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Recent Sequencing-Related Papers of Note: Jul 1, 2014


bammds: A tool for assessing the ancestry of low depth whole genome data using multidimensional scaling (MDS).
Malaspinas AS, Tange O, Moreno-Mayar JV, Rasmussen M, et al.
Bioinformatics. 2014 Jun 28. [Epub ahead of print]

Towards better understanding of artifacts in variant calling from high-coverage samples.
Li H.
Bioinformatics. 2014 Jun 27. [Epub ahead of print]

High-quality and high-throughput massively parallel sequencing of the human mitochondrial genome using the Illumina MiSeq.
King JL, LaRue BL, Novroski NM, Stoljarova M, et al.
Forensic Sci Int Genet. 2014 Jun 7;12C:128-135. [Epub ahead of print]

MAP-RSeq: Mayo analysis pipeline for RNA sequencing.
Kalari KR, Nair AA, Bhavsar JD, O Brien DR, et al.
BMC Bioinformatics. 2014 Jun 27;15(1):224.

Microbial sequencing analyses suggest the presence of a fecal veneer on indoor climbing wall holds.
Bräuer SL, Vuono D, Carmichael MJ, Pepe-Ranney C, et al.
Curr Microbiol. 2014 Jun 28. [Epub ahead of print]

Integrated RNA and DNA sequencing improves mutation detection in low purity tumors.
Wilkerson MD, Cabanski CR, Sun W, Hoadley KA, et al.
Nucleic Acids Res. 2014 Jun 26. [Epub ahead of print]

LUMPY: A probabilistic framework for structural variant discovery.
Layer RM, Chiang C, Quinlan AR, Hall IM.
Genome Biol. 2014 Jun 26;15(6):R84.

Effect of confinement on DNA, solvent and counterion dynamics in a model biological nanopore.
Markosyan S, De Biase PM, Czapla L, Samoylova O, et al.
Nanoscale. 2014 Jun 27. [Epub ahead of print]

Bayesian genome assembly and assessment by Markov chain Monte Carlo sampling.
Howison M, Zapata F, Edwards EJ, Dunn CW.
PLOS One. 2014 Jun 26;9(6):e99497.

Library preparation for highly accurate population sequencing of RNA viruses.
Acevedo A, Andino R.
Nat Protoc. 2014 Jun;9(7):1760-1769.

Genome-wide identification of transcript start and end sites by transcript isoform sequencing.
Pelechano V, Wei W, Jakob P, Steinmetz LM.
Nat Protoc. 2014 Jun;9(7):1740-1759.

A de novo genome assembly algorithm for repeats and nonrepeats.
Lian S, Li Q, Dai Z, Xiang Q, Dai X .
Biomed Res Int. 2014;2014:736473.

H3M2: Detection of runs of homozygosity from whole-exome sequencing data.
Magi A, Tattini L, Palombo F, Benelli M, et al.
Bioinformatics. 2014 Jun 24. [Epub ahead of print]

CNV-guided multi-read allocation for ChIP-seq.
Zhang Q, Keleş S.
Bioinformatics. 2014 Jun 24. [Epub ahead of print]

Fabrication of sub-20 nm nanopore arrays in membranes with embedded metal electrodes at wafer scales.
Bai J, Wang D, Nam SW, Peng H, et al.
Nanoscale. 2014 Jun 26. [Epub ahead of print]

Decoding long nanopore sequencing reads of natural DNA.
Laszlo AH, Derrington IM, Ross BC, Brinkerhoff H, et al.
Nat Biotechnol. 2014 Jun 25. [Epub ahead of print]

Evaluation and optimisation of indel detection workflows for Ion Torrent sequencing of the BRCA1 and BRCA2 genes.
Yeo ZX, Wong JC, Rozen SG, Lee AS.
BMC Genomics. 2014 Jun 24;15(1):516.

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments.
Dolzhenko E, Smith AD.
BMC Bioinformatics. 2014 Jun 24;15(1):215.

Defining a personal, allele-specific, and single-molecule long-read transcriptome.
Tilgner H, Grubert F, Sharon D, Snyder MP.
Proc Natl Acad Sci U S A. 2014 Jun 24. [Epub ahead of print]

Slowing single-stranded DNA translocation through a solid-state nanopore by decreasing the nanopore diameter.
Akahori R, Haga T, Hatano T, Yanagi I, et al.
Nanotechnology. 2014 Jun 24;25(27):275501.

The marine microbial eukaryote transcriptome sequencing project (MMETSP): illuminating the functional diversity of eukaryotic life in the oceans through transcriptome sequencing.
Keeling PJ, Burki F, Wilcox HM, Allam B, et al.
PLOS Biol. 2014 Jun 24;12(6):e1001889.

"Deep" Sequencing accuracy and reproducibility using Roche/454 technology for inferring co-receptor usage in HIV-1.
Knapp DJ, McGovern RA, Poon AF, Zhong X, et al.
PLOS One. 2014 Jun 24;9(6):e99508.

Comparison of good- and bad-quality cork: application of high-throughput sequencing of phellogenic tissue.
Teixeira RT, Fortes AM, Pinheiro C, Pereira H.
J Exp Bot. 2014 Jun 22. [Epub ahead of print]

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi.
Riley R, Salamov AA, Brown DW, Nagy LG, et al.
Proc Natl Acad Sci U S A. 2014 Jun 23. [Epub ahead of print]

Detection of genomic variations and DNA polymorphisms and impact on analysis of meiotic recombination and genetic mapping.
Qi J, Chen Y, Copenhaver GP, Ma H.
Proc Natl Acad Sci U S A. 2014 Jun 23. [Epub ahead of print]

Enhanced fluid flow through nanopores by polymer brushes.
Chen Q.
Langmuir. 2014 Jun 23. [Epub ahead of print]

Local alignment tool based on Hadoop framework and GPU architecture.
Hung CL, Hua GJ.
Biomed Res Int. 2014;2014:541490.

Software for pre-processing Illumina next-generation sequencing short read sequences.
Chen C, Khaleel SS, Huang H, Wu CH.
Source Code Biol Med. 2014 May 3;9:8.

MBD ultra-sequencing: a novel method for identifying inter-individual and cell-type-specific variation in DNA methylation.
Li X, Baker-Andresen D, Zhao Q, Marshall V, Bredy TW.
Genes Brain Behav. 2014 Jun 20. [Epub ahead of print]

Inferring human population size and separation history from multiple genome sequences.
Schiffels S, Durbin R.
Nat Genet. 2014 Jun 22. [Epub ahead of print]

The sheep genome illuminates biology of the rumen and lipid metabolism.
Jiang Y, Xie M, Chen W, Talbot R, et al.
Science. 2014 Jun 6;344(6188):1168-73.