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In Print: Last Week's Sequencing-Related Papers of Note: Oct 9, 2012


DNA template strand sequencing of single-cells maps genomic rearrangements at high resolution.
Falconer E, Hills M, Naumann U, Poon SS, et al.
Nat Methods. 2012 Oct 7. [Epub ahead of print]

Sequence verification of synthetic DNA by assembly of sequencing reads.
Wilson ML, Cai Y, Hanlon R, Taylor S, et al.
Nucleic Acids Res. 2012 Oct 4. [Epub ahead of print]

Population genetic inference from personal genome data: impact of ancestry and admixture on human genomic variation.
Kidd JM, Gravel S, Byrnes J, Moreno-Estrada A, et al.
Am J Hum Genet. 2012 Oct 5;91(4):660-71.

Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth.
Fromer M, Moran JL, Chambert K, Banks E, et al.
Am J Hum Genet. 2012 Oct 5;91(4):597-607.

Oxygen minimum zones harbour novel viral communities with low diversity.
Cassman N, Prieto-Davó A, Walsh K, Silva GG, et al.
Environ Microbiol. 2012 Sep 11. [Epub ahead of print]

Estimation of metagenome size and structure in an experimental soil microbiota from low coverage next generation sequence data.
Frisli T, Haverkamp TH, Jakobsen KS, Stenseth NC, Rudi K.
J Appl Microbiol. 2012 Oct 8. [Epub ahead of print]

A calibrated human Y-chromosomal phylogeny based on resequencing.
Wei W, Ayub Q, Chen Y, McCarthy S, et al.
Genome Res. 2012 Oct 4. [Epub ahead of print]

1,8-Naphthyridine-2,7-diamine: a potential universal reader of Watson-Crick base pairs for DNA sequencing by electron tunneling.
Liang F, Lindsay S, Zhang P.
Org Biomol Chem. 2012 Oct 4. [Epub ahead of print]

Detecting and visualizing gene fusions.
Supper J, Gugenmus C, Wollnik J, Drueke T, Scherf M, Hahn A, Grote K, Bretschneider N, Klocke B, Zinser C, Cartharius K, Seifert M.
Methods. 2012 Oct 1. [Epub ahead of print]

Sequence capture and massively parallel sequencing to detect mutations associated with malignant hyperthermia.
Schiemann AH, Dürholt EM, Pollock N, Stowell KM.
Br J Anaesth. 2012 Oct 3. [Epub ahead of print]

The methylomes of six bacteria.
Murray IA, Clark TA, Morgan RD, Boitano M, et al.
Nucleic Acids Res. 2012 Oct 2. [Epub ahead of print]

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling.
Boyle P, Clement K, Gu H, Smith ZD, et al.
Genome Biol. 2012 Oct 3;13(10):R92.

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions.
Hansen KD, Langmead B, Irizarry RA.
Genome Biol. 2012 Oct 3;13(10):R83.

BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.
Lim JQ, Tennakoon C, Li G, Wong E, et al.
Genome Biol. 2012 Oct 3;13(10):R82.

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles.
Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, et al.
Genome Biol. 2012 Oct 3;13(10):R87.

SERE: Single-parameter quality control and sample comparison for RNA-seq.
Schulze SK, Kanwar R, Gölzenleuchter M, Therneau TM, Beutler AS.
BMC Genomics. 2012 Oct 3;13(1):524.

Meiotic maps of sockeye salmon derived from massively parallel DNA sequencing.
Everett MV, Miller MR, Seeb JE.
BMC Genomics. 2012 Oct 3;13(1):521.

Influence of polymer-pore interaction on the translocation of a polymer through a nanopore.
Luo MB, Cao WP.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Sep;86(3-1):031914.

Comparative metagenomic analysis of soil microbial communities across three hexachlorocyclohexane contamination levels.
Sangwan N, Lata P, Dwivedi V, Singh A, et al.
PLoS One. 2012;7(9):e46219.

Paired-end sequencing of long-range DNA fragments for de novo assembly of large, complex mammalian genomes by direct intra-molecule ligation.
Asan, Geng C, Chen Y, Wu K, et al.
PLoS One. 2012;7(9):e46211.

Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.
Yao F, Ariyaratne PN, Hillmer AM, Lee WH, et al.
PLoS One. 2012;7(9):e46152.

Voltage-driven translocation of DNA through a high throughput conical solid-state nanopore.
Liu Q, Wu H, Wu L, Xie X, et al.
PLoS One. 2012;7(9):e46014.

Improving indel detection specificity of the Ion Torrent PGM benchtop sequencer.
Yeo ZX, Chan M, Yap YS, Ang P, et al.
PLoS One. 2012;7(9):e45798.

Choosing the best plant for the job: a cost-effective assay to prescreen ancient plant remains destined for shotgun sequencing.
Wales N, Romero-Navarro JA, Cappellini E, Gilbert MT.
PLoS One. 2012;7(9):e45644.

WaveSeq: a novel data-driven method of detecting histone modification enrichments using wavelets.
Mitra A, Song J.
PLoS One. 2012;7(9):e45486.

High-resolution transcriptome of human macrophages.
Beyer M, Mallmann MR, Xue J, Staratschek-Jox A, et al.
PLoS One. 2012;7(9):e45466.

An integrated pipeline for de novo assembly of microbial genomes.
Tritt A, Eisen JA, Facciotti MT, Darling AE.
PLoS One. 2012;7(9):e42304.

Preparation of small RNA libraries for high-throughput sequencing.
Malone C, Brennecke J, Czech B, Aravin A, Hannon GJ.
Cold Spring Harb Protoc. 2012 Oct 1;2012(10).

KungFQ: a simple and powerful approach to compress Fastq files.
Grassi E, Di Gregorio F, Molineris I.
IEEE/ACM Trans Comput Biol Bioinform. 2012 Sep 25. [Epub ahead of print]

ChIP-exo method for identifying genomic location of DNA-binding proteins with near-single-nucleotide accuracy.
Rhee HS, Pugh BF.
Curr Protoc Mol Biol. 2012 Oct;Chapter 21:Unit21.24.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.