Annual Scientific Report 2015

037. Chiapparino A, Maeda K, Turei D, et al. (2015) The orchestra of
lipid-transfer proteins at the crossroads between metabolism
and signaling. Prog. Lipid Res. 61:30-39. doi:10.1016/j.
plipres.2015.10.004
038. Church DM, Schneider VA, Steinberg KM, et al. (2015) Extending
reference assembly models. Genome Biol. 16:13. doi:10.1186/
s13059-015-0587-3
039. Clark MB, Mercer TR, Bussotti G, et al. (2015) Quantitative gene
profiling of long noncoding RNAs with targeted RNA sequencing.
Nat. Methods 12:339-342. doi:10.1038/nmeth.3321
040. Collier N, Groza T, Smedley D, et al. (2015) PhenoMiner: from text
to a database of phenotypes associated with OMIM diseases.
Database (Oxford) 2015: doi:10.1093/database/bav104
041. Collier N, Oellrich A, Groza T (2015) Concept selection for
phenotypes and diseases using learn to rank J. Biomed. Semantics
6:24. doi:10.1186/s13326-015-0019-z
042. Cook CE, Bergman MT, Finn RD, et al. (2015) The European
Bioinformatics Institute in 2016: Data growth and integration.
Nucleic Acids Res. 44:D20-D26. doi:10.1093/nar/gkv1352
043. Cortes-Ciriano I, Murrell DS, van Westen GJ, et al. (2015)
Prediction of the potency of mammalian cyclooxygenase inhibitors
with ensemble proteochemometric modeling. J Cheminform 7:1.
doi:10.1186/s13321-014-0049-z
044. Cortes-Ciriano I, Ul Ain Q, Subramanian V, et al. (2015)
Polypharmacology modelling using proteochemometrics (PCM):
Recent methodological developments, applications to target
families, and future prospects. Med. Chem. Comm. 6:24-50.
doi:10.1039/c4md00216d
045. Cortés-Ciriano I, van Westen GJ, Bouvier G, et al. (2015) Improved
large-scale prediction of growth inhibition patterns using the NCI60
cancer cell line panel. Bioinformatics (in press); doi:10.1093/
bioinformatics/btv529
046. Cunningham F, Moore B, Ruiz-Schultz N, et al. (2015) Improving
the Sequence Ontology terminology for genomic variant
annotation. J. Biomed. Semantics 6:32. doi:10.1186/s13326-015-
0030-4
047. Dahlman I, Sinha I, Gao H, et al. (2015) The fat cell epigenetic
signature in post-obese women is characterized by global
hypomethylation and differential DNA methylation of adipogenesis
genes. Int. J. Obes. (Lond) 39:910-919. doi:10.1038/ijo.2015.31
048. Davies M, Dedman N, Hersey A, et al. (2015) ADME SARfari:
comparative genomics of drug metabolizing systems.
Bioinformatics 31:1695-1697. doi:10.1093/bioinformatics/btv010
049. Davies M, Nowotka M, Papadatos G, et al. (2015) ChEMBL web
services: streamlining access to drug discovery data and utilities.
Nucleic Acids Res. 43:w612-w620. doi:10.1093/nar/gkv352
050. de Lange KM, Barrett JC (2015) Understanding inflammatory
bowel disease via immunogenetics. J. Autoimmun. 64:91-100.
doi:10.1016/j.jaut.2015.07.013
051. de Villavicencio-Díaz TN, Gómez YR, Argüelles BO, et al. (2015)
Comparative proteomics analysis of the antitumor effect of
CIGB-552 peptide in HT-29 colon adenocarcinoma cells. J.
Proteomics 126:163-171. doi:10.1016/j.jprot.2015.05.024
052. Deans AR, Lewis SE, Huala E, et al. (2015) Finding our way
through phenotypes. PLoS Biol. 13:e1002033. doi:10.1371/
journal.pbio.1002033
053. Denas O, Sandstrom R, Cheng Y, et al. (2015) Genome-wide
comparative analysis reveals human-mouse regulatory landscape
and evolution BMC Genomics 16:87. doi:10.1186/s12864-015-
1245-6
054. Deutsch EW, Albar JP, Binz PA, et al. (2015) Development of data
representation standards by the human proteome organization
proteomics standards initiative. J. Am. Med. Inform. Assoc.
22:495-506. doi:10.1093/jamia/ocv001
055. Diaz-Muñoz MD, Bell SE, Fairfax K, et al. (2015) The RNA-binding
protein HuR is essential for the B cell antibody response. Nat.
