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In Print: Jun 3, 2011

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Bioinformatics Tool-Related Papers of Note, May 2011

Alon A, Wlodawer A, Fass D,
Improved molecular replacement by density- and energy-guided protein structure optimization.
Nature. 2011 May 26;473(7348):540-3.


Anderson CL, Strope CL, Moriyama EN.
SuiteMSA: Visual Tools for Multiple Sequence Alignment Comparison and Molecular Sequence Simulation.
BMC Bioinformatics. 2011 May 21;12(1):184.


Bouhassira E, Lajugie J.
GenPlay, a multi-purpose genome analyzer and browser.
Bioinformatics. 2011 May 19. [Epub ahead of print]


Butte AJ, Chiang AP, Pouliot Y.
Predicting Adverse Drug Reactions Using Publicly Available PubChem BioAssay Data.
Clin Pharmacol Ther. 2011 May 25. [Epub ahead of print]


Capriotti E, Fernald GH, Karczewski KJ, Daneshjou R, Altman RB.
Bioinformatics Challenges for Personalized Medicine.
Bioinformatics. 2011 May 19. [Epub ahead of print]


Chee B, Schatz B, Zhai C,
BeeSpace Navigator: exploratory analysis of gene function using semantic indexing of biological literature.
Nucleic Acids Res. 2011 May 9. [Epub ahead of print]


Chute CG, Masys DR, Pathak J, Wang J, Basford M, Li R, Kashyap S.
Mapping clinical phenotype data elements to standardized metadata repositories and controlled terminologies: the eMERGE Network experience.
J Am Med Inform Assoc. 2011 May 19. [Epub ahead of print]


Foster JM, Griss J, Gatto L,
A posteriori quality control for the curation and reuse of public proteomics data.
Proteomics. 2011 Jun;11(11):2182-94.


Gnirke A, Regev A, Haas BJ,
Full-length transcriptome assembly from RNA-Seq data without a reference genome.
Nat Biotechnol. 2011 May 15. [Epub ahead of print]


Gogol-Doering A, Rybak A, Alvarado AS,
De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics.
Genome Res. 2011 May 2. [Epub ahead of print]


Greenberg DA, Drill EN, Stewart WC.
Predicting Adverse Drug Reactions Using Publicly Available PubChem BioAssay Data.
Eur J Hum Genet. 2011 May 25. [Epub ahead of print]


Guan JH, Deng L, Dong QW, Zhou SG.
SemiHS: An Iterative Semi-supervised Approach for Predicting Protein-protein Interaction Hot Spots.
Protein Pept Lett. 2011 May 2. [Epub ahead of print]


Holt RA, Warren RL.
Targeted assembly of short sequence reads.
PLoS One. 2011 May 11;6(5):e19816.


Kostic AD, Ojesina AI, Pedamallu CS, Getz G, Jung J, Meyerson M, Verhaak RG.
PathSeq: software to identify or discover microbes by deep sequencing of human tissue.
Nat Biotechnol. 2011 May;29(5):393-6.


Lai F, Chen WH, Hwu WL, Chien YH, Lu YW.
Integrating Human Genome Database into Electronic Health Record with Sequence Alignment and Compression Mechanism.
J Med Syst. 2011 May 11. [Epub ahead of print]


Ma DC, Wu J, Li ML, Diao YB, Zhang YQ, Guo YZ, Li YZ.
A Novel Method to Predict Protein-Protein Interactions Based on the Information of Protein-Protein Interaction Networks and Protein Sequence.
Protein Pept Lett. 2011 May 2. [Epub ahead of print]


Merz KM, Zheng Z.
Ligand Identification Scoring Algorithm (LISA).
J Chem Inf Model. 2011 May 25. [Epub ahead of print]


Ozturk C, Otu HH, Jones J, Isci S.
Pathway Analysis of High Throughput Biological Data within a Bayesian Network Framework.
Bioinformatics. 2011 May 5. [Epub ahead of print]


Pesch E, Blazewicz J, Kierzynka M, Wojciechowski P, Frohmberg W.
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs.
BMC Bioinformatics. 2011 May 20;12(1):181.


Rogers AS, Williams GW, Spieth J, Davis PA, Ozersky P, Bieri T.
Methods and strategies for gene structure curation in WormBase.
Database (Oxford). 2011 May 3;2011:baq039.


Schaefer CF, Buetow KH, Greenblum SI, Efroni S.
The PathOlogist: an automated tool for pathway-centric analysis.
BMC Bioinformatics. 2011 May 4;12:133.


Spitzmüller A, Klebe G, Velec HF.
MiniMuDS: A New Optimizer using Knowledge-Based Potentials Improves Scoring of Docking Solutions.
J Chem Inf Model. 2011 May 11. [Epub ahead of print]


Stein L, Grossman R, Feng X.
PeakRanger: A cloud-enabled peak caller for ChIP-seq data.
BMC Bioinformatics. 2011 May 9;12(1):139.


Trapnell C, Garber M, Grabherr MG, Guttman M.
Computational methods for transcriptome annotation and quantification using RNA-seq.
Nat Methods. 2011 Jun;8(6):469-77.


Vandekerckhove J, Gevaert K, Martens L, Colaert N.
A case study on the comparison of different software tools for automated quantification of peptides.
Methods Mol Biol. 2011;753:373-98.


Yesupriya A, Wulf A, Hindorff LA, Khoury MJ, Gwinn M, Dowling N,Yu W.
GWAS Integrator: a bioinformatics tool to explore human genetic associations reported in published genome-wide association studies.
Eur J Hum Genet. 2011 May 25. [Epub ahead of print]


Yildiz F, Samayoa J, Karplus K.
Identification of Prokaryotic Small Proteins using a Comparative Genomic Approach.
Bioinformatics. 2011 May 5. [Epub ahead of print]


The Scan

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.

Study Points to Synonymous Mutation Effects on E. Coli Enzyme Activity

Researchers in Nature Chemistry saw signs of enzyme activity shifts in the presence of synonymous mutations in a multiscale modeling analysis of three Escherichia coli genes.

Team Outlines Paternal Sample-Free Single-Gene Approach for Non-Invasive Prenatal Screening

With data for nearly 9,200 pregnant individuals, researchers in Genetics in Medicine demonstrate the feasibility of their carrier screening and reflex single-gene non-invasive prenatal screening approach.

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.