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In Print: Sep 30, 2011

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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].


The Scan

Study Reveals New Details About Genetics of Major Cause of Female Infertility

Researchers in Nature Medicine conducted a whole-exome sequencing study of mote than a thousand patients with premature ovarian insufficiency.

Circulating Tumor DNA Shows Potential as Biomarker in Rare Childhood Cancer

A study in the Journal of Clinical Oncology has found that circulating tumor DNA levels in rhabdomyosarcoma may serve as a biomarker for prognosis.

Study Recommends Cancer Screening for Dogs Beginning Age Seven, Depending on Breed

PetDx researchers report in PLOS One that annual cancer screening for dogs should begin by age seven.

White-Tailed Deer Harbor SARS-CoV-2 Variants No Longer Infecting Humans, Study Finds

A new study in PNAS has found that white-tailed deer could act as a reservoir of SARS-CoV-2 variants no longer found among humans.