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Last Week's Sequencing-Related Papers of Note: Apr 29, 2014


CANOES: detecting rare copy number variants from whole exome sequencing data.
Backenroth D, Homsy J, Murillo LR, Glessner J, et al.
Nucleic Acids Res. 2014 Apr 25. [Epub ahead of print]

Sequencing and annotated analysis of full genome of Holstein breed bull.
Kõks S, Reimann E, Lilleoja R, Lättekivi F, et al.
Mamm Genome. 2014 Apr 26. [Epub ahead of print]

Nucleosome acetylation sequencing to study the establishment of chromatin acetylation.
Mittal C, Blacketer MJ, Shogren-Knaak MA.
Anal Biochem. 2014 Apr 24. [Epub ahead of print]

Simulation of Finnish population history, guided by empirical genetic data, to assess power of rare-variant tests in Finland.
Wang SR, Agarwala V, Flannick J, Chiang CW, et al.
Am J Hum Genet. 2014 Apr 23. [Epub ahead of print]

ShrinkBayes: a versatile R-package for analysis of count-based sequencing data in complex study designs.
van de Wiel MA, Neerincx M, Buffart TE, Sie D, Verheul HM.
BMC Bioinformatics. 2014 Apr 26;15(1):116.

Mudi, a web tool for identifying mutations by bioinformatics analysis of whole-genome sequence.
Iida N, Yamao F, Nakamura Y, Iida T.
Genes Cells. 2014 Apr 28. [Epub ahead of print]

Somatic mutations found in the healthy blood compartment of a 115-yr-old woman demonstrate oligoclonal hematopoiesis.
Holstege H, Pfeiffer W, Sie D, Hulsman M, et al.
Genome Res. 2014 Apr 23. [Epub ahead of print]

The emerging biofuel crop Camelina sativa retains a highly undifferentiated hexaploid genome structure.
Kagale S, Koh C, Nixon J, Bollina V, et al.
Nat Commun. 2014 Apr 23;5:3706.

The genome sequence of a widespread apex predator, the Golden Eagle (Aquila chrysaetos).
Doyle JM, Katzner TE, Bloom PH, Ji Y, et al.
PLOS One. 2014 Apr 23;9(4):e95599.

Mammalian Y chromosomes retain widely expressed dosage-sensitive regulators.
Bellott DW, Hughes JF, Skaletsky H, Brown LG, et al.
Nature. 2014 Apr 24;508(7497):494-9.

Origins and functional evolution of Y chromosomes across mammals.
Cortez D, Marin R, Toledo-Flores D, Froidevaux L, et al.
Nature. 2014 Apr 24;508(7497):488-93.

Interpreting the conductance blockades of DNA translocations through solid-state nanopores.
Carlsen AT, Zahid OK, Ruzicka J, Taylor EW, Hall AR.
ACS Nano. 2014 Apr 23. [Epub ahead of print]

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads.
Kajitani R, Toshimoto K, Noguchi H, Toyoda A, et al.
Genome Res. 2014 Apr 22. [Epub ahead of print]

The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates.
Berthelot C, Brunet F, Chalopin D, Juanchich A, et al.
Nat Commun. 2014 Apr 22;5:3657.

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution.
Booth MJ, Marsico G, Bachman M, Beraldi D, Balasubramanian S.
Nat Chem. 2014 May;6(5):435-40.
(See our coverage of this paper here.)

Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair.
Dal GM, Ergüner B, Sağıroğlu MS, Yüksel B, et al.
J Med Genet. 2014 Apr 24. [Epub ahead of print]

Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.
International Glossina Genome Initiative
Science. 2014 Apr 25;344(6182):380-6.

Patterns of coding variation in the complete exomes of three Neandertals.
Castellano S, Parra G, Sánchez-Quinto FA, Racimo F, et al.
Proc Natl Acad Sci U S A. 2014 Apr 21. [Epub ahead of print]

Bioinformatics pipelines for targeted resequencing and whole-exome sequencing of human and mouse genomes: a virtual appliance approach for instant deployment.
Li J, Doyle MA, Saeed I, Wong SQ, et al.
PLOS One. 2014 Apr 21;9(4):e95217.

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms.
Patro R, Mount SM, Kingsford C.
Nat Biotechnol. 2014 Apr 20. [Epub ahead of print]

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer.
Lohr JG, Adalsteinsson VA, Cibulskis K, Choudhury AD, et al.
Nat Biotechnol. 2014 Apr 20. [Epub ahead of print]

Indexing a sequence for mapping reads with a single mismatch.
Crochemore M, Langiu A, Rahman MS.
Philos Trans A Math Phys Eng Sci. 2014 Apr 21;372(2016):20130167.

ExonSampler: a computer program for genome-wide and candidate gene exon sampling for targeted next-generation sequencing.
Cosart T, Beja-Pereira A, Luikart G.
Mol Ecol Resour. 2014 Apr 22. [Epub ahead of print]