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In Print: Jan 21, 2011

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Bioinformatics Tool-Related Papers of Note, December 2010

Mishra RK, Singh V
RISCI - Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes.
BMC Bioinformatics. 2010 Dec 26;11(1):609.


Gupta A, Ponomarenko J, Baitaluk M, Sedova M, Kozhenkov S, Dubinina Y.
BiologicalNetworks 2.0 - an integrative view of genome biology data.
BMC Bioinformatics. 2010 Dec 29;11(1):610.


Benson AK, Russell DJ, Sayood K, Way SF.
A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences.
BMC Bioinformatics. 2010 Dec 17;11(1):601.


Franke A, Melum E, Holm K, Karlsen TH.
SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels.
BMC Bioinformatics. 2010 Dec 17;11(1):600.


Allison L, Cao MD, Dix TI.
A genome alignment algorithm based on compression.
BMC Bioinformatics. 2010 Dec 16;11(1):599.


Apostolos J, Bonneville R, Jin VX, Wu W, Lan X.
W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data.
Bioinformatics. 2010 Dec 7. [Epub ahead of print]


Adadey A, Kertesz-Farkas A, Doughty E, Thompson G, Kann MG, Bodenreider O, Peterson T.
Toward an automatic method for extracting cancer- and other disease-related point mutations from the biomedical literature.
Bioinformatics. 2010 Dec 7. [Epub ahead of print]


Napoli A, Devignes MD, Smail-Tabbone M, Poch O, Benabderrahmane S.
IntelliGO: a new vector-based semantic similarity measure including annotation origin.
BMC Bioinformatics. 2010 Dec 1;11(1):588.


Yoon K, Robbins KA, Doderer MS.
SIDEKICK: Genomic data driven analysis and decision-making framework.
BMC Bioinformatics. 2010 Dec 30;11(1):611.


Kuchinsky A, States DJ, Meng F, Su G, Morris JH.
GLay: community structure analysis of biological networks.
Bioinformatics. 2010 Dec 15;26(24):3135-7.


Gorodkin J, Menzel P, Stadler PF.
maxAlike: Maximum-likelihood based sequence reconstruction with application to improved primer design for unknown sequences.
Bioinformatics. 2010 Dec 1. [Epub ahead of print]


Wiuf C, Andersen CL, Lamy P, Orntoft TF.
Rseg - an R package to optimize segmentation of SNP array data.
Bioinformatics. 2010 Dec 5. [Epub ahead of print]


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Ruscheinski J, Ono K, Smoot ME, Wang PL, Ideker T.
Cytoscape 2.8: New Features for Data Integration and Network Visualization.
Bioinformatics. 2010 Dec 12. [Epub ahead of print]


Salzberg SL , Angiuoli SV.
Mugsy: Fast multiple alignment of closely related whole genomes.
Bioinformatics. 2010 Dec 9. [Epub ahead of print]


Shimizu K, Tsuda K.
SlideSort: All Pairs Similarity Search for Short Reads.
Bioinformatics. 2010 Dec 9. [Epub ahead of print]


Jolley KA, Maiden MC.
BIGSdb: Scalable analysis of bacterial genome variation at the population level.
BMC Bioinformatics. 2010 Dec 10;11:595.


Schliep KP.
phangorn: Phylogenetic analysis in R.
Bioinformatics. 2010 Dec 17. [Epub ahead of print]


Ni B, Leung KS, Lo LY, Lou S, Kwok-Wing Tsui S, Chan TF.
ABMapper: a suffix array-based tool for multi-location searching and splice-junction mapping.
Bioinformatics. 2010 Dec 17. [Epub ahead of print]


Brazma A, Prokopenko I, Dietrich J, Fernandez-Banet J, Rung J, Gostev M, Krestyaninova M, McCarthy MI, Ripatti S.
SAIL - a software system for sample and phenotype availability across biobanks and cohorts.
Bioinformatics. 2010 Dec 17. [Epub ahead of print]


He A, Schmidt B, Maskell DL, Lee K, Kuttippurathu L, Hsing M, Kong SW, Pu WT, Liu Y.
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.
Bioinformatics. 2010 Dec 23. [Epub ahead of print]


Nobel AB, Wright FA, Walter V.
DiNAMIC: A Method To Identify Recurrent DNA Copy Number Aberrations in Tumors.
Bioinformatics. 2010 Dec 23. [Epub ahead of print]


Gnirke A, Berlin AM, Walker BJ, Nusbaum C, Aird D, Jaffe DB, Przybylski D, Lander ES, Ribeiro FJ, Hall G, Maccallum I, Burton JN, Williams L, Costello M, Daza R, Nicol R, Gnerre S, Sykes S, Sharpe T, Shea TP.
High-quality draft assemblies of mammalian genomes from massively parallel sequence data.
Proc Natl Acad Sci U S A. 2010 Dec 27. [Epub ahead of print]


Hoffman EP, Yu G, Li H, Shih IM, Xuan J, Clarke R, Ha S, Madhavan S, Wang Y.
PUGSVM: A caBIGTM analytical tool for multiclass gene selection and predictive classification.
Bioinformatics. 2010 Dec 24. [Epub ahead of print]


The Scan

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.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.