses the fatty acid hydroperoxide group toward the redox center.

Accurate human papillomavirus genotyping by 454 pyrosequencing

Linear motifs in the C-terminus of D. melanogaster cryptochrome

Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data

Reducing bias in RNA sequencing data: a novel approach to compute counts

The SSEA server for protein secondary structure alignment.

Protein disulfide isomerase and glutathione are alternative substrates in the one Cys catalytic cycle of glutathione peroxidase 7.

Mapping and characterization of G-quadruplexes in Mycobacterium tuberculosis gene promoter regions.

Selenocysteine oxidation in glutathione peroxidase catalysis: an MS-supported quantum mechanics study.

G-quadruplex forming sequences in the genome of all known human viruses: A comprehensive guide

Novel West Nile virus lineage 1a full genome sequences from human cases of infection in north-eastern Italy, 2011.

Enhancing protein function prediction with taxonomic constraints--The Argot2.5 web server.

Characterization of Intra-Type Variants of Oncogenic Human Papillomaviruses by Next-Generation Deep Sequencing of the E6/E7 Region

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

Primary structure of the nuclear forms of phospholipid hydroperoxide glutathione peroxidase (PHGPx) in rat spermatozoa

Reproducibility: In praise of open research measures

Improving the quality of protein structure models by selecting from alignment alternatives

Peroxiredoxin 6 from the Antarctic emerald rockcod: molecular characterization of its response to warming

Quantitative label-free redox proteomics of reversible cysteine oxidation in red blood cell membranes

Characterization of a novel complex BRAF mutation in a follicular variant papillary thyroid carcinoma

Human cytomegalovirus productively infects adrenocortical cells and induces an early cortisol response

Transcriptome and Cell Physiological Analyses in Different Rice Cultivars Provide New Insights Into Adaptive and Salinity Stress Responses.

Third generation sequencing technologies applied to diagnostic microbiology: benefits and challenges in applications and data analysis

Simplifying amino acid alphabets by means of a branch and bound algorithm and substitution matrices

Insight into the mechanism of ferroptosis inhibition by ferrostatin-1