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In Print: Last Week's Sequencing-Related Papers of Note: Oct 15, 2013


Benchmarking RNA-seq quantification tools.
Chandramohan R, Wu PY, Phan JH, Wang MD.
Conf Proc IEEE Eng Med Biol Soc. 2013 Jul;2013:647-650.

In-depth analysis of interrelation between quality scores and real errors in Illumina reads.
Kwon S, Park S, Lee B, Yoon S.
Conf Proc IEEE Eng Med Biol Soc. 2013 Jul;2013:635-638.

Nucleotide sequence alignment using sparse coding and belief propagation.
Roozgard A, Barzigar N, Wang S, Jiang X, et al.
Conf Proc IEEE Eng Med Biol Soc. 2013 Jul;2013:588-591.

A CMOS enhanced solid-state nanopore based single molecule detection platform.
Chen C, Yemenicioglu S, Uddin A, Corgliano E, Theogarajan L.
Conf Proc IEEE Eng Med Biol Soc. 2013 Jul;2013:164-167.

Robust adjustment of sequence tag abundance.
Baumann DD, Doerge RW.
Bioinformatics. 2013 Oct 9. [Epub ahead of print]

A single-molecule long-read survey of the human transcriptome.
Sharon D, Tilgner H, Grubert F, Snyder M.
Nat Biotechnol. 2013 Oct 13. [Epub ahead of print]

RRBS-Analyser: a comprehensive web server for reduced representation bisulfite sequencing data analysis.
Wang T, Liu Q, Li X, Wang X, et al.
Hum Mutat. 2013 Sep 18. [Epub ahead of print]

Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma.
Nabilsi NH, Deleyrolle LP, Darst RP, Riva A, et al.
Genome Res. 2013 Oct 8. [Epub ahead of print]

RNA sequencing-based identification of aberrant imprinting in cloned mice.
Okae H, Matoba S, Nagashima T, Mizutani E, et al.
Hum Mol Genet. 2013 Oct 8. [Epub ahead of print]

Population genomics from pool sequencing.
Ferretti L, Ramos-Onsins SE, Pérez-Enciso M.
Mol Ecol. 2013 Sep 14. [Epub ahead of print]

Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities.
Logares R, Sunagawa S, Salazar G, Cornejo-Castillo FM, et al.
Environ Microbiol. 2013 Aug 18. [Epub ahead of print]

Microbial basis of oral malodor development in humans.
Yang F, Huang S, He T, Catrenich C, et al.
J Dent Res. 2013 Oct 7. [Epub ahead of print]

Study on the polymer translocation induced blockade ionic current inside a nanopore by Langevin dynamics simulation.
Sun LZ, Luo MB.
J Phys Condens Matter. 2013 Oct 7;25(46):465101.

High-efficiency RNA cloning enables accurate quantification of miRNA expression by deep sequencing.
Zhang Z, Lee JE, Riemondy K, Anderson EM, Yi R.
Genome Biol. 2013 Oct 7;14(10):R109.

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.