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Papers of Note: Jul 26, 2011


Structural variation in two human genomes mapped at single-nucleotide resolution by whole genome de novo assembly.
Li Y, Zheng H, Luo R, Wu H, et al.
Nat Biotechnol. 2011 Jul 24. [Epub ahead of print]

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing.
Lee EJ, Pei L, Srivastava G, Joshi T, et al.
Nucleic Acids Res. 2011 Jul 23. [Epub ahead of print]

FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism.
Darnell JC, Van Driesche SJ, Zhang C, Hung KY, et al.
Cell. 2011 Jul 22;146(2):247-61.

Force-driven polymer translocation through a nanopore: an old problem revisited.
Rowghanian P, Grosberg AY.
J Phys Chem B. 2011 Jul 22. [Epub ahead of print]

High resolution detection and analysis of CpG dinucleotides methylation using MBD-seq technology.
Lan X, Adams C, Landers M, Dudas M, et al.
PLoS One. 2011;6(7):e22226.

Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-seq data.
Chung D, Kuan PF, Li B, Sanalkumar R, et al.
PLoS Comput Biol. 2011 Jul;7(7):e1002111.

Multiple sequence assembly from reads alignable to a common reference genome.
Peng Q, Smith AD.
IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1283-95.

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A novel method to perform genomic walks using a combination of single strand DNA circularization and rolling circle amplification.
Gadkar VJ, Filion M.
J Microbiol Methods. 2011 Jul 14. [Epub ahead of print]

An integrated semiconductor device enabling non-optical genome sequencing.
Rothberg JM, Hinz W, Rearick TM, Schultz J, et al.
Nature. 2011 Jul 20;475(7356):348-52.
(see article, this issue)

Analyses of X-linked and autosomal genetic variation in population-scale whole genome sequencing.
Gottipati S, Arbiza L, Siepel A, Clark AG, Keinan A.
Nat Genet. 2011 Jul 24. [Epub ahead of print]

RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries.
Hafner M, Renwick N, Brown M, Mihailovic A, et al.
RNA. 2011 Jul 20. [Epub ahead of print]

coMOTIF: A mixture framework for identifying transcription factor and a co-regulator motif in ChIP-seq data.
Xu M, Weinberg CR, Umbach DM, Li L.
Bioinformatics. 2011 Jul 19. [Epub ahead of print]

miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants.
Yang X, Li L.
Bioinformatics. 2011 Jul 19. [Epub ahead of print]

Comparative analysis of RNA-seq alignment algorithms and the RNA-seq Unified Mapper (RUM).
Grant GR, Farkas MH, Pizarro A, Lahens N, et al.
Bioinformatics. 2011 Jul 19. [Epub ahead of print]

De novo assembly of expressed transcripts and global analysis of Phalaenopsis aphrodite transcriptome.
Su CL, Chao YT, Alex Chang YC, Chen WC, et al.
Plant Cell Physiol. 2011 Jul 19. [Epub ahead of print]

Accurate and comprehensive sequencing of personal genomes.
Ajay SS, Parker SC, Ozel Abaan H, Fuentes Fajardo KV, Margulies EH.
Genome Res. 2011 Jul 19. [Epub ahead of print]

FAAST: Flow-space Assisted Alignment Search Tool.
Lysholm F, Andersson B Dr, Persson B Dr.
BMC Bioinformatics. 2011 Jul 19;12(1):293.

Bias detection and correction in RNA-sequencing data.
Zheng W, Chung LM, Zhao H.
BMC Bioinformatics. 2011 Jul 19;12(1):290.