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June's Bioinformatics Papers of Note


Ausiello G, Bianchi V, et al.
webPDBinder: a server for the identification of ligand binding sites on protein structures.
Nucleic Acids Res. 2013 June 3. [Epub ahead of print]

Droit A, Gevry N, et al.
NGS++: a library for rapid prototyping of epigenomics software tools.
Bioinformatics. 2013 June 4. [Epub ahead of print]

Chorny I, Chuang HY, et al.
Isaac: Ultra-fast whole genome secondary analysis on Illumina sequencing platforms.
Bioinformatics. 2013 June 4. [Epub ahead of print]

Felipe JC, Miyoshi NS, et al.
Computational framework to support integration of biomolecular and clinical data within a translational approach.
BMC Bioinformatics. 2013 June 6. [Epub ahead of print]

Brouwer C, Luo W.
Pathview: an R/Bioconductor package for pathway based data integration and visualization.
Bioinformatics. 2013 June 4. [Epub ahead of print]

Beltrame L, Bianco L, et al.
Pathway Processor 2.0: a Web resource for pathway-based analysis of high throughput data.
Bioinformatics. 2013 June 5. [Epub ahead of print]

Good BM, Su AI
Crowdsourcing for Bioinformatics.
Bioinformatics. 2013 June 19. [Epub ahead of print]

Hackl H, Snajder R, Trajanoski Z.
GPViz: dynamic visualization of genomic regions and variants affecting protein domains.
Bioinformatics. 2013 June 19. [Epub ahead of print]

Chen ZZ, Deng F, Wang L.
Exact algorithms for haplotype assembly from whole-genome sequence data.
Bioinformatics. 2013 June 18. [Epub ahead of print]

Goodson M, Heger A, et al.
GAT: a simulation framework for testing the association of genomic intervals.
Bioinformatics. 2013 June 18. [Epub ahead of print]

Chung RH, Shih CC.
SeqSIMLA: a sequence and phenotype simulation tool for complex disease studies.
BMC Bioinformatics. 2013 June 20. [Epub ahead of print]

Humphreys DT, Suter CM.
miRspring: a compact standalone research tool for analyzing miRNA-seq data.
Nucleic Acids Res. 2013 June 17. [Epub ahead of print]

Brass A, Duck G, et al.
bioNerDS: exploring bioinformatics' database and software use through literature mining.
BMC Bioinformatics. 2013 Jun 15;14(1):194. [Epub ahead of print]

Chang CJ, Liu C, et al.
FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.
BMC Bioinformatics. 2013 Jun 15;14(1):193. [Epub ahead of print]

Gao Q, Mitsopoulos C, et al.
ROCK: a resource for integrative breast cancer data analysis.
Breast Cancer Res Treat. 2013 Jun 12. [Epub ahead of print]

Aksoy BA, Cerami E, et al.
PiHelper: An Open Source Framework for Drug-Target and Antibody-Target Data.
Bioinformatics. 2013 Jun 12. [Epub ahead of print]

Baroukh C, Chen EY, et al.
ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells.
Database (Oxford). 2013 Jun 21.

Hanson NW, Hallam SJ, et al.
MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information.
BMC Bioinformatics. 2013 Jun 21;14(1):202. [Epub ahead of print]

D'Amato M, Greco D, et al.
Drug Repositioning: A Machine-Learning Approach through Data Integration.
J Cheminform. 2013 Jun 22;5(1):30. [Epub ahead of print]

Eren AM, Morrison HG, et al.
A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology.
PLoS One. 2013 Jun 17;8(6):e66643. Print 2013.

Adams DJ, Rashid M, et al.
Cake: a bioinformatics pipeline for the integrated analysis of somatic variants in cancer genomes.
Bioinformatics. 2013 Jun 25. [Epub ahead of print]

Fan H, Jaeger E, et al.
Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing.
BMC Genomics. 2013 Jun 27;14(1):425. [Epub ahead of print]

Abreu-Goodger C, Bartonicek N, et al.
Kraken: A set of tools for quality control and analysis of high-throughput sequence data.
Methods. 2013 Jun 28. [Epub ahead of print]

Eller LA, Harbolick EA, et al.
Nautilus: a Bioinformatics Package for the Analysis of HIV-1 Targeted Deep Sequencing Data.
AIDS Res Hum Retroviruses. 2013 Jun 28. [Epub ahead of print]

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