List of works - Luisa Castagnoli

A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules

scientific article

A novel approach to protein-protein interaction: complex formation between the p53 tumor suppressor and the HIV Tat proteins.

scientific article published in January 1995

A strategy to optimize translation initiation in recombinant mRNA: application to the Rop gene.

scientific article published on June 1989

A subset of RAB proteins modulates PP2A phosphatase activity

scientific article published on 09 September 2016

A two-hybrid system based on chimeric operator recognition for studying protein homo/heterodimerization in Escherichia coli

scientific article published on 01 June 2001

Alterations in the phosphoproteomic profile of cells expressing a non-functional form of the SHP2 phosphatase.

scientific article published on 24 August 2015

Alternative bacteriophage display systems.

scientific article

Analysis of dominant copy number mutants of the plasmid pMB1

scientific article

Approaches to Analyze Protein Interactions.

scientific article

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins

scientific article

Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases

scientific article

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction

scientific article

Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases

scientific article published on 3 February 2017

CUBAN, a Case Study of Selective Binding: Structural Details of the Discrimination between Ubiquitin and NEDD8 ⬇️

scientific article published on 08 March 2019

Can we infer peptide recognition specificity mediated by SH3 domains?

scientific article

Characterization by mass cytometry of different methods for the preparation of muscle mononuclear cells.

scientific article

Characterization of a promoter up mutation in the -35 region of the promoter of the primer for ColE1 replication.

scientific article

Cloning of several cDNA segments coding for human liver proteins

scientific article

CoCUN, a Novel Ubiquitin Binding Domain Identified in N4BP1

scientific article published on 17 July 2019

Combining affinity proteomics and network context to identify new phosphatase substrates and adapters in growth pathways.

scientific article published on 7 May 2014

Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae and H. sapiens

scientific article published on 06 December 2010

Construction, exploitation and evolution of a new peptide library displayed at high density by fusion to the major coat protein of filamentous phage

scientific article published on June 1997

Control of ColE1 plasmid replication by antisense RNA.

scientific article

Control of initiation of pMB1 replication: purified Rop protein and RNA I affect primer formation in vitro

scientific article published on 01 July 1984

Control of pMB1 replication: inhibition of primer formation by Rop requires RNA1.

scientific article published on June 1984

Counteracting effects operating on Src homology 2 domain-containing protein-tyrosine phosphatase 2 (SHP2) function drive selection of the recurrent Y62D and Y63C substitutions in Noonan syndrome

scientific article published on 18 June 2012

DISNOR: a disease network open resource.

scientific article published on 3 October 2017

DOMINO: a database of domain-peptide interactions

scientific article

Deep Proteomics of Breast Cancer Cells Reveals that Metformin Rewires Signaling Networks Away from a Pro-growth State.

scientific article published on 3 March 2016

Diverse driving forces underlie the invariant occurrence of the T42A, E139D, I282V and T468M SHP2 amino acid substitutions causing Noonan and LEOPARD syndromes

scientific article

Domain repertoires as a tool to derive protein recognition rules.

scientific article

Enriching the viral-host interactomes with interactions mediated by SH3 domains

scientific article

Erratum: Nepravishta, R., et al. CoCUN, a Novel Ubiquitin Binding Domain Identified in N4BP1. Biomolecules 2019, 9, 284

scientific article published on 28 November 2019

Fibro-adipogenic progenitors of dystrophic mice are insensitive to NOTCH regulation of adipogenesis

scientific article published on 25 June 2019

Genetic and structural analysis of the ColE1 Rop (Rom) protein

scientific article published on February 1989

Group I Paks support muscle regeneration and counteract cancer-associated muscle atrophy.

scientific article

HiPPO and PANDA: two bioinformatics tools to support analysis of high-dimensional mass cytometry data

High-Dimensional Single-Cell Quantitative Profiling of Skeletal Muscle Cell Population Dynamics during Regeneration

scientific article published on 18 July 2020

How does Rop work?

