Publications by authors named "Laurent Gatto"

50Publications

MSnbase, Efficient and Elegant R-Based Processing and Visualization of Raw Mass Spectrometry Data.

J Proteome Res 2020 Sep 28. Epub 2020 Sep 28.

Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy.

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http://dx.doi.org/10.1021/acs.jproteome.0c00313DOI Listing
September 2020

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

Stat Appl Genet Mol Biol 2019 12 12;18(6). Epub 2019 Dec 12.

MRC Biostatistics Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1515/sagmb-2018-0065DOI Listing
December 2019

Reproducibility and Transparency by Design.

Mol Cell Proteomics 2019 08 4;18(8 suppl 1):S202-S204. Epub 2019 Jul 4.

¶Brigham Young University, Provo UT

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http://dx.doi.org/10.1074/mcp.IP119.001567DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6692781PMC
August 2019

A Bioconductor workflow for the Bayesian analysis of spatial proteomics.

F1000Res 2019 11;8:446. Epub 2019 Apr 11.

Université catholique de Louvain, Brussels, 1200, Belgium.

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http://dx.doi.org/10.12688/f1000research.18636.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6509962PMC
June 2020

Assessing sub-cellular resolution in spatial proteomics experiments.

Curr Opin Chem Biol 2019 02 14;48:123-149. Epub 2018 Dec 14.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK.

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http://dx.doi.org/10.1016/j.cbpa.2018.11.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391913PMC
February 2019

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

Bioinformatics 2019 09;35(17):3151-3153

Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.

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http://dx.doi.org/10.1093/bioinformatics/btz031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736197PMC
September 2019

Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics.

Nat Commun 2019 01 18;10(1):331. Epub 2019 Jan 18.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.

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http://dx.doi.org/10.1038/s41467-018-08191-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338729PMC
January 2019

A Bayesian mixture modelling approach for spatial proteomics.

PLoS Comput Biol 2018 11 27;14(11):e1006516. Epub 2018 Nov 27.

Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, UK.

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http://dx.plos.org/10.1371/journal.pcbi.1006516
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http://dx.doi.org/10.1371/journal.pcbi.1006516DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258510PMC
November 2018

Preprints help journalism, not hinder it.

Nature 2018 08;560(7720):553

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http://dx.doi.org/10.1038/d41586-018-06055-3DOI Listing
August 2018

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

EMBO Rep 2018 08 12;19(8). Epub 2018 Jun 12.

Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge, Cambridge, UK

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http://dx.doi.org/10.15252/embr.201745642DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6073214PMC
August 2018

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

Nat Protoc 2017 Jun 4;12(6):1110-1135. Epub 2017 May 4.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1038/nprot.2017.026DOI Listing
June 2017

A Bioconductor workflow for processing and analysing spatial proteomics data.

F1000Res 2016 28;5:2926. Epub 2016 Dec 28.

Computational Proteomics Unit, Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.12688/f1000research.10411.2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053703PMC
December 2016

Ten Simple Rules for Taking Advantage of Git and GitHub.

PLoS Comput Biol 2016 07 14;12(7):e1004947. Epub 2016 Jul 14.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1004947DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4945047PMC
July 2016

Learning from Heterogeneous Data Sources: An Application in Spatial Proteomics.

PLoS Comput Biol 2016 05 13;12(5):e1004920. Epub 2016 May 13.

Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1004920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866734PMC
May 2016

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

J Proteome Res 2016 Apr 1;15(4):1116-25. Epub 2016 Mar 1.

Univ. Grenoble Alpes , iRTSV-BGE, F-38000 Grenoble, France.

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http://dx.doi.org/10.1021/acs.jproteome.5b00981DOI Listing
April 2016

A draft map of the mouse pluripotent stem cell spatial proteome.

Nat Commun 2016 Jan 12;7:8992. Epub 2016 Jan 12.

Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK.

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http://dx.doi.org/10.1038/ncomms9992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729960PMC
January 2016

Testing and Validation of Computational Methods for Mass Spectrometry.

J Proteome Res 2016 Mar 17;15(3):809-14. Epub 2015 Nov 17.

CECAD, University of Cologne , 50931 Cologne, Germany.

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http://dx.doi.org/10.1021/acs.jproteome.5b00852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4804830PMC
March 2016

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

Stem Cells 2015 Sep 23;33(9):2712-25. Epub 2015 Jun 23.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.

