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In Print: Nov 12, 2010

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Bioinformatics Tool-Related Papers of Note, October 2010

Note: In addition to the below listing, papers for Nucleic Acids Research's annual database issue are available under advance access here.

Kokocinski F, Harrow J, Hubbard T.
AnnoTrack — a tracking system for genome annotation.
BMC Genomics. 2010 Oct 5;11:538.


Methé BA, Rusch DB, Tanenbaum DM, Goll J, Li K, Thiagarajan M, Yooseph S.
METAREP: JCVI metagenomics reports--an open source tool for high-performance comparative metagenomics.
Bioinformatics. 2010 Oct 15;26(20):2631-2. Epub 2010 Aug 26.


Biswas A, Parab G, Mynampati KC, Rao R, Umashankar S, Reuben S, Swarup S, Kannan VS.
MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation.
Bioinformatics. 2010 Oct 15;26(20):2639-40. Epub 2010 Aug 11.


Willighagen E, Wohlgemuth G, Fiehn O, Haldiya PK , Kind T.
The Chemical Translation Service--a web-based tool to improve standardization of metabolomic reports.
Bioinformatics. 2010 Oct 15;26(20):2647-8. Epub 2010 Sep 9.


Bier E, Esteves FF, Karten HJ, Do LH.
Booly: a new data integration platform.
BMC Bioinformatics. 2010 Oct 13;11(1):513. [Epub ahead of print]


Daily K, Baldi P, Rigor P, Christley S, Xie X.
Data structures and compression algorithms for high-throughput sequencing technologies.
BMC Bioinformatics. 2010 Oct 14;11(1):514. [Epub ahead of print]


Evans AM, Dehaven CD, Dai H, Lawton KA.
Organization of GC/MS and LC/MS Metabolomics Data into Chemical Libraries.
J Cheminform. 2010 Oct 18;2(1):9. [Epub ahead of print]


Statnikov A, Aliferis CF, Lytkin NI, Narendra V.
A comprehensive assessment of methods for de-novo reverse-engineering of genome-scale regulatory networks.
Genomics. 2010 Oct 13. [Epub ahead of print]


Viglietto G, Cerulo L, Ceccarelli M, Morganella S.
VEGA: Variational segmentation for copy number detection.
Bioinformatics. 2010 Oct 19. [Epub ahead of print]


Laviolette F, Corbeil J, Boisvert S.
Ray: Simultaneous Assembly of Reads from a Mix of High-Throughput Sequencing Technologies.
J Comput Biol. 2010 Oct 20. [Epub ahead of print]


Duncavage EJ, Abel HJ, Pfeifer JD, Armstrong JR, Becker N, Magrini VJ.
SLOPE: A quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data.
Bioinformatics. 2010 Sep 27. [Epub ahead of print]


Nellessen D, Walossek J, Arndt KM, Müller KM, Staab P, Grünberg R.
SynBioWave - a real-time communication platform for molecular and synthetic biology.
Bioinformatics. 2010 Sep 13. [Epub ahead of print]


Zhou A, Zhang F, Chen JY.
PEPPI: a peptidomic database of human protein isoforms for proteomics experiments.
BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S7.


Harrington ED, Relman DA, Raes J, Arumugam M, Bork P.
SmashCell: A software framework for the analysis of single-cell amplified genome sequences.
Bioinformatics. 2010 Oct 21. [Epub ahead of print]


Hildebrandt A, Bertsch A, Dehof AK, Rurainski A, Moll A, Stockel D, Lenhof HP, Schumann M, Toussaint NC, Nickels S, Mueller SC, Kohlbacher O.
BALL - Biochemical Algorithms Library 1.3.
BMC Bioinformatics. 2010 Oct 25;11(1):531. [Epub ahead of print]


Papanicolaou A, Heckel DG.
The GMOD Drupal Bioinformatic Server Framework.
Bioinformatics. 2010 Oct 22. [Epub ahead of print]


Topol EJ, Bhatia G, Frazer K, Schork NJ, Harismendy O, Bafna V, Bansal V.
A Covering Method for Detecting Genetic Associations between Rare Variants and Common Phenotypes.
PLoS Comput Biol. 2010 Oct 14;6(10):e1000954.


Barua D, Kim J, Reed JL.
An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models.
PLoS Comput Biol. 2010 Oct 28;6(10):e1000970.


Brudno M, Dzamba M, Fiume M, Medvedev P, Smith T.
Detecting copy number variation with mated short reads.
Genome Res. 2010 Sep 21. [Epub ahead of print]


The Scan

Not Immediately Told

The US National Institutes of Health tells lawmakers that one of its grantees did not immediately report that it had developed a more infectious coronavirus, Science says.

Seems Effective in Kids

The Associated Press reports that the Pfizer-BioNTech SARS-CoV-2 vaccine for children appears to be highly effective at preventing symptomatic disease.

Intelligence Warning on Bioeconomy Threats

US intelligence warns over China's focus on technologies and data related to the bioeconomy, the New York Times reports.

PLOS Papers on Campylobacteriosis Sources, Inherited Retinal Dystrophies, Liver Cancer Prognosis

In PLOS this week: approach to uncover source of Campylobacteriosis, genetic risk factors for inherited retinal dystrophies, and more.