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In Print: Last Week's Sequencing-Related Papers of Note: Oct 29, 2013


Next-generation sequencing reveals how RNA catalysts evolve from random space.
Ameta S, Winz ML, Previti C, Jäschke A.
Nucleic Acids Res. 2013 Oct 23. [Epub ahead of print]

Semiconductor-based DNA sequencing of histone modification states.
Cheng CS, Rai K, Garber M, Hollinger A, et al.
Nat Commun. 2013 Oct 25;4:2672.

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community.
Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K.
ISME J. 2013 Oct 24. [Epub ahead of print]

Compact representation of k-mer de Bruijn graphs for genome read assembly.
Rødland EA.
BMC Bioinformatics. 2013 Oct 23;14(1):313.

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.
Schumacher A, Pireddu L, Niemenmaa M, Kallio A, et al.
Bioinformatics. 2013 Oct 22. [Epub ahead of print]

A hierarchical Poisson log-normal model for network inference from RNA sequencing data.
Gallopin M, Rau A, Jaffrézic F.
PLoS One. 2013 Oct 17;8(10):e77503.

dPeak: High resolution identification of transcription factor binding sites from PET and SET ChIP-seq data.
Chung D, Park D, Myers K, Grass J, et al.
PLoS Comput Biol. 2013 Oct;9(10):e1003246.

PacBio sequencing of gene families − a case study with wheat gluten genes.
Zhang W, Ciclitira P, Messing J.
Gene. 2013 Oct 18. [Epub ahead of print]

eALPS: Estimating abundance levels in pooled sequencing using available genotyping data.
Eskin I, Hormozdiari F, Conde L, Riby J, et al.
J Comput Biol. 2013 Oct 21. [Epub ahead of print]

A nanopore-nanofiber mesh biosensor to control DNA translocation.
Squires AH, Hersey JS, Grinstaff MW, Meller A.
J Am Chem Soc. 2013 Oct 21. [Epub ahead of print]

Combining different mRNA capture methods to analyze the transcriptome: analysis of the Xenopus laevis transcriptome.
Blower MD, Jambhekar A, Schwarz DS, Toombs JA.
PLoS One. 2013 Oct 15;8(10):e77700.

AutoAssemblyD: a graphical user interface system for several genome assemblers.
Veras AA, de Sá PH, Azevedo V, Silva A, Ramos RT.
Bioinformation. 2013 Sep 23;9(16):840-1.

PEAR: A fast and accurate Illumina Paired-End reAd mergeR.
Zhang J, Kobert K, Flouri T, Stamatakis A.
Bioinformatics. 2013 Oct 18. [Epub ahead of print]

Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, et al.
Nat Methods. 2013 Oct 20. [Epub ahead of print]

Quantitative assessment of single-cell RNA-sequencing methods.
Wu AR, Neff NF, Kalisky T, Dalerba P, et al.
Nat Methods. 2013 Oct 20. [Epub ahead of print]

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.