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In Print: Last Week's Sequencing-Related Papers of Note: Nov 13, 2012


Next generation sequence analysis and computational genomics using graphical pipeline workflows.
Torri F, Dinov ID, Zamanyan A, Hobel S, et al.
Genes. 2012 Aug 30;3(3):545-575.

Targeted transcript profiling by sequencing.
Zajac P, Ahmadian A.
Sci Rep. 2012;2:821. Epub 2012 Nov 8.

Library preparation and multiplex capture for massive parallel sequencing applications made efficient and easy.
Neiman M, Sundling S, Grönberg H, Hall P, et al.
PLoS One. 2012;7(11):e48616.

Prediction of altered 3'- UTR miRNA-binding sites from RNA-seq data: the swine leukocyte antigen complex (SLA) as a model region.
Endale Ahanda ML, Fritz ER, Estellé J, Hu ZL, et al.
PLoS One. 2012;7(11):e48607.

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.
Fang G, Munera D, Friedman DI, Mandlik A, et al.
Nat Biotechnol. 2012 Nov 8. [Epub ahead of print]

Quality control of next-generation sequencing library through an integrative digital microfluidic platform.
Thaitrong N, Kim H, Renzi RF, Bartsch MS, et al.
Electrophoresis. 2012 Sep 28. [Epub ahead of print]

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring.
Lamichhaney S, Barrio AM, Rafati N, Sundström G, et al.
Proc Natl Acad Sci U S A. 2012 Nov 7. [Epub ahead of print]

Next-generation sequencing of human mitochondrial reference genomes uncovers high heteroplasmy frequency.
Sosa MX, Sivakumar IK, Maragh S, Veeramachaneni V, et al.
PLoS Comput Biol. 2012 Oct;8(10):e1002737.

RNA-seq pinpoints a Xanthomonas TAL-effector activated resistance gene in a large-crop genome.
Strauß T, van Poecke RM, Strauß A, Römer P, et al.
Proc Natl Acad Sci U S A. 2012 Nov 6. [Epub ahead of print]

D-peaks: A visual tool to display ChIP-seq peaks along the genome.
Brohée S, Bontempi G.
Transcription. 2012 Sep 1;3(5).

Exploring the parallel development of microbial systems in neonates with cystic fibrosis.
Rogers GB, Bruce KD.
MBio. 2012 Nov 6;3(6).

Automated degenerate PCR primer design for high-throughput sequencing improves efficiency of viral sequencing.
Li K, Shrivastava S, Brownley A, Katzel D, et al.
Virol J. 2012 Nov 6;9(1):261.

Complex effects of nucleotide variants in a mammalian cis-regulatory element.
Kwasnieski JC, Mogno I, Myers CA, Corbo JC, Cohen BA.
Proc Natl Acad Sci U S A. 2012 Nov 5. [Epub ahead of print]

MetaGeneTack: Ab initio detection of frameshifts in metagenomic sequences.
Tang S, Antonov I, Borodovsky M.
Bioinformatics. 2012 Nov 4. [Epub ahead of print]

An integrated map of genetic variation from 1,092 human genomes.
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, et al.
Nature. 2012 Nov 1;491(7422):56-65.

Achieving high throughput sequencing of cDNA library utilizing an alternative protocol for the bench top next-generation sequencing system.
Wan M, Faruq J, Rosenberg JN, Xia J, et al.
Microbiol Methods. 2012 Nov 2. [Epub ahead of print]

A model system for assessing and comparing the ability of exon microarray and tag sequencing to detect genes specific for malignant B-cells.
Kloster MB, Bilgrau AE, Rodrigo-Domingo M, Bergkvist KS, et al.
BMC Genomics. 2012 Nov 5;13(1):596.

Resolving candidate genes of mouse skeletal muscle QTL via RNA-seq and expression network analyses.
Lionikas A, Meharg C, Derry JM, Ratkevicius A, et al.
BMC Genomics. 2012 Nov 5;13(1):592.

MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling.
Kitchen JL, Moore JD, Palmer SA, Allaby RG.
BMC Bioinformatics. 2012 Nov 5;13(1):287.

The Scan

Possibly as Transmissible

Officials in the UK say the B.1.617.2 variant of SARS-CoV-2 may be as transmitted as easily as the B.1.1.7 variant that was identified in the UK, New Scientist reports.

Gene Therapy for SCID 'Encouraging'

The Associated Press reports that a gene therapy appears to be effective in treating severe combined immunodeficiency syndrome.

To Watch the Variants

Scientists told US lawmakers that SARS-CoV-2 variants need to be better monitored, the New York Times reports.

Nature Papers Present Nautilus Genome, Tool to Analyze Single-Cell Data, More

In Nature this week: nautilus genome gives peek into its evolution, computational tool to analyze single-cell ATAC-seq data, and more.