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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.