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Member - Wellcome Trust Sanger Institute

The members of the campus are: Wellcome Trust Sanger Institute European Bioinformatics Institute The Wellcome Trust is an independent research-funding charity that aims to improve human and animal health

http://www.wellcome.ac.uk/

Research staff and students at the Sanger Institute:

Sanger Institute is a Member which means you can publish in any BioMed Central, Chemistry Central or SpringerOpen journal with a 15% discount on the fee. The article-processing charge is paid centrally by your institution and then costed back to your project/dept code.

Work published with BioMed Central, Chemistry Central and SpringerOpen by researchers at Wellcome Trust Sanger Institute

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	1.	Commentary Dissemination of metabolomics results: role of MetaboLights and COSMOS Reza M Salek, Kenneth Haug, Christoph Steinbeck GigaScience 2013, 2:8 (17 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary There is a need to disseminate the increasing amount of metabolomic data in standard reproducible ways. Hosted and coordinated by the EBI, the open source MetaboLights repository, and COSMOS community standards consortium tackle this
	2.	Research article Structural and functional annotation of the porcine immunome Harry D Dawson, Jane E Loveland, Géraldine Pascal, James GR Gilbert, Hirohide Uenishi, Katherine M Mann, Yongming Sang, Jie Zhang, Denise Carvalho-Silva, Toby Hunt, Matthew Hardy, Zhiliang Hu, Shu-Hong Zhao, Anna Anselmo, Hiroki Shinkai, Celine Chen, Bouabid Badaoui, Daniel Berman, Clara Amid, Mike Kay, David Lloyd, Catherine Snow, Takeya Morozumi, Ryan Pei-Yen Cheng, Megan Bystrom, Ronan Kapetanovic, John C Schwartz, Ranjit Kataria, Matthew Astley, Eric Fritz et al. BMC Genomics 2013, 14:332 (15 May 2013) Abstract \| Full text \| PDF \| PubMed
	3.	Gene family update Update on the Kelch-like (KLHL) gene family Bajinder S Dhanoa, Tiziana Cogliati, Akhila G Satish, Elspeth A Bruford, James S Friedman Human Genomics 2013, 7:13 (15 May 2013) Abstract \| Full text \| PDF \| PubMed
	4.	Research *A member of the Plasmodium falciparum* PHIST family binds to the erythrocyte cytoskeleton component band 4.1** Lindsay A Parish, Deborah W Mai, Matthew L Jones, Erika L Kitson, Julian C Rayner Malaria Journal 2013, 12:160 (11 May 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Identification of a novel interaction between the erythrocyte Band 4.1 protein and a P. falciparum component from the PHIST family of proteins. The paper should be of interest to groups working on the parasite "exportome".
	5.	Letter to the Editor Vive la différence: naming structural variants in the human reference genome Ruth L Seal, Mathew W Wright, Kristian A Gray, Elspeth A Bruford Human Genomics 2013, 7:12 (1 May 2013) Abstract \| Full text \| PDF \| PubMed
	6.	Method EMu: probabilistic inference of mutational processes and their localization in the cancer genome Andrej Fischer, Christopher JR Illingworth, Peter J Campbell, Ville Mustonen Genome Biology 2013, 14:R39 (29 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A method to infer mutational processes from cancer sequencing data and to determine the genomic sites at which they are active
	7.	Research Phosphoproteomics data classify hematological cancer cell lines according to tumor type and sensitivity to kinase inhibitors Pedro Casado, Maria P Alcolea, Francesco Iorio, Juan-Carlos Rodríguez-Prados, Bart Vanhaesebroeck, Julio Saez-Rodriguez, Simon Joel, Pedro R Cutillas Genome Biology 2013, 14:R37 (29 April 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary A phosphoproteomic approach helps to distinguish between different types of blood cancers and gauges their sensitivity to kinase inhibitors
	8.	Opinion Sixty years of genome biology W Doolittle, Peter Fraser, Mark B Gerstein, Brenton R Graveley, Steven Henikoff, Curtis Huttenhower, Alicia Oshlack, Chris P Ponting, John L Rinn, Michael C Schatz, Jernej Ule, Detlef Weigel, George M Weinstock Genome Biology 2013, 14:113 (25 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Members of Genome Biology's Editorial Board select their highlights from the 60 years of genome biology that followed the double helix
