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In Print: August's Bioinformatics Papers of Note

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Goldstein S, Lin HC, et al.
AGORA: Assembly Guided by Optical Restriction Alignment.
BMC Bioinformatics. 2012 Aug 2;13(1):189.


Carbajo D, Tramontano A.
A resource for benchmarking the usefulness of protein structure models.
BMC Bioinformatics. 2012 Aug 2;13(1):188.


Brendel VP, Standage DS.
ParsEval: parallel comparison and analysis of gene structure annotations.
BMC Bioinformatics. 2012 Aug 1;13(1):187.


Broet P, Moreau T.
A model-based statistic for detecting molecular markers associated with complex survival patterns in early-stage cancer.
J Clin Bioinforma. 2012 Aug 6;2(1):14.


Berardini TZ, Chetty R, et al.
Assessment of community-submitted ontology annotations from a novel database-journal partnership.
Database (Oxford). 2012 Aug 1;2012(0):bas030.


Dai DF, Hsieh EJ, et al.
Topograph, a software platform for precursor enrichment corrected global protein turnover measurements.
Mol Cell Proteomics. 2012 Aug 3. [Epub ahead of print]


Chang LC, Kaminski N, et al.
An R package Suite for Microarray Meta-analysis in Quality Control, Differentially Expressed Gene Analysis and Pathway Enrichment Detection.
Bioinformatics. 2012 Aug 3. [Epub ahead of print]


Fischer M, Dander A, et al.
SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data.
PLoS One. 2012;7(8):e41948.


Kjems J, Knudsen B, et al.
PPfold 3.0: Fast RNA secondary structure prediction using phylogeny and auxiliary data.
Bioinformatics. 2012 Aug 9. [Epub ahead of print]


Cheng W, Nie P, et al.
WinHAP: An Efficient Haplotype Phasing Algorithm Based on Scalable Sliding Windows.
PLoS One. 2012;7(8):e43163.


Bar-Joseph Z, Gitter A, Navlakha S.
A Network-based Approach for Predicting Missing Pathway Interactions.
PLoS Comput Biol. 2012 Aug;8(8):e1002640.


Blanchette P, Borozan I, et al.
CaPSID: A bioinformatics platform for computational pathogen sequence identification in human genomes and transcriptomes.
BMC Bioinformatics. 2012 Aug 17;13(1):206.


Deng R, Huang J, et al.
metaPIS: a sequence-based meta-server for protein interaction site prediction.
Protein Pept Lett. 2012 Aug 7. [Epub ahead of print]


Downard KM, Lun AT, Wong JW.
Flushuffle and Fluresort: new algorithms to identify reassorted strains of the influenza virus by mass spectrometry.
BMC Bioinformatics. 2012 Aug 20;13(1):208.


Chapman BA, Cock PJ, et al.
Bio.Phylo: A unified toolkit for processing, analyzing and visualizing phylogenetic trees in biopython.
BMC Bioinformatics. 2012 Aug 21;13(1):209.


Katze MG, Jones DC, et al.
Compression of next-generation sequencing reads aided by highly efficient de novo assembly.
Nucleic Acids Res. 2012 Aug 16. [Epub ahead of print]


Nair PS, Vihinen M.
VariBench: A benchmark database for variations.
Hum Mutat. 2012 Aug 17. [Epub ahead of print]


Chang I, Kim S, et al.
PACSY, a relational database management system for protein structure and chemical shift analysis.
J Biomol NMR. 2012 Aug 19. [Epub ahead of print]


Ahlers V, Beckmann N, et al.
Genometa — a fast and accurate classifier for short metagenomic shotgun reads.
PLoS One. 2012;7(8):e41224.


Sahraeian SM, Yoon BJ.
A network synthesis model for generating protein interaction network families.
PLoS One. 2012;7(8):e41474.


Zhou B.
An Empirical Bayes Mixture Model for SNP Detection in Pooled Sequencing Data.
Bioinformatics. 2012 Aug 22. [Epub ahead of print]


Andersen SU, Gupta V, et al.
shortran: A pipeline for small RNA-seq data analysis.
Bioinformatics. 2012 Aug 22. [Epub ahead of print]


Carbonell J, Conesa A, et al.
Qualimap: evaluating next generation sequencing alignment data.
Bioinformatics. 2012 Aug 22. [Epub ahead of print]


Li B, Leal SM, Wang G.
SimRare: a program to generate and analyze sequence-based data for association studies of quantitative and qualitative traits.
Bioinformatics. 2012 Aug 22. [Epub ahead of print]


Ma H, Zhao H.
FacPad: Bayesian Sparse Factor Modeling for the Inference of Pathways Responsive to Drug Treatment.
Bioinformatics. 2012 Aug 24. [Epub ahead of print]


Cuevas-Diaz-Duran R, Falciani F, et al.
COMPADRE: An R and Web Resource for Pathway Activity Analysis by Component Decompositions.
Bioinformatics. 2012 Aug 24. [Epub ahead of print]


Anisimova M, Hauser A, et al.
Repeat or not repeat? — Statistical validation of tandem repeat prediction in genomic sequences.
Nucleic Acids Res. 2012 Aug 25. [Epub ahead of print]


Akmaev VR, Hendrickson B, et al.
A GC-Wave Correction Algorithm that Improves the Analytical Performance of aCGH.
J Mol Diagn. 2012 Aug 23. [Epub ahead of print]


Granqvist E, Hartley M, Morris RJ.
BaSAR-A tool in R for frequency detection.
Biosystems. 2012 Aug 18. [Epub ahead of print]


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