Annual Scientific Report 2015

Publications in 2015
076. Fu G, Batchelor C, Dumontier M, et al. (2015) PubChemRDF:
towards the semantic annotation of PubChem compound and
substance databases. J. Cheminformatics 7:34. doi:10.1186/
s13321-015-0084-4
077. Furnham N, Dawson NL, Rahman SA, et al. (2015) Large-scale
analysis exploring evolution of catalytic machineries and
mechanisms in enzyme superfamilies. J. Mol. Biol. (in press);
doi:10.1016/j.jmb.2015.11.010
078. Fuster-Matanzo A, Gessler F, Leonardi T, et al. (2015) Acellular
approaches for regenerative medicine: on the verge of clinical trials
with extracellular membrane vesicles? Stem Cell Res. Ther. 6:227.
doi:10.1186/s13287-015-0232-9
079. Galardini M, Mengoni A, Bazzicalupo M (2015) Mapping
contigs using CONTIGuator. Methods Mol. Biol. 1231:163-176.
doi:10.1007/978-1-4939-1720-4_11
080. Galardini M, Mengoni A, Mocali S (2015) From pangenome to
panphenome and back. Methods Mol. Biol. 1231:257-270.
doi:10.1007/978-1-4939-1720-4_16
081. Gardner PP, Fasold M, Burge SW, et al. (2015) Conservation
and losses of non-coding RNAs in avian genomes. PLoS ONE
10:e0121797. doi:10.1371/journal.pone.0121797
082. Gatto L, Hansen KD, Hoopmann MR, et al. (2015) Testing and
validation of computational methods for Mass Spectrometry. J.
Proteome Res. (in press); doi:10.1021/acs.jproteome.5b00852
083. Gaulton A, Kale N, van Westen GJ, et al. (2015) A large-scale
crop protection bioassay data set. Sci. Data 2:150032-150032.
doi:10.1038/sdata.2015.32
084. Gaulton KJ, Ferreira T, Lee Y, et al. (2015) Genetic fine mapping
and genomic annotation defines causal mechanisms at type
2 diabetes susceptibility loci. Nat. Genet. 47:1415-1425.
doi:10.1038/ng.3437
085. Geihs M, Yan Y, Walter K, et al. (2015) An interactive genome
browser of association results from the UK10K cohorts project.
Bioinformatics 31:4029-4031. doi:10.1093/bioinformatics/btv491
086. Gibson R, Alako B, Amid C, et al. (2015) Biocuration of functional
annotation at the European Nucleotide Archive. Nucleic Acids Res.
44:D58-D66. doi:10.1093/nar/gkv1311
087. Golanowska M, Galardini M, Bazzicalupo M, et al. (2015) Draft
genome sequence of a highly virulent strain of the plant pathogen
Dickeya solani, IFB0099. Genome Announc. 3:e00109-15-e00109-
15. doi:10.1128/genomeA.00109-15
088. Griss J (2015) Spectral library searching in proteomics. Proteomics
16:729-740. doi:10.1002/pmic.201500296
089. Griss J, Perez-Riverol Y, Hermjakob H, et al. (2015) Identifying
novel biomarkers through data mining - a realistic scenario?
Proteomics Clin Appl 9:437-443. doi:10.1002/prca.201400107
090. Groza T, Köhler S, Moldenhauer D, et al. (2015) The Human
Phenotype Ontology: Semantic unification of common and
rare disease. Am. J. Hum. Genet. 97:111-124. doi:10.1016/j.
ajhg.2015.05.020
091. Gutmanas A, Adams PD, Bardiaux B, et al. (2015) NMR Exchange
Format: A unified and open standard for representation of NMR
restraint data. Nat. Struct. Mol. Biol. 22:433-434. doi:10.1038/
nsmb.3041
092. Hagmann J, Becker C, Müller J, et al. (2015) Century-scale
Methylome stability in a recently diverged Arabidopsis thaliana
lineage. PLoS Genet. 11: e1004920. doi:10.1371/journal.
pgen.1004920
093. Hamann J, Aust G, Arac D, et al. (2015) International Union of
Basic and Clinical Pharmacology. XCIV. Adhesion G proteincoupled
receptors. Pharmacol. Rev. 67:338-367. doi:10.1124/
pr.114.009647
094. Hastings J, Jeliazkova N, Owen G, et al. (2015) eNanoMapper:
harnessing ontologies to enable data integration for nanomaterial
risk assessment. J. Biomed. Semantics 6:10. doi:10.1186/s13326-
015-0005-5
095. Hastings J, Owen G, Dekker A, et al. (2015) ChEBI in 2016:
Improved services and an expanding collection of metabolites.
Nucleic Acids Res (in press); doi:10.1093/nar/gkv1031
096. Heinzel A, Muhlberger I, Stelzer G, et al. (2015) Molecular disease
presentation in diabetic nephropathy Nephrol. Dial. Transplant.
