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April and May's Bioinformatics Papers of Note


Horridge M, Musen MA, et al.
WebProtege: A Collaborative Web Based Platform for Editing Biomedical Ontologies.
Bioinformatics. 2014 Apr 26. [Epub ahead of print]

Borchers CH, Deelder AM, et al.
PeptidePicker: A scientific workflow with web interface for selecting appropriate peptides for targeted proteomics experiments.
J Proteomics 2014 Apr 22. [Epub ahead of print]

Buffart TE, Neerincx M, et al.
ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs.
BMC Bioinformatics. 2014 Apr 26;15(1):116. [Epub ahead of print]

Bouckaert R, Drummond AJ, et al.
BEAST 2: a software platform for Bayesian evolutionary analysis.
PLoS Comput Biol. 2014 Apr 10.

Caporaso JG, Keim P, et al.
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes.
PeerJ. 2014 Apr 1;2:e332. doi: 10.7717/peerj.332. eCollection 2014

Tokheim C, Park JW, Xing Y.
PrimerSeq: Design and Visualization of RT-PCR Primers for Alternative Splicing Using RNA-seq Data.
Genomics Proteomics Bioinformatics. 2014 Apr 18.[Epub ahead of print]

Pfeifer B, Lercher MJ, et al.
PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R.
Mol Biol Evol. 2014 May 5. [Epub ahead of print]

Barril X, Defelipe LA, et al.
TuberQ: a Mycobacterium tuberculosis protein druggability database.
Database (Oxford). 2014 May 8.

Slowikowski K, Hu X, Raychaudhuri S.
SNPsea: an algorithm to identify cell types, tissues, and pathways affected by risk loci.
Bioinformatics. 2014 May 10. [Epub ahead of print]

Gille C, Gille A, et al.
Alignment-Annotator web server: rendering and annotating sequence alignments.
Nucleic Acids Res. 2014 May 9. [Epub ahead of print]

Dhakan DB, Gupta A, et al.
MP3: A Software Tool for the Prediction of Pathogenic Proteins in Genomic and Metagenomic Data.
PLoS One. 2014 Apr 15.

Denroche RE, Fehringer G, et al.
A two-dimensional pooling strategy for rare variant detection on next-generation sequencing platforms.
PLoS One. 2014 Apr 11.

Xu R, Li L, Wang Q.
dRiskKB: a large-scale disease-disease risk relationship knowledge base constructed from biomedical text.
BMC Bioinformatics. 2014 Apr 12;15:105. doi: 10.1186/1471-2105-15-105.

Cantarel BL, Mackey AJ, et al.
BAYSIC: a Bayesian method for combining sets of genome variants with improved specificity and sensitivity.
BMC Bioinformatics. 2014 Apr 12;15:104. doi: 10.1186/1471-2105-15-104

Carroll RJ1, Bastarache L, Denny JC.
R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment.
Bioinformatics. 2014 May 7. [Epub ahead of print]

Daina A, Gfeller D, et al.
SwissTargetPrediction: a web server for target prediction of bioactive small molecules.
Nucleic Acids Res. 2014 May 3. [Epub ahead of print]

Chen YT, Hsieh WP, et al.
HaplotypeCN: Copy Number Haplotype Inference with Hidden Markov Model and Localized Haplotype Clustering.
PLoS One. 2014 May 21.

Barnes MR, Gagliano SA, et al.
A bayesian method to incorporate hundreds of functional characteristics with association evidence to improve variant prioritization.
PLoS One. 2014 May 20.

Down TA, Hubbard T, et al.
A Comparison of Peak Callers Used for DNase-Seq Data.
PLoS One. 2014 May 8.

Bi M, Chen L, et al.
RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction.
RNA. 2014 May 6. [Epub ahead of print]

Dündar F, Diehl S, et al.
deepTools: a flexible platform for exploring deep-sequencing data.
Nucleic Acids Res. 2014 May 5. [Epub ahead of print]

Hao Y, Juan L, et al.
The personal genome browser: visualizing functions of genetic variants.
Nucleic Acids Res. 2014 May 5. [Epub ahead of print]

Brudno M, Dubchak I, et al.
GenomeVISTA - an integrated software package for whole-genomealignment and visualization.
Bioinformatics. 2014 May 23. [Epub ahead of print]

Lam TW, Luo R, et al.
FaSD-somatic: A fast and accurate somatic SNV detection algorithm for cancer genome sequencing data.
Bioinformatics. 2014 May 14. [Epub ahead of print]

Balakrishnan L, Chatterjee A, et al.
Pancreatic Cancer Database: An integrative resource for pancreatic cancer.
Cancer Biol Ther. 2014 May 19;15(8). [Epub ahead of print]

Gawrysiak P, Messina A, et al.
SparkSeq: fast, scalable, cloud-ready tool for the interactive genomic data analysis with nucleotide precision.
Bioinformatics. 2014 May 19. pii: btu343. [Epub ahead of print]

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