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http://doi.wiley.com/10.1002/stem.2067
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http://dx.doi.org/10.1002/stem.2067DOI Listing
September 2015

Visualization of proteomics data using R and bioconductor.

Proteomics 2015 Apr;15(8):1375-89

Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK; Department of Biochemistry, Computational Proteomics Unit, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201400392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510819PMC
April 2015

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

Plant Physiol 2014 Oct 13;166(2):1033-43. Epub 2014 Aug 13.

Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom (N.N., P.V.S., L.G., P.D., K.S.L.); Computational Proteomics Unit (L.G.), and Cambridge Centre for Proteomics, Cambridge Systems Biology Centre (N.N., P.S., L.G., K.L.), Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, United Kingdom

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http://dx.doi.org/10.1104/pp.114.245589DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213074PMC
October 2014

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

Mol Cell Proteomics 2014 Aug 28;13(8):2147-67. Epub 2014 May 28.

From the ‡Univ. Grenoble Alpes, F-38000 Grenoble, France; **CEA, iRTSV, Laboratoire Biologie à Grande Echelle, F-38054 Grenoble, France; ‡‡ INSERM, U1038, F-38054 Grenoble, France;

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http://dx.doi.org/10.1074/mcp.M114.040923DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125743PMC
August 2014

A foundation for reliable spatial proteomics data analysis.

Mol Cell Proteomics 2014 Aug 20;13(8):1937-52. Epub 2014 May 20.

From the ‡Cambridge Centre for Proteomics, Department of Biochemistry, Tennis Court Road, University of Cambridge, Cambridge, CB2 1QR, United Kingdom;

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http://dx.doi.org/10.1074/mcp.M113.036350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4125728PMC
August 2014

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

Bioinformatics 2014 May 11;30(9):1322-4. Epub 2014 Jan 11.

Computational Proteomics Unit and Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK and Université Grenoble-Alpes, CEA (iRSTV/BGE), INSERM (U1038), CNRS (FR3425), 38054 Grenoble, France.

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http://dx.doi.org/10.1093/bioinformatics/btu013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3998135PMC
May 2014

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

J Proteome Res 2014 Feb 17;13(2):763-76. Epub 2014 Jan 17.

Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge , 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom.

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http://dx.doi.org/10.1021/pr4008464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3929368PMC
February 2014

Using R and Bioconductor for proteomics data analysis.

Biochim Biophys Acta 2014 Jan 18;1844(1 Pt A):42-51. Epub 2013 May 18.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK. Electronic address:

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http://dx.doi.org/10.1016/j.bbapap.2013.04.032DOI Listing
January 2014

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

J Proteome Res 2013 Jun 2;12(6):2323-39. Epub 2013 May 2.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, United Kingdom.

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http://dx.doi.org/10.1021/pr300775kDOI Listing
June 2013

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

J Proteome Res 2013 Jun 17;12(6):2340-53. Epub 2013 Apr 17.

Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom.

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http://dx.doi.org/10.1021/pr300776tDOI Listing
June 2013

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

Bioinformatics 2012 Jan 22;28(2):288-9. Epub 2011 Nov 22.

Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Tennis Court Road, CB2 1QR, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr645DOI Listing
January 2012

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

Anal Chem 2011 Dec 16;83(24):9267-72. Epub 2011 Nov 16.

Laboratorio Biotecnologie Unità Tecnica BIORAD, ENEA CR Casaccia, Roma, Italy.

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http://dx.doi.org/10.1021/ac201733mDOI Listing
December 2011

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

Proteomics 2011 Jun 2;11(11):2182-94. Epub 2011 May 2.

EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201000602DOI Listing
June 2011

Challenges for proteomics core facilities.

Proteomics 2011 Mar 16;11(6):1017-25. Epub 2011 Feb 16.

Cambridge Centre for Proteomics, Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201000693DOI Listing
March 2011

Organelle proteomics experimental designs and analysis.

Proteomics 2010 Nov 2;10(22):3957-69. Epub 2010 Nov 2.

