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September's Bioinformatics Papers of Note

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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

NFTs for Genome Sharing

Nature News writes that non-fungible tokens could be a way for people to profit from sharing genomic data.

Wastewater Warning System

Time magazine writes that cities and college campuses are monitoring sewage for SARS-CoV-2, an approach officials hope lasts beyond COVID-19.

Networks to Boost Surveillance

Scientific American writes that new organizations and networks aim to improve the ability of developing countries to conduct SARS-CoV-2 genomic surveillance.

Genome Biology Papers on Gastric Cancer Epimutations, BUTTERFLY, GUNC Tool

In Genome Biology this week: recurrent epigenetic mutations in gastric cancer, correction tool for unique molecular identifier-based assays, and more.