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Last Week's Sequencing-Related Papers of Note: Aug 9, 2011


Genome-wide epigenetic analysis of human pluripotent stem cells by ChIP and ChIP-seq.
Hitchler MJ, Rice JC.
Methods Mol Biol. 2011;767:253-67.

An unbiased genome-wide analysis of zinc-finger nuclease specificity.
Gabriel R, Lombardo A, Arens A, Miller JC, et al.
Nat Biotechnol. 2011 Aug 7. [Epub ahead of print]

Whole genome sequencing and phenotypic analysis of mutations found in Bacillus subtilis following evolution under relaxed selection for sporulation.
Brown CT, Fishwick LK, Chokshi BM, Cuff MA, et al.
Appl Environ Microbiol. 2011 Aug 5. [Epub ahead of print]

Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data.
Chien CH, Sun YM, Chang WC, Chiang-Hsieh PY, et al.
Nucleic Acids Res. 2011 Aug 5. [Epub ahead of print]

Genome-wide profiling of DNA methylation in human cancer cells.
Ogoshi K, Hashimoto SI, Nakatani Y, Qu W, et al.
Genomics. 2011 Jul 29. [Epub ahead of print]

MicroRNAs of rat articular cartilage at different developmental stages identified by Solexa sequencing.
Sun J, Zhong N, Li Q, Min Z, et al.
Osteoarthritis Cartilage. 2011 Jul 22. [Epub ahead of print]

Pyrosequencing for mini-barcoding of fresh and old museum specimens.
Shokralla S, Zhou X, Janzen DH, Hallwachs W, et al.
PLoS One. 2011;6(7):e21252.

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Synthetic spike-in standards for RNA-seq experiments.
Jiang L, Schlesinger F, Davis CA, Zhang Y, et al.
Genome Res. 2011 Aug 4. [Epub ahead of print]

RSEM: accurate transcript quantification from RNA-seq data with or without a reference genome.
Li B, Dewey CN.
BMC Bioinformatics. 2011 Aug 4;12(1):323.

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing.
Shen Y, Venu RC, Nobuta K, Wu X, et al.
Genome Res. 2011 Aug 3. [Epub ahead of print]

A comprehensively molecular haplotype-resolved genome of a European individual.
Suk EK, McEwen GK, Duitama J, Nowick K, et al.
Genome Res. 2011 Aug 3. [Epub ahead of print]

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data.
Wei Z, Wang W, Hu P, Lyon GJ, Hakonarson H.
Nucleic Acids Res. 2011 Aug 3. [Epub ahead of print]

Analysis of the melon (Cucumis melo) small RNAome by high-throughput pyrosequencing.
Gonzalez-Ibeas D, Blanca J, Donaire L, Saladie M, et al.
BMC Genomics. 2011 Aug 3;12(1):393.

RNA-seq analysis and de novo transcriptome assembly of Hevea brasiliensis.
Xia Z, Xu H, Zhai J, Li D, et al.
Plant Mol Biol. 2011 Aug 3. [Epub ahead of print]

Rare and common regulatory variation in population-scale sequenced human genomes.
Montgomery SB, Lappalainen T, Gutierrez-Arcelus M, Dermitzakis ET.
PLoS Genet. 2011 Jul;7(7):e1002144.

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Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits.
Zaboli G, Ameur A, Igl W, Johansson A, et al.
Eur J Hum Genet. 2011 Aug 3. [Epub ahead of print]

AlleleSeq: analysis of allele-specific expression and binding in a network framework.
Rozowsky J, Abyzov A, Wang J, Alves P, et al.
Mol Syst Biol. 2011 Aug 2;7:522.

Mauve assembly metrics.
Darling A, Tritt A, Eisen JA, Facciotti MT.
Bioinformatics. 2011 Aug 2. [Epub ahead of print]

A powerful and flexible approach to the analysis of RNA sequence count data.
Zhou YH, Xia K, Wright FA.
Bioinformatics. 2011 Aug 2. [Epub ahead of print]

De novo assembly and characterization of the carrot transcriptome reveals novel genes, new markers, and genetic diversity.
Iorizzo M, Senalik DA, Grzebelus D, Bowman M, et al.
BMC Genomics. 2011 Aug 2;12(1):389.

A complete genome assembly of Glaciecola mesophila sp. nov. sequenced by using BIGIS-4 sequencer system.
Yuan L, Ren L, Li Y, Han W, et al.
Sci China Life Sci. 2011 Aug 1. [Epub ahead of print]

High-throughput Illumina strand-specific RNA sequencing library preparation.
Zhong S, Joung JG, Zheng Y, Chen YR, et al.
Cold Spring Harb Protoc. 2011 Aug 1;2011(8).

High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche Genome Sequencer FLX platform.
Fordyce SL, Avila-Arcos MC, Rockenbauer E, Børsting C, et al.
Biotechniques. 2011 Aug;51(2):127-133.

Chaperone-assisted translocation of a polymer through a nanopore.
Yu W, Luo K.
J Am Chem Soc. 2011 Aug 1. [Epub ahead of print]

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.