Cambridge Centre for Proteomics, Cambridge Systems Biology Centre, Department of Biochemistry, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1002/pmic.201000244DOI Listing
November 2010

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

Authors:
Leming Shi Gregory Campbell Wendell D Jones Fabien Campagne Zhining Wen Stephen J Walker Zhenqiang Su Tzu-Ming Chu Federico M Goodsaid Lajos Pusztai John D Shaughnessy André Oberthuer Russell S Thomas Richard S Paules Mark Fielden Bart Barlogie Weijie Chen Pan Du Matthias Fischer Cesare Furlanello Brandon D Gallas Xijin Ge Dalila B Megherbi W Fraser Symmans May D Wang John Zhang Hans Bitter Benedikt Brors Pierre R Bushel Max Bylesjo Minjun Chen Jie Cheng Jing Cheng Jeff Chou Timothy S Davison Mauro Delorenzi Youping Deng Viswanath Devanarayan David J Dix Joaquin Dopazo Kevin C Dorff Fathi Elloumi Jianqing Fan Shicai Fan Xiaohui Fan Hong Fang Nina Gonzaludo Kenneth R Hess Huixiao Hong Jun Huan Rafael A Irizarry Richard Judson Dilafruz Juraeva Samir Lababidi Christophe G Lambert Li Li Yanen Li Zhen Li Simon M Lin Guozhen Liu Edward K Lobenhofer Jun Luo Wen Luo Matthew N McCall Yuri Nikolsky Gene A Pennello Roger G Perkins Reena Philip Vlad Popovici Nathan D Price Feng Qian Andreas Scherer Tieliu Shi Weiwei Shi Jaeyun Sung Danielle Thierry-Mieg Jean Thierry-Mieg Venkata Thodima Johan Trygg Lakshmi Vishnuvajjala Sue Jane Wang Jianping Wu Yichao Wu Qian Xie Waleed A Yousef Liang Zhang Xuegong Zhang Sheng Zhong Yiming Zhou Sheng Zhu Dhivya Arasappan Wenjun Bao Anne Bergstrom Lucas Frank Berthold Richard J Brennan Andreas Buness Jennifer G Catalano Chang Chang Rong Chen Yiyu Cheng Jian Cui Wendy Czika Francesca Demichelis Xutao Deng Damir Dosymbekov Roland Eils Yang Feng Jennifer Fostel Stephanie Fulmer-Smentek James C Fuscoe Laurent Gatto Weigong Ge Darlene R Goldstein Li Guo Donald N Halbert Jing Han Stephen C Harris Christos Hatzis Damir Herman Jianping Huang Roderick V Jensen Rui Jiang Charles D Johnson Giuseppe Jurman Yvonne Kahlert Sadik A Khuder Matthias Kohl Jianying Li Li Li Menglong Li Quan-Zhen Li Shao Li Zhiguang Li Jie Liu Ying Liu Zhichao Liu Lu Meng Manuel Madera Francisco Martinez-Murillo Ignacio Medina Joseph Meehan Kelci Miclaus Richard A Moffitt David Montaner Piali Mukherjee George J Mulligan Padraic Neville Tatiana Nikolskaya Baitang Ning Grier P Page Joel Parker R Mitchell Parry Xuejun Peng Ron L Peterson John H Phan Brian Quanz Yi Ren Samantha Riccadonna Alan H Roter Frank W Samuelson Martin M Schumacher Joseph D Shambaugh Qiang Shi Richard Shippy Shengzhu Si Aaron Smalter Christos Sotiriou Mat Soukup Frank Staedtler Guido Steiner Todd H Stokes Qinglan Sun Pei-Yi Tan Rong Tang Zivana Tezak Brett Thorn Marina Tsyganova Yaron Turpaz Silvia C Vega Roberto Visintainer Juergen von Frese Charles Wang Eric Wang Junwei Wang Wei Wang Frank Westermann James C Willey Matthew Woods Shujian Wu Nianqing Xiao Joshua Xu Lei Xu Lun Yang Xiao Zeng Jialu Zhang Li Zhang Min Zhang Chen Zhao Raj K Puri Uwe Scherf Weida Tong Russell D Wolfinger

Nat Biotechnol 2010 Aug 30;28(8):827-38. Epub 2010 Jul 30.

National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, USA.

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http://dx.doi.org/10.1038/nbt.1665DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315840PMC
August 2010

Assessing the applicability of the GTR nucleotide substitution model through simulations.

Evol Bioinform Online 2007 Feb 4;2:145-55. Epub 2007 Feb 4.

Laboratory of Evolutionary Genetics, Institute for Molecular Biology and Medicine, Université Libre de Bruxelles, CP300, rue Jeener et Brachet 12, 6041 Gosselies, Belgium.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674669PMC
February 2007