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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.

The Scan

Mosquitos Genetically Modified to Prevent Malaria Spread

A gene drive approach could be used to render mosquitos unable to spread malaria, researchers report in Science Advances.

Gut Microbiomes Allow Bears to Grow to Similar Sizes Despite Differing Diets

Researchers in Scientific Reports find that the makeup of brown bears' gut microbiomes allows them to reach similar sizes even when feasting on different foods.

Finding Safe Harbor in the Human Genome

In Genome Biology, researchers present a new approach to identify genomic safe harbors where transgenes can be expressed without affecting host cell function.

New Data Point to Nuanced Relationship Between Major Depression, Bipolar Disorder

Lund University researchers in JAMA Psychiatry uncover overlapping genetic liabilities for major depression and bipolar disorder.