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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.	Review Toward knowledge support for analysis and interpretation of complex traits Nigel Collier, Anika Oellrich, Tudor Groza Genome Biology 2013, 14:214 (30 September 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Nigel Collier reviews how algorithmic advances are set to enhance the description of complex traits through high-throughput phenotype analysis
	2.	Research article Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets Gerard JP van Westen, Remco F Swier, Isidro Cortes-Ciriano, Jörg K Wegner, John P Overington, Adriaan P IJzerman, Herman WT van Vlijmen, Andreas Bender Journal of Cheminformatics 2013, 5:42 (24 September 2013) Abstract \| Full text \| PDF \| PubMed
	3.	Research article Benchmarking of protein descriptor sets in proteochemometric modeling (part 1): comparative study of 13 amino acid descriptor sets Gerard JP van Westen, Remco F Swier, Jörg K Wegner, Adriaan P IJzerman, Herman WT van Vlijmen, Andreas Bender Journal of Cheminformatics 2013, 5:41 (23 September 2013) Abstract \| Full text \| PDF \| PubMed
	4.	Research article A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease Yu-fei Lin, David A, Shuang Guan, Lira Mamanova, Kenneth J McDowall BMC Genomics 2013, 14:620 (14 September 2013) Abstract \| Full text \| PDF \| PubMed
	5.	Research article Two Pfam protein families characterized by a crystal structure of protein lpg2210 from Legionella pneumophila Penelope Coggill, Ruth Y Eberhardt, Robert D Finn, Yuanyuan Chang, Lukasz Jaroszewski, Adam Godzik, Debanu Das, Qingping Xu, Herbert L Axelrod, L Aravind, Alexey G Murzin, Alex Bateman BMC Bioinformatics 2013, 14:265 (3 September 2013) Abstract \| Full text \| PDF \| PubMed
	6.	Methodology article Ontology based molecular signatures for immune cell types via gene expression analysis Terrence F Meehan, Nicole A Vasilevsky, Christopher J Mungall, David S Dougall, Melissa A Haendel, Judith A Blake, Alexander D Diehl BMC Bioinformatics 2013, 14:263 (30 August 2013) Abstract \| Full text \| PDF \| PubMed
	7.	Software LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions Ségolène Caboche Journal of Cheminformatics 2013, 5:40 (29 August 2013) Abstract \| Full text \| PDF \| PubMed
	8.	Research The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery Roz Laing, Taisei Kikuchi, Axel Martinelli, Isheng J Tsai, Robin N Beech, Elizabeth Redman, Nancy Holroyd, David J Bartley, Helen Beasley, Collette Britton, David Curran, Eileen Devaney, Aude Gilabert, Martin Hunt, Frank Jackson, Stephanie Johnston, Ivan Kryukov, Keyu Li, Alison A Morrison, Adam J Reid, Neil Sargison, Gary Saunders, James D Wasmuth, Adrian Wolstenholme, Matthew Berriman, John S Gilleard, James A Cotton Genome Biology 2013, 14:R88 (28 August 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary The genome and transcriptome of Haemonchus contortus, a nematode parasite of sheep, provides insights into antihelminthic resistance
	9.	Software KNIME-CDK: Workflow-driven cheminformatics Stephan Beisken, Thorsten Meinl, Bernd Wiswedel, Luis F de Figueiredo, Michael Berthold, Christoph Steinbeck BMC Bioinformatics 2013, 14:257 (22 August 2013) Abstract \| Full text \| PDF
	10.	Meeting abstract Histone deacetylase (HDAC) 1 and 2 are essential for normal T cell development and genomic stability in mice Oliver M Dovey, George Vasilliou, Allan Bradley, Shaun M Cowley Clinical Epigenetics 2013, 5(Suppl 1):S11 (19 August 2013) Full text \| PDF
	11.	Research article *Transcription of a protein-coding gene on B chromosomes of the Siberian roe deer (Capreolus pygargus)* Vladimir A Trifonov, Polina V Dementyeva, Denis M Larkin, Patricia CM O’Brien, Polina L Perelman, Fengtang Yang, Malcolm A Ferguson-Smith, Alexander S Graphodatsky BMC Biology 2013, 11:90 (6 August 2013) Abstract \| Full text \| PDF \| PubMed
	12.	Comment So, you want to sequence a genome... Derek L Stemple Genome Biology 2013, 14:128 (30 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Derek Stemple discusses lessons learned from the zebrafish genome project
	13.	Methodology article Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology David P Hill, Nico Adams, Mike Bada, Colin Batchelor, Tanya Z Berardini, Heiko Dietze, Harold J Drabkin, Marcus Ennis, Rebecca E Foulger, Midori A Harris, Janna Hastings, Namrata S Kale, Paula de Matos, Christopher J Mungall, Gareth Owen, Paola Roncaglia, Christoph Steinbeck, Steve Turner, Jane Lomax BMC Genomics 2013, 14:513 (29 July 2013) Abstract \| Full text \| PDF \| PubMed