scientific article published on 01 January 1984

HuPho: the human phosphatase portal

scientific article published on 24 August 2012

Hybrid Rop-pIII proteins for the display of constrained peptides on filamentous phage capsids

scientific article published on January 1993

Identification of new substrates of the protein-tyrosine phosphatase PTP1B by Bayesian integration of proteome evidence

scientific article published on December 2010

Increasing the immunogenicity of protein antigens through the genetic insertion of VQGEESNDK sequence of human IL-1 beta into their sequence.

scientific article published in August 1993

Intersectin, a novel adaptor protein with two Eps15 homology and five Src homology 3 domains.

scientific article

Linking an easily detectable phenotype to the folding of a common structural motif. Selection of rare turn mutations that prevent the folding of Rop.

scientific article published on April 1994

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data

scientific article

MINT, the molecular interaction database: 2009 update

scientific article (publication date: 2010)

MINT, the molecular interaction database: 2012 update

scientific article

MINT: the Molecular INTeraction database

scientific article

Mapping protein-protein interactions with phage-displayed combinatorial peptide libraries

scientific article

Mapping the human phosphatome on growth pathways

scientific article

Metformin Delays Satellite Cell Activation and Maintains Quiescence.

scientific article published on 24 April 2019

Metformin Induces Apoptosis and Downregulates Pyruvate Kinase M2 in Breast Cancer Cells Only When Grown in Nutrient-Poor Conditions

scientific article published on 20 August 2015

Metformin protects skeletal muscle from cardiotoxin induced degeneration

scientific article

Methods to reveal domain networks

scientific article

Microfluidic-enhanced 3D bioprinting of aligned myoblast-laden hydrogels leads to functionally organized myofibers in vitro and in vivo

scientific article published on 23 March 2017

Multiple modification and protein interaction signals drive the Ring finger protein 11 (RNF11) E3 ligase to the endosomal compartment

scientific article

Osteogenic differentiation of skeletal muscle progenitor cells is activated by the DNA damage response

scientific article published on 01 April 2019

Phage displayed peptide libraries

scientific article

Physical and Functional Interaction between p53 Mutants and Different Isoforms of p73

scientific article published in Journal of Biological Chemistry

Physical interaction with Yes-associated protein enhances p73 transcriptional activity

scientific article

Processing of eukaryotic tRNA precursors: secondary structure of the precursor specific sequences affects the rate but not the accuracy of processing reactions.

scientific article published on July 1982

Promoter of a eukaryotic tRNAPro gene is composed of three noncontiguous regions.

scientific article

Protein interaction networks by proteome peptide scanning

scientific article

RNF11 at the Crossroads of Protein Ubiquitination

scientific article published on 11 November 2020

RNF11 is a GGA protein cargo and acts as a molecular adaptor for GGA3 ubiquitination mediated by Itch.

scientific article published on 8 September 2014

Reactive oxygen species and epidermal growth factor are antagonistic cues controlling SHP-2 dimerization

scientific article published on 12 March 2012

Recognition specificity of individual EH domains of mammals and yeast

scientific article

Regulation of myoblast differentiation by metabolic perturbations induced by metformin.

scientific article

Report and Abstracts of the 14th Meeting of IIM, the Interuniversity Institute of Myology, - Assisi (Italy), October 12-15, 2017

article

Role of 14-3-3 proteins in the regulation of neutral trehalase in the yeast Saccharomyces cerevisiae

scientific article

SIGNOR: a database of causal relationships between biological entities.

scientific article

Selection from a peptide library of the antigenic determinants of a protein

scientific article published on January 1993

Selection of antibody ligands from a large library of oligopeptides expressed on a multivalent exposition vector.

scientific article

Selection of ligands by panning of domain libraries displayed on phage lambda reveals new potential partners of synaptojanin 1

scientific article (publication date: 13 April 2001)

Selectivity and promiscuity in the interaction network mediated by protein recognition modules

scientific article published on June 2004

The 4G10, pY20 and p-TYR-100 antibody specificity: profiling by peptide microarrays

scientific article published on 13 December 2011

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

scientific article

The SH2 domain interaction landscape

scientific article

The SH3 domains of endophilin and amphiphysin bind to the proline-rich region of synaptojanin 1 at distinct sites that display an unconventional binding specificity

scientific article (publication date: 5 November 1999)