30:17-25. doi:10.1093/ndt/gfv267
097. Henriques D, Rocha M, Saez-Rodriguez J, et al. (2015) Reverse
engineering of logic-based differential equation models using a
mixed-integer dynamic optimisation approach. Bioinformatics
31:2999-3007. doi:10.1093/bioinformatics/btv314
098. Herrero-Zazo M, Segura-Bedmar I, Hastings J, et al. (2015)
DINTO: Using OWL ontologies and SWRL rules to Infer
drug-drug interactions and their mechanisms J. Chem Inf. Model.
55:1698-1707. doi:10.1021/acs.jcim.5b00119
099. Hersey A, Chambers J, Bellis L, et al. (2015) Chemical databases:
curation or integration by user-defined equivalence? Drug Discov.
Today Technol. 14:17-24. doi:10.1016/j.ddtec.2015.01.005
100. Hodson N, Invergo B, Rayner JC, et al. (2015) Palmitoylation and
palmitoyl-transferases in Plasmodium parasites. Biochem. Soc.
Trans. 43:240-245. doi:10.1042/BST20140289
101. Holliday GL, Bairoch A, Bagos PG, et al. (2015) Key challenges
for the creation and maintenance of specialist protein resources.
Proteins 83:1005-1013. doi:10.1002/prot.24803
102. Holmes RK, Tuck AC, Zhu C, et al. (2015) Loss of the yeast
SR protein Npl3 alters gene expression due to transcription
readthrough. PLoS Genet. 11: e1005735. doi:10.1371/journal.
pgen.1005735
103. Horikoshi M, Mӓgi R, van de Bunt M, et al. (2015) Discovery and
fine-mapping of glycaemic and obesity-related trait loci using
high-density imputation. PLoS Genet. 11: e1005230. doi:10.1371/
journal.pgen.1005230
104. Horvatovich P, Lundberg EK, Chen YJ, et al. (2015) Quest for
missing proteins: update 2015 on chromosome-centric Human
Proteome Project. J. Proteome Res. 14:3415-3431. doi:10.1021/
pr5013009
105. Hostas J, Jakubec D, Laskowski RA, et al. (2015) Representative
amino acid side-chain interactions in protein-DNA complexes:
A comparison of highly accurate correlated ab initio quantum
mechanical calculations and efficient approaches for applications
to large systems J. Chem. Theory Comput. 11:4086-4092.
doi:10.1021/acs.jctc.5b00398
106. Howe KL, Bolt BJ, Cain S, et al. (2015) WormBase 2016:
expanding to enable helminth genomic research. Nucleic Acids
Res. 44:D774-D780. doi:10.1093/nar/gkv1217
107. Huang YH, Xu BS, Zhou XY, et al. (2015) Systematic
characterization and prediction of post-translational modification
cross-talk. Mol. Cell. Proteomics 14:761-770. doi:10.1074/mcp.
M114.037994
108. Hubley R, Finn RD, Clements J, et al. (2015) The Dfam database
of repetitive DNA families. Nucleic Acids Res. 44:D81-D89.
doi:10.1093/nar/gkv1272
109. Hucka M, Bergmann FT, Dräger A, et al. (2015) Systems Biology
Markup Language (SBML) Level 2 Version 5: Structures and
Facilities for Model Definitions. J Integr Bioinform 12:271.
doi:10.2390/biecoll-jib-2015-271
110. Hucka M, Nickerson DP, Bader GD, et al. (2015) Promoting
Coordinated Development of Community-Based Information
Standards for Modeling in Biology: The COMBINE Initiative. Front
Bioeng Biotechnol 3:19. doi:10.3389/fbioe.2015.00019
111. Ing-Simmons E, Seitan V, Faure A, et al. (2015) Spatial enhancer
clustering and regulation of enhancer-proximal genes by cohesin.
Genome Res. 25:504-513. doi:10.1101/gr.184986.114
112. Iorio F, Shrestha RL, Levin N, et al. (2015) A semi-supervised
approach for refining transcriptional signatures of drug response
and repositioning predictions. PLoS One 10(10):e0139446-
e0139446. doi:10.1371/journal.pone.0139446
113. Ison J, Rapacki K, Ménager H, et al. (2015) Tools and data services
registry: a community effort to document bioinformatics resources.
Nucleic Acids Res. 44:D38-D47. doi:10.1093/nar/gkv1116
114. Ivanov DK, Escott-Price V, Ziehm M, et al. (2015) Longevity GWAS
using the Drosophila genetic reference panel. J. Gerontol. A Biol.
Sci. Med. Sci. 70:1470-1478. doi:10.1093/gerona/glv047
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2015 EMBL-EBI Annual Scientific Report