	14.	Research Gene expression changes with age in skin, adipose tissue, blood and brain Daniel Glass, Ana Viñuela, Matthew N Davies, Adaikalavan Ramasamy, Leopold Parts, David Knowles, Andrew A Brown, Åsa K Hedman, Kerrin S Small, Alfonso Buil, Elin Grundberg, Alexandra C Nica, PaolaDi Meglio, Frank O Nestle, Mina Ryten, Richard Durbin, Mark I McCarthy, Panagiotis Deloukas, Emmanouil T Dermitzakis, Michael E Weale, Veronique Bataille, Tim D Spector Genome Biology 2013, 14:R75 (26 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of microarray experiments in subjects of varying age shows that gene expression in four different tissues changes with time
	15.	Software DepthTools: an R package for a robust analysis of gene expression data Aurora Torrente, Sara López-Pintado, Juan Romo BMC Bioinformatics 2013, 14:237 (25 July 2013) Abstract \| Full text \| PDF \| PubMed
	16.	Research article Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974 Kelly L Wyres, Andries van Tonder, Lotte M Lambertsen, Regine Hakenbeck, Julian Parkhill, Stephen D Bentley, Angela B Brueggemann BMC Genomics 2013, 14:500 (24 July 2013) Abstract \| Full text \| PDF \| PubMed
	17.	Software The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases Panagiotis Moulos, Julie Klein, Simon Jupp, Robert Stevens, Jean-Loup Bascands, Joost P Schanstra BMC Bioinformatics 2013, 14:235 (24 July 2013) Abstract \| Full text \| PDF \| PubMed
	18.	Research *Assemblathon 2: evaluating de novo* methods of genome assembly in three vertebrate species** Keith R Bradnam, Joseph N Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, Inanç Birol, Sébastien Boisvert, Jarrod A Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen-Chi Chou, Jacques Corbeil, Cristian Del Fabbro, T Docking, Richard Durbin, Dent Earl, Scott Emrich, Pavel Fedotov, Nuno A Fonseca, Ganeshkumar Ganapathy, Richard A Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph B Hiatt, Isaac Y Ho et al. GigaScience 2013, 2:10 (22 July 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Assemblathon 2 is the largest systematic assessment of how the process of genome assembly is carried out, with 21 participating teams submitting 43 entries based on data from 3 different genomes
	19.	Research Identification of a neuronal transcription factor network involved in medulloblastoma development Maria Łastowska, Hani Al-Afghani, Haya H Al-Balool, Harsh Sheth, Emma Mercer, Jonathan M Coxhead, Chris PF Redfern, Heiko Peters, Alastair D Burt, Mauro Santibanez-Koref, Chris M Bacon, Louis Chesler, Alistair G Rust, David J Adams, Daniel Williamson, Steven C Clifford, Michael S Jackson Acta Neuropathologica Communications 2013, 1:35 (11 July 2013) Abstract \| Full text \| PDF
	20.	Methodology article The systems biology simulation core algorithm Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, Andreas Dräger BMC Systems Biology 2013, 7:55 (5 July 2013) Abstract \| Full text \| PDF \| PubMed
	21.	Research Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene Mar Gonzàlez-Porta, Adam Frankish, Johan Rung, Jennifer Harrow, Alvis Brazma Genome Biology 2013, 14:R70 (1 July 2013) Abstract \| Provisional PDF \| PubMed \| Editor’s summary Analysis of RNA-seq data across different tissues and cell lines reveals that the majority of genes have a single dominant transcript
	22.	Research article Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum Katherine Lawler, Kim Hammond-Kosack, Alvis Brazma, Richard MR Coulson BMC Systems Biology 2013, 7:52 (27 June 2013) Abstract \| Full text \| PDF \| PubMed
	23.	Research article Quantifying single nucleotide variant detection sensitivity in exome sequencing Alison M Meynert, Louise S Bicknell, Matthew E Hurles, Andrew P Jackson, Martin S Taylor BMC Bioinformatics 2013, 14:195 (18 June 2013) Abstract \| Full text \| PDF \| PubMed \| f1000
	24.	Research article Large scale variation in DNA copy number in chicken breeds Richard PMA Crooijmans, Mark S Fife, Tomas W Fitzgerald, Shurnevia Strickland, Hans H Cheng, Pete Kaiser, Richard Redon, Martien AM Groenen BMC Genomics 2013, 14:398 (13 June 2013) Abstract \| Full text \| PDF \| PubMed
	25.	Software bioWeb3D: an online webGL 3D data visualisation tool Jean-Baptiste Pettit, John C Marioni BMC Bioinformatics 2013, 14:185 (7 June 2013) Abstract \| Full text \| PDF \| PubMed