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In Print: Last Week's Sequencing-Related Papers of Note: May 21, 2013


Transcriptome sequencing of neonatal thymic epithelial cells.
St-Pierre C, Brochu S, Vanegas JR, Dumont-Lagacé M, et al.
Sci Rep. 2013 May 17;3:1860.

ACCUSA2: Multi-purpose SNV calling enhanced by probabilistic integration of quality scores.
Piechotta M, Dieterich C.
Bioinformatics. 2013 May 16. [Epub ahead of print]

Electrophoresis of a DNA coil near a nanopore.
Rowghanian P, Grosberg AY.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Apr;87(4-1):042723.

Electrophoretic capture of a DNA chain into a nanopore.
Rowghanian P, Grosberg AY.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Apr;87(4-1):042722.

Translocation of a polymer through a nanopore across a viscosity gradient.
de Haan HW, Slater GW.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Apr;87(4-1):042604.

454-pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters.
Sundberg C, Al-Soud WA, Larsson M, Alm E, et al.
FEMS Microbiol Ecol. 2013 May 16. [Epub ahead of print]

Translocating kilobase RNA through the staphylococcal α-hemolysin nanopore.
Cracknell JA, Japrung D, Bayley H.
Nano Lett. 2013 May 16. [Epub ahead of print]

Comparative analysis of RNA sequencing methods for degraded or low-input samples.
Adiconis X, Borges-Rivera D, Satija R, Deluca DS, et al.
Nat Methods. 2013 May 19. [Epub ahead of print]

Specificity control for read alignments using an artificial reference genome guided false discovery rate.
Giese SH, Zickmann F, Renard BY.
Bioinformatics. 2013 May 17. [Epub ahead of print]

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.
Shalek AK, Satija R, Adiconis X, Gertner RS, et al.
Nature. 2013 May 19. [Epub ahead of print]

Optimizing preservation protocols to extract high-quality RNA from different tissues of echinoderms for next-generation sequencing.
Pérez-Portela R, Riesgo A.
Mol Ecol Resour. 2013 May 20. [Epub ahead of print]

ReviSTER: An automated pipeline to revise misaligned reads to simple tandem repeats.
Tae H, McMahon KW, Settlage RE, Bavarva JH, Garner HR.
Bioinformatics. 2013 May 15. [Epub ahead of print]

Updating RNA-seq analyses after re-annotation.
Roberts A, Schaeffer L, Pachter L.
Bioinformatics. 2013 May 14. [Epub ahead of print]

Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies.
Supple MA, Hines HM, Dasmahapatra KK, Lewis JJ, et al.
Genome Res. 2013 May 14. [Epub ahead of print]

The genomics of selection in dogs and the parallel evolution between dogs and humans.
Wang GD, Zhai W, Yang HC, Fan RX, et al.
Nat Commun. 2013 May 14;4:1860.

Single-cell and metagenomic analyses indicate a fermentative and saccharolytic lifestyle for members of the OP9 lineage.
Dodsworth JA, Blainey PC, Murugapiran SK, Swingley WD, et al.
Nat Commun. 2013 May 14;4:1854.

Optimizing de novo assembly of short-read RNA-seq data for phylogenomics.
Yang Y, Smith SA.
BMC Genomics. 2013 May 14;14(1):328.

DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.
Nakato R, Itoh T, Shirahige K.
Genes Cells. 2013 May 15. [Epub ahead of print]

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data.
Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B.
Nucleic Acids Res. 2013 May 13. [Epub ahead of print]

Fine de novo sequencing of a fungal genome using only SOLiD short read data: verification on Aspergillus oryzae RIB40.
Umemura M, Koyama Y, Takeda I, Hagiwara H, et al.
PLoS One. 2013 May 7;8(5):e63673.

A multi-platform draft de novo genome assembly and comparative analysis for the scarlet Macaw (Ara macao).
Seabury CM, Dowd SE, Seabury PM, Raudsepp T, et al.
PLoS One. 2013 May 8;8(5):e62415.

A next-generation sequencing method for genotyping-by-sequencing of highly heterozygous autotetraploid potato.
Uitdewilligen JG, Wolters AM, D'hoop BB, Borm TJ, et al.
PLoS One. 2013 May 8;8(5):e62355.

High-throughput tetrad analysis.
Ludlow CL, Scott AC, Cromie GA, Jeffery EW, et al.
Nat Methods. 2013 May 12. [Epub ahead of print]

Sequence comparative analysis using networks (SCAN): software for evaluating de novo transcript assembly from next generation sequencing.
Misner I, Bicep C, Lopez P, Halary S, et al.
Mol Biol Evol. 2013 May 10. [Epub ahead of print]

Identification of a Tibetan-specific mutation in the hypoxic gene EGLN1 and its contribution to high-altitude adaptation.
Xiang K, Ouzhuluobu, Peng Y, Yang Z, et al.
Mol Biol Evol. 2013 May 10. [Epub ahead of print]

Sequence-based mapping of the polyploid wheat genome.
Saintenac C, Zhang D, Wang S, Akhunov E.
G3 (Bethesda). 2013 May 11. [Epub ahead of print]

A statistical framework for power calculations in ChIP-seq experiments.
Zuo C, Keles S.
Bioinformatics. 2013 May 10. [Epub ahead of print]

GAGE-B: An evaluation of genome assemblers for bacterial organisms.
Magoc T, Pabinger S, Canzar S, Liu X, et al.
Bioinformatics. 2013 May 10. [Epub ahead of print]

A bi-Poisson model for clustering gene expression profiles by RNA-seq.
Wang N, Wang Y, Hao H, Wang L, et al.
Brief Bioinform. 2013 May 10. [Epub ahead of print]

Efficient isolation of polymorphic microsatellites from high-throughput sequence data based on number of repeats.
Cardoso SD, Gonçalves D, Robalo JI, Almada VC, et al.
Mar Genomics. 2013 May 7. [Epub ahead of print]

Strand-seq: a unifying tool for studies of chromosome segregation.
Falconer E, Lansdorp PM.
Semin Cell Dev Biol. 2013 May 7. [Epub ahead of print]

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.
Gifford CA, Ziller MJ, Gu H, Trapnell C, et al.
Cell. 2013 May 7. [Epub ahead of print]

Sequencing platform and library preparation choices impact viral metagenomes.
Solonenko SA, Ignacio-Espinoza JC, Alberti A, Cruaud C, et al.
BMC Genomics. 2013 May 10;14(1):320.

Characterization of human plasma-derived exosomal RNAs by deep sequencing.
Huang X, Yuan T, Tschannen M, Sun Z, et al.
BMC Genomics. 2013 May 10;14(1):319.

Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.).
Ming R, Vanburen R, Liu Y, Yang M, et al.
Genome Biol. 2013 May 10;14(5):R41.

Lane-by-lane sequencing using Illumina's Genome Analyzer II.
Gravina MT, Lin JH, Levine SS.
Biotechniques. 2013 May;54(5):265-9.

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.