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In Print: Jun 3, 2011


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

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According to the New York Times, Pfizer and BioNTech are seeking full US Food and Drug Administration approval for their SARS-CoV-2 vaccine.

Viral Integration Study Critiqued

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Giraffe Species Debate

The Scientist reports that a new analysis aiming to end the discussion of how many giraffe species there are has only continued it.

Science Papers Examine Factors Shaping SARS-CoV-2 Spread, Give Insight Into Bacterial Evolution

In Science this week: genomic analysis points to role of human behavior in SARS-CoV-2 spread, and more.