@article{bandle,
  title={Inferring differential subcellular localisation in comparative spatial proteomics using BANDLE},
  author={Crook, Oliver M and Davies, Colin TR and Gatto, Laurent and Kirk, Paul DW and Lilley, Kathryn S},
  journal={bioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory},
  url = {doi: https://doi.org/10.1101/2021.01.04.425239}
}


@Manual{Rstat,
    title = {R: A Language and Environment for Statistical Computing},
    author = {{R Development Core Team}},
    organization = {R Foundation for Statistical Computing},
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@Article{Gentleman:2004,
	Abstract = {The Bioconductor project is an initiative for the
		  collaborative creation of extensible software for
		  computational biology and bioinformatics. The goals
		  of the project include: fostering collaborative
		  development and widespread use of innovative
		  software, reducing barriers to entry into
		  interdisciplinary scientific research, and promoting
		  the achievement of remote reproducibility of
		  research results. We describe details of our aims
		  and methods, identify current challenges, compare
		  Bioconductor to other open bioinformatics projects,
		  and provide working examples.},
	Doi = {10.1186/gb-2004-5-10-r80},
	File = {Gentleman_et_al_GenomeBiology_2004.pdf:/home/lgatto/Biblio/Gentleman_et_al_GenomeBiology_2004.pdf:PDF},
	Keywords = {Computational Biology; Internet; Repro; Software;
		  ducibility of Results},
	Owner = {lgatto},
	Pii = {gb-2004-5-10-r80},
	Pmid = {15461798},
	Timestamp = {2006.09.27},
	Url = {https://doi.org/10.1186/gb-2004-5-10-r80},
	author = {Gentleman, Robert C. and Carey, Vincent J. and
		  Bates, Douglas M. and Bolstad, Ben and Dettling,
		  Marcel and Dudoit, Sandrine and Ellis, Byron and
		  Gautier, Laurent and Ge, Yongchao and Gentry, Jeff
		  and Hornik, Kurt and Hothorn, Torsten and Huber,
		  Wolfgang and Iacus, Stefano and Irizarry, Rafael and
		  Leisch, Friedrich and Li, Cheng and Maechler, Martin
		  and Rossini, Anthony J. and Sawitzki, Gunther and
		  Smith, Colin and Smyth, Gordon and Tierney, Luke and
		  Yang, Jean Y. H. and Zhang, Jianhua},
	title = {Bioconductor: open software development for computational biology and bioinformatics.},
	journal = {Genome Biol},
	volume = {5},
	number = {10},
	pages = {-80},
	year = {2004},
	tags = "reproducible research, software, R, Bioconductor, statistics"
}


@Article{Gatto:2012,
  author =       {Gatto, Laurent and Lilley, Kathryn S},
  title =        {{MS}nbase -- an {R}/{B}ioconductor package for isobaric
		 tagged mass spectrometry data visualization,
		 processing and quantitation.},
  journal =      {Bioinformatics},
  year =         {2012},
  month =        {Jan},
  number =       {2},
  volume =       {28},
  pages =        {288-9},
  doi =          {10.1093/bioinformatics/btr645},
  PMID =         {22113085}}


@Article{Christoforou:2016,
  author =       {Christoforou, Andy and Mulvey, Claire M and
                  Breckels, Lisa M and Geladaki, Aikaterini and
                  Hurrell, Tracey and Hayward, Penelope C and Naake,
                  Thomas and Gatto, Laurent and Viner, Rosa and
                  Martinez Arias, Alfonso and Lilley, Kathryn S},
  title =        {A draft map of the mouse pluripotent stem cell
                 spatial proteome.},
  journal =      {Nat Commun},
  year =         {2016},
  month =        {},
  number =       {},
  volume =       {7},
  pages =        {8992},
  doi =          {10.1038/ncomms9992},
  PMID =         {26754106}}


@book{Gilks:1995,
  title={Markov chain Monte Carlo in practice},
  author={Gilks, Walter R and Richardson, Sylvia and Spiegelhalter, David},
  year={1995},
  publisher={CRC press}
}


@Article{pRoloc:2014,
	title = {Mass-spectrometry based spatial proteomics data analysis using pRoloc and pRolocdata},
	author = {Laurent Gatto and Lisa M. Breckels and Samuel Wieczorek and Thomas Burger and Kathryn S. Lilley},
	journal = {Bioinformatics},
	year = {2014},
}

@Article{thplopit,
  doi = {10.1038/s41467-021-26000-9},
  url = {https://doi.org/10.1038/s41467-021-26000-9},
  year = {2021},
  month = oct,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {12},
  number = {1},
  author = {Claire M. Mulvey and Lisa M. Breckels and Oliver M. Crook and David J. Sanders and Andre L. R. Ribeiro and Aikaterini Geladaki and Andy Christoforou and Nina Ko{\v{c}}evar Britov{\v{s}}ek and Tracey Hurrell and Michael J. Deery and Laurent Gatto and Andrew M. Smith and Kathryn S. Lilley},
  title = {Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the {THP}-1 human leukaemia cell line},
  journal = {Nature Communications}
}

@article{Tan:2009,
	title={Mapping organelle proteins and protein complexes in drosophila melanogaster},
	author={Tan, Denise JL and Dvinge, Heidi and Christoforou, Andrew and Bertone, Paul and Martinez Arias, Alfonso and Lilley, Kathryn S},
	journal={Journal of proteome research},
	volume={8},
	number={6},
	pages={2667--2678},
	year={2009},
	publisher={ACS Publications}
}

@article{Mulvey:2017,
  doi = {10.1038/nprot.2017.026},
  url = {https://doi.org/10.1038/nprot.2017.026},
  year = {2017},
  month = may,
  publisher = {Springer Science and Business Media {LLC}},
  volume = {12},
  number = {6},
  pages = {1110--1135},
  author = {Claire M Mulvey and Lisa M Breckels and Aikaterini Geladaki and Nina Ko{\v{c}}evar Britov{\v{s}}ek and Daniel J H Nightingale and Andy Christoforou and Mohamed Elzek and Michael J Deery and Laurent Gatto and Kathryn S Lilley},
  title = {Using {hyperLOPIT} to perform high-resolution mapping of the spatial proteome},
  journal = {Nature Protocols}
}