Lista de obras - Laurent Gatto - Dominio Público Uruguay

A Bayesian Mixture Modelling Approach For Spatial Proteomics

A Bayesian mixture modelling approach for spatial proteomics

artículo científico publicado en 2018

A Bioconductor workflow for processing and analysing spatial proteomics data

scientific article published on 28 December 2016

A Bioconductor workflow for the Bayesian analysis of spatial proteomics

artículo científico publicado en 2019

A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R

artículo científico publicado en 2022

A cross-platform toolkit for mass spectrometry and proteomics

artículo científico publicado en 2012

A draft map of the mouse pluripotent stem cell spatial proteome

artículo científico publicado en 2016

A foundation for reliable spatial proteomics data analysis.

artículo científico publicado en 2014

A posteriori quality control for the curation and reuse of public proteomics data

artículo científico publicado en 2011

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection

artículo científico publicado en 2020

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection

artículo científico publicado en 2020

A subcellular map of the human proteome

artículo científico publicado en 2017

Aberrant Membrane Composition and Biophysical Properties Impair Erythrocyte Morphology and Functionality in Elliptocytosis

artículo científico publicado en 2020

Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies.

artículo científico publicado en 2016

Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches

artículo científico publicado en 2016

Assessing sub-cellular resolution in spatial proteomics experiments

Assessing the applicability of the GTR nucleotide substitution model through simulations

artículo científico publicado en 2006

BRAF Induction in Thyrocytes Triggers Important Changes in the miRNAs Content and the Populations of Extracellular Vesicles Released in Thyroid Tumor Microenvironment

artículo científico publicado en 2022

BioContainers: An open-source and community-driven framework for software standardization

artículo científico publicado en 2017

Cardiovirus leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic

artículo científico publicado en 2022

Challenges for proteomics core facilities

artículo científico publicado en 2011

Chapter 14. R for Proteomics

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics

artículo científico publicado en 2019

Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor

artículo científico publicado en 2021

Curated single cell multimodal landmark datasets for R/Bioconductor

artículo científico publicado en 2023

DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics

artículo científico publicado en 2016

Data Management Plan for a Biotechnology and Biological Sciences Research Council (BBSRC) Tools and Resources Development Fund (TRDF) Grant

Deciphering thylakoid sub-compartments using a mass spectrometry-based approach.

artículo científico publicado en 2014

Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells

artículo científico publicado en 2015

Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies

artículo científico publicado en 2013

Exploiting the DepMap cancer dependency data using the depmap R package

artículo científico publicado en 2021

Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics

scientific article published on 12 December 2019

Global mapping of protein subcellular location in apicomplexans: the parasite as we’ve never seen it before

artículo científico publicado en 2019

Gut microbiome modulates tacrolimus pharmacokinetics through the transcriptional regulation of ABCB1

artículo científico publicado en 2023

HYGIEIA: HYpothesizing the Genesis of Infectious Diseases and Epidemics through an Integrated Systems Biology Approach

artículo científico publicado en 2022

Human urinary exosomes as innate immune effectors

artículo científico publicado en 2014

Identification and implication of tissue-enriched ligands in epithelial-endothelial crosstalk during pancreas development

artículo científico publicado en 2022

Identification of RSK substrates using an analog-sensitive kinase approach

artículo científico publicado en 2024

Identification of trans-golgi network proteins in Arabidopsis thaliana root tissue

artículo científico publicado en 2014

Improving qualitative and quantitative performance for MS(E)-based label-free proteomics

artículo científico publicado en 2013

Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE

artículo científico publicado en 2021

Interferon regulatory factor 7-mediated responses are defective in cord blood plasmacytoid dendritic cells

article

LC-MS/MS methods for absolute quantification and identification of proteins associated with chimeric plant oil bodies

artículo científico publicado en 2011

LOPIT-DC: A simpler approach to high-resolution spatial proteomics

Label-free protein quantification for plant Golgi protein localization and abundance.

artículo científico publicado en 2014

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics

artículo científico publicado en 2016

MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data

artículo científico publicado en 2020

MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data

artículo científico publicado en 2020

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation

artículo científico publicado en 2011

Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata.

