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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]

Filed under

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.