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June's Bioinformatics Papers of Note

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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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The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.