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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.	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 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 \| Provisional PDF
	2.	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
	3.	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
	4.	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 \| Provisional 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.
	5.	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
	6.	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
	7.	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
	8.	Research article Structural analysis of the genome of breast cancer cell line ZR-75-30 identifies twelve expressed fusion genes Ina Schulte, Elizabeth M Batty, Jessica CM Pole, Katherine A Blood, Steven Mo, Susanna L Cooke, Charlotte Ng, Kevin L Howe, Suet-Feung Chin, James D Brenton, Carlos Caldas, Karen D Howarth, Paul AW Edwards BMC Genomics 2012, 13:719 (22 December 2012) Abstract \| Full text \| PDF \| PubMed
	9.	Proceedings Mapping small molecule binding data to structural domains Felix A Kruger, Raghd Rostom, John P Overington BMC Bioinformatics 2012, 13(Suppl 17):S11 (13 December 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	10.	Software Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework Steven Lewis, Attila Csordas, Sarah Killcoyne, Henning Hermjakob, Michael R Hoopmann, Robert L Moritz, Eric W Deutsch, John Boyle BMC Bioinformatics 2012, 13:324 (5 December 2012) Abstract \| Full text \| PDF \| PubMed
	11.	Research article *Investigations into genome diversity of Haemophilus influenzae* using whole genome sequencing of clinical isolates and laboratory transformants** Peter M Power, Stephen D Bentley, Julian Parkhill, E Moxon, Derek W Hood BMC Microbiology 2012, 12:273 (23 November 2012) Abstract \| Full text \| PDF \| PubMed
	12.	Software GraphAlignment: Bayesian pairwise alignment of biological networks Michal Kolář, Jörn Meier, Ville Mustonen, Michael Lässig, Johannes Berg BMC Systems Biology 2012, 6:144 (21 November 2012) Abstract \| Full text \| PDF \| PubMed
	13.	Research The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success Kelly L Wyres, Lotte M Lambertsen, Nicholas J Croucher, Lesley McGee, Anne von Gottberg, Josefina Liñares, Michael R Jacobs, Karl G Kristinsson, Bernard W Beall, Keith P Klugman, Julian Parkhill, Regine Hakenbeck, Stephen D Bentley, Angela B Brueggemann Genome Biology 2012, 13:R103 (16 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Sequencing of a collection of isolates of Streptococcus pneumoniae reveals extensive gene transfer between the virulent strain PMEN1 and other strains
	14.	Research article Structural and molecular basis of interaction of HCV non-structural protein 5A with human casein kinase 1α and PKR Govindarajan Sudha, Subburaj Yamunadevi, Nidhi Tyagi, Saumitra Das, Narayanaswamy Srinivasan BMC Structural Biology 2012, 12:28 (13 November 2012) Abstract \| Full text \| PDF \| PubMed
	15.	Software Copynumber: Efficient algorithms for single- and multi-track copy number segmentation Gro Nilsen, Knut Liestøl, Peter Van Loo, Hans Kristian Moen Vollan, Marianne B Eide, Oscar M Rueda, Suet-Feung Chin, Roslin Russell, Lars O Baumbusch, Carlos Caldas, Anne-Lise Børresen-Dale, Ole Christian Lingjærde BMC Genomics 2012, 13:591 (4 November 2012) Abstract \| Full text \| PDF \| PubMed
	16.	Research article *Comparative genomics of the classical Bordetella* subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens** Jihye Park, Ying Zhang, Anne M Buboltz, Xuqing Zhang, Stephan C Schuster, Umesh Ahuja, Minghsun Liu, Jeff F Miller, Mohammed Sebaihia, Stephen D Bentley, Julian Parkhill, Eric T Harvill BMC Genomics 2012, 13:545 (10 October 2012) Abstract \| Full text \| PDF \| PubMed
	17.	Review Using mouse models to study function of transcriptional factors in T cell development Peng Li, Yiren Xiao, Zhixin Liu, Pentao Liu Cell Regeneration 2012, 1:8 (10 October 2012) Abstract \| Full text \| PDF \| Editor’s summary I am very happy to accept this review by Dr Peng Li. Please publish it in October 2012. Many thanks.
	18.	Research Digital transcriptome profiling of normal and glioblastoma-derived neural stem cells identifies genes associated with patient survival Pär G Engström, Diva Tommei, Stefan H Stricker, Christine Ender, Steven M Pollard, Paul Bertone Genome Medicine 2012, 4:76 (9 October 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary High-throughput sequencing of transcript tags revealed a gene expression signature that correlates with tumor stage and patient survival in a glioblastoma-derived neural stem cell model.
	19.	Technical Note LibKiSAO: a Java library for Querying KiSAO Anna Zhukova, Richard Adams, Camille Laibe, Nicolas Le Novère BMC Research Notes 2012, 5:520 (24 September 2012) Abstract \| Full text \| PDF \| PubMed
	20.	Proceedings Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology Anika Oellrich, Georgios V Gkoutos, Robert Hoehndorf, Dietrich Rebholz-Schuhmann Journal of Biomedical Semantics 2012, 3(Suppl 2):S1 (21 September 2012) Abstract \| Full text \| PDF \| PubMed
	21.	Review Pluripotency and its layers of complexity Jolene Ooi, Pentao Liu Cell Regeneration 2012, 1:7 (14 September 2012) Abstract \| Full text \| PDF
	22.	Research article Integrating cytogenetics and genomics in comparative evolutionary studies of cichlid fish Juliana Mazzuchelli, Thomas Kocher, Fengtang Yang, Cesar Martins BMC Genomics 2012, 13:463 (9 September 2012) Abstract \| Full text \| PDF \| PubMed
	23.	Research article *Comparative genomics of Brachyspira pilosicoli* strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity** Luke J Mappley, Michael L Black, Manal AbuOun, Alistair C Darby, Martin J Woodward, Julian Parkhill, A Turner, Matthew I Bellgard, Tom La, Nyree D Phillips, Roberto M La Ragione, David J Hampson BMC Genomics 2012, 13:454 (5 September 2012) Abstract \| Full text \| PDF \| PubMed
	24.	Research Modeling gene expression using chromatin features in various cellular contexts Xianjun Dong, Melissa C Greven, Anshul Kundaje, Sarah Djebali, James B Brown, Chao Cheng, Thomas R Gingeras, Mark Gerstein, Roderic Guigó, Ewan Birney, Zhiping Weng Genome Biology 2012, 13:R53 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Models for linking gene expression with chromatin features vary according to cellular context and RNA measurement method
	25.	Research *Analysis of variation at transcription factor binding sites in Drosophila* and humans** Mikhail Spivakov, Junaid Akhtar, Pouya Kheradpour, Kathryn Beal, Charles Girardot, Gautier Koscielny, Javier Herrero, Manolis Kellis, Eileen EM Furlong, Ewan Birney Genome Biology 2012, 13:R49 (5 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Transcription factor binding site variability in fly and human provides evidence for a buffering phenomenon