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Annual Scientific Report 2015

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192. Perez-Riverol Y, Xu QW, Wang R, et al. (<strong>2015</strong>) PRIDE Inspector<br />

Toolsuite: Moving toward a universal visualization tool for<br />

proteomics data standard formats and quality assessment of<br />

ProteomeXchange datasets. Mol. Cell. Proteomics 15:305-317.<br />

doi:10.1074/mcp.O115.050229<br />

193. Perna D, Karreth FA, Rust AG, et al. (<strong>2015</strong>) BRAF inhibitor<br />

resistance mediated by the AKT pathway in an oncogenic<br />

BRAF mouse melanoma model. Proc. Natl. Acad. Sci. U.S.A.<br />

112:E536-45. doi:10.1073/pnas.1418163112<br />

194. Philippakis AA, Azzariti DR, Beltran S, et al. (<strong>2015</strong>) The Matchmaker<br />

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36:915-921. doi: 10.1002/humu.22858<br />

195. PLoS Medicine Editors, Beck A, Birney E, et al. (<strong>2015</strong>) Progress<br />

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196. Porras P, Duesbury M, Fabregat A, et al. (<strong>2015</strong>) A visual review<br />

of the interactome of LRRK2: Using deep-curated molecular<br />

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197. Porta-Pardo E, Garcia-Alonso L, Hrabe T, et al. (<strong>2015</strong>) a<br />

pan-cancer catalogue of cancer driver protein interaction<br />

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198. Prakash A, Bateman A (<strong>2015</strong>) Domain atrophy creates rare<br />

cases of functional partial protein domains. Genome Biol. 16:88.<br />

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199. Proserpio V, Lönnberg T (<strong>2015</strong>) Single-cell technologies are<br />

revolutionizing the approach to rare cells. Immunol. Cell Biol. (in<br />

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200. Proserpio V, Mahata B (<strong>2015</strong>) Single-cell technologies to study<br />

the immune system. Immunology 147:133-140. doi:10.1111/<br />

imm.12553<br />

201. Pundir S, Magrane M, Martin MJ, et al. (<strong>2015</strong>) Searching and<br />

navigating UniProt databases. Curr Protoc Bioinformatics<br />

50:1.27.1-1.27.10. doi:10.1002/0471250953.bi0127s50<br />

202. Punta M, Simon I, Dosztányi Z (<strong>2015</strong>) Prediction and analysis of<br />

intrinsically disordered proteins. Methods Mol. Biol. 1261:35-59.<br />

doi:10.1007/978-1-4939-2230-7_3<br />

203. Rahman SA, Singh Y, Kohli S, et al. (<strong>2015</strong>) Reply to<br />

‘”Mycobacterium indicus pranii” is a strain of Mycobacterium<br />

intracellulare’: “M. indicus pranii” is a distinct strain, not derived<br />

from M. intracellulare, and is an organism at an evolutionary<br />

transition point between a fast grower and slow grower. MBio 6:<br />

doi:10.1128/mbio.00352-15<br />

204. Raposo AA, Vasconcelos FF, Drechsel D, et al. (<strong>2015</strong>) Ascl1<br />

coordinately regulates gene expression and the chromatin<br />

landscape during neurogenesis. Cell Rep (in press); doi:10.1016/j.<br />

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205. Ravenhall M, Škunca N, Lassalle F, et al. (<strong>2015</strong>) Inferring horizontal<br />

gene transfer. PLoS Comput. Biol. 11: e1004095. doi:10.1371/<br />

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206. Rawlings ND (<strong>2015</strong>) Bacterial calpains and the evolution of the<br />

calpain (C2) family of peptidases. Biol. Direct 10:66. doi:10.1186/<br />

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207. Rawlings ND (<strong>2015</strong>) Peptidase specificity from the substrate<br />

cleavage collection in the MEROPS database and a tool to<br />

measure cleavage site conservation. Biochimie (in press);<br />

doi:10.1016/j.biochi.<strong>2015</strong>.10.003<br />

208. Rawlings ND, Barrett AJ, Finn R (<strong>2015</strong>) Twenty years of the<br />

MEROPS database of proteolytic enzymes, their substrates and<br />

inhibitors. Nucleic Acids Res. 44:D343-D350. doi:10.1093/nar/<br />

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209. Rebollo-Lopez MJ, Lelièvre J, Alvarez-Gomez D, et al. (<strong>2015</strong>)<br />