Immunol. 16:415-425. doi:10.1038/ni.3115
056. Ding Z, Ni Y, Timmer SW, et al. (2015) Correction: Quantitative
genetics of CTCF binding reveal local sequence effects and
different modes of X-chromosome association. PLoS Genet. 11:
e1005177. doi:10.1371/journal.pgen.1005177
057. Dong H, Nebert DW, Bruford EA, et al. (2015) Update of the
human and mouse Fanconi anemia genes. Hum. Genomics 9:32.
doi:10.1186/s40246-015-0054-y
058. Dritsou V, Topalis P, Windbichler N, et al. (2015) A draft genome
sequence of an invasive mosquito: an Italian Aedes albopictus.
Pathog. Glob. Health 109:207-220. doi:10.1179/204777321
5Y.0000000031
059. Duarte AM, Psomopoulos FE, Blanchet C, et al. (2015) Future
opportunities and trends for e-infrastructures and life sciences:
going beyond the grid to enable life science data analysis. Front
Genet 6:197. doi:10.3389/fgene.2015.00197
060. Dubin MJ, Zhang P, Meng D, et al. (2015) DNA methylation in
Arabidopsis has a genetic basis and shows evidence of local
adaptation. Elife 4: e05255 doi:10.7554/elife.05255
061. Dutta-Roy R, Rosenmund C, Edelstein SJ, et al. (2015) Liganddependent
opening of the multiple AMPA receptor conductance
States: a concerted model. PLoS ONE 10: e0116616.
doi:10.1371/journal.pone.0116616
062. Dyke SOM, Cheung WA, Joly Y, et al. (2015) Epigenome data
release: A participant-centered approach to privacy protection.
Genome Biol. 16:142. doi:10.1186/s13059-015-0723-0
063. Eduati F, Mangravite LM, Wang T, et al. (2015) Prediction of human
population responses to toxic compounds by a collaborative
competition. Nat. Biotechnol. 33:933-U172. doi:10.1038/nbt.3299
064. Emwas AH, Luchinat C, Turano P, et al. (2015) Standardizing the
experimental conditions for using urine in NMR-based metabolomic
studies with a particular focus on diagnostic studies: a review.
Metabolomics 11:872-894. doi:10.1007/s11306-014-0746-7
065. Eory L, Gilbert MTP, Li C, et al. (2015) Avianbase: a community
resource for bird genomics Genome Biol. 16:21. doi:10.1186/
s13059-015-0588-2
066. Fabregat A, Sidiropoulos K, Garapati P, et al. (2015) The Reactome
Pathway Knowledgebase. Nucleic Acids Res. 44:D481-D487.
doi:10.1093/nar/gkv1351
067. Faddeeva A, Studer RA, Kraaijeveld K, et al. (2015) Collembolan
transcriptomes highlight molecular evolution of hexapods and
provide clues on the adaptation to terrestrial life. PLoS ONE 10:
e0130600. doi:10.1371/journal.pone.0130600
068. Farnell EJ, Tyagi N, Ryan S, et al. (2015) Known allergen structures
predict Schistosoma mansoni IgE-binding antigens in human
infection. Front. Immunol. 6:26. doi:10.3389/fimmu.2015.00026
069. Ferreira P, Fonseca NA, Dutra I, et al. (2015) Predicting
malignancy from mammography findings and image-guided core
biopsies Int. J. Data Min. Bioinform. 11:257-276. doi:10.1504/
IJDMB.2015.067319
070. Fiehn O, Putri SP, Saito K, et al. (2015) Metabolomics continues
to expand: highlights from the 2015 metabolomics conference.
Metabolomics 11:1036-1040. doi:10.1007/s11306-015-0846-z
071. Finn RD, Clements J, Arndt W, et al. (2015) HMMER web server:
2015 update. Nucleic Acids Res. 43:w30-w38. doi:10.1093/nar/
gkv397
072. Finn RD, Coggill P, Eberhardt RY, et al. (2015) The Pfam protein
families database: towards a more sustainable future. Nucleic
Acids Res. 44:D279-D285. doi:10.1093/nar/gkv1344
073. Forster SC, Browne HP, Kumar N, et al. (2015) HPMCD: the
database of human microbial communities from metagenomic
datasets and microbial reference genomes. Nucleic Acids Res.
44:D604-D609. doi:10.1093/nar/gkv1216
074. Foulger RE, Osumi-Sutherland D, McIntosh BK, et al. (2015)
Representing virus-host interactions and other multi-organism
processes in the Gene Ontology. BMC Microbiol. 15:146.
doi:10.1186/s12866-015-0481-x
075. Frankish A, Uszczynska B, Ritchie GRS, et al. (2015) Comparison
of GENCODE and RefSeq gene annotation and the impact of
reference geneset on variant effect prediction. BMC Genomics 16:
doi:10.1186/1471-2164-16-S8-S2
2015 EMBL-EBI Annual Scientific Report 69