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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]

Filed under

The Scan

Comfort of Home

The Guardian reports that AstraZeneca is to run more clinical trials from people's homes with the aim of increasing participant diversity.

Keep Under Control

Genetic technologies are among the tools suggested to manage invasive species and feral animals in Australia, Newsweek says.

Just Make It

The New York Times writes that there is increased interest in applying gene synthesis to even more applications.

Nucleic Acids Research Papers on OncoDB, mBodyMap, Genomicus

In Nucleic Acids Research this week: database to analyze large cancer datasets, human body microbe database, and more.