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List of works by Laurent Gatto

A Bayesian Mixture Modelling Approach For Spatial Proteomics

A Bayesian mixture modelling approach for spatial proteomics

scientific article published on 27 November 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

scientific article published on 11 April 2019

A Modular and Expandable Ecosystem for Metabolomics Data Annotation in R

scientific article published on 11 February 2022

A cross-platform toolkit for mass spectrometry and proteomics

scientific article

A draft map of the mouse pluripotent stem cell spatial proteome

scientific article published on 12 January 2016

A foundation for reliable spatial proteomics data analysis.

scientific article

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

scientific article

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

scientific article published on 09 November 2020

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

scientific article published on 5 May 2020

A subcellular map of the human proteome

scientific article

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

scientific article published on 29 July 2020

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

scientific article

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

scientific article

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

scientific article published in January 2006

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

scientific article published on 23 March 2022

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

scientific article

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

scientific article published on 16 June 2022

Challenges for proteomics core facilities

scientific article

Chapter 14. R for Proteomics

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics

scientific article published in Nature Communications

Curated Single Cell Multimodal Landmark Datasets for R/Bioconductor

scientific article published on 28 October 2021

Curated single cell multimodal landmark datasets for R/Bioconductor

scientific article published on 25 August 2023

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

scientific article published on 6 September 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.

scientific article

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

scientific article published on 8 June 2015

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

scientific article

Exploiting the DepMap cancer dependency data using the depmap R package

scientific article published on 25 May 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

scientific article published in 2019

Gut microbiome modulates tacrolimus pharmacokinetics through the transcriptional regulation of ABCB1

scientific article published on 6 July 2023

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

scientific article published on 24 June 2022

Human urinary exosomes as innate immune effectors

scientific article

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

scientific article published on 19 April 2022

Identification of RSK substrates using an analog-sensitive kinase approach

scientific article published in 2024

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

scientific article published on 17 January 2014

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

scientific article published on 17 April 2013

Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE

scientific article published on 5 January 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

scientific article

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

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

scientific article published on 13 August 2014

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics

scientific article

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

scientific article published on 09 September 2020

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

scientific article published on 30 April 2020

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

scientific article

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

scientific article

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)

scientific article

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

scientific article published on 6 April 2021

Orchestrating high-throughput genomic analysis with Bioconductor

scientific article

Organelle proteomics experimental designs and analysis

scientific article

Preprints help journalism, not hinder it

scientific article published in Nature

ProtFinder: finding subcellular locations of proteins using protein interaction networks

scientific article published on 12 January 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

scientific article (publication date: March 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.

scientific article

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

scientific article

Replication of single-cell proteomics data reveals important computational challenges

scientific article published on 12 April 2021

Reproducibility and Transparency by Design

scientific article published on 04 July 2019

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

scientific article published on 2 August 2023

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

scientific article published on 01 October 2021

Ten Simple Rules for Taking Advantage of Git and GitHub

scientific article (publication date: July 2016)

Ten Simple Rules for Taking Advantage of git and GitHub

Testing and Validation of Computational Methods for Mass Spectrometry

scientific article published on 9 November 2015

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

scientific article

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

scientific article published on 21 March 2013

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

scientific article published on 12 April 2022

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

scientific article

Towards reproducible MSMS data preprocessing, quality control and quantification

Using R and Bioconductor for proteomics data analysis

scientific article

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

scientific article

Visualization of proteomics data using R and bioconductor

2015 scientific article

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.

scientific article published on 5 June 2018

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

scientific article published on 23 April 2014

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