The adapter protein CD2AP binds to p53 protein in the cytoplasm and can discriminate its polymorphic variants P72R.

scientific article published on 26 September 2014

The cell-autonomous mechanisms underlying the activity of metformin as an anticancer drug

scientific article

The central proline rich region of POB1/REPS2 plays a regulatory role in epidermal growth factor receptor endocytosis by binding to 14-3-3 and SH3 domain-containing proteins

scientific article

The genes encoding the transcription factor yTAFII60, the G4p1 protein and a putative glucose transporter are contained in a 12.3 kb DNA fragment on the left arm of Saccharomyces cerevisiae chromosome VII.

scientific article

The human phosphatase interactome: An intricate family portrait

scientific article

The immunosuppressant drug azathioprine restrains adipogenesis of muscle Fibro/Adipogenic Progenitors from dystrophic mice by affecting AKT signaling

scientific article published on 13 March 2019

The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.

scientific article

The plasmid as a tool for plasmid genetics. I. Fine structure of the beta-lactamase gene

scientific article published on 01 December 1982

The plasmid as a tool for plasmid genetics. II. Isolation of point mutations that affect replication of a ColE1-related plasmid

scientific article published on 01 December 1982

The protein interaction network mediated by human SH3 domains

scientific article published on 29 June 2011

Transcription by RNA polymerase III.

scientific article published on January 1983

Tumor suppressor density-enhanced phosphatase-1 (DEP-1) inhibits the RAS pathway by direct dephosphorylation of ERK1/2 kinases

scientific article

Unusual binding properties of the SH3 domain of the yeast actin-binding protein Abp1: structural and functional analysis

scientific article

VirusMINT: a viral protein interaction database

scientific article

mentha: a resource for browsing integrated protein-interaction networks

scientific article published in August 2013

List of works by Luisa Castagnoli

A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules

A novel approach to protein-protein interaction: complex formation between the p53 tumor suppressor and the HIV Tat proteins.

A strategy to optimize translation initiation in recombinant mRNA: application to the Rop gene.

A subset of RAB proteins modulates PP2A phosphatase activity

A two-hybrid system based on chimeric operator recognition for studying protein homo/heterodimerization in Escherichia coli

Alterations in the phosphoproteomic profile of cells expressing a non-functional form of the SHP2 phosphatase.

Alternative bacteriophage display systems.

Analysis of dominant copy number mutants of the plasmid pMB1

Approaches to Analyze Protein Interactions.

Bayesian modeling of the yeast SH3 domain interactome predicts spatiotemporal dynamics of endocytosis proteins

Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction

Both Intrinsic Substrate Preference and Network Context Contribute to Substrate Selection of Classical Tyrosine Phosphatases

CUBAN, a Case Study of Selective Binding: Structural Details of the Discrimination between Ubiquitin and NEDD8 ⬇️

Can we infer peptide recognition specificity mediated by SH3 domains?

Characterization by mass cytometry of different methods for the preparation of muscle mononuclear cells.

Characterization of a promoter up mutation in the -35 region of the promoter of the primer for ColE1 replication.

Cloning of several cDNA segments coding for human liver proteins

CoCUN, a Novel Ubiquitin Binding Domain Identified in N4BP1

Combining affinity proteomics and network context to identify new phosphatase substrates and adapters in growth pathways.

Combining peptide recognition specificity and context information for the prediction of the 14-3-3-mediated interactome in S. cerevisiae and H. sapiens

Construction, exploitation and evolution of a new peptide library displayed at high density by fusion to the major coat protein of filamentous phage

Control of ColE1 plasmid replication by antisense RNA.

Control of initiation of pMB1 replication: purified Rop protein and RNA I affect primer formation in vitro

Control of pMB1 replication: inhibition of primer formation by Rop requires RNA1.

Counteracting effects operating on Src homology 2 domain-containing protein-tyrosine phosphatase 2 (SHP2) function drive selection of the recurrent Y62D and Y63C substitutions in Noonan syndrome

DISNOR: a disease network open resource.

DOMINO: a database of domain-peptide interactions

Deep Proteomics of Breast Cancer Cells Reveals that Metformin Rewires Signaling Networks Away from a Pro-growth State.

