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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

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.

Study Looks at Parent Uncertainties After Children's Severe Combined Immunodeficiency Diagnoses

A qualitative study in EJHG looks at personal, practical, scientific, and existential uncertainties in parents as their children go through SCID diagnoses, treatment, and post-treatment stages.

Antimicrobial Resistance Study Highlights Key Protein Domains

By screening diverse versions of an outer membrane porin protein in Vibrio cholerae, researchers in PLOS Genetics flagged protein domain regions influencing antimicrobial resistance.

Latent HIV Found in White Blood Cells of Individuals on Long-Term Treatments

Researchers in Nature Microbiology find HIV genetic material in monocyte white blood cells and in macrophages that differentiated from them in individuals on HIV-suppressive treatment.