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Papers of Note: Jul 13, 2010


DNA translocation through graphene nanopores.
Schneider GF, Kowalczyk SW, Calado VE, et al.
Nano Lett. 2010 Jul 7. [Epub ahead of print]

Optimus Primer: A PCR enrichment primer design program for next-generation sequencing of human exonic regions.
Brown AM, Lo KS, Guelpa P, et al.
BMC Res Notes. 2010 Jul 7;3(1):185. [Epub ahead of print]

Deep mapping: A novel mutagen-based strategy for direct mapping and mutation identification using whole genome sequencing.
Zuryn S, Le Gras S, Jamet K, Jarriault S.
Genetics. 2010 Jul 6. [Epub ahead of print]

Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.
Hestand MS, Klingenhoff A, Scherf M, Ariyurek Y, et al.
Nucleic Acids Res. 2010 Jul 7. [Epub ahead of print]

Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing.
Walsh T, Lee MK, Casadei S, Thornton AM, et al.
Proc Natl Acad Sci U S A. 2010 Jun 28. [Epub ahead of print]

Whole human exome capture for high-throughput sequencing.
Kim DW, Nam SH, Kim RN, Choi SH, Park HS.
Genome. 2010 Jul;53(7):568-74.

G-SQZ: Compact encoding of genomic sequence and quality data.
Tembe W, Lowey J, Suh E.
Bioinformatics. 2010 Jul 6. [Epub ahead of print]

Whole exome sequencing and homozygosity mapping identify mutation in the cell polarity protein GPSM2 as the cause of nonsyndromic hearing loss DFNB82.
Walsh T, Shahin H, Elkan-Miller T, Lee MK, et al.
Am J Hum Genet. 2010 Jul 9;87(1):90-94. Epub 2010 Jun 17.

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Massively parallel display of genomic DNA fragments by rolling-circle amplification and strand displacement amplification on chip.
Zhao H, Gao L, Luo J, Zhou D, Lu Z.
Talanta. 2010 Jul 15;82(2):477-482. Epub 2010 May 11.

Next-generation sequencing: The solution for high-resolution, unambiguous HLA typing.
Lind C, Ferriola D, Mackiewicz K, Heron S, et al.
Hum Immunol. 2010 Jul 2. [Epub ahead of print]

HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-seq data.
Qin ZS, Yu J, Shen J, Maher CA, et al.
BMC Bioinformatics. 2010 Jul 2;11(1):369. [Epub ahead of print]

An efficient annotation and gene-expression derivation tool for Illumina Solexa datasets.
Hosseini P, Tremblay A, Matthews BF, Alkharouf NW.
BMC Res Notes. 2010 Jul 2;3(1):183. [Epub ahead of print]

A method for full genome sequencing of all four serotypes of the dengue virus.
Christenbury JG, Aw PP, Ong SH, Schreiber MJ, et al.
J Virol Methods. 2010 Jul 2. [Epub ahead of print]

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data.
Wang K, Li M, Hakonarson H.
Nucleic Acids Res. 2010 Jul 3. [Epub ahead of print]

Sequencing of 50 human exomes reveals adaptation to high altitude.
Yi X, Liang Y, Huerta-Sanchez E, Jin X, et al.
Science. 2010 Jul 2;329(5987):75-78.

MicroRNA profiling of clear cell renal cell carcinoma by whole-genome small RNA deep sequencing of paired frozen and formalin-fixed, paraffin-embedded tissue specimens.
Weng L, Wu X, Gao H, Mu B et al.
J Pathol. 2010 May 21. [Epub ahead of print]

Optimization of protocol for sequencing of difficult templates.
Kieleczawa J, Mazaika E.
J Biomol Tech. 2010 Jul;21(2):97-102.

Comparison of the Illumina Genome Analyzer and Roche 454 GS FLX for resequencing of hypertrophic cardiomyopathy-associated genes.
Dames S, Durtschi J, Geiersbach K, Stephens J, Voelkerding KV.
J Biomol Tech. 2010 Jul;21(2):73-80.

The Scan

Just Breathing

A new analysis suggests that most Mycobacterium tuberculosis is spread by aerosols from breathing, rather than by coughing, the New York Times reports.

Just Like This One

NPR reports that the World Health Organization has hired a South African biotech company to recreate mRNA vaccine for SARS-CoV-2 that is similar to the one developed by Moderna.

Slow Start

The Wall Street Journal reports that Biogen's Alzheimer's disease treatment had revenues for July through September that totaled $300,000.

Genome Research Papers on Cancer Chromatin, Splicing in the Thymus, Circular RNAs in Cancer

In Genome Research this week: analysis of bivalent chromatin sites, RBFOX splicing factors' role in thymic epithelial cells, and more.