Annual Scientific Report 2015

Publications in 2015
230. Scialdone A, Natarajan KN, Saraiva LR, et al. (2015) Computational
assignment of cell-cycle stage from single-cell transcriptome data.
Methods 85:54-61. doi:10.1016/j.ymeth.2015.06.021
231. Scoriels L, Salek RM, Goodby E, et al. (2015) Behavioural
and molecular endophenotypes in psychotic disorders reveal
heritable abnormalities in glutamatergic neurotransmission. Transl.
Psychiatry 5:e540. doi:10.1038/tp.2015.26
232. Scruggs SB, Watson K, Su AI, et al. (2015) Harnessing the
heart of big data. Circ. Res. 116:1115-1119. doi:10.1161/
circresaha.115.306013
233. Senger S, Bartek L, Papadatos G, et al. (2015) Managing
expectations: Assessment of chemistry databases generated
by automated extraction of chemical structures from patents. J.
Cheminform. 7: 49. doi:10.1186/s13321-015-0097-z
234. Skinner BM, Sargent CA, Churcher C, et al. (2015) The pig X and Y
Chromosomes: structure, sequence, and evolution. Genome Res.
26:130-139. doi:10.1101/gr.188839.114
235. Smedley D, Haider S, Durinck S, et al. (2015) The BioMart
community portal: an innovative alternative to large, centralized
data repositories. Nucleic Acids Res. 43:W589-W598.
doi:10.1093/nar/gkv350
236. Smith JA, Leonardi T, Huang B, et al. (2015) Extracellular vesicles
and their synthetic analogues in aging and age-associated brain
diseases. Biogerontology 16:147-185. doi:10.1007/s10522-014-
9510-7
237. Sousa FL, Parente DJ, Shis DL, et al. (2015) AlloRep: a repository
of sequence, structural and mutagenesis data for the LacI/GalR
transcription regulators. J. Mol. Biol. (in press); doi:10.1016/j.
jmb.2015.09.015
238. Spjuth O, Krestyaninova M, Hastings J, et al. (2015) Harmonising
and linking biomedical and clinical data across disparate data
archives to enable integrative cross-biobank research. Eur. J. Hum.
Genet. (in press); doi:10.1038/ejhg.2015.165
239. Squizzato S, Park YM, Buso N, et al. (2015) The EBI Search
engine: providing search and retrieval functionality for biological
data from EMBL-EBI. Nucleic Acids Res. 43:w585-w588.
doi:10.1093/nar/gkv316
240. Stanford NJ, Wolstencroft K, Golebiewski M, et al. (2015) The
evolution of standards and data management practices in systems
biology. Mol. Syst. Biol. 11:851. doi:10.15252/msb.20156053
241. Stauch B, Fisher SJ, Cianci M (2015) Open and closed states of
Candida antarctica Lipase B: Protonation and the mechanism of
interfacial activation. J. Lipid Res. 56:2348-2358. doi:10.1194/jlr.
M063388
242. Stavrakas V, Melas IN, Sakellaropoulos T, et al. (2015) Network
reconstruction based on proteomic data and prior knowledge of
protein connectivity using graph theory. PLoS ONE 10: e0128411.
doi:10.1371/journal.pone.0128411
243. Stegle O, Teichmann SA, Marioni JC (2015) Computational and
analytical challenges in single-cell transcriptomics. Nat. Rev. Genet.
16:133-145. doi:10.1038/nrg3833
244. Stephan J, Stegle O, Beyer A (2015) A random forest approach
to capture genetic effects in the presence of population structure.
Nat. Commun. 6:7432; doi:10.1038/ncomms8432
245. Strumillo M, Beltrao P (2015) Towards the computational design
of protein post-translational regulation. Bioorg. Med. Chem.
23:2877-2882. doi:10.1016/j.bmc.2015.04.056
246. Stubbington MJ, Mahata B, Svensson V, et al. (2015) An atlas
of mouse CD4(+) T cell transcriptomes. Biol. Direct 10:14.
doi:10.1186/s13062-015-0045-x
247. Su J, Ekman C, Oskolkov N, et al. (2015) A novel atlas of gene
expression in human skeletal muscle reveals molecular changes
associated with aging. Skelet. Muscle 5:35. doi:10.1186/s13395-
015-0059-1
248. Sudmant PH, Rausch T, Gardner EJ, et al. (2015) An integrated
map of structural variation in 2,504 human genomes. Nature
526:75-81. doi:10.1038/nature15394
249. Surakka I, Horikoshi M, Mägi R, et al. (2015) The impact of
low-frequency and rare variants on lipid levels. Nat. Genet.
