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July's Bioinformatics Papers of Note

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Adams R, Dörr A, et al.
The systems biology simulation core algorithm.
BMC Syst Biol. 2013 July 5.


Aherne ST, Clarke C, et al.
BreastMark: an integrated approach to mining publicly available transcriptomic datasets relating to breast cancer outcome.
Breast Cancer Res. 2013 Jul 2;15(4):R52. [Epub ahead of print]


Ma X, Zhang X.
NURD: an implementation of a new method to estimate isoform expression from non-uniform RNA-seq data.
BMC Bioinformatics. 2013 Jul 10.


Erdmann JJ, Johnson JE, et al.
MMuFLR: missense mutation and frameshift location reporter.
Bioinformatics. 2013 Jul 25. [Epub ahead of print]


Bian J, Kachroo P, et al.
SNVHMM: predicting single nucleotide variants from next generation sequencing.
BMC Bioinformatics. 2013 Jul 15


Chapman BA, Kirchner R, et al.
GEMINI: integrative exploration of genetic variation and genome annotations.
PLoS Comput Biol. Epub 2013 Jul 18.


Ackley A, Knowling S, et al.
An algorithm for generating small RNAs capable of epigenetically modulating transcriptional gene silencing and activation in human cells.
Mol Ther Nucleic Acids. 2013 Jul 9


Bot JJ, Galas DJ, et al.
RCytoscape: tools for exploratory network analysis.
BMC Bioinformatics. 2013 Jul 9;14(1):217. [Epub ahead of print]


Alonso A, Canela-Xandri O, et al.
GStream: improving SNP and CNV coverage on genome-wide association studies.
PLoS One. 2013 Jul 3


Adolf-Bryfogle J, Dunbrack RL Jr.
The PyRosetta toolkit: a graphical user interface for the Rosetta software suite.
PLoS One. 2013 Jul 9.


Kuo TC, Tian TF, Tseng YJ.
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data.
BMC Syst Biol. 2013 Jul 23;7:64. doi: 10.1186/1752-0509-7-64


Ander BP, Peng B, et al.
An integrative framework for bayesian variable selection with informative priors for identifying genes and pathways.
PLoS One. 2013 Jul 3


Boerwinkle E, Jian X, Liu X.
dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations.
Hum Mutat. 2013 Jul 10. doi: 10.1002/humu.22376. [Epub ahead of print]


Cheng C, Mullighan C et al.
A genomic random interval model for statistical analysis of genomic lesion data.
Bioinformatics. 2013 Jul 18. [Epub ahead of print]


Adelson DL, Branford S, et al.
A comparative analysis of algorithms for somatic SNV detection in cancer.
Bioinformatics. 2013 Jul 13. [Epub ahead of print]


Bapteste E, Halary S, et al.
EGN: a wizard for construction of gene and genome similarity networks.
BMC Evol Biol. 2013 Jul 11


Gang DR, Nelson W, et al.
TCW: transcriptome computational workbench.
PLoS One. 2013 Jul 17


Nagy A, Patthy L.
MisPred: a resource for identification of erroneous protein sequences in public databases.
PLoS One. 2013 Jul 17;2013:bat053. doi: 10.1093/database/bat053. Print 2013.


Araki H, Black MA, et al.
MelanomaDB: a web tool for integrative analysis of melanoma genomic information to identify disease-associated molecular pathways.
Front Oncol. 2013 Jul 16.


Campagne F, Chambwe N, et al.
GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data.
PLoS One. 2013 Jul 23.


Sahraeian SM, Yoon BJ.
SMETANA: accurate and scalable algorithm for probabilistic alignment of large-scale biological networks.
PLoS One. 2013 Jul 12.


Dobbs D, El-Manzalawy Y, et al.
DockRank: ranking docked conformations using partner-specific sequence homology based protein interface prediction.
Proteins. 2013 Jul 20. doi: 10.1002/prot.24370. [Epub ahead of print]


Gonzalez-Perez A, Lopez-Bigas N, Tamborero D
OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes.
Bioinformatics. 2013 Jul 31. [Epub ahead of print]


Berman MA, Conlin LK, et al.
PECONPI: a novel software for uncovering pathogenic copy number variations in non-syndromic sensorineural hearing loss and other genetically heterogeneous disorders.
Am J Med Genet A. 2013 Jul 29. doi: 10.1002/ajmg.a.36038. [Epub ahead of print]


Das AA, Krishna R, et al.
PepBind: a comprehensive database and computational tool for analysis of protein-peptide interactions.
Genomics Proteomics Bioinformatics. 2013 Jul 26


Belcastro V, Cano S,et al.
Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data.
BMC Genomics. 2013 Jul 29;14(1):514. [Epub ahead of print]


Chen SJ, Chen TW, et al.
CPAP: cancer panel analysis pipeline.
Hum Mutat. 2013 Jul 24. doi: 10.1002/humu.22386. [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.