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In Print: August's Bioinformatics Papers of Note


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]

Filed under

The Scan

Boosters Chasing Variants

The New York Times reports that an FDA advisory panel is to weigh updated booster vaccines for COVID-19.

Not Yet

The World Health Organization says monkeypox is not yet a global emergency, the Washington Post reports.

More Proposed for Federal Research

Science reports that US House of Representatives panels are seeking to increase federal research funding.

PLOS Papers on Breast Cancer Metastasis, Left-Sided Cardiac Defects, SARS-CoV-2 Monitoring

In PLOS this week: link between breast cancer metastasis and CLIC4, sequencing analysis of left-sided cardiac defects, and more.