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November's Bioinformatics Papers of Note

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Aloria K, Arizmendi JM, et al.
PAnalyzer: A software tool for protein inference in shotgun proteomics.
BMC Bioinformatics. 2012 Nov 5;13(1):288.


Allen-Soltero SR, Chan JE, et al.
Bioinformatic identification of genes suppressing genome instability.
Proc Natl Acad Sci U S A. Epub 2012 Nov 5.


Butler J, Daley M, et al.
HD-CNV: Hotspot Detector for Copy Number Variants.
Bioinformatics. 2012 Nov 4. [Epub ahead of print]


Hall IM, Layer RM, et al.
Binary Interval Search (BITS): A Scalable Algorithm for Counting Interval Intersections.
Bioinformatics. 2012 Nov 4. [Epub ahead of print]


Bork P, Gonçalves E, et al.
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Bioinformatics. 2012 Nov 4. [Epub ahead of print]


Lin H, Li Y, et al.
A single kernel-based approach to extract drug-drug interactions from biomedical literature.
PLoS One. Epub 2012 Nov 1.


Chen MS, Dai Z, et al.
Improving accuracy for cancer classification with a new algorithm for genes selection.
BMC Bioinformatics. 2012 Nov 13;13(1):298.


Chinnaiyan AM, Iyer MK, Veeneman BA.
Oculus: faster sequence alignment by streaming read compression.
BMC Bioinformatics. 2012 Nov 13;13(1):297.


Jeong SK, Kim H, et al.
PanelComposer: A Web-Based Panel Construction Tool for Multivariate Analysis of Disease Biomarker Candidates.
J Proteome Res. 2012 Nov 16. [Epub ahead of print]


Eng JK, Hoopmann MR, Jahan TA.
Comet: an open source tandem mass spectrometry sequence database search tool.
Proteomics. 2012 Nov 12. [Epub ahead of print]


Berg J, Kolar M, et al.
GraphAlignment: Bayesian pairwise alignment of biological networks.
BMC Syst Biol. 2012 Nov 21;6(1):144.


Heijsman D, Hiltemann SD, et al.
Huvariome: a web server resource of whole genome next-generation sequencing allelic frequencies to aid in pathological candidate gene selection.
J Clin Bioinforma. 2012 Nov 19;2(1):19.


Flassig RJ, Heise S, et al.
An Effective Framework for Reconstructing Gene Regulatory Networks From Genetical Genomics Data.
Bioinformatics 2012 Nov 21. [Epub ahead of print]


Glinskii OV, Glinsky VV, Li F.
Glycobioinformatics: current strategies and tools for data mining in mass spectrometry based glycoproteomics.
Proteomics. 2012 Nov 23. [Epub ahead of print]


Powell DR, Seemann T.
VAGUE: a graphical user interface for the Velvet assembler.
Bioinformatics. 2012 Nov 17. [Epub ahead of print]


Chen Y, M Tannir N, et al.
VirusSeq: Software to identify viruses and their integration sites using next generation sequencing of human cancer tissue.
Bioinformatics. 2012 Nov 17. [Epub ahead of print]


Anthony J, Marth G, et al.
Scribl: An HTML5 Canvas-based graphics library for visualizing genomic data over the web.
Bioinformatics. 2012 Nov 19. [Epub ahead of print]


Amos C, Fang S, et al.
Building a statistical model for predicting cancer genes.
PLoS One. Epub 2012 Nov 15.


Manrique M, Pareja E, et al.
BG7: A New Approach for Bacterial Genome Annotation Designed for Next Generation Sequencing Data.
PLoS One. Epub 2012 Nov 21.


Zhang J, Xu D.
Fast algorithm for population-based protein structural model analysis.
Proteomics. 2012 Nov 26. [Epub ahead of print]


Afgan E, Chapman B.
CloudMan as a platform for tool, data, and analysis distribution.
BMC Bioinformatics. 2012 Nov 27;13(1):315.


Filed under

The Scan

Alzheimer's Risk Gene Among Women

CNN reports that researchers have found that variants in MGMT contribute to Alzheimer's disease risk among women but not men.

Still Hanging Around

The Guardian writes that persistent pockets of SARS-CoV-2 in the body could contribute to long COVID.

Through a Little Spit

Enteric viruses like norovirus may also be transmitted through saliva, not just the fecal-oral route, according to New Scientist.

Nature Papers Present Method to Detect Full Transcriptome, Viruses Infecting Asgard Archaea, More

In Nature this week: VASA-seq approach to detect full transcriptome, analysis of viruses infecting Asgard archaea, and more.