Release of 50 new, drug-like compounds and their computational<br />

target predictions for open source anti-tubercular drug discovery.<br />

PLoS One 10: e0142293. doi:10.1371/journal.pone.0142293<br />

210. Reisinger F, Del-Toro N, Ternent T, et al. (<strong>2015</strong>) Introducing<br />

the PRIDE Archive RESTful web services. Nucleic Acids Res.<br />

43:W599-W604. doi:10.1093/nar/gkv382<br />

211. Ring N, Meehan TF, Blake A, et al. (<strong>2015</strong>) A mouse informatics<br />

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212. Roberts AM, Ware JS, Herman DS, et al. (<strong>2015</strong>) Integrated allelic,<br />

transcriptional, and phenomic dissection of the cardiac effects of<br />

titin truncations in health and disease. Sci. Transl. Med. 7:270ra6.<br />

doi:10.1126/scitranslmed.3010134<br />

213. Rocca-Serra P, Salek RM, Arita M, et al. (<strong>2015</strong>) Data standards can<br />

boost metabolomics research, and if there is a will, there is a way.<br />

Metabolomics 12: doi:10.1007/s11306-015-0879-3<br />

214. Rodriguez N, Thomas A, Watanabe L, et al. (<strong>2015</strong>) JSBML 1.0:<br />

providing a smorgasbord of options to encode systems biology<br />

models. Bioinformatics 31:3383-3386. doi:10.1093/bioinformatics/<br />

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215. Rohwer N, Bindel F, Grimm C, et al. (<strong>2015</strong>) Annexin A1 sustains<br />

tumor metabolism and cellular proliferation upon stable loss of<br />

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216. Rompp A, Wang R, Albar JP, et al. (<strong>2015</strong>) A public repository<br />

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217. Ruiz Hernandez SE, Streeter I, de Leeuw NH (<strong>2015</strong>) The effect<br />

of water on the binding of glycosaminoglycan saccharides to<br />

hydroxyapatite surfaces: a molecular dynamics study. Phys. Chem.<br />

Chem. Phys. 17:22377-22388. doi:10.1039/c5cp02630j<br />

218. Saez-Rodriguez J, MacNamara A, Cook S (<strong>2015</strong>) Modeling<br />

signaling networks to advance new cancer therapies. Annu. Rev.<br />

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219. Salek RM, Arita M, Dayalan S, et al. (<strong>2015</strong>) Embedding standards<br />

in metabolomics: the Metabolomics Society data standards task<br />

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220. Salek RM, Neumann S, Schober D, et al. (<strong>2015</strong>) COordination of<br />

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metabolomics data access. Metabolomics 11:1587-1597.<br />

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221. Sali A, Berman HM, Schwede T, et al. (<strong>2015</strong>) Outcome of the first<br />

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222. Saraiva LR, Ahuja G, Ivandic I, et al. (<strong>2015</strong>) Molecular and neuronal<br />

homology between the olfactory systems of zebrafish and mouse.<br />

Sci. Rep. 5:11487. doi:10.1038/srep11487<br />

223. Saraiva LR, Ibarra-Soria X, Khan M, et al. (<strong>2015</strong>) Hierarchical<br />

deconstruction of mouse olfactory sensory neurons: from whole<br />

mucosa to single-cell RNA-seq. Sci. Rep. 5:18178. doi:10.1038/<br />

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224. Sariyar M, Schluender I, Smee C, et al. (<strong>2015</strong>) Sharing and reuse<br />

of sensitive data and samples: supporting researchers in identifying<br />

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doi:10.1089/bio.<strong>2015</strong>.0014<br />

225. Schmid M, Smith J, Burt DW, et al. (<strong>2015</strong>) Third report on chicken<br />

genes and chromosomes <strong>2015</strong>. Cytogenet. Genome Res.<br />

145:78-179. doi:10.1159/000430927<br />

226. Schoenfelder S, Furlan-Magaril M, Mifsud B, et al. (<strong>2015</strong>) The<br />

pluripotent regulatory circuitry connecting promoters to their<br />

long-range interacting elements Genome Res. 25:582-597.<br />

doi:10.1101/gr.185272.114<br />

227. Schoenfelder S, Sugar R, Dimond A, et al. (<strong>2015</strong>) Polycomb<br />

repressive complex PRC1 spatially constrains the mouse<br />

embryonic stem cell genome. Nat. Genet. 47:1179-1186.<br />

doi:10.1038/ng.3393<br />

228. Schwarz RF, Branicky R, Grundy LJ, et al. (<strong>2015</strong>) Changes in<br />

postural syntax characterize sensory modulation and natural<br />

variation of C. elegans locomotion. PLoS Comput. Biol. 11:<br />

e1004322. doi:10.1371/journal.pcbi.1004322<br />

229. Scialdone A, Howard M (<strong>2015</strong>) How plants manage food reserves<br />

at night: quantitative models and open questions. Front Plant Sci<br />

6:294. doi:10.3389/fpls.<strong>2015</strong>.00204<br />

<strong>2015</strong> EMBL-EBI <strong>Annual</strong> <strong>Scientific</strong> <strong>Report</strong> 73

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