artículo científico publicado en 2014

Molecular networks in Network Medicine: Development and applications

scientific article published on 19 April 2020

Morphological and mitochondrial DNA analyses indicate the presence of a hybrid zone between two species of leaf beetle (Coleoptera; Chrysomelidae) in Southern Spain

article

NSF 19-501 AccelNet Proposal: Community of Open Scholarship Grassroots Networks (COSGN)

artículo científico publicado en 2020

Negative feedback via RSK modulates Erk-dependent progression from naïve pluripotency

scientific article published on 12 June 2018

On the many advantages of using the VariantExperiment class to store, exchange and analyze SARS-CoV-2 genomic data and associated metadata

artículo científico publicado en 2021

Orchestrating high-throughput genomic analysis with Bioconductor

artículo científico publicado en 2015

Organelle proteomics experimental designs and analysis

artículo científico publicado en 2010

Preprints help journalism, not hinder it

scientific article published in Nature

ProtFinder: finding subcellular locations of proteins using protein interaction networks

artículo científico publicado en 2022

Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism

scientific article published on 02 October 2019

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

artículo científico publicado en 2014

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.

artículo científico publicado en 2013

Recent developments in scholarly publishing to improve research practices in the life sciences

Replication of single-cell proteomics data reveals important computational challenges

artículo científico publicado en 2021

Replication of single-cell proteomics data reveals important computational challenges

artículo científico publicado en 2021

Reproducibility and Transparency by Design

scientific article published on 04 July 2019

Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics

artículo científico publicado en 2023

Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line

artículo científico publicado en 2021

Ten Simple Rules for Taking Advantage of Git and GitHub

artículo científico publicado en 2016

Ten Simple Rules for Taking Advantage of git and GitHub

Testing and Validation of Computational Methods for Mass Spectrometry

artículo científico publicado en 2015

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

artículo científico publicado en 2010

The effect of organelle discovery upon sub-cellular protein localisation.

artículo científico publicado en 2013

The intra-mitochondrial O-GlcNAcylation system rapidly modulates OXPHOS function and ROS release in the heart

artículo científico publicado en 2022

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

artículo científico publicado en 2014

Towards reproducible MSMS data preprocessing, quality control and quantification

Using R and Bioconductor for proteomics data analysis

artículo científico publicado en 2013

Using hyperLOPIT to perform high-resolution mapping of the spatial proteome.

artículo científico publicado en 2017

Visualization of proteomics data using R and bioconductor

artículo científico publicado en 2015

ensembldb: an R package to create and use Ensembl-based annotation resources

scientific article published on 01 September 2019

hiPSC hepatocyte model demonstrates the role of unfolded protein response and inflammatory networks in α1-antitrypsin deficiency.

artículo científico publicado en 2018

qcML: an exchange format for quality control metrics from mass spectrometry experiments

artículo científico

Lista de obras de Laurent Gatto

A Bayesian Mixture Modelling Approach For Spatial Proteomics

A Bayesian mixture modelling approach for spatial proteomics

A Bioconductor workflow for processing and analysing spatial proteomics data

A Bioconductor workflow for the Bayesian analysis of spatial proteomics

A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R

A cross-platform toolkit for mass spectrometry and proteomics

A draft map of the mouse pluripotent stem cell spatial proteome

A foundation for reliable spatial proteomics data analysis.

A posteriori quality control for the curation and reuse of public proteomics data

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection

A semi-supervised Bayesian approach for simultaneous protein sub-cellular localisation assignment and novelty detection

A subcellular map of the human proteome

Aberrant Membrane Composition and Biophysical Properties Impair Erythrocyte Morphology and Functionality in Elliptocytosis

Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies.

Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label-free proteomics approaches

Assessing sub-cellular resolution in spatial proteomics experiments

Assessing sub-cellular resolution in spatial proteomics experiments

Assessing the applicability of the GTR nucleotide substitution model through simulations

BRAF Induction in Thyrocytes Triggers Important Changes in the miRNAs Content and the Populations of Extracellular Vesicles Released in Thyroid Tumor Microenvironment

BioContainers: An open-source and community-driven framework for software standardization

Cardiovirus leader proteins retarget RSK kinases toward alternative substrates to perturb nucleocytoplasmic traffic

Challenges for proteomics core facilities

Chapter 14. R for Proteomics

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics

Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor

Curated single cell multimodal landmark datasets for R/Bioconductor

DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics

Data Management Plan for a Biotechnology and Biological Sciences Research Council (BBSRC) Tools and Resources Development Fund (TRDF) Grant

Deciphering thylakoid sub-compartments using a mass spectrometry-based approach.

Dynamic Proteomic Profiling of Extra-Embryonic Endoderm Differentiation in Mouse Embryonic Stem Cells

Effects of traveling wave ion mobility separation on data independent acquisition in proteomics studies

Exploiting the DepMap cancer dependency data using the depmap R package

Fast approximate inference for variable selection in Dirichlet process mixtures, with an application to pan-cancer proteomics

Global mapping of protein subcellular location in apicomplexans: the parasite as we’ve never seen it before

Gut microbiome modulates tacrolimus pharmacokinetics through the transcriptional regulation of ABCB1

HYGIEIA: HYpothesizing the Genesis of Infectious Diseases and Epidemics through an Integrated Systems Biology Approach

Human urinary exosomes as innate immune effectors

Identification and implication of tissue-enriched ligands in epithelial-endothelial crosstalk during pancreas development

Identification of RSK substrates using an analog-sensitive kinase approach

Identification of trans-golgi network proteins in Arabidopsis thaliana root tissue

Improving qualitative and quantitative performance for MS(E)-based label-free proteomics

Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE

Interferon regulatory factor 7-mediated responses are defective in cord blood plasmacytoid dendritic cells

LC-MS/MS methods for absolute quantification and identification of proteins associated with chimeric plant oil bodies

LOPIT-DC: A simpler approach to high-resolution spatial proteomics

Label-free protein quantification for plant Golgi protein localization and abundance.

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics

MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data

MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data

MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation

Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata.

Molecular networks in Network Medicine: Development and applications

Morphological and mitochondrial DNA analyses indicate the presence of a hybrid zone between two species of leaf beetle (Coleoptera; Chrysomelidae) in Southern Spain

NSF 19-501 AccelNet Proposal: Community of Open Scholarship Grassroots Networks (COSGN)

Negative feedback via RSK modulates Erk-dependent progression from naïve pluripotency

On the many advantages of using the VariantExperiment class to store, exchange and analyze SARS-CoV-2 genomic data and associated metadata

Orchestrating high-throughput genomic analysis with Bioconductor

Organelle proteomics experimental designs and analysis

Preprints help journalism, not hinder it

ProtFinder: finding subcellular locations of proteins using protein interaction networks

Proteome Mapping of a Cyanobacterium Reveals Distinct Compartment Organization and Cell-Dispersed Metabolism

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

RNA-seq reveals the RNA binding proteins, Hfq and RsmA, play various roles in virulence, antibiotic production and genomic flux in Serratia sp. ATCC 39006.

Recent developments in scholarly publishing to improve research practices in the life sciences

Recent developments in scholarly publishing to improve research practices in the life sciences

Replication of single-cell proteomics data reveals important computational challenges

Replication of single-cell proteomics data reveals important computational challenges

Reproducibility and Transparency by Design

Revisiting the Thorny Issue of Missing Values in Single-Cell Proteomics

Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line

Ten Simple Rules for Taking Advantage of Git and GitHub

Ten Simple Rules for Taking Advantage of git and GitHub

Testing and Validation of Computational Methods for Mass Spectrometry

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

The effect of organelle discovery upon sub-cellular protein localisation.

The intra-mitochondrial O-GlcNAcylation system rapidly modulates OXPHOS function and ROS release in the heart

The mzTab data exchange format: communicating mass-spectrometry-based proteomics and metabolomics experimental results to a wider audience

Towards reproducible MSMS data preprocessing, quality control and quantification

Using R and Bioconductor for proteomics data analysis