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Last Week's Sequencing-Related Papers of Note: Apr 22, 2014


Validation of noise models for single-cell transcriptomics.
Grün D, Kester L, van Oudenaarden A.
Nat Methods. 2014 Apr 20. [Epub ahead of print]

DSRC 2-Industry-oriented compression of FASTQ files.
Roguski L, Deorowicz S.
Bioinformatics. 2014 Apr 18. [Epub ahead of print]

An atlas of active enhancers across human cell types and tissues.
Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, et al.
Nature. 2014 Mar 27;507(7493):455-61.

FANSe2: a robust and cost-efficient alignment tool for quantitative next-generation sequencing applications.
Xiao CL, Mai ZB, Lian XL, Zhong JY, et al.
PLOS One. 2014 Apr 17;9(4):e94250.

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq.
Treutlein B, Brownfield DG, Wu AR, Neff NF, et al.
Nature. 2014 Apr 13. [Epub ahead of print]

Microsecond simulations of DNA and ion transport in nanopores with novel ion-ion and ion-nucleotides effective potentials.
De Biase PM, Markosyan S, Noskov S.
J Comput Chem. 2014 Apr 5;35(9):711-21.

Rearrangement structure-independent strategy of CNV breakpoint analysis.
Xiao J, Zhang L, Wang J, Jiang Y, et al.
Mol Genet Genomics. 2014 Apr 16. [Epub ahead of print]

The impacts of read length and transcriptome complexity for de novo assembly: a simulation study.
Chang Z, Wang Z, Li G.
PLOS One. 2014 Apr 15;9(4):e94825.

Long-read sequencing of chicken transcripts and identification of new transcript isoforms.
Thomas S, Underwood JG, Tseng E, Holloway AK, et al.
PLOS One. 2014 Apr 15;9(4):e94650.

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases.
Shen L, Shao N, Liu X, Nestler E.
BMC Genomics. 2014 Apr 15;15(1):284.

BisQC: an operational pipeline for multiplexed bisulfite sequencing.
Chen GG, Diallo AB, Poujol R, Nagy C, et al.
BMC Genomics. 2014 Apr 16;15(1):290.

Sequencing-by-ligation using oligonucleotide probes with 3'-thio-deoxyinosine.
Pu D, Chen J, Bai Y, Tu J, et al.
J Biomed Nanotechnol. 2014 May;10(5):751-9.

Copy number variation detection using next generation sequencing read counts.
Wang H, Nettleton D, Ying K.
BMC Bioinformatics. 2014 Apr 14;15(1):109.

The Scan

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.

New Insights Into TP53-Driven Cancer

Researchers examine in Nature how TP53 mutations arise and spark tumor development.

Mapping Single-Cell Genomic, Transcriptomic Landscapes of Colorectal Cancer

In Genome Medicine, researchers present a map of single-cell genomic and transcriptomic landscapes of primary and metastatic colorectal cancer.

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.