Lista de obras - Stefano Toppo - Dominio Público Uruguay

A comparison of thiol peroxidase mechanisms

artículo científico publicado en 2010

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

artículo científico publicado en 2007

A large-scale evaluation of computational protein function prediction

artículo científico publicado en 2013

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

artículo científico publicado en 2002

Accurate human papillomavirus genotyping by 454 pyrosequencing

artículo científico publicado en 2013

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

artículo científico publicado en 2006

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

artículo científico publicado en 2016

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

artículo científico publicado en 2012

Applications of next-generation sequencing technologies to diagnostic virology

artículo científico publicado en 2011

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

artículo científico publicado en 2012

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

artículo científico publicado en 2016

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

artículo científico publicado en 2008

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

artículo científico publicado en 2012

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

artículo científico publicado en 2002

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

artículo científico publicado en 2008

Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates

artículo científico publicado en 2010

Eliciting the Functional Taxonomy from protein annotations and taxa

artículo científico publicado en 2016

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

artículo científico

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.

artículo científico publicado en 2008

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

artículo científico publicado en 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.

artículo científico publicado en 2005

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

artículo científico publicado en 2018

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

artículo científico publicado en 2013

Glutathione Peroxidase 4

artículo científico publicado en 2016

Glutathione Peroxidase-4

artículo científico publicado en 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.

artículo científico publicado en 2017

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

artículo científico publicado en 2015

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

artículo científico publicado en 2022

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

artículo científico publicado en 2009

Human papillomavirus genotyping by 454 next generation sequencing technology

artículo científico publicado en 2011

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

artículo científico publicado en 2016

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

artículo científico publicado en 2006

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

artículo científico publicado en 2019

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

artículo científico publicado en 2019

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

artículo científico publicado en 2006

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

artículo científico publicado en 2007

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

artículo científico publicado en 2018

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

artículo científico publicado en 2008

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

artículo científico

Mass Spectrometry Data Analysis in the Proteomics Era

artículo científico publicado en 2007

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

artículo científico publicado en 2010

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

artículo científico publicado en 2018

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

artículo científico publicado en 2022

Next-generation sequencing technologies in diagnostic virology

artículo científico publicado en 2013

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

artículo científico publicado en 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.

artículo científico publicado en 2013

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

artículo científico publicado en 2017

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

artículo científico publicado en 2003

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

artículo científico publicado en 2015

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

artículo científico publicado en 2015

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

artículo científico publicado en 2005

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

artículo científico publicado en 2013

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

artículo científico publicado en 2020

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

artículo científico publicado en 2014

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

artículo científico publicado en 2022

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

artículo científico publicado en 2009

Redox status in a model of cancer stem cells.

artículo científico publicado en 2016

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

artículo científico publicado en 2014

Reproducibility: In praise of open research measures

artículo científico publicado en 2013

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

artículo científico publicado en 2015

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

artículo científico publicado en 2000

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

artículo científico publicado en 2002

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

artículo científico publicado en 2017

Studying interactions by molecular dynamics simulations at high concentration

artículo científico publicado en 2012

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

artículo científico publicado en 2020

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

artículo científico publicado en 2020

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

artículo científico

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.

artículo científico publicado en 2004

The catalytic site of glutathione peroxidases.

artículo científico publicado en 2008

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

artículo científico publicado en 2010

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

artículo científico publicado en 2006

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

artículo científico publicado en 2016

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

artículo científico publicado en 2013

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

artículo científico publicado en 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.

artículo científico publicado en 2008

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

artículo científico publicado en 2018

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

artículo científico

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

artículo científico publicado en 2022

Zebrafish spata2 is expressed at early developmental stages.

artículo científico publicado en 2007

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

artículo científico publicado en 2014

Lista de obras de Stefano Toppo

A comparison of thiol peroxidase mechanisms

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

A large-scale evaluation of computational protein function prediction

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

Accurate human papillomavirus genotyping by 454 pyrosequencing

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

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

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

Applications of next-generation sequencing technologies to diagnostic virology

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

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

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

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

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

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

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

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

Draft genome sequences of two Neisseria meningitidis serogroup C clinical isolates

Eliciting the Functional Taxonomy from protein annotations and taxa

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

Evolutionary Study of the Crassphage Virus at Gene Level

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

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

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.

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

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

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

Glutathione Peroxidase 4

Glutathione Peroxidase-4

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.

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

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

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

Human papillomavirus genotyping by 454 next generation sequencing technology

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

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

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

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

Insight into the mechanism of ferroptosis inhibition by ferrostatin-1

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

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

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

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

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

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

Mass Spectrometry Data Analysis in the Proteomics Era

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

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

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

Next-generation sequencing technologies in diagnostic virology

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

Optimizing PCR primers targeting the bacterial 16S ribosomal RNA gene

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

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

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

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

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

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

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

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

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

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

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

Redox status in a model of cancer stem cells.

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

Reproducibility: In praise of open research measures

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

Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana

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

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

Studying interactions by molecular dynamics simulations at high concentration

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

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

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

Telethonin, a novel sarcomeric protein of heart and skeletal muscle

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

The SSEA server for protein secondary structure alignment.

The catalytic site of glutathione peroxidases.

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