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In Print: Nov 12, 2010


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

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.