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Last Week's Sequencing-Related Papers of Note: Sep 27, 2011


Transcriptome analysis and comparison reveal divergence between two invasive whitefly cryptic species.
Wang XW, Luan JB, Li JM, Su YL, et al.
BMC Genomics. 2011 Sep 22;12(1):458.

Unveiling in situ interactions between marine protists and bacteria through single cell sequencing.
Martinez-Garcia M, Brazel D, Poulton NJ, Swan BK, et al.
ISME J. 2011 Sep 22. [Epub ahead of print]

SEM-induced shrinking of solid-state nanopores for single molecule detection.
Prabhu AS, Freedman KJ, Robertson JW, Nikolov Z, et al.
Nanotechnology. 2011 Sep 22;22(42):425302.

Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles.
Guo S, Liu J, Zheng Y, Huang M, et al.
BMC Genomics. 2011 Sep 21;12(1):454.

CDinFusion — submission-ready, on-line integration of sequence and contextual data.
Hankeln W, Wendel NJ, Gerken J, Waldmann J, et al.
PLoS One. 2011;6(9):e24797. Epub 2011 Sep 13.

ChIP-Seq: technical considerations for obtaining high-quality data.
Kidder BL, Hu G, Zhao K.
Nat Immunol. 2011 Sep 20;12(10):918-22.

Nanopore-based single molecule mass spectrometry on a lipid membrane microarray.
Baaken G, Ankri N, Schuler AK, Rühe J, Behrends JC.
ACS Nano. 2011 Sep 20. [Epub ahead of print]

Droplet-based pyrosequencing using digital microfluidics.
Boles DJ, Benton JL, Siew GJ, Levy MH, et al.
Anal Chem. 2011 Sep 20. [Epub ahead of print]

Application of high-resolution, massively parallel pyrosequencing for estimation of haplotypes and gene expression levels of swine leukocyte antigen (SLA) class I genes.
Kita YF, Ando A, Tanaka K, Suzuki S, et al.
Immunogenetics. 2011 Sep 20. [Epub ahead of print]

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Novel molecular and computational methods improve the accuracy of insertion site analysis in sleeping beauty-induced tumors.
Brett BT, Berquam-Vrieze KE, Nannapaneni K, Huang J, et al.
PLoS One. 2011;6(9):e24668. Epub 2011 Sep 13.

Ralstonia syzygii, the blood disease bacterium and some Asian R. solanacearum strains form a single genomic species despite divergent lifestyles.
Remenant B, de Cambiaire JC, Cellier G, Jacobs JM, et al.
PLoS One. 2011;6(9):e24356. Epub 2011 Sep 8.

Genome-wide prediction and analysis of human chromatin boundary elements.
Wang J, Lunyak VV, Jordan IK.
Nucleic Acids Res. 2011 Sep 19. [Epub ahead of print]

Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers.
Wei W, Qi X, Wang L, Zhang Y, et al.
BMC Genomics. 2011 Sep 19;12(1):451. [Epub ahead of print]

Opera: Reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.
Gao S, Sung WK, Nagarajan N.
J Comput Biol. 2011 Sep 19. [Epub ahead of print]

Gate manipulation of DNA capture into nanopore.
He Y, Tsutsui M, Fan C, Taniguchi M, Kawai T.
ACS Nano. 2011 Sep 19. [Epub ahead of print]

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.