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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

Could Mix It Up

The US Food and Drug Administration is considering a plan that would allow for the mixing-and-matching of SARS-CoV-2 vaccines and boosters, the New York Times says.

Closest to the Dog

New Scientist reports that extinct Japanese wolf appears to be the closest known wild relative of dogs.

Offer to Come Back

The Knoxville News Sentinel reports that the University of Tennessee is offering Anming Hu, a professor who was acquitted of charges that he hid ties to China, his position back.

PNAS Papers on Myeloid Differentiation MicroRNAs, Urinary Exosomes, Maize Domestication

In PNAS this week: role of microRNAs in myeloid differentiation, exosomes in urine, and more.