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In Print: Last Week's Sequencing-Related Papers of Note: Nov 6, 2012


A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples.
Maehara K, Odawara J, Harada A, Yoshimi T, et al.
Nucleic Acids Res. 2012 Nov 3. [Epub ahead of print]

Slowing down DNA translocation through a nanopore by lowering fluid temperature.
Yeh LH, Zhang M, Joo SW, Qian S.
Electrophoresis. 2012 Sep 4. [Epub ahead of print]

PyroTrimmer: a software with GUI for pre-processing 454 amplicon sequences.
Oh J, Kim BK, Cho WS, Hong SG, Kim KM.
J Microbiol. 2012 Oct;50(5):766-9.

Surveying the microbiome of ants: Comparing 454 pyrosequencing with traditional methods to uncover bacterial diversity.
Kautz S, Rubin BE, Russell JA, Moreau CS.
Appl Environ Microbiol. 2012 Nov 2. [Epub ahead of print]

Early pregnancy diagnosis in dairy cows using circulating nucleic acids.
Mayer J, Soller JT, Beck J, Purwins V, et al.
Theriogenology. 2012 Oct 31. pii: S0093-691X(12)00547-X. [Epub ahead of print]

Reanalysis of RNA-sequencing data reveals several additional fusion genes with multiple isoforms.
Kangaspeska S, Hultsch S, Edgren H, Nicorici D, et al.
PLoS One. 2012;7(10):e48745.

FREQ-Seq: A rapid, cost-effective, sequencing-based method to determine allele frequencies directly from mixed populations.
Chubiz LM, Lee MC, Delaney NF, Marx CJ.
PLoS One. 2012;7(10):e47959.

Denoising PCR-amplified metagenome data.
Rosen MJ, Callahan BJ, Fisher DS, Holmes SP.
BMC Bioinformatics. 2012 Oct 31;13(1):283.

Capturing native long-range contiguity by in situ library construction and optical sequencing.
Schwartz JJ, Lee C, Hiatt JB, Adey A, Shendure J.
Proc Natl Acad Sci U S A. 2012 Oct 29. [Epub ahead of print]

ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs.
Yasuda T, Suzuki S, Nagasaki M, Miyano S.
BMC Bioