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Last Week's Sequencing-Related Papers of Note: Mar 25, 2014


The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, et al.
Nat Biotechnol. 2014 Mar 23. [Epub ahead of print]

Nanopore fabrication by controlled dielectric breakdown.
Kwok H, Briggs K, Tabard-Cossa V.
PLOS One. 2014 Mar 21;9(3):e92880.

Function-based identification of mammalian enhancers using site-specific integration.
Dickel DE, Zhu Y, Nord AS, Wylie JN, et al.
Nat Methods. 2014 Mar 23. [Epub ahead of print]

spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data.
Vitting-Seerup K, Porse BT, Sandelin A, Waage J.
BMC Bioinformatics. 2014 Mar 23;15(1):81.

Comparison of single-molecule sequencing and hybrid approaches for finishing the genome of Clostridium autoethanogenum and analysis of CRISPR systems in industrial relevant Clostridia.
Brown SD, Nagaraju S, Utturkar S, De Tissera S, et al.
Biotechnol Biofuels. 2014 Mar 21;7(1):40.

Sequencing and assembly of the 22-gb loblolly pine genome.
Zimin A, Stevens KA, Crepeau MW, Holtz-Morris A, et al.
Genetics. 2014 Mar;196(3):875-90.

Performance comparison between rapid sequencing platforms for ultra-low coverage sequencing strategy.
Chen S, Li S, Xie W, Li X, et al.
PLOS One. 2014 Mar 20;9(3):e92192.

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.
Neale DB, Wegrzyn JL, Stevens KA, Zimin AV, et al.
Genome Biol. 2014 Mar 20;15(3):R59.

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens.
Shokralla S, Gibson JF, Nikbakht H, Janzen DH, et al.
Mol Ecol Resour. 2014 Feb 19. [Epub ahead of print]

Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing.
Treutlein B, Gokce O, Quake SR, Südhof TC.
Proc Natl Acad Sci U S A. 2014 Mar 17. [Epub ahead of print]

High-resolution antibody dynamics of vaccine-induced immune responses.
Laserson U, Vigneault F, Gadala-Maria D, Yaari G, et al.
Proc Natl Acad Sci U S A. 2014 Mar 17. [Epub ahead of print]

Integrated analysis of DNA methylation and RNA transcriptome during in vitro differentiation of human pluripotent stem cells into retinal pigment epithelial cells.
Liu Z, Jiang R, Yuan S, Wang N, et al.
PLOS One. 2014 Mar 17;9(3):e91416.

Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing.
Ameur A, Meiring TL, Bunikis I, Häggqvist S, et al.
Sci Rep. 2014 Mar 18;4:4398.

RepARK—de novo creation of repeat libraries from whole-genome NGS reads.
Koch P, Platzer M, Downie BR.
Nucleic Acids Res. 2014 Mar 14. [Epub ahead of print]

Genome-guided transcript assembly by integrative analysis of RNA sequence data.
Boley N, Stoiber MH, Booth BW, Wan KH, et al.
Nat Biotechnol. 2014 Mar 16. [Epub ahead of print]

Sequencing degraded RNA addressed by 3' tag counting.
Sigurgeirsson B, Emanuelsson O, Lundeberg J.
PLOS One. 2014 Mar 14;9(3):e91851.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.