Annual Scientific Report 2015

Publications in 2015
154. Mak L, Marcus D, Howlett A, et al. (2015) Metrabase: A
cheminformatics and bioinformatics database for small molecule
transporter data analysis and (Q)SAR modeling. J. Cheminform
7:31. doi:10.1186/s13321-015-0083-5
155. Maree S, Maree FF, Putterill JF, et al. (2015) Synthesis of empty
African horse sickness virus particles. Virus Res. 213:184-194.
doi:10.1016/j.virusres.2015.12.006
156. Marsh JA, Rees HA, Ahnert SE, et al. (2015) Structural and
evolutionary versatility in protein complexes with uneven
stoichiometry. Nat. Commun. 6:6394; doi:10.1038/ncomms7394
157. Marsh JA, Teichmann SA (2015) Structure, dynamics, assembly,
and evolution of protein complexes. Annu. Rev. Biochem.
84:551-575. doi:10.1146/annurev-biochem-060614-034142
158. Martin H, Shales M, Fernandez-Piñar P, et al. (2015) Differential
genetic interactions of yeast stress response MAPK pathways.
Mol. Syst. Biol. 11:800. doi:10.15252/msb.20145606
159. Martínez Cuesta S, Rahman SA, Furnham N, et al. (2015) The
classification and evolution of enzyme function. Biophys. J.
109:1082-1086. doi:10.1016/j.bpj.2015.04.020
160. Martínez H, Tárraga J, Medina I, et al. (2015) Concurrent and
accurate short read mapping on multicore processors. IEEE/
ACM Trans. Comput. Biol. Bioinform. 12:995-1007. doi:10.1109/
tcbb.2015.2392077
161. Mattila J, Havula E, Suominen E, et al. (2015) Mondo-Mlx mediates
organismal sugar sensing through the gli-similar transcription
factor sugarbabe. Cell Rep 13:350-364. doi:10.1016/j.
celrep.2015.08.081
162. McEntyre J, Sarkans U, Brazma A (2015) The BioStudies
database. Mol. Syst. Biol. 11:847. doi:10.15252/msb.20156658
163. Medina-Rivera A, Defrance M, Sand O, et al. (2015) RSAT
2015: Regulatory sequence analysis tools. Nucleic Acids Res.
43:w50-w56. doi:10.1093/nar/gkv362
164. Melas IN, Sakellaropoulos T, Iorio F, et al. (2015) Identification
of drug-specific pathways based on gene expression data:
application to drug induced lung injury. Integr. Biol. 7:904-920.
doi:10.1039/c4ib00294f
165. Mesquita RD, Vionette-Amaral RJ, Lowenberger C, et al. (2015)
Genome of Rhodnius prolixus, an insect vector of Chagas disease,
reveals unique adaptations to hematophagy and parasite infection.
Proc. Natl. Acad. Sci. U.S.A. 112:14936-14941. doi:10.1073/
pnas.1506226112
166. Mitchell A, Bucchini F, Cochrane G, et al. (2015) EBI
Metagenomics in 2016 - an expanding and evolving resource for
the analysis and archiving of metagenomic data. Nucleic Acids
Res. 44:D595-D603. doi:10.1093/nar/gkv1195
167. Moreno P, Beisken S, Harsha B, et al. (2015) BiNChE: A web tool
and library for chemical enrichment analysis based on the ChEBI
ontology. BMC Bioinformatics 16: doi:10.1186/s12859-015-0486-
3
168. Moretto M, Sonego P, Dierckxsens N, et al. (2015) COLOMBOS
v3.0: leveraging gene expression compendia for cross-species
analyses. Nucleic Acids Res. 44:D620-D623. doi:10.1093/nar/
gkv1251
169. Mugumbate G, Abrahams KA, Cox JA, et al. (2015) Mycobacterial
dihydrofolate reductase inhibitors identified using chemogenomic
methods and in vitro validation. PLoS ONE 10:e0121492.
doi:10.1371/journal.pone.0121492
170. Mugumbate G, Overington JP (2015) The relationship between
target-class and the physicochemical properties of antibacterial
drugs. Bioorg. Med. Chem. 23:5218-5224. doi:10.1016/j.
bmc.2015.04.063
171. Murn J, Zarnack K, Yang YJ, et al. (2015) Control of a neuronal
morphology program by an RNA-binding zinc finger protein,
Unkempt. Genes Dev. 29:501-512. doi:10.1101/gad.258483.115
172. Murrell DS, Cortes-Ciriano I, van Westen GJP, et al. (2015)
Chemically Aware Model Builder (camb): an R package for property
and bioactivity modelling of small molecules J. Cheminform. 7:45.
doi:10.1186/s13321-015-0086-2
173. Mussa HY, Marcus D, Mitchell JB, et al. (2015) Verifying the fully
“Laplacianised” posterior Naive Bayesian approach and more. J.
