List of works by Stefano Toppo

A comparison of thiol peroxidase mechanisms

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

A two-step strategy for constructing specifically self-subtracted cDNA libraries

scientific article

Accurate human papillomavirus genotyping by 454 pyrosequencing.

scientific article published on 10 April 2013

Align: a C++ class library and web server for rapid sequence alignment prototyping.

scientific article

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

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

Applications of next-generation sequencing technologies to diagnostic virology

scientific article published on 14 November 2011

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

scientific article

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

scientific article published on 17 April 2009

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

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

scientific article published on 21 April 2008

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

scientific article

Copper/Zinc Superoxide Dismutase from the Crocodile Icefish Chionodraco hamatus: Antioxidant Defense at Constant Sub-Zero Temperature

scientific article published on 17 April 2020

Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs

scientific article

Differential liquid phase proteomic analysis of the effect of selenium supplementation in LNCaP cells.

scientific article

Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates

scientific article published on 30 July 2010

Eliciting the Functional Taxonomy from protein annotations and taxa

scientific article published on 18 August 2016

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

scientific article published on 27 August 2015

Evolutionary Study of the Crassphage Virus at Gene Level

scientific article published on 17 September 2020

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

scientific article

Full Genome Sequence-Based Comparative Study of Wild-Type and Vaccine Strains of Infectious Laryngotracheitis Virus from Italy

scientific article published on 18 February 2016

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

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

article published in 2018

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

scientific article published on 11 June 2018

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

scientific article

Glutathione Peroxidase 4

scientific article published in 2016

Glutathione Peroxidase-4

scientific article published in 2011

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

Glutathione peroxidase 8 is transcriptionally regulated by HIFα and modulates growth factor signaling in HeLa cells.

scientific article published on January 2015

Human Virus Genomes Are Enriched in Conserved Adenine/Thymine/Uracil Multiple Tracts That Pause Polymerase Progression

scientific article published in 2022

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

scientific article

Human papillomavirus genotyping by 454 next generation sequencing technology

scientific article

Identification by MS/MS of disulfides produced by a functional redox transition

scientific article published on January 2010

Identification of novel X-linked gain-of-function RPGR-ORF15 mutation in Italian family with retinitis pigmentosa and pathologic myopia

scientific article published on 20 December 2016

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

scientific article

Inactivation of the glutathione peroxidase GPx4 by the ferroptosis-inducing molecule RSL3 requires the adaptor protein 14-3-3ε

scientific article published on 20 October 2019

Insight into the mechanism of ferroptosis inhibition by ferrostatin-1

scientific article published on 20 September 2019

Lack of glutathione peroxidase-8 in the ER impacts on lipid composition of HeLa cells microsomal membranes

scientific article published on 16 December 2019

Large-scale prediction of protein structure and function from sequence.

scientific article

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

scientific article published on 9 February 2007

Loss of cardiac Wnt/β-catenin signalling in Desmoplakin-deficient AC8 zebrafish models is rescuable by genetic and pharmacological intervention.

scientific article published on 7 March 2018

MPA: a multiple peak alignment algorithm to perform multiple comparisons of liquid-phase proteomic profiles.

scientific article published in January 2008

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

scientific article published on 18 July 2017

Mass Spectrometry Data Analysis in the Proteomics Era

scientific article published in January 2007

Matching up Phosphosites to Kinases: A Survey of Available Predictive Programs

scientific article published in June 2010

NeSSie: a tool for the identification of approximate DNA sequence symmetries.

scientific article published on 7 March 2018

Neutralising reactivity against SARS-CoV-2 Delta and Omicron variants by vaccination and infection history

scientific article published in 2022

Next-generation sequencing technologies in diagnostic virology

scientific article published on 21 March 2013

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

Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene

article

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

scientific article published on 14 March 2013

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms.

scientific article

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

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

scientific article published on 3 October 2015

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

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

scientific article published in January 2005

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

QPARSE: searching for long-looped or multimeric G-quadruplexes potentially distinctive and druggable

scientific article published on 01 January 2020

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

scientific article published on 15 March 2014

Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes

scientific article published in 2022

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

scientific article

Redox status in a model of cancer stem cells.

scientific article published on 13 September 2016

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

scientific article

Reproducibility: In praise of open research measures

scientific article published in June 2013

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

scientific article published on 7 July 2015

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

scientific article

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

scientific article published on 01 August 2002

Sox10 contributes to the balance of fate choice in dorsal root ganglion progenitors

scientific article

Studying interactions by molecular dynamics simulations at high concentration

scientific article published on 22 February 2012

Suppression of COVID-19 outbreak in the municipality of Vo, Italy

scientific article published on 18 April 2020

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

scientific article published on 30 June 2020

TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts.

scientific article published on March 2003

Telethonin, a novel sarcomeric protein of heart and skeletal muscle

scientific journal article

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

The SSEA server for protein secondary structure alignment.

scientific article

The catalytic site of glutathione peroxidases.

scientific article published in September 2008

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

scientific article

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

scientific article published on 13 October 2006

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

scientific article

Toward More Transparent and Reproducible Omics Studies Through a Common Metadata Checklist and Data Publications

scientific article

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

scientific article (publication date: 2014)

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

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

Understanding mammalian glutathione peroxidase 7 in the light of its homologs.

scientific article published on 25 February 2015

Vimentin binds to G-quadruplex repeats found at telomeres and gene promoters

scientific article published on 01 February 2022

Zebrafish spata2 is expressed at early developmental stages.

scientific article published on January 2007

keeSeek: searching distant non-existing words in genomes for PCR-based applications.

scientific article published on 27 May 2014

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