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September's Bioinformatics Papers of Note


Bi C, Berman HM, et al.
RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB ProteinData Bank.
Bioinformatics. 2014 Sep 2. pii: btu596. [Epub ahead of print]

Smith DR
Buying in to bioinformatics: an introduction to commercial sequence analysis software.
Bioinformatics. 2014 Sep 2. pii: btu596. [Epub ahead of print]

Abate F, Acquaviva A, et al.
Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer.
BMC Syst Biol. 2014 Sep 4;8(1):97. [Epub ahead of print]

Diament B, Eng JK, et al.
Crux: Rapid Open Source Protein Tandem Mass Spectrometry Analysis.
J Proteome Res. 2014 Sep 9. [Epub ahead of print]

Abbott KL, Abrahante J, et al.
The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice.
Nucleic Acids Res. 2014 Sep 4. pii: gku770. [Epub ahead of print]

Cingolani P, Sladek R, Blanchette M.
BigDataScript: A scripting language for data pipelines.
Bioinformatics. 2014 Sep 3. pii: btu595. [Epub ahead of print]

Li Y, Peng C, et al.
SignalSpider: Probabilistic Pattern Discovery on Multiple Normalized ChIP-Seq Signal Profiles.
Bioinformatics. 2014 Sep 5. pii: btu604. [Epub ahead of print]

Bahar I, Cobanoglu MC, et al.
BalestraWeb: Efficient, online evaluation of drug-target interactions.
Bioinformatics. 2014 Sep 5. pii: btu599. [Epub ahead of print]

Albersmeier A, Albaum S, et al.
GABenchToB: A Genome Assembly Benchmark Tuned on Bacteria and Benchtop Sequencers.
PLoS One. 2014 Sep 8;9(9):e107014. doi: 10.1371/journal.pone.0107014.

Bailey-Wilson JE, Carter TC, et al.
Generalized Functional Linear Models for Gene-Based Case-Control Association Studies.
Genet Epidemiol. 2014 Sep 9. doi: 10.1002/gepi.21840. [Epub ahead of print].

Sarovich DS, Price EP.
SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets.
BMC Res Notes. 2014 Sep 8;7(1):618. doi: 10.1186/1756-0500-7-618.

An L, Jiang H, et al.
Statistical approach of functional profiling for a microbial community.
PLoS One. 2014 Sep 8;9(9):e106588. doi: 10.1371/journal.pone.0106588.

Cao S, Deng HW, et al.
A Unified Sparse Representation for Sequence Variant Identification for Complex Traits.
Genet Epidemiol. 2014 Sep 4. doi: 10.1002/gepi.21849. [Epub ahead of print].

Ching T, Garmire LX, et al.
A novel model to combine clinical and pathway-based transcriptomic information for the prognosis prediction of breast cancer.
PLoS Comput Biol. 2014 Sep 18;10(9):e1003851. doi: 10.1371/journal.pcbi.1003851.

Budden DM, Crampin EJ, et al.
NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks.
Bioinformatics. 2014 Sep 21. pii: btu612. [Epub ahead of print].

Guo M, Li P, et al.
An overview of SNP interactions in genome-wide association studies.
Brief Funct Genomics. 2014 Sep 19. pii: elu036. [Epub ahead of print]

Buettner F, Mueller NS, et al.
RAMONA: a web application for gene set analysis on multilevel omics data.
Bioinformatics. 2014 Sep 18. pii: btu610. [Epub ahead of print]

Beal K, Flicek P, et al.
The Ensembl REST API: Ensembl Data for Any Language.
Bioinformatics. 2014 Sep 17. pii: btu613. [Epub ahead of print]

Borneman J, Chrobak M, et al.
PRISE2: Software for designing sequence-selective PCR primers and probes.
BMC Bioinformatics. 2014 Sep 25;15(1):317. [Epub ahead of print]

Filed under

The Scan

Tara Pacific Expedition Project Team Finds High Diversity Within Coral Reef Microbiome

In papers appearing in Nature Communications and elsewhere, the team reports on findings from the two-year excursion examining coral reefs.

Study Examines Relationship Between Cellular Metabolism, DNA Damage Repair

A new study in Molecular Systems Biology finds that an antioxidant enzyme shifts from mitochondria to the nucleus as part of the DNA damage response.

Stem Cell Systems Target Metastatic Melanoma in Mouse Model

Researchers in Science Translational Medicine describe a pair of stem cell systems aimed at boosting immune responses against metastatic melanoma in the brain.

Open Pediatric Brain Tumor Atlas Team Introduces Genomic Data Collection, Analytical Tools

A study in Cell Genomics outlines open-source methods being used to analyze and translate whole-genome, exome, and RNA sequence data from the Pediatric Brain Tumor Atlas.