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In Print: Last Week's Sequencing-Related Papers of Note: May 8, 2012


Transverse electric field dragging of DNA in a nanochannel.
Tsutsui M, He Y, Furuhashi M, Rahong S, et al.
Sci Rep. 2012;2:394.

Digital gene expression analysis based on integrated de novo transcriptome assembly of sweet potato [Ipomoea batatas (L.) Lam].
Tao X, Gu YH, Wang HY, Zheng W, et al.
PLoS One. 2012;7(4):e36234.

Generation and analysis of a mouse intestinal metatranscriptome through Illumina based RNA-sequencing.
Xiong X, Frank DN, Robertson CE, Hung SS, et al.
PLoS One. 2012;7(4):e36009.

Factors that affect large subunit ribosomal DNA amplicon sequencing studies of fungal communities: classification method, primer choice, and error.
Porter TM, Golding GB.
PLoS One. 2012;7(4):e35749.

Utilizing RNA-seq data for de-novo coexpression network inference.
Iancu OD, Kawane S, Bottomly D, Searles R, et al.
Bioinformatics. 2012 May 3. [Epub ahead of print]

SEQCHIP: a powerful method to integrate sequence and genotype data for the detection of rare variant associations.
Liu DJ, Leal SM.
Bioinformatics. 2012 May 3. [Epub ahead of print]

Bacterial communities in different sections of a municipal wastewater treatment plant revealed by 16S rDNA 454 pyrosequencing.
Ye L, Zhang T.
Appl Microbiol Biotechnol. 2012 May 5. [Epub ahead of print]

HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies.
Huang S, Chen Z, Huang G, Yu T, et al.
Genome Res. 2012 May 3. [Epub ahead of print]

Mutation mapping and identification by whole genome sequencing.
Leshchiner I, Alexa K, Kelsey P, Adzhubei I, et al.
Genome Res. 2012 May 3. [Epub ahead of print]

Genome-wide copy number analysis of single cells.
Baslan T, Kendall J, Rodgers L, Cox H, et al.
Nat Protoc. 2012 May 3;7(6):1024-41.

Hypervariable loci in the human gut virome.
Minot S, Grunberg S, Wu GD, Lewis JD, Bushman FD.
Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3962-6.

Fractal MapReduce decomposition of sequence alignment.
Almeida JS, Gruneberg A, Maass W, Vinga S.
Algorithms Mol Biol. 2012 May 2;7(1):12.

Reliable detection of subclonal single-nucleotide variants in tumour cell populations.
Gerstung M, Beisel C, Rechsteiner M, Wild P, et al.
Nat Commun. 2012 May 1;3:811.

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome.
Iorizzo M, Senalik D, Szklarczyk M, Grzebelus D, et al.
BMC Plant Biol. 2012 May 1;12(1):61.

A context-based approach to identify the most likely mapping for RNA-seq experiments.
Bonfert T, Csaba G, Zimmer R, Friedel CC.
BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S9.

High-resolution genetic mapping with pooled sequencing.
Edwards MD, Gifford DK.
BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S8.

PAIR: polymorphic Alu insertion recognition.
Sveinbjörnsson JI, Halldórsson BV.
BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S7.

An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data.
Zhang J, Wang J, Wu Y.
BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S6.

KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.
Sacomoto GA, Kielbassa J, Chikhi R, Uricaru R, et al.
BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S5.

Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments.
Khrameeva EE, Gelfand MS.
BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S4.

Haplotype reconstruction using perfect phylogeny and sequence data.
Efros A, Halperin E.
BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S3.

MGMR: leveraging RNA-seq population data to optimize expression estimation.
Rozov R, Halperin E, Shamir R.
BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S2.

Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data.
Kakaradov B, Xiong HY, Lee LJ, Jojic N, Frey BJ.
BMC Bioinformatics. 2012 Apr 19;13 Suppl 6:S11.

Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets.
Hughes A, Ruan Y, Ekanayake S, Bae SH, et al.
BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S9.

A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data.
Han Z, Tian L, Pécot T, Huang T, et al.
BMC Bioinformatics. 2012 Mar 13;13 Suppl 2:S2.

The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.