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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

Call to Look Again

More than a dozen researchers penned a letter in Science saying a previous investigation into the origin of SARS-CoV-2 did not give theories equal consideration.

Not Always Trusted

In a new poll, slightly more than half of US adults have a great deal or quite a lot of trust in the Centers for Disease Control and Prevention, the Hill reports.

Identified Decades Later

A genetic genealogy approach has identified "Christy Crystal Creek," the New York Times reports.

Science Papers Report on Splicing Enhancer, Point of Care Test for Sexual Transmitted Disease

In Science this week: a novel RNA structural element that acts as a splicing enhancer, and more.