47:589-597. doi:10.1038/ng.3300
250. Suzek BE, Wang YQ, Huang HZ, et al. (2015) UniRef clusters: A
comprehensive and scalable alternative for improving sequence
similarity searches. Bioinformatics 31:926-932. doi:10.1093/
bioinformatics/btu739
251. Swat MJ, Moodie S, Wimalaratne SM, et al. (2015)
Pharmacometrics Markup Language (PharmML): Opening new
perspectives for model exchange in drug development. CPT
Pharmacometrics Syst. Pharmacol. 4:316-319. doi:10.1002/
psp4.57
252. Tan G, Gil M, Löytynoja AP, et al. (2015) Simple chained guide
trees give poorer multiple sequence alignments than inferred trees
in simulation and phylogenetic benchmarks. Proc. Natl. Acad. Sci.
U.S.A. 112:e99-100. doi:10.1073/pnas.1417526112
253. Tan G, Muffato M, Ledergerber C, et al. (2015) Current methods
for automated filtering of multiple sequence alignments frequently
worsen single-gene phylogenetic inference. Syst. Biol. 64:778-791.
doi:10.1093/sysbio/syv033
254. Tello-Ruiz MK, Stein J, Wei S, et al. (2015) Gramene 2016:
comparative plant genomics and pathway resources. Nucleic
Acids Res. 44:D1133-D1140. doi:10.1093/nar/gkv1179
255. Ten Hoopen P, Pesant S, Kottmann R, et al. (2015) Marine
microbial biodiversity, bioinformatics and biotechnology (M2B3)
data reporting and service standards. Stand. Genomic Sci. 10:20.
doi:10.1186/s40793-015-0001-5
256. Terfve CD, Wilkes EH, Casado P, et al. (2015) Large-scale
models of signal propagation in human cells derived from
discovery phosphoproteomic data. Nat. Commun. 6:8033-8033.
doi:10.1038/ncomms9033
257. The Cancer Cell Line Encyclopedia Consortium & The Genomics of
Drug Sensitivity in Cancer Consortium (2015) Pharmacogenomic
agreement between two cancer cell line data sets. Nature
528:84-87. doi:10.1038/nature15736
258. The UniProt Consortium (2015) UniProt: a hub for protein
information Nucleic Acids Res. 43(D1):D204-D212. doi:10.1093/
nar/gku989
259. Thiele S, Cerone L, Saez-Rodriguez J, et al. (2015) Extended
notions of sign consistency to relate experimental data to signaling
and regulatory network topologies. BMC Bioinformatics 16:345.
doi:10.1186/s12859-015-0733-7
260. Thornton J (2015) What you need to know to make the most
of big data in biology. Lancet 385:S5-6. doi:10.1016/s0140-
6736(15)60321-x
261. Touloumis A, Tavare S, Marioni JC (2015) Testing the mean matrix
in high-dimensional transposable data. Biometrics 71:157-166.
doi:10.1111/biom.12257
262. Truszkowski J, Goldman N (2015) Maximum likelihood phylogenetic
inference is consistent on multiple sequence alignments, with
or without gaps. Syst. Biol. 65(2):328-333. doi:10.1093/sysbio/
syv089
263. Tsang JC, Yu Y, Burke S, et al. (2015) Single-cell transcriptomic
reconstruction reveals cell cycle and multi-lineage differentiation
defects in Bcl11a-deficient hematopoietic stem cells. Genome Biol.
16:178. doi:10.1186/s13059-015-0739-5
264. Tyagi N, Farnell EJ, Fitzsimmons CM, et al. (2015) Comparisons
of allergenic and Metazoan parasite proteins: Allergy the price of
immunity. PLoS Comput. Biol. 11: e1004546. doi:10.1371/journal.
pcbi.1004546
265. Tyler-Smith C, Yang HM, Landweber LF, et al. (2015) Where next
for genetics and genomics? PLoS Biol 13: e1002216. doi:10.1371/
journal.pbio.1002216
266. UK10K Consortium, Walter K, Min JL, et al. (2015) The UK10K
project identifies rare variants in health and disease. Nature
526:82-90. doi:10.1038/nature14962
267. Vallejos CA, Marioni JC, Richardson S (2015) BASiCS: Bayesian
Analysis of Single-Cell Sequencing data. PLoS Comput. Biol. 11:
e1004333. doi:10.1371/journal.pcbi.1004333
268. van de Wetering M, Francies HE, Francis JM, et al. (2015)
Prospective derivation of a living organoid biobank of colorectal
cancer patients. Cell 161:933-945. doi:10.1016/j.cell.2015.03.053
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2015 EMBL-EBI Annual Scientific Report