Diverse driving forces underlie the invariant occurrence of the T42A, E139D, I282V and T468M SHP2 amino acid substitutions causing Noonan and LEOPARD syndromes

Domain repertoires as a tool to derive protein recognition rules.

Enriching the viral-host interactomes with interactions mediated by SH3 domains

Erratum: Nepravishta, R., et al. CoCUN, a Novel Ubiquitin Binding Domain Identified in N4BP1. Biomolecules 2019, 9, 284

Fibro-adipogenic progenitors of dystrophic mice are insensitive to NOTCH regulation of adipogenesis

Genetic and structural analysis of the ColE1 Rop (Rom) protein

Group I Paks support muscle regeneration and counteract cancer-associated muscle atrophy.

HiPPO and PANDA: two bioinformatics tools to support analysis of high-dimensional mass cytometry data

High-Dimensional Single-Cell Quantitative Profiling of Skeletal Muscle Cell Population Dynamics during Regeneration

How does Rop work?

HuPho: the human phosphatase portal

Hybrid Rop-pIII proteins for the display of constrained peptides on filamentous phage capsids

Identification of new substrates of the protein-tyrosine phosphatase PTP1B by Bayesian integration of proteome evidence

Increasing the immunogenicity of protein antigens through the genetic insertion of VQGEESNDK sequence of human IL-1 beta into their sequence.

Intersectin, a novel adaptor protein with two Eps15 homology and five Src homology 3 domains.

Linking an easily detectable phenotype to the folding of a common structural motif. Selection of rare turn mutations that prevent the folding of Rop.

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data

MINT, the molecular interaction database: 2009 update

MINT, the molecular interaction database: 2012 update

MINT: the Molecular INTeraction database

Mapping protein-protein interactions with phage-displayed combinatorial peptide libraries

Mapping the human phosphatome on growth pathways

Metformin Delays Satellite Cell Activation and Maintains Quiescence.

Metformin Induces Apoptosis and Downregulates Pyruvate Kinase M2 in Breast Cancer Cells Only When Grown in Nutrient-Poor Conditions

Metformin protects skeletal muscle from cardiotoxin induced degeneration

Methods to reveal domain networks

Microfluidic-enhanced 3D bioprinting of aligned myoblast-laden hydrogels leads to functionally organized myofibers in vitro and in vivo

Multiple modification and protein interaction signals drive the Ring finger protein 11 (RNF11) E3 ligase to the endosomal compartment

Osteogenic differentiation of skeletal muscle progenitor cells is activated by the DNA damage response

Phage displayed peptide libraries

Physical and Functional Interaction between p53 Mutants and Different Isoforms of p73

Physical interaction with Yes-associated protein enhances p73 transcriptional activity

Processing of eukaryotic tRNA precursors: secondary structure of the precursor specific sequences affects the rate but not the accuracy of processing reactions.

Promoter of a eukaryotic tRNAPro gene is composed of three noncontiguous regions.

Protein interaction networks by proteome peptide scanning

RNF11 at the Crossroads of Protein Ubiquitination

RNF11 is a GGA protein cargo and acts as a molecular adaptor for GGA3 ubiquitination mediated by Itch.

Reactive oxygen species and epidermal growth factor are antagonistic cues controlling SHP-2 dimerization

Recognition specificity of individual EH domains of mammals and yeast

Regulation of myoblast differentiation by metabolic perturbations induced by metformin.

Report and Abstracts of the 14th Meeting of IIM, the Interuniversity Institute of Myology, - Assisi (Italy), October 12-15, 2017

Role of 14-3-3 proteins in the regulation of neutral trehalase in the yeast Saccharomyces cerevisiae

SIGNOR: a database of causal relationships between biological entities.

Selection from a peptide library of the antigenic determinants of a protein

Selection of antibody ligands from a large library of oligopeptides expressed on a multivalent exposition vector.

Selection of ligands by panning of domain libraries displayed on phage lambda reveals new potential partners of synaptojanin 1

Selectivity and promiscuity in the interaction network mediated by protein recognition modules

The 4G10, pY20 and p-TYR-100 antibody specificity: profiling by peptide microarrays

The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text

The SH2 domain interaction landscape