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November's 2013 Bioinformatics Papers of Note


Del Pozo A, Izarzugaza JM, et al.
wKinMut: An integrated tool for the analysis and interpretation of mutations in human protein kinases.
BMC Bioinformatics. 2013 Nov 29;14(1):345. [Epub ahead of print]

Cairns BR, Carrell DT, et al.
Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.
BMC Bioinformatics. 2013 Nov 21;14(1):337. [Epub ahead of print]

Arvestad L, Elias I, et al.
Fastphylo: Fast tools for phylogenetics.
BMC Bioinformatics. 2013 Nov 20;14(1):334. [Epub ahead of print]

Dunn CW, Howison M, Zapata F.
Agalma: an automated phylogenomics workflow.
BMC Bioinformatics. 2013 Nov 19;14(1):330. [Epub ahead of print]

Al-Shahib A, Underwood A.
Snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing.
BMC Bioinformatics. 2013 Nov 19;14(1):326. [Epub ahead of print]

Aebersold R, Bühlmann P, et al.
Statistical approach to protein quantification.
Mol Cell Proteomics. 2013 Nov 19. [Epub ahead of print]

Numa H, Itoh T.
MEGANTE: A Web-based System for Integrated Plant Genome Annotation.
Plant Cell Physiol. 2013 Nov 18. [Epub ahead of print]

Chen R, Coin LJ, et al.
YHap: a population model for probabilistic assignment of Y haplogroups from re-sequencing data.
BMC Bioinformatics. 2013 Nov 19;14(1):331. doi: 10.1186/1471-2105-14-331.

Araújo E, Espindola G, et al.
SpliceProt: a protein sequence repository of predicted human splice variants.
Proteomics. 2013 Nov 25. doi: 10.1002/pmic.201300078. [Epub ahead of print]

Büchel F, Chaouiya C, et al.
Path2Models: large-scale generation of computational models from biochemical pathway maps.
BMC Syst Biol. 2013 Nov 1;7(1):116. [Epub ahead of print]

Dellicour S, Mardulyn P.
SPADS 1.0: a toolbox to perform spatial analyses on DNA sequence datasets.
Mol Ecol Resour. 2013 Nov 11. doi: 10.1111/1755-0998.12200. [Epub ahead of print]

Dalgleish R, Gaspar P, et al.
Variobox: Automatic Detection and Annotation of Human Genetic Variants.
Hum Mutat. 2013 Nov 4. doi: 10.1002/humu.22474. [Epub ahead of print]

Alioto T, Behr J, et al.
Systematic evaluation of spliced alignment programs for RNA-seq data.
Nat Methods. 2013 Nov 3. doi: 10.1038/nmeth.2722. [Epub ahead of print]

Goodswen SJ, Kennedy PJ, Ellis JT.
A novel strategy for classifying the output from an in silico vaccine discovery pipeline for eukaryotic pathogens using machine learning algorithms.
BMC Bioinformatics. 2013 Nov 2;14(1):315. [Epub ahead of print]

Caprari S, Di Stefano M, et al.
ASSIST: a fast versatile local structural comparison tool.
Bioinformatics. 2013 Nov 15. [Epub ahead of print]

Fernie AR, Herter T, et al.
Mercator: A fast and simple web server for genome scale functional annotation of plant sequence data.
Plant Cell Environ. 2013 Nov 15. doi: 10.1111/pce.12231. [Epub ahead of print]

Arshadi N, Beck T, et al.
WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.
Bioinformatics. 2013 Nov 26. [Epub ahead of print]

Domenico TD, Martin AJ, et al.
PANADA: Protein Association Network Annotation, Determination and Analysis.
PLoS One. 2013 Nov 12;8(11):e78383.

Chen M, Gunel M, Zhao H.
SomatiCA: Identifying, Characterizing and Quantifying Somatic Copy Number Aberrations from Cancer Genome Sequencing Data.
PLoS One. 2013 Nov 12;8(11):e78143.

Atkinson F, Davies M, et al.
MyChEMBL: A virtual machine implementation of open data and cheminformatics tools.
Bioinformatics. 2013 Nov 20. [Epub ahead of print]

Diao L, Guo F, et al.
CAPER2.0: an interactive, configurable and extensible workflow-based platform to analyze datasets from the Chromosome-centric Human Proteome Project.
J Proteome Res. 2013 Nov 22. [Epub ahead of print]

Vuong H, Stephens RM, Volfovsky N.
AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations.
Bioinformatics. 2013 Nov 29. [Epub ahead of print]

Franzke A, German DA, et al.
BrassiBase: Introduction to a Novel Knowledge Database on Brassicaceae Evolution.
Plant Cell Physiol. 2013 Nov 19. [Epub ahead of print]

Kim J, Ma J.
PSAR-Align: improving multiple sequence alignment using probabilistic sampling.
Bioinformatics. 2013 Nov 29. [Epub ahead of print]

Liao Y, Smyth GK, Shi W.
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.
Bioinformatics. 2013 Nov 30. [Epub ahead of print]

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