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In Print: Last Week's Sequencing-Related Papers of Note: Jul 17, 2012


BROMOC-D: Brownian dynamics/Monte-Carlo program suite to study ion and DNA permeation in nanopores.
De Biase PM, Solano CJ, Markosyan S, Czapla L, Noskov SY.
J Chem Theory Comput. 2012 Jul 10;8(7):2540-2551.

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.
Lam ET, Hastie A, Lin C, Ehrlich D, et al.
Nat Biotechnol. 2012 Jul 15. [Epub ahead of print]
(See our coverage of this paper here.)

A regression model for estimating DNA copy number data applied to capture sequencing data.
Rigaill GJ, Cadot S, Kluin RJ, Xue Z, et al.
Bioinformatics. 2012 Jul 13. [Epub ahead of print]

The cervical microbiome over 7 years and a comparison of methodologies for its characterization.
Smith BC, McAndrew T, Chen Z, Harari A, et al.
PLoS One. 2012;7(7):e40425.

IMG/M-HMP: a metagenome comparative analysis system for the human microbiome project.
Markowitz VM, Chen IM, Chu K, Szeto E, et al.
PLoS One. 2012;7(7):e40151.

Targeted recovery of novel phylogenetic diversity from next-generation sequence data.
Lynch MD, Bartram AK, Neufeld JD.
ISME J. 2012 Jul 12. [Epub ahead of print]

CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.
Li P, Ji G, Dong M, Schmidt E, et al.
Bioinformatics. 2012 Jul 12. [Epub ahead of print]

Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants.
Sellitto M, Bai G, Serena G, Fricke WF, et al.
PLoS One. 2012;7(3):e33387.

Single-molecule electrical random resequencing of DNA and RNA.
Ohshiro T, Matsubara K, Tsutsui M, Furuhashi M, et al.
Sci Rep. 2012;2:501.

Fast and automatic processing of multi-level events in nanopore translocation experiments.
Raillon C, Granjon P, Graf M, Steinbock LJ, Radenovic A.
Nanoscale. 2012 Jul 11. [Epub ahead of print]

NDesign: software for study design for the detection of rare variants from next-generation sequencing data.
Sugaya Y, Akazawa Y, Saito A, Kamitsuji S.
J Hum Genet. 2012 Jul 12. [Epub ahead of print]

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells.
Peters BA, Kermani BG, Sparks AB, Alferov O, et al.
Nature. 2012 Jul 11;487(7406):190-5.
(See our coverage of this paper here.)

Bis-SNP: combined DNA methylation and SNP calling for bisulfite-seq data.
Liu Y, Siegmund KD, Laird PW, Berman BP.
Genome Biol. 2012 Jul 11;13(7):R61.

Efficient error correction for next-generation sequencing of viral amplicons.
Skums P, Dimitrova Z, Campo DS, Vaughan G, et al.
BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S6.

Improving genome assemblies by sequencing PCR products with PacBio.
Zhang X, Davenport KW, Gu W, Daligault HE, et al.
Biotechniques. 2012 Jul;53(1):61-2.

Assessing graphene nanopores for sequencing DNA.
Wells DB, Belkin M, Comer J, Aksimentiev A.
Nano Lett. 2012 Jul 10. [Epub ahead of print]

From sequencer to supercomputer: an automatic pipeline for managing and processing next generation sequencing data.
Camerlengo T, Ozer HG, Onti-Srinivasan R, Yan P, et al.
AMIA Summits Transl Sci Proc. 2012;2012:1-10.

Small RNA expression profiling by high-throughput sequencing: implications of enzymatic manipulation.
Zhuang F, Fuchs RT, Robb GB.
J Nucleic Acids. 2012;2012:360358.

Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling.
Chang CT, Tsai CN, Tang CY, Chen CH, et al.
ScientificWorldJournal. 2012;2012:365104.

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.