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In Print: Last Week's Sequencing-Related Papers of Note: Jan 14, 2014


Assessment of whole genome amplification for sequence capture and massively parallel sequencing.
Hasmats J, Gréen H, Orear C, Validire P, et al.
PLOS One. 2014 Jan 7;9(1):e84785.

Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells.
Deng Q, Ramsköld D, Reinius B, Sandberg R.
Science. 2014 Jan 10;343(6167):193-6.

Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples.
Lee YK, Jin S, Duan S, Lim YC, et al.
Biol Proced Online. 2014 Jan 9;16(1):1.

Comparative analysis of nucleotide translocation through protein nanopores using steered molecular dynamics and an adaptive biasing force.
Martin HS, Jha S, Coveney PV.
J Comput Chem. 2014 Jan 9. [Epub ahead of print]

Genetics of single-cell protein abundance variation in large yeast populations.
Albert FW, Treusch S, Shockley AH, Bloom JS, Kruglyak L.
Nature. 2014 Jan 8. [Epub ahead of print]

Base preferences in non-templated nucleotide incorporation by MMLV-derived reverse transcriptases.
Zajac P, Islam S, Hochgerner H, Lönnerberg P, Linnarsson S.
PLOS One. 2013 Dec 31;8(12):e85270.

Low-bandwidth and non-compute intensive remote identification of microbes from raw sequencing reads.
Gautier L, Lund O.
PLOS One. 2013 Dec 31;8(12):e83784.

Preparing unbiased T-cell receptor and antibody cDNA libraries for the deep next generation sequencing profiling.
Mamedov IZ, Britanova OV, Zvyagin IV, Turchaninova MA, et al.
Front Immunol. 2013 Dec 23;4:456.

Bias from removing read duplication in ultra-deep sequencing experiments.
Zhou W, Chen T, Zhao H, Eterovic AK, et al.
Bioinformatics. 2014 Jan 2. [Epub ahead of print]

Diminishing return for increased mappability with longer sequencing reads: implications of the k-mer distributions in the human genome.
Li W, Freudenberg J, Miramontes P.
BMC Bioinformatics. 2014 Jan 3;15(1):2.

An unbiased resource of novel SNP markers provides a new chronology for the human Y chromosome and reveals a deep phylogenetic structure in Africa.
Scozzari R, Massaia A, Trombetta B, Bellusci G, et al.
Genome Res. 2014 Jan 6. [Epub ahead of print]

Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs.
Friedersdorf MB, Keene JD.
Genome Biol. 2014 Jan 7;15(1):R2.

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.
Zhang Y, Wong CH, Birnbaum RY, Li G, et al.
Nature. 2013 Dec 12;504(7479):306-10.

The Scan

Looking for Omicron

NPR reports that SARS-CoV-2 testing in the US has gotten better but also that some experts say more needs to be done to better track the Omicron variant.

Holmes Alleges Abuse

The Associated Press reports that Theranos' Elizabeth Holmes has testified at her wire fraud trial that her business and romantic partner abused her.

Bit More Diverse, But More to Do

While Black and Hispanic patients are more likely to participate in cancer clinical trials than previously, they are still underrepresented, according to US News & World Report.

PNAS Papers on Yeast Gene Silencing, Zika Virus Inhibition, Immunoglobulin Hypermutation

In PNAS this week: gene silencing in Saccharomyces cerevisiae, possible neuroprotective role for SHFL in a mouse model of Zika virus infection, and more.