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In Print: Dec 17, 2010

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Bioinformatics Tool-Related Papers of Note, November 2010

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

Nenadic A, Goble CA, Sulakhe D, Foster I, Madduri R, Soiland-Reyes S, Tan W.
CaGrid Workflow Toolkit: a Taverna based workflow tool for cancer grid.
BMC Bioinformatics. 2010 Nov 2;11:542.


Birren BW, Ryan EM, Henn MR, Lennon NJ, Yu Q, Allen TM.
PriSM: A Primer Selection and Matching tool for amplification and sequencing of viral genomes.
Bioinformatics. 2010 Nov 9. [Epub ahead of print]


Jonsson AL , Simms AM, Schaeffer RD, Daggett V.
Generation of a Consensus Protein Domain Dictionary.
Bioinformatics. 2010 Nov 9. [Epub ahead of print]


Klockenbusch C, Zhang C, Evans DM, Kast J, Rogalski JC, Beavis RC.
In Silico Protein Interaction Analysis Using the Global Proteome Machine Database.
J Proteome Res. 2010 Nov 10. [Epub ahead of print]


Bader GD, Jain S.
An improved method for scoring protein-protein interactions using semantic similarity within the Gene Ontology.
BMC Bioinformatics. 2010 Nov 15;11(1):562.


Issac H, Cloonan N, Koehler R, Grimmond SM.
The Uniqueome: A mappability resource for short-tag sequencing.
Bioinformatics. 2010 Nov 12. [Epub ahead of print]


Harrington ED, Raes J, Foerstner KU, Arumugam M, Bork P.
SmashCommunity: A metagenomic annotation and analysis tool.
Bioinformatics. 2010 Oct 19. [Epub ahead of print]


Dickerson JA, Hemert JV, Xia T.
OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data.
Bioinformatics. 2010 Oct 14. [Epub ahead of print]


Zinovyev A, Barillot E , Vert JP, Bleakley K, Janoueix-Lerosey I, Delattre O, Boeva V.
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization.
Bioinformatics. 2010 Nov 15. [Epub ahead of print]


Ruppin E, Zur H, Shlomi T.
iMAT: an integrative metabolic analysis tool.
Bioinformatics. 2010 Dec 15;26(24):3140-2. Epub 2010 Nov 15.


Dlugosch KM, Dinh L, Rieseberg LH, King MG, Barker MS, Kane NC, Challa RS.
EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics.
Evol Bioinform Online. 2010 Oct 20;6:143-149.


Diehnelt CW, Emery J, Fu J, Gonzalez-Moa MJ, Greving MP, Woodbury NW, Belcher PE, Johnston SA.
Thermodynamic additivity of sequence variations: an algorithm for creating high affinity peptides without large libraries or structural information.
PLoS One. 2010 Nov 11;5(11):e15432.


Agrawal A, Choudhary A, Misra S, Liao WK.
Anatomy of a Hash-based Long Read Sequence Mapping Algorithm for Next Generation DNA Sequencing.
Bioinformatics. 2010 Nov 18. [Epub ahead of print]


Sahinidis NV, Vouzis PD.
GPU-BLAST: Using graphics processors to accelerate protein sequence alignment.
Bioinformatics. 2010 Nov 18. [Epub ahead of print]


Nyamundanda G, Gormley IC, Brennan L.
Probabilistic Principal Component Analysis for Metabolomic Data.
BMC Bioinformatics. 2010 Nov 23;11(1):571.


Sherlock G, Martin J, Blow M, Snyder M, Zhang T, Bruno VM, Meng X, Fang Z, Wang Z.
Rnnotator: an automated de novo transcriptome assembly pipeline from stranded RNA-Seq reads.
BMC Genomics. 2010 Nov 24;11(1):663.


Loytynoja A, Goldman N.
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser.
BMC Bioinformatics. 2010 Nov 26;11(1):579.


Kelley DR, Schatz MC, Salzberg SL.
Quake: quality-aware detection and correction of sequencing errors.
Genome Biol. 2010 Nov 29;11(11):R116.


Goble CA, Winder C, Broomhead D, Jameson D, Kell DB, Weichart D, Simeonidis E, Khan F, Messiha HL, Westerhoff HV, Spasic I, Dada JO, Wishart J, Carroll K, Malys N, Paton NW, Swainston N, Li P, Mendes P, Gaskell SJ, Dunn W.
Systematic integration of experimental data and models in systems biology.
BMC Bioinformatics. 2010 Nov 29;11(1):582.


The Scan

Comfort of Home

The Guardian reports that AstraZeneca is to run more clinical trials from people's homes with the aim of increasing participant diversity.

Keep Under Control

Genetic technologies are among the tools suggested to manage invasive species and feral animals in Australia, Newsweek says.

Just Make It

The New York Times writes that there is increased interest in applying gene synthesis to even more applications.

Nucleic Acids Research Papers on OncoDB, mBodyMap, Genomicus

In Nucleic Acids Research this week: database to analyze large cancer datasets, human body microbe database, and more.