Annual Scientific Report 2015
EMBL_EBI_ASR_2015_DigitalEdition
EMBL_EBI_ASR_2015_DigitalEdition
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Publications in <strong>2015</strong><br />
EMBL is proud to be a member of the ORCID Foundation, the public, open registry<br />
of unique researcher identifiers that helps researchers take credit for their work.<br />
This list, based on ORCIDs and affiliation data extracted from Web of Science,<br />
represents EMBL-EBI articles published online in <strong>2015</strong>.<br />
001. 1000 Genomes Project Consortium (<strong>2015</strong>) A global reference<br />
for human genetic variation. Nature 526:68-74. doi:10.1038/<br />
nature15393<br />
002. Achim K, Pettit JB, Saraiva LR, et al. (<strong>2015</strong>) High-throughput<br />
spatial mapping of single-cell RNA-seq data to tissue of origin. Nat.<br />
Biotechnol. 33:503-509. doi:10.1038/nbt.3209<br />
003. Agirre X, Castellano G, Pascual M, et al. (<strong>2015</strong>) Whole-epigenome<br />
analysis in multiple myeloma reveals DNA hypermethylation of B<br />
cell-specific enhancers. Genome Res. 25:478-487. doi:10.1101/<br />
gr.180240.114<br />
004. Aguiar B, Vieira J, Cunha AE, et al. (<strong>2015</strong>) Convergent evolution at<br />
the gametophytic self-incompatibility system in malus and prunus.<br />
PLoS ONE 10: e0126138. doi:10.1371/journal.pone.0126138<br />
005. Ahnert SE, Marsh JA, Hernández H, et al. (<strong>2015</strong>) Principles of<br />
assembly reveal a periodic table of protein complexes. Science<br />
350: aaa2245. doi:10.1126/science.aaa2245<br />
006. Alvaro N, Conway M, Doan S, et al. (<strong>2015</strong>) Crowdsourcing Twitter<br />
annotations to identify first-hand experiences of prescription drug<br />
use. J. Biomed. Inform. 58:280-287. doi:10.1016/j.jbi.<strong>2015</strong>.11.004<br />
007. Andersson L, Archibald AL, Bottema CD, et al. (<strong>2015</strong>) Coordinated<br />
international action to accelerate genome-to-phenome with<br />
FAANG, the Functional Annotation of Animal Genomes project<br />
Genome Biol. 16:57. doi:10.1186/s13059-015-0622-4<br />
008. Anjum S, Morganella S, D’Angelo F, et al. (<strong>2015</strong>) VEGAWES:<br />
variational segmentation on whole exome sequencing for copy<br />
number detection. BMC Bioinformatics 16:315-315. doi:10.1186/<br />
s12859-015-0748-0<br />
009. Arrowsmith CH, Audia JE, Austin C, et al. (<strong>2015</strong>) The promise<br />
and peril of chemical probes Nat. Chem. Biol. 11:536-541.<br />
doi:10.1038/nchembio.1867<br />
010. Audain E, Ramos Y, Hermjakob H, et al. (<strong>2015</strong>) Accurate estimation<br />
of isoelectric point of protein and peptide based on amino acid<br />
sequences. Bioinformatics (in press); doi:10.1093/bioinformatics/<br />
btv674<br />
011. Babbitt PC, Bagos PG, Bairoch A, et al. (<strong>2015</strong>) Creating a<br />
specialist protein resource network: a meeting report for the<br />
protein bioinformatics and community resources retreat. Database<br />
<strong>2015</strong>:bav063. doi:10.1093/database/bav063<br />
012. Bacci G, Ceccherini MT, Bani A, et al. (<strong>2015</strong>) Exploring<br />
the dynamics of bacterial community composition in soil:<br />
the pan-bacteriome approach. Antonie Van Leeuwenhoek<br />
107:785-797. doi:10.1007/s10482-014-0372-4<br />
013. Barrett JC, Dunham I, Birney E (<strong>2015</strong>) Using human genetics to<br />
make new medicines. Nat. Rev. Genet. 16:561-562. doi:10.1038/<br />
nrg3998<br />
014. Bastian FB, Chibucos MC, Gaudet P, et al. (<strong>2015</strong>) The Confidence<br />
Information Ontology: a step towards a standard for asserting<br />
confidence in annotations. Database (Oxford) <strong>2015</strong>. doi:10.1093/<br />
database/bav043<br />
015. Baxevanis AD, Bateman A (<strong>2015</strong>) The importance of biological<br />
databases in biological discovery. Curr Protoc Bioinformatics<br />
50:1.1.1-8. doi:10.1002/0471250953.bi0101s50<br />
016. Beisken S, Conesa P, Haug K, et al. (<strong>2015</strong>) SpeckTackle:<br />
JavaScript charts for spectroscopy. J Cheminform 7:17.<br />
doi:10.1186/s13321-015-0065-7<br />
017. Benjelloun B, Alberto FJ, Streeter I, et al. (<strong>2015</strong>) Characterizing<br />
neutral genomic diversity and selection signatures in indigenous<br />
populations of Moroccan goats (Capra hircus) using WGS data.<br />
Front Genet 6:107. doi:10.3389/fgene.<strong>2015</strong>.00107<br />
