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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.

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.