Cheminform. 7:27. doi:10.1186/s13321-015-0075-5
174. Naldi A, Monteiro PT, Mussel C, et al. (2015) Cooperative
development of logical modelling standards and tools with
CoLoMoTo. Bioinformatics 31:1154-1159. doi:10.1093/
bioinformatics/btv013
175. Natarajan P, Punta M, Kumar A, et al. (2015) Structure and
sequence analyses of Bacteroides proteins BVU_4064 and
BF1687 reveal presence of two novel predominantly-beta domains,
predicted to be involved in lipid and cell surface interactions. BMC
Bioinformatics 16: doi:10.1186/s12859-014-0434-7
176. Neafsey DE, Waterhouse RM, Abai MR, et al. (2015) Mosquito
genomics. Highly evolvable malaria vectors: the genomes of 16
Anopheles mosquitoes. Science 347: 1258522. doi:10.1126/
science.1258522
177. Nguyen N, Hickey G, Zerbino DR, et al. (2015) Building a
pan-genome reference for a population. J. Comput. Biol.
22:387-401. doi:10.1089/cmb.2014.0146
178. Nik-Zainal S, Kucab JE, Morganella S, et al. (2015) The genome
as a record of environmental exposure. Mutagenesis 30:763-770.
doi:10.1093/mutage/gev073
179. Nsamba P, de Beer TA, Chitray M, et al. (2015) Determination of
common genetic variants within the non-structural proteins of
foot-and-mouth disease viruses isolated in sub-Saharan Africa.
Vet. Microbiol. 177:106-122. doi:10.1016/j.vetmic.2015.03.007
180. Núñez de Villavicencio-Díaz T, Ramos Gómez Y, Oliva Argüelles
B, et al. (2015) Data for comparative proteomics analysis
of the antitumor effect of CIGB-552 peptide in HT-29 colon
adenocarcinoma cells. Data Brief. 4:468-473. doi:10.1016/j.
dib.2015.06.024
181. Ochoa D, Beltrao P (2015) Kinase-two-hybrid: towards the
conditional interactome. Mol. Syst. Biol. 11:798. doi:10.15252/
msb.20156107
182. Oellrich A, Collier N, Smedley D, et al. (2015) Generation of silver
standard concept annotations from biomedical texts with special
relevance to phenotypes. PLoS ONE 10:e0116040. doi:10.1371/
journal.pone.0116040
183. Oprea TI, Overington JP (2015) Computational and practical
aspects of drug repositioning. Assay Drug Dev. Technol.
13:299-306. doi:10.1089/adt.2015.29011.tiodrrr
184. Orchard S, Hermjakob H (2015) Shared resources, shared
costs-leveraging biocuration resources. Database (Oxford) 2015.
doi:10.1093/database/bav009
185. Papadatos G, Davies M, Dedman N, et al. (2015) SureChEMBL:
a large-scale, chemically annotated patent document database.
Nucleic Acids Res. 44:D1220-D1228. doi:10.1093/nar/gkv1253
186. Papadatos G, Gaulton A, Hersey A, et al. (2015) Activity, assay
and target data curation and quality in the ChEMBL database. J.
Comput. Aided Mol. Des. 29:885-896. doi:10.1007/s10822-015-
9860-5
187. Partridge L, Thornton J, Bates G (2015) The new science
of ageing. Philos Trans R Soc. Lond. B Biol. Sci. 370:1676.
doi:10.1098/rstb.2015.0249
188. Patel S, Roncaglia P, Lovering RC (2015) Using Gene Ontology
to describe the role of the neurexin-neuroligin-SHANK complex
in human, mouse and rat and its relevance to autism. BMC
Bioinformatics 16: doi:10.1186/s12859-015-0622-0
189. Pavlopoulos GA, Malliarakis D, Papanikolaou N, et al. (2015)
Visualizing genome and systems biology: technologies, tools,
implementation techniques and trends, past, present and future.
Gigascience 4:38. doi:10.1186/s13742-015-0077-2
190. Pedro H, Maheswari U, Urban M, et al. (2015) PhytoPath: an
integrative resource for plant pathogen genomics. Nucleic Acids
Res 44(D1):D688-D693. doi:10.1093/nar/gkv1052
191. Perez-Riverol Y, Uszkoreit J, Sanchez A, et al. (2015) msdata-core-api:
An open-source, metadata-oriented library
for computational proteomics. Bioinformatics 31:2903-2905.
doi:10.1093/bioinformatics/btv250
72
2015 EMBL-EBI Annual Scientific Report