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In Print : Sep 10, 2010


Bioinformatics Tool-Related Papers of Note, August 2010

Cantacessi C, Jex AR, Hall RS, Young ND, Campbell BE, Joachim A, Nolan MJ, Abubucker S, Sternberg PW, Ranganathan S, Mitreva M, Gasser RB.
A practical, bioinformatic workflow system for large data sets generated by next-generation sequencing.
Nucleic Acids Res. 2010 Aug 3. [Epub ahead of print]

Chavez L, Jozefczuk J, Grimm C, Dietrich J, Timmermann B, Lehrach H, Herwig R, Adjaye J.
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage.
Genome Res. 2010 Aug 27. [Epub ahead of print]

Cheng WC, Tsai ML, Chang CW, Huang CL, Chen CR, Shu WY, Lee YS, Wang TH, Hong JH, Li CY, Hsu IC.
Microarray meta-analysis database (M2DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database
BMC Bioinformatics. 2010 Aug 10;11(1):421.

Clancy K, Voigt CA.
Programming cells: towards an automated 'Genetic Compiler'
Curr Opin Biotechnol. 2010 Aug 9. [Epub ahead of print]

Dudley JT, Pouliot Y, Chen R, Morgan AA, Butte AJ.
Translational bioinformatics in the cloud: an affordable alternative.
Genome Med. 2010 Aug 6;2(8):51.

Edgar RC.
Search and clustering orders of magnitude faster than BLAST.
Bioinformatics. 2010 Aug 12. [Epub ahead of print]

Gao J, Thelen JJ, Dunker AK, Xu D.
Musite: a tool for global prediction of general and kinase-specific phosphorylation sites.
Mol Cell Proteomics. 2010 Aug 11. [Epub ahead of print]

Goecks J, Nekrutenko A, Taylor J, Galaxy Team T.
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences.
Genome Biol. 2010 Aug 25;11(8):R86.

Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T.
BioRuby: Bioinformatics software for the Ruby programming language.
Bioinformatics. 2010 Aug 25. [Epub ahead of print]

Hardcastle TJ, Kelly KA.
baySeq: Empirical Bayesian Methods For Identifying Differential Expression In Sequence Count Data.
BMC Bioinformatics. 2010 Aug 10;11(1):422.

Henkel R, Endler L, Peters A, Le Novère N, Waltemath D.
Ranked retrieval of computational biology models
BMC Bioinformatics. 2010 Aug 11;11:423.

Hoehme S, Drasdo D.
A cell-based simulation software for multicellular systems.
Bioinformatics. 2010 Aug 13. [Epub ahead of print]

Kim TM, Luquette LJ, Xi R, Park PJ.
rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data.
BMC Bioinformatics. 2010 Aug 18;11(1):432.

Langmead B, Hansen KD, Leek JT.
Cloud-scale RNA-sequencing differential expression analysis with Myrna.
Genome Biol. 2010 Aug 11;11(8):R83.

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Medina-Aunon JA, Paradela A, Macht M, Thiele H, Corthals G, Albar JP.
Protein Information and Knowledge Extractor: Discovering biological information from proteomics data.
Proteomics. 2010 Sep;10(18):3262-71.

Miclaus K, Chierici M, Lambert C, Zhang L, Vega S, Hong H, Yin S, Furlanello C, Wolfinger R, Goodsaid F.
Variability in GWAS analysis: the impact of genotype calling algorithm inconsistencies.
Pharmacogenomics J. 2010 Aug;10(4):324-35.

Pahl R, Schäfer H.
PERMORY: an LD-exploiting permutation test algorithm for powerful genome-wide association testing.
Bioinformatics. 2010 Sep 1;26(17):2093-100.

Pedamallu CS, Posfai J.
Open source tool for prediction of genome wide protein-protein interaction network based on ortholog information.
Source Code Biol Med. 2010 Aug 4;5(1):8.

Pitt JN, Rajapakse I, Ferré-D'Amaré AR.
SEWAL: an open-source platform for next-generation sequence analysis and visualization.
Nucleic Acids Res. 2010 Aug 6. [Epub ahead of print]

Rizk G, Lavenier D.
GASSST: Global Alignment Short Sequence Search Tool.
Bioinformatics. 2010 Aug 24. [Epub ahead of print]

Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA.
ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.
Bioinformatics. 2010 Sep 15;26(18):2354-2356

Schneider J, Vorhölter FJ, Trost E, Blom J, Musa YR, Neuweger H, Niehaus K, Schatschneider S, Tauch A, Goesmann A.
CARMEN — Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks.
Genet Mol Res. 2010 Aug 24;9(3):1660-72.

Surget-Groba Y, Montoya-Burgos JI.
Optimization of de novo transcriptome assembly from next-generation sequencing data.
Genome Res. 2010 Aug 30. [Epub ahead of print]

Tudor CO, Schmidt CJ, Vijay-Shanker K.
eGIFT: Mining Gene Information from the Literature.
BMC Bioinformatics. 2010 Aug 9;11(1):418.

Zadeh JN, Wolfe BR, Pierce NA.
Nucleic acid sequence design via efficient ensemble defect optimization.
J Comput Chem. 2010 Aug 17. [Epub ahead of print]

Zhmurov A, Dima RI, Kholodov Y, Barsegov V.
Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors.
Proteins. 2010 Jul 23. [Epub ahead of print]

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.