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In Print: Last Week's Sequencing-Related Papers of Note: Apr 9, 2013


QC-Chain: fast and holistic quality control method for next-generation sequencing data.
Zhou Q, Su X, Wang A, Xu J, Ning K.
PLoS One. 2013;8(4):e60234.

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform.
McLean JS, Lombardo MJ, Ziegler MG, Novotny M, et al.
Genome Res. 2013 Apr 5. [Epub ahead of print]

Pyrosequencing analysis of the bacterial community in drinking water wells.
Navarro-Noya YE, Suárez-Arriaga MC, Rojas-Valdes A, Montoya-Ciriaco NM, et al.
Microb Ecol. 2013 Apr 6. [Epub ahead of print]

Multiplexed ionic current sensing with glass nanopores.
Bell NA, Thacker VV, Hernández-Ainsa S, Fuentes-Perez ME, et al.
Lab Chip. 2013 Apr 8. [Epub ahead of print]

Updating benchtop sequencing performance comparison.
Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, et al.
Nat Biotechnol. 2013 Apr;31(4):294-6.
(See our coverage of this paper here.)

Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance.
Kelly AD, Hill KE, Correll M, Hu L, et al.
Genomics. 2013 Apr 2. [Epub ahead of print]

A tool for RNA sequencing sample identity check.
Huang J, Chen J, Lathrop M, Liang L.
Bioinformatics. 2013 Apr 4. [Epub ahead of print]

Single-molecule detection of 5-hydroxymethylcytosine in DNA through chemical modification and nanopore analysis.
Li WW, Gong L, Bayley H.
Angew Chem Int Ed Engl. 2013 Apr 4. [Epub ahead of print]

Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing.
Wan Y, Qu K, Ouyang Z, Chang HY.
Nat Protoc. 2013 Apr 4;8(5):849-69.

Peregrine: A rapid and unbiased method to produce strand-specific RNA-Seq libraries from small quantities of starting material.
Langevin SA, Bent ZW, Solberg OD, Curtis DJ, et al.
RNA Biol. 2013 Apr 1;10(4).

Probabilistic error correction for RNA sequencing.
Le HS, Schulz MH, McCauley BM, Hinman VF, Bar-Joseph Z.
Nucleic Acids Res. 2013 Apr 4. [Epub ahead of print]

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.
Liao Y, Smyth GK, Shi W.
Nucleic Acids Res. 2013 Apr 4. [Epub ahead of print]

Integration of mate pair sequences to improve shotgun assemblies of flow-sorted chromosome arms of hexaploid wheat.
Belova T, Zhan B, Wright J, Caccamo M, et al.
BMC Genomics. 2013 Apr 4;14(1):222.

PASTA: splice junction identification from RNA-sequencing data.
Tang S, Riva A.
BMC Bioinformatics. 2013 Apr 4;14(1):116.

Identification of SNPs in closely related temperate japonica rice cultivars using restriction enzyme-phased sequencing.
Kim SI, Tai TH.
PLoS One. 2013;8(3):e60176.

RNA-seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches.
Fan H, Xiao Y, Yang Y, Xia W, et al.
PLoS One. 2013;8(3):e59997.

Multiple single-cell genomes provide insight into functions of uncultured deltaproteobacteria in the human oral cavity.
Campbell AG, Campbell JH, Schwientek P, Woyke T, et al.
PLoS One. 2013;8(3):e59361.

Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 genomes data.
Quinn EM, Cormican P, Kenny EM, Hill M, et al.
PLoS One. 2013;8(3):e58815.

State-of-the-art fusion-finder algorithms sensitivity and specificity.
Carrara M, Beccuti M, Lazzarato F, Cavallo F, et al.
Biomed Res Int. 2013;2013:340620.

Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing.
De Meyer T, Mampaey E, Vlemmix M, Denil S, et al.
PLoS One. 2013;8(3):e59068.

A method to detect differentially methylated loci with next-generation sequencing.
Xu H, Podolsky RH, Ryu D, Wang X, et al.
Genet Epidemiol. 2013 Apr 1. [Epub ahead of print]

Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing.
Xie G, Wang L, Gao Q, Yu W, et al.
J Sci Food Agric. 2013 Jan 19. [Epub ahead of print]

First insights into the metagenome of Egyptian mummies using next-generation sequencing.
Khairat R, Ball M, Chang CC, Bianucci R, et al.
J Appl Genet. 2013 Apr 4. [Epub ahead of print]

Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription.
Vilfan ID, Tsai YC, Clark TA, Wegener J, et al.
J Nanobiotechnology. 2013 Apr 3;11(1):8.

The plover neurotranscriptome assembly: transcriptomic analysis in an ecological model species without a reference genome.
Moghadam HK, Harrison PW, Zachar G, Székely T, Mank JE.
Mol Ecol Resour. 2013 Mar 29. [Epub ahead of print]

Whole-exome targeted sequencing of the uncharacterized pine genome.
Neves LG, Davis JM, Brad Barbazuk W, Kirst M.
Plant J. 2013 Apr 4. [Epub ahead of print]

RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling.
Arnold B, Corbett-Detig RB, Hartl D, Bomblies K.
Mol Ecol. 2013 Apr 3. [Epub ahead of print]

PRICE: software for the targeted assembly of components of (meta)genomic sequence data.
Ruby JG, Bellare P, Derisi JL.
G3 (Bethesda). 2013 Mar 23. [Epub ahead of print]

The genomic and transcriptomic landscape of a HeLa cell line.
Landry JJ, Pyl PT, Rausch T, Zichner T, et al.
G3 (Bethesda). 2013 Mar 26. [Epub ahead of print]

RNA sequencing reveals small RNAs differentially expressed between incipient Japanese threespine sticklebacks.
Kitano J, Yoshida K, Suzuki Y.
BMC Genomics. 2013 Apr 2;14(1):214.

Genome sequencing of bacteria: sequencing, de novo assembly and rapid analysis using open source tools.
Kisand V, Lettieri T.
BMC Genomics. 2013 Apr 1;14(1):211.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.