	9.	Research Artemisinin resistance in rodent malaria - mutation in the AP2 adaptor μ-chain suggests involvement of endocytosis and membrane protein trafficking Gisela Henriques, Axel Martinelli, Louise Rodrigues, Katarzyna Modrzynska, Richard Fawcett, Douglas R Houston, Sofia T Borges, Umberto d’Alessandro, Halidou Tinto, Corine Karema, Paul Hunt, Pedro Cravo Malaria Journal 2013, 12:118 (5 April 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In the rodent malaria parasite Plasmodium chabaudi, an increased artemisinin-resistant phenotype occurs along with a mutation in a functional element of the AP2 adaptor protein complex. This suggests that endocytosis and trafficking of membrane proteins may be involved, generating new insights into possible mechanisms of resistance.
	10.	Database TRACER: a resource to study the regulatory architecture of the mouse genome Chao-Kung Chen, Orsolya Symmons, Veli Vural Uslu, Taro Tsujimura, Sandra Ruf, Damian Smedley, François Spitz BMC Genomics 2013, 14:215 (2 April 2013) Abstract \| Full text \| PDF \| PubMed
	11.	Methodology article Application of text-mining for updating protein post-translational modification annotation in UniProtKB Anne-Lise Veuthey, Alan Bridge, Julien Gobeill, Patrick Ruch, Johanna R McEntyre, Lydie Bougueleret, Ioannis Xenarios BMC Bioinformatics 2013, 14:104 (22 March 2013) Abstract \| Full text \| PDF \| PubMed
	12.	Poster presentation Expanding natural product chemistry resources at the EBI Janna Hastings, Pablo Conesa, Adriano Dekker, Marcus Ennis, Kenneth Haug, Kalai Jayaseelan, Namrata Kale, Tejasvi Mahendraker, Pablo Moreno, Venkatesh Muthukrishnan, Gareth Owen, Reza Salek, Steve Turner, Christoph Steinbeck Journal of Cheminformatics 2013, 5(Suppl 1):P43 (22 March 2013) Full text \| PDF
	13.	Correspondence The Enzyme Portal: a case study in applying user-centred design methods in bioinformatics Paula de Matos, Jennifer A Cham, Hong Cao, Rafael Alcántara, Francis Rowland, Rodrigo Lopez, Christoph Steinbeck BMC Bioinformatics 2013, 14:103 (20 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The first ‘how to’ guide for applying User-Centred Design (UCD) to websites for bioinformatics involves biomedical researchers rather than developers to design better web experiences, for example The Enzyme Portal
	14.	Research highlight Go retro and get a GRIP Kim Wong, David J Adams, Thomas M Keane Genome Biology 2013, 14:108 (19 March 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary David Adams and colleagues grapple with the GRIPs (gene retrocopy insertion polymorphisms) identified by Ewing et al in this month's issue
	15.	Research article *Inferring patient to patient transmission of Mycobacterium tuberculosis* from whole genome sequencing data** Josephine M Bryant, Anita C Schürch, Henk van Deutekom, Simon R Harris, Jessica L de Beer, Victor de Jager, Kristin Kremer, Sacha A F T van Hijum, Roland J Siezen, Martien Borgdorff, Stephen D Bentley, Julian Parkhill, Dick van Soolingen BMC Infectious Diseases 2013, 13:110 (27 February 2013) Abstract \| Full text \| PDF \| PubMed
	16.	Poster presentation Migraine without aura: genome-wide association analysis identifies several novel susceptibility B De Vries, T Freilinger, V Anttila, R Malik, GM Terwindt, P Pozo-Rosich, B Winsvold, D Nyholt, WPJ van Oosterhout, V Artto, M Todt, E Hämäläinen, J Fernandez-Moralez, M Louter, MA Kaunisto, J Schoenen, O Raitakari, T Lehtimäki, M Ville-Pueyo, H Göbel, E Wichman, C Sintas, A Uitterlinden, A Hofman, F Rivadeneira, A Heinze, E Tronvik, CM van Duin, J Kaprio, B Cormand, M Wessman, RR Frants, T Meitinger, B Müller-Myhsok, JA Zwart, M Färkkilä, A Macaya, MD Ferrari, C Kubisch, A Palotie, M Dichgans, AMJ van den Maagdenberg et al. The Journal of Headache and Pain 2013, $article.volume.volumeNumber(Suppl 1):P21 (21 February 2013) Full text \| PDF
