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In Print: Aug 5, 2011


Bioinformatics Tool-Related Papers of Note, July 2011

Klipp E, Krause F, Schulz M, Le Novère N, Liebermeister W.
Retrieval, alignment, and clustering of computational models based on semantic annotations.
Mol Syst Biol. 2011 Jul 19;7:512..

Bujnicki JM, Jeleniewicz J, Milanowska K, Rother K, Puton T, Rother M.
ModeRNA server: an online tool for modeling RNA 3D structures.
Bioinformatics. 2011 Jul 4. [Epub ahead of print].

Reva B, Sander C, Antipin Y.
Predicting the functional impact of protein mutations: application to cancer genomics.
Nucleic Acids Res. 2011 Jul 3. [Epub ahead of print].

Montana G, Berk M, Ebbels T.
A statistical framework for biomarker discovery in metabolomic time course data.
Bioinformatics. 2011 Jul 15;27(14):1979-85.

Singla D, Dash D, Raghava GP, Anurag M.
A Web Server for Predicting Inhibitors against Bacterial Target GlmU Protein.
BMC Pharmacol. 2011 Jul 6;11(1):5.

Lopez D, Casero D, Pellegrini M, Cokus SJ, Merchant SS.
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.
BMC Bioinformatics. 2011 Jul 12;12:282.

Kadie C, Meek C, Heckerman D, Huang JC.
Conditional random fields for fast, large-scale genome-wide association studies.
PLoS One. 2011;6(7):e21591.

Fournier D, Andrade-Navarro MA.
PDBpaint, a visualization webservice to tag protein structures with sequence annotations.
Bioinformatics. 2011 Jul 14. [Epub ahead of print].

Al Olama AA, Antoniou AC, Ardern-Jones AT, et al;.
A risk prediction algorithm based on family history and common genetic variants: application to prostate cancer with potential clinical impact.
Genet Epidemiol. 2011 Jul 18. [Epub ahead of print]

Brittnacher MJ, Fong C, Hayden HS, Jacobs MA, Radey M, Rohmer L.
PGAT: A multi-strain analysis resource for microbial genomes.
Bioinformatics. 2011 Jul 15. [Epub ahead of print].

Balázs B, Benke Z, Győrffy B, Lánczky A, Schäfer R, Szállási Z, Timár J.
RecurrenceOnline: an online analysis tool to determine breast cancer recurrence and hormone receptor status using microarray data.
Breast Cancer Res Treat. 2011 Jul 16. [Epub ahead of print].

Brunk B, Farkas MH, Grant GR, et al.
Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM).
Bioinformatics. 2011 Jul 19. [Epub ahead of print].

Bennett MJ, Chanda SK, Craik CS, et al.
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data.
BMC Bioinformatics. 2011 Jul 22;12(1):298.

Dwivedi GR, Gupta S, Khan F, Mishra M, Parihar R, Sen N, Sharma A.
DbMDR: A Relational Database for Multidrug Resistance Genes as Potential Drug Targets.
Chem Biol Drug Des. 2011 Jul 22. [Epub ahead of print].

Cooper GF, Gopalakrishnan V, Lustgarten JL, Visweswaran S.
Application of an efficient Bayesian discretization method to biomedical data.
Bioinformatics. 2011 Jul 27 [Epub ahead of print].

Chen T, Chen Y, Clark A, et al.
RseqFlow: Workflows for RNA-Seq data analysis.
BMC Res Notes. 2011 Jul 28;4(1):261.

Al-Ars Z, Hasan L, Kentie M.
DOPA: GPU-based Protein Alignment Using Database and Memory Access Optimizations.
BMC Res Notes. 2011 Jul 28;4(1):261.

Friedman BA, Maniatis T.
ExpressionPlot: A web-based framework for analysis of RNA-Seq and microarray gene expression data.
Genome Biol. 2011 Jul 28;12(7):R69.

Agrawal NJ, Helk B, Kumar S, Singh SK, Trout BL, Wang X.
Aggregation in protein-based biotherapeutics: Computational studies and tools to identify aggregation-prone regions.
Genome Biol. 2011 Jul 28;12(7):R69.

Boffelli D, Dubchak I, Lukashin I, et al.
VISTA Region Viewer (RViewer) — a computational system for prioritizing genomic intervals for biomedical studies.
Bioinformatics. 2011 Jul 26. [Epub ahead of print]

Ames J, Clark AP, Dinov ID, et al.Applications of the Pipeline Environment for Visual Informatics and Genomics Computations.
BMC Bioinformatics. 2011 Jul 26;12(1):304.

The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.