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In Print: Last Week's Sequencing-Related Papers of Note: Nov 19, 2013


Targeted RNA-sequencing with competitive multiplex-PCR amplicon libraries.
Blomquist TM, Crawford EL, Lovett JL, Yeo J, et al.
PLOS One. 2013 Nov 13;8(11):e79120.

Genome-wide chromatin analysis in mature mouse and human spermatozoa.
Hisano M, Erkek S, Dessus-Babus S, Ramos L, et al.
Nat Protoc. 2013 Dec;8(12):2449-70.

featureCounts: an efficient general-purpose program for assigning sequence reads to genomic features.
Liao Y, Smyth GK, Shi W.
Bioinformatics. 2013 Nov 13. [Epub ahead of print]

MEDIPS: genome wide differential coverage analysis of sequencing data derived from DNA enrichment experiments.
Lienhard M, Grimm C, Morkel M, Herwig R, Chavez L .
Bioinformatics. 2013 Nov 13. [Epub ahead of print]

The gut microbiotassay: a high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity.
Hermann-Bank ML, Skovgaard K, Stockmarr A, Larsen N, Mølbak L.
BMC Genomics. 2013 Nov 14;14(1):788.

Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.
Zaghlool A, Ameur A, Nyberg L, Halvardson J, et al.
BMC Biotechnol. 2013 Nov 13;13(1):99.

Towards sensitive graphene nanoribbon-nanopore devices by preventing electron beam induced damage.
Puster M, Rodríguez-Manzo JA, Balan A, Drndic M.
ACS Nano. 2013 Nov 13. [Epub ahead of print]

Prospective identification of parasitic sequences in phage display screens.
Matochko WL, Cory Li S, Tang SK, Derda R.
Nucleic Acids Res. 2013 Nov 11. [Epub ahead of print]

Microsatellite marker discovery using single molecule real-time circular consensus sequencing on the Pacific Biosciences RS.
Grohme MA, Soler RF, Wink M, Frohme M.
Biotechniques. 2013 Nov;55(5):253-6.

Finding the active genes in deep RNA-seq gene expression studies.
Hart T, Komori HK, Lamere S, Podshivalova K, Salomon DR.
BMC Genomics. 2013 Nov 11;14(1):778.

RNAseqViewer: visualization tool for RNA-seq data.
Rogé X, Zhang X.
Bioinformatics. 2013 Nov 8. [Epub ahead of print]

Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing.
Doi K, Monjo T, Hoang PH, Yoshimura J, et al.
Bioinformatics. 2013 Nov 8. [Epub ahead of print]

DriverDB: an exome sequencing database for cancer driver gene identification.
Cheng WC, Chung IF, Chen CY, Sun HJ, et al.
Nucleic Acids Res. 2013 Nov 7. [Epub ahead of print]

High-resolution microbial community reconstruction by integrating short reads from multiple 16S rRNA regions.
Amir A, Zeisel A, Zuk O, Elgart M, et al.
Nucleic Acids Res. 2013 Nov 7. [Epub ahead of print]

Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells.
Gole J, Gore A, Richards A, Chiu YJ, et al.
Nat Biotechnol. 2013 Nov 10. [Epub ahead of print]
(See our coverage of this paper here.)

Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations.
Zhang Y, Wong CH, Birnbaum RY, Li G, et al.
Nature. 2013 Nov 10. [Epub ahead of print]

IgG variable region and VH CDR3 diversity in unimmunized mice analyzed by massively parallel sequencing.
Lu J, Panavas T, Thys K, Aerssens J, et al.
Mol Immunol. 2013 Nov 7;57(2):274-283.

Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data.
Spencer DH, Tyagi M, Vallania F, Bredemeyer A, et al.
J Mol Diagn. 2013 Nov 5. pii: S1525-1578(13)00210-9. [Epub ahead of print]

Accurate local-ancestry inference in exome-sequenced admixed individuals via off-target sequence reads.
Hu Y, Willer C, Zhan X, Kang HM, Abecasis GR.
Am J Hum Genet. 2013 Nov 7;93(5):891-9.

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.
Guo W, Fiziev P, Yan W, Cokus S, et al.
BMC Genomics. 2013 Nov 10;14(1):774.

The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.