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Recent Sequencing-Related Papers of Note: Jul 22, 2014

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Surface modification of solid-state nanopores for sticky-free translocation of single-stranded DNA.
Tang Z, Lu B, Zhao Q, Wang J, et al.
Small. 2014 Jul 14. [Epub ahead of print]


Altitude adaptation in Tibetans caused by introgression of Denisovan-like DNA.
Huerta-Sánchez E, Jin X, Asan, Bianba Z, et al.
Nature. 2014 Jul 2. [Epub ahead of print]


Genome sequencing of normal cells reveals developmental lineages and mutational processes.
Behjati S, Huch M, van Boxtel R, Karthaus W, et al.
Nature. 2014 Jun 29. [Epub ahead of print]


Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
Smallwood SA, Lee HJ, Angermueller C, Krueger F, et al.
Nat Methods. 2014 Jul 20. [Epub ahead of print]


Unlocking the secondary gene-pool of barley with next-generation sequencing.
Wendler N, Mascher M, Nöh C, Himmelbach A, et al.
Plant Biotechnol J. 2014 Jul 6. [Epub ahead of print]


Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing.
Aflitos S, Schijlen E, de Jong H, de Ridder D, et al.
Plant J. 2014 Jul 12. [Epub ahead of print]


Variant detection sensitivity and biases in whole genome and exome sequencing.
Meynert AM, Ansari M, FitzPatrick DR, Taylor MS.
BMC Bioinformatics. 2014 Jul 19;15(1):247.


The common marmoset genome provides insight into primate biology and evolution.
The Marmoset Genome Sequencing and Analysis Consortium. Collaborators: Worley KC, Warren WC, Rogers J, et al.
Nat Genet. 2014 Jul 20. [Epub ahead of print]


Assessing the impact of water treatment on bacterial biofilms in drinking water distribution systems using high-throughput DNA sequencing.
Shaw JL, Monis P, Fabris R, Ho L, et al.
Chemosphere. 2014 Jul 16;117C:185-192.


Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics.
Kidd KK, Pakstis AJ, Speed WC, Lagacé R, et al.
Forensic Sci Int Genet. 2014 Jul 1;12C:215-224. [Epub ahead of print]


Bis-class: a new classification tool of methylation status using bayes classifier and local methylation information.
Huh I, Yang X, Park T, Yi SV.
BMC Genomics. 2014 Jul 18;15(1):608.


Stepwise threshold clustering: a new method for genotyping MHC loci using next-generation sequencing technology.
Stutz WE, Bolnick DI.
PLOS One. 2014 Jul 18;9(7):e100587.


A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome.
International Wheat Genome Sequencing Consortium (IWGSC). Collaborators: Mayer KF, Rogers J, Doležel J, Pozniak C, et al.
Science. 2014 Jul 18;345(6194):1251788.


Genome interplay in the grain transcriptome of hexaploid bread wheat.
Pfeifer M, Kugler KG, Sandve SR, Zhan B, International Wheat Genome Sequencing Consortium, et al.
Science. 2014 Jul 18;345(6194):1250091.


Structural and functional partitioning of bread wheat chromosome 3B.
Choulet F, Alberti A, Theil S, Glover N, et al.
Science. 2014 Jul 18;345(6194):1249721.


Long-range PCR in next-generation sequencing: comparison of six enzymes and evaluation on the MiSeq sequencer.
Jia H, Guo Y2, Zhao W3, Wang K4.
Sci Rep. 2014 Jul 18;4:5737.


SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-seq data of normal and diseased samples.
Yalamanchili HK, Li Z, Wang P, Wong MP, et al.
Nucleic Acids Res. 2014 Jul 17. [Epub ahead of print]


Targeted chromatin capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements.
Kolovos P, van de Werken HJ, Kepper N, Zuin J, et al.
Epigenetics Chromatin. 2014 Jun 16;7:10.


AAV type 2 wild-type and vector-mediated genomic integration profiles in human diploid fibroblasts analyzed by 3rd generation PacBio DNA sequencing.
Hüser D, Gogol-Döring A, Chen W, Heilbronn R.
J Virol. 2014 Jul 16. [Epub ahead of print]


Fast and cost-effective genetic mapping in apple using next-generation sequencing.
Gardner KM, Brown PJ, Cooke TF, Cann S, et al.
G3. 2014 Jul 16. [Epub ahead of print]


SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples.
Kimes PK, Cabanski CR, Wilkerson MD, Zhao N, et al.
Nucleic Acids Res. 2014 Jul 16. [Epub ahead of print]


Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds.
Herrero-Medrano JM, Megens HJ, Groenen MA, Bosse M, et al.
BMC Genomics. 2014 Jul 16;15(1):601.


MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing.
Calabrese C, Simone D, Diroma MA, Santorsola M, et al.
Bioinformatics. 2014 Jul 14. [Epub ahead of print]


Resolving complex tandem repeats with long reads.
Ummat A, Bashir A.
Bioinformatics. 2014 Jul 15. [Epub ahead of print]


Whole-exome imputation of sequence variants identified two novel alleles associated with adult body height in African Americans.
Du M, Auer PL, Jiao S, Haessler J, et al.
Hum Mol Genet. 2014 Jul 15. [Epub ahead of print]


Decoding ChIP-seq peaks with a double-binding signal refines binding peaks to single-nucleotide and predicts cooperative interaction.
Gomes AL, Abeel T, Peterson M, Azizi E, et al.
Genome Res. 2014 Jul 14. [Epub ahead of print]


False positives in multiplex polymerase chain reaction-based next-generation sequencing have unique signatures.
McCall CM, Mosier S, Thiess M, Debeljak M, et al.
J Mol Diagn. 2014 Jul 10. [Epub ahead of print]


Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications.
Rimmer A, Phan H, Mathieson I, Iqbal Z, et al.
Nat Genet. 2014 Jul 13. [Epub ahead of print]


Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle.
Daetwyler HD, Capitan A, Pausch H, Stothard P, et al.
Nat Genet. 2014 Jul 13. [Epub ahead of print]

The Scan

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Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.