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Last Week's Sequencing-Related Papers of Note: Mar 4, 2014

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Highly multiplexed subcellular RNA sequencing in situ.
Lee JH, Daugharthy ER, Scheiman J, Kalhor R, et al.
Science. 2014 Feb 27. [Epub ahead of print]


ngsCAT: a tool to assess the efficiency of targeted enrichment sequencing.
López-Domingo FJ, Florido JP, Rueda A, Dopazo J, Santoyo-Lopez J.
Bioinformatics. 2014 Feb 26. [Epub ahead of print]


Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH).
Helwak A, Tollervey D.
Nat Protoc. 2014 Mar;9(3):711-728.


Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases.
Ahmed T, Haraldsen JT, Rehr JJ, Di Ventra M, et al.
Nanotechnology. 2014 Feb 27;25(12):125705.


A glance at quality score: implication for de novo transcriptome reconstruction of Illumina reads.
Mbandi SK, Hesse U, Rees DJ, Christoffels A.
Front Genet. 2014 Feb 12;5:17.


FineSplice, enhanced splice junction detection and quantification: a novel pipeline based on the assessment of diverse RNA-Seq alignment solutions.
Gatto A, Torroja-Fungairiño C, Mazzarotto F, Cook SA, et al.
Nucleic Acids Res. 2014 Feb 25. [Epub ahead of print]


High-throughput detection of clinically relevant mutations in archived tumor samples by multiplexed PCR and next generation sequencing.
Bourgon R, Lu S, Yan Y, Lackner MR, et al.
Clin Cancer Res. 2014 Feb 26. [Epub ahead of print]


Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility.
Kielpinski LJ, Vinther J.
Nucleic Acids Res. 2014 Feb 24. [Epub ahead of print]


Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries.
Carpenter ML, Buenrostro JD, Valdiosera C, Schroeder H, et al.
Am J Hum Genet. 2013 Nov 7;93(5):852-64.


False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing.
Campana MG, Robles García N, Rühli FJ, Tuross N.
BMC Res Notes. 2014 Feb 25;7(1):111.


Ray Wu as Fifth Business: Deconstructing collective memory in the history of DNA sequencing.
Onaga LA.
Stud Hist Philos Biol Biomed Sci. 2014 Feb 21;46C:1-14.


MOABS: model based analysis of bisulfite sequencing data.
Sun D, Xi Y, Rodriguez B, Park HJ, et al.
Genome Biol. 2014 Feb 24;15(2):R38.


iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data.
Mimori T, Nariai N, Kojima K, Takahashi M, et al.
BMC Syst Biol. 2013;7 Suppl 6:S8.


HSA: a Heuristic Splice Alignment tool.
Bu J, Chi X, Jin Z.
BMC Syst Biol. 2013;7 Suppl 2:S10.


Detection and classification of peaks in 5' cap RNA sequencing data.
Strbenac D, Armstrong NJ, Yang JY.
BMC Genomics. 2013;14 Suppl 5:S9.


MetaID: A novel method for identification and quantification of metagenomic samples.
Srinivasan SM, Guda C.
BMC Genomics. 2013;14 Suppl 8:S4.


Reducing bias in RNA sequencing data: a novel approach to compute counts.
Finotello F, Lavezzo E, Bianco L, Barzon L, et al.
BMC Bioinformatics. 2014;15 Suppl 1:S7.


An efficient and scalable graph modeling approach for capturing information at different levels in next generation sequencing reads.
Warnke JD, Ali HH.
BMC Bioinformatics. 2013;14 Suppl 11:S7.


Efficient digest of high-throughput sequencing data in a reproducible report.
Zhang Z, Leipzig J, Sasson A, Yu AM, et al.
BMC Bioinformatics. 2013;14 Suppl 11:S3.


Impact of different ChIP-Seq protocols on DNA integrity and quality of bioinformatics analysis results.
Felsani A, Gudmundsson B, Nanni S, Brini E, et al.
Brief Funct Genomics. 2014 Feb 21. [Epub ahead of print]


A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data.
Feng H, Conneely KN, Wu H.
Nucleic Acids Res. 2014 Feb 22. [Epub ahead of print]


Whole-genome haplotyping using long reads and statistical methods.
Kuleshov V, Xie D, Chen R, Pushkarev D, et al.
Nat Biotechnol. 2014 Feb 23. [Epub ahead of print]


An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform.
Fadrosh DW, Ma B, Gajer P, Sengamalay N, et al.
Microbiome. 2014 Feb 24;2(1):6.

The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.