018. Birney E, Soranzo N (<strong>2015</strong>) Human genomics: The end<br />
of the start for population sequencing. Nature 526:52-53.<br />
doi:10.1038/526052a<br />
019. Blake JA, Christie KR, Dolan ME, et al. (<strong>2015</strong>) Gene Ontology<br />
Consortium: going forward. Nucleic Acids Res. 43(D1):D1049-<br />
D1056. doi:10.1093/nar/gku1179<br />
020. Blumenthal T, Davis P, Garrido-Lecca A (<strong>2015</strong>) Operon and<br />
non-operon gene clusters in the C. elegans genome. WormBook<br />
<strong>2015</strong>:1-20. doi:10.1895/wormbook.1.175.1<br />
021. Boeckmann B, Marcet-Houben M, Rees JA, et al. (<strong>2015</strong>) Quest for<br />
orthologs entails quest for tree of life: In search of the gene stream.<br />
Genome Biol. Evol. 7:1988-1999. doi:10.1093/gbe/evv121<br />
022. Bolser D, Staines DM, Pritchard E, et al. (<strong>2015</strong>) Ensembl<br />
Plants: integrating tools for visualizing, mining, and analyzing<br />
plant genomics data. Methods Mol. Biol. 1374:115-140.<br />
doi:10.1007/978-1-4939-3167-5_6<br />
023. Boroviak T, Loos R, Lombard P, et al. (<strong>2015</strong>) Lineage-specific<br />
profiling delineates the emergence and progression of naive<br />
pluripotency in mammalian embryogenesis. Dev. Cell 35:366-382.<br />
doi:10.1016/j.devcel.<strong>2015</strong>.10.011<br />
024. Bosi E, Donati B, Galardini M, et al. (<strong>2015</strong>) MeDuSa: A multi-draft<br />
based scaffolder. Bioinformatics 31:2443-2451. doi:10.1093/<br />
bioinformatics/btv171<br />
025. Brage S, Westgate K, Franks PW, et al. (<strong>2015</strong>) Estimation of<br />
free-living energy expenditure by heart rate and movement<br />
sensing: A doubly-labelled water study. PLoS One 10:e0137206.<br />
doi:10.1371/journal.pone.0137206<br />
026. Brooksbank C, Johnson C (<strong>2015</strong>) Europe: Lifelong learning for all in<br />
biomedicine. Nature 524:415-415. doi:10.1038/524415c<br />
027. Bruford EA, Lane L, Harrow J (<strong>2015</strong>) Devising a consensus<br />
framework for validation of novel human coding loci. J. Proteome<br />
Res. 14:4945-4948. doi:10.1021/acs.jproteome.5b00688<br />
028. Bruford MW, Ginja C, Hoffmann I, et al. (<strong>2015</strong>) Prospects and<br />
challenges for the conservation of farm animal genomic resources,<br />
<strong>2015</strong>-2025. Front Genet 6:314. doi:10.3389/fgene.<strong>2015</strong>.00314<br />
029. Budd A, Dinkel H, Corpas M, et al. (<strong>2015</strong>) Ten simple rules for<br />
organizing an unconference. PLoS Comput. Biol. 11: e1003905.<br />
doi:10.1371/journal.pcbi.1003905<br />
030. Buettner F, Natarajan KN, Casale FP, et al. (<strong>2015</strong>) Computational<br />
analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing<br />
data reveals hidden subpopulations of cells. Nat. Biotechnol.<br />
33:155-160. doi:10.1038/nbt.3102<br />
031. Cannone JJ, Sweeney BA, Petrov AI, et al. (<strong>2015</strong>) R3D-2-MSA: the<br />
RNA 3D structure-to-multiple sequence alignment server. Nucleic<br />
Acids Res. 43:W15-W23. doi:10.1093/nar/gkv543<br />
032. Carén H, Stricker SH, Bulstrode H, et al. (<strong>2015</strong>) Glioblastoma<br />
stem cells respond to differentiation cues but fail to undergo<br />
commitment and terminal cell-cycle arrest. Stem Cell <strong>Report</strong>s<br />
5:829-842. doi:10.1016/j.stemcr.<strong>2015</strong>.09.014<br />
033. Carvalho PC, Padron G, Calvete JJ, et al. (<strong>2015</strong>) Computational<br />
proteomics: Integrating mass spectral data into a biological<br />
context. J. Proteomics 129:1-2. doi:10.1016/j.jprot.<strong>2015</strong>.10.013<br />
034. Casale FP, Rakitsch B, Lippert C, et al. (<strong>2015</strong>) Efficient set tests for<br />
the genetic analysis of correlated traits. Nat. Methods 12:755-U93.<br />
doi:10.1038/NMETH.3439<br />
035. Chaouiya C, Keating SM, Berenguier D, et al. (<strong>2015</strong>) The Systems<br />
Biology Markup Language (SBML) Level 3 Package: Qualitative<br />
Models, Version 1, Release 1. J Integr. Bioinform. 12:270.<br />
doi:10.2390/biecoll-jib-<strong>2015</strong>-270<br />
036. Chiang Z, Vastermark A, Punta M, et al. (<strong>2015</strong>) The complexity,<br />
challenges and benefits of comparing two transporter classification<br />
systems in TCDB and Pfam. Brief. Bioinform. 16:865-872.<br />
doi:10.1093/bib/bbu053<br />
68<br />
<strong>2015</strong> EMBL-EBI <strong>Annual</strong> <strong>Scientific</strong> <strong>Report</strong>
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