	17.	Poster presentation Migraine without aura: genome-wide association analysis identifies several novel susceptibility Boukje de Vries, Tobias Freilinger, Verneri Anttila, Rainer Malik, Mikko Kallela, Gisela M Terwindt, Patricia Pozo-Rosich, Bendik Winsvold, Dale R Nyholt, Willebrordus PJ van Oosterhout, Ville Artto, Unda Todt, Eija Hämäläinen, Jèssica Fernández-Morales, Mark A Louter, Mari A Kaunisto, Jean Schoenen, Olli Raitakari, Terho Lehtimäki, Marta Vila-Pueyo, Hartmut Göbel, Erich Wichmann, Cèlia Sintas, Andre G Uitterlinden, Albert Hofman, Fernando Rivadeneira, Axel Heinze, Erling Tronvik, Cornelia M van Duijn, Jaakko Kaprio, Bru Cormand, Maija Wessman, Rune R Frants, Thomas Meitinger, Bertram Müller-Myhsok, John-Anker Zwart, Markus Färkkilä, Alfons Macaya, Michel D Ferrari, Christian Kubisch, Aarno Palotie, Martin Dichgans, Arn MJM van den Maagdenberg, et al. The Journal of Headache and Pain 2013, $article.volume.volumeNumber(Suppl 1):P18 (21 February 2013) Full text \| PDF
	18.	Research *Genome of Acanthamoeba castellanii* highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling** Michael Clarke, Amanda J Lohan, Bernard Liu, Ilias Lagkouvardos, Scott Roy, Nikhat Zafar, Claire Bertelli, Christina Schilde, Arash Kianianmomeni, Thomas R Bürglin, Christian Frech, Bernard Turcotte, Klaus O Kopec, John M Synnott, Caleb Choo, Ivan Paponov, Aliza Finkler, Chris Heng Tan, Andrew P Hutchins, Thomas Weinmeier, Thomas Rattei, Jeffery SC Chu, Gregory Gimenez, Manuel Irimia, Daniel J Rigden, David A Fitzpatrick, Jacob Lorenzo-Morales, Alex Bateman, Cheng-Hsun Chiu, Petrus Tang, Peter Hegemann, Hillel Fromm, Didier Raoult, Gilbert Greub, Diego Miranda-Saavedra, Nansheng Chen, Piers Nash et al. Genome Biology 2013, 14:R11 (1 February 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of Acanthamoeba castellanii's genome reveals the role of lateral gene transfer and the evolution of tyrosine kinase signaling
	19.	Research Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data Jong Kim, John C Marioni Genome Biology 2013, 14:R7 (28 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new framework for modeling stochastic gene expression in single cells yields insights into the regulatory role of histone modifications
	20.	Research Restriction of V3 region sequence divergence in the HIV-1 envelope gene during antiretroviral treatment in a cohort of recent seroconverters Astrid Gall, Steve Kaye, Stéphane Hué, David Bonsall, Richard Rance, Gregory J Baillie, Sarah J Fidler, Jonathan N Weber, Myra O McClure, Paul Kellam, Retrovirology 2013, 10:8 (18 January 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The authors show, through a cross-sectional study of sequence diversity of the env V3 in 30 antiretroviral-naive patients during primary infection that considerable population structure diversity exists, with some individuals exhibiting highly constrained plasma virus diversity. Diversity was independent of clinical markers (viral load, time from seroconversion, CD4 cell count) of infection.
	21.	Software CySBGN: A Cytoscape plug-in to integrate SBGN maps Emanuel Gonçalves, Martijn Iersel, Julio Saez-Rodriguez BMC Bioinformatics 2013, 14:17 (16 January 2013) Abstract \| Full text \| PDF \| PubMed
	22.	Database UniChem: a unified chemical structure cross-referencing and identifier tracking system Jon Chambers, Mark Davies, Anna Gaulton, Anne Hersey, Sameer Velankar, Robert Petryszak, Janna Hastings, Louisa Bellis, Shaun McGlinchey, John P Overington Journal of Cheminformatics 2013, 5:3 (14 January 2013) Abstract \| Full text \| PDF \| PubMed
	23.	Research article *Identifying targets of the Sox domain protein Dichaete in the Drosophila* CNS via targeted expression of dominant negative proteins** Shih Pei Shen, Jelena Aleksic, Steven Russell BMC Developmental Biology 2013, 13:1 (5 January 2013) Abstract \| Full text \| PDF \| PubMed
	24.	Methodology article *A simplified counter-selection recombineering protocol for creating fluorescent protein reporter constructs directly from C. elegans* fosmid genomic clones** Nisha Hirani, Marcel Westenberg, Minaxi S Gami, Paul Davis, Ian A Hope, Colin T Dolphin BMC Biotechnology 2013, 13:1 (3 January 2013) Abstract \| Full text \| PDF \| PubMed
	25.	Research article New approaches for unravelling reassortment pathways Victoria Svinti, James A Cotton, James O McInerney BMC Evolutionary Biology 2013, 13:1 (1 January 2013) Abstract \| Full text \| PDF \| PubMed