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In Print: Last Week's Sequencing-Related Papers of Note: Oct 2, 2012


SNVerGUI: a desktop tool for variant analysis of next-generation sequencing data.
Wang W, Hu W, Hou F, Hu P, Wei Z.
J Med Genet. 2012 Sep 28. [Epub ahead of print]

A single-cell genome for Thiovulum sp.
Marshall IP, Blainey PC, Spormann AM, Quake SR.
Appl Environ Microbiol. 2012 Sep 28. [Epub ahead of print]

DNA pooling and statistical tests for the detection of single nucleotide polymorphisms.
Ramsey DM, Futschik A.
Stat Appl Genet Mol Biol. 2012 Sep 25;11(5).

A metagenome-wide association study of gut microbiota in type 2 diabetes.
Qin J, Li Y, Cai Z, Li S, et al.
Nature. 2012 Sep 26. [Epub ahead of print]

Cell type-specific termination of transcription by transposable element sequences.
Conley AB, Jordan IK.
Mob DNA. 2012 Sep 30;3(1):15.

A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens).
Hildebrand F, Ebersbach T, Nielsen HB, Li X, et al.
BMC Genomics. 2012 Sep 28;13(1):514.

A duck RH panel and its potential for assisting NGS genome assembly.
Rao M, Morisson M, Faraut T, Bardes S, et al.
BMC Genomics. 2012 Sep 28;13(1):513.

Fragmentation of DNA in a sub-microliter microfluidic sonication device.
Tseng Q, Lomonosov AM, Furlong EE, Merten CA.
Lab Chip. 2012 Sep 26. [Epub ahead of print]

SpolPred: Rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences.
Coll F, Mallard K, Preston MD, Bentley S, et al.
Bioinformatics. 2012 Sep 26. [Epub ahead of print]

Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease.
Sifrim A, Van Houdt JK, Tranchevent LC, Nowakowska B, et al.
Genome Med. 2012 Sep 26;4(9):73.

Guiding the design of synthetic DNA-binding molecules with massively parallel sequencing.
Meier JL, Yu A, Korf I, Segal DJ, Dervan PB.
J Am Chem Soc. 2012 Sep 26. [Epub ahead of print]

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes.
Gorkin DU, Lee D, Reed X, Fletez-Brant C, et al.
Genome Res. 2012 Sep 27. [Epub ahead of print]

The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine.
Pastor WA, Huang Y, Henderson HR, Agarwal S, Rao A.
Nat Protoc. 2012 Oct;7(10):1909-17.

Deep sequencing of systematic combinatorial libraries reveals β-lactamase sequence constraints at high resolution.
Deng Z, Huang W, Bakkalbasi E, Brown NG, et al.
J Mol Biol. 2012 Sep 24. pii: S0022-2836(12)00771-1.

Combining laser microdissection and RNA-seq to chart the transcriptional landscape of fungal development.
Teichert I, Wolff G, Kück U, Nowrousian M.
BMC Genomics. 2012 Sep 27;13(1):511.

Performance of VIDISCA-454 in feces-suspensions and serum.
de Vries M, Oude Munnink BB, Deijs M, Canuti M, et al.
Viruses. 2012 Aug;4(8):1328-34.

Complete genome sequence of Amycolatopsis mediterranei S699 based on de novo assembly via a combinatorial sequencing strategy.
Tang B, Zhao W, Zheng H, Zhuo Y, et al.
J Bacteriol. 2012 Oct;194(20):5699-700.

Gigabase-scale transcriptome analysis on four species of pearl oysters.
Huang XD, Zhao M, Liu WG, Guan YY, et al.
Mar Biotechnol (NY) . 2012 Sep 26. [Epub ahead of print]

Single-stranded DNA within nanopores: conformational dynamics and implications for sequencing; a molecular dynamics simulation study.
Guy AT, Piggot TJ, Khalid S.
Biophys J. 2012 Sep 5;103(5):1028-36.

ESTclean: a cleaning tool for next-gen transcriptome shotgun sequencing.
Tae H, Ryu D, Sureshchandra S, Choi JH.
BMC Bioinformatics. 2012 Sep 26;13(1):247.

Separating metagenomic short reads into genomes via clustering.
Tanaseichuk O, Borneman J, Jiang T.
Algorithms Mol Biol. 2012 Sep 26;7(1):27.

Viral metagenomics demonstrates that domestic pigs are a potential reservoir for Ndumu virus.
Masembe C, Michuki G, Onyango M, Rumberia C, et al.
Virol J. 2012 Sep 24;9(1):218.

Effective driving force applied on DNA inside a solid-state nanopore.
Lu B, Hoogerheide DP, Zhao Q, Yu D.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Jul;86(1-1):011921.

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.