Bioinformatics Tool-Related Papers of Note, June 2011
An J, Jones SJ, Li YY.
A computational approach to finding novel targets for existing drugs.
PLoS Comput Biol. 2011 Sep;7(9):e1002139. Epub 2011 Sep 1.
Lippert C, Kadie CM, Heckerman D, Listgarten J, Davidson RI, Liu Y.
FaST linear mixed models for genome-wide association studies.
Nat Methods. 2011 Sep 4. [Epub ahead of print].
Lomize AL, Joo H, Mosberg HI, Pogozheva ID, Lomize MA.
OPM database and PPM web server: resources for positioning of proteins in membranes.
Nucleic Acids Res. 2011 Sep 2. [Epub ahead of print].
Kuhn DN, Rigoutsos I, Parida L, Haiminen N.
Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results.
PLoS One. 2011;6(9):e24182. Epub 2011 Sep 7.
Kamburov A, Keun HC, Cavill R, Herwig R, Ebbels TM.
Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA.
Bioinformatics. 2011 Sep 4. [Epub ahead of print].
Marchiori E, Nabuurs SB, van Laarhoven T.
Gaussian interaction profile kernels for predicting drug-target interaction.
Bioinformatics. 2011 Sep 4. [Epub ahead of print].
Martin JA, Wang Z.
Next-generation transcriptome assembly.
Nat Rev Genet. 2011 Sep 7;12(10):671-82.
Warren A, Wattam AR, Wang C, et al.
PATRIC: The Comprehensive Bacterial Bioinformatics Resource with a Focus on Human Pathogenic Species.
Infect Immun. 2011 Sep 6. [Epub ahead of print].
Lim HC, Mittler J, Curlin M.
HIV Therapy Simulator: a graphical user interface for comparing the effectiveness of novel therapy regimens.
Bioinformatics. 2011 Sep 12. [Epub ahead of print].
Salzberg SL, Magoc T.
FLASH: Fast Length Adjustment of Short Reads to Improve Genome Assemblies.
Bioinformatics. 2011 Sep 7. [Epub ahead of print].
Li H.
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.
Bioinformatics. 2011 Sep 8. [Epub ahead of print].
Friedman AJ, McCammon JA, Durrant JD.
CrystalDock: A Novel Approach to Fragment-Based Drug Design.
J Chem Inf Model. 2011 Sep 13. [Epub ahead of print].
Pop M, Koren S, Treangen TJ.
Bambus 2: Scaffolding Metagenomes.
Bioinformatics. 2011 Sep 16. [Epub ahead of print].
Smith AT, Thomas CE, Searfoss GH, et al.
Predictive Power Estimation Algorithm (PPEA) — A New Algorithm to Reduce Overfitting for Genomic Biomarker Discovery.
PLoS One. 2011;6(9):e24233. Epub 2011 Sep 15.
Bogdanov B, Wang B, McClain C, et al.
MetSign: A Computational Platform for High-Resolution Mass Spectrometry-Based Metabolomics.
Anal Chem. 2011 Sep 20. [Epub ahead of print].
Feng J, Jiang T, Li W.
IsoLasso: A LASSO Regression Approach to RNA-Seq Based Transcriptome Assembly.
J Comput Biol. 2011 Sep 27. [Epub ahead of print].