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Sequencing Papers of Note


Rapid and precise scanning helium ion microscope milling of solid-state nanopores for biomolecule detection.
Yang J, Ferranti DC, Stern LA, et al.
Nanotechnology. 2011 Jul 15;22(28):285310.

Complete genome sequence of Treponema paraluiscuniculi, Strain Cuniculi A: The loss of infectivity to humans is associated with genome decay.
Smajs D, Zobaníková M, Strouhal M, et al.
PLoS One. 2011;6(5):e20415.

A dominant mutation in RPE65 identified by whole-exome sequencing causes retinitis pigmentosa with choroidal involvement.
Bowne SJ, Humphries MM, Sullivan LS, et al.
Eur J Hum Genet. 2011 Jun 8. [Epub ahead of print]

A probabilistic method for the detection and genotyping of small indels from population-scale sequence data.
Bansal V, Libiger O.
Bioinformatics. 2011 Jun 7. [Epub ahead of print]

De novo discovery of mutated driver pathways in cancer.
Vandin F, Upfal E, Raphael BJ.
Genome Res. 2011 Jun 7. [Epub ahead of print]

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity.
Young MD, Willson TA, Wakefield MJ, et al.
Nucleic Acids Res. 2011 Jun 7. [Epub ahead of print]

Effects of short read quality and quantity on a de novo vertebrate transcriptome assembly.
Garcia TI, Shen Y, Catchen J, et al.
Comp Biochem Physiol C Toxicol Pharmacol. 2011 Jun 1. [Epub ahead of print]

Btrim: A fast, lightweight adapter and quality trimming program for next-generation sequencing technologies.
Kong Y.
Genomics. 2011 May 30. [Epub ahead of print]

Ensuring the safety of vaccine cell substrates by massively parallel sequencing of the transcriptome.
Onions D, Côté C, Love B, et al.
Vaccine. 2011 Jun 4. [Epub ahead of print]

De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants.
Ness RW, Siol M, Barrett SC.
BMC Genomics. 2011 Jun 7;12(1):298. [Epub ahead of print]

Reference-guided assembly of four diverse Arabidopsis thaliana genomes.
Schneeberger K, Ossowski S, Ott F, et al.
Proc Natl Acad Sci U S A. 2011 Jun 6. [Epub ahead of print]

Systematic bias in high-throughput sequencing data and its correction by BEADS.
Cheung MS, Down TA, Latorre I, Ahringer J.
Nucleic Acids Res. 2011 Jun 6. [Epub ahead of print]

PileLineGUI: a desktop environment for handling genome position files in next-generation sequencing studies.
López-Fernández H, Glez-Peña D, Reboiro-Jato M, et al.
Nucleic Acids Res. 2011 Jun 6. [Epub ahead of print]

CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping.
Nguyen T, Shi W, Ruden D.
BMC Res Notes. 2011 Jun 6;4(1):171. [Epub ahead of print]

RNA-seq : technical variability and sampling.
McInt yre LM, Lopiano KK, Morse AM, et al.
BMC Genomics. 2011 Jun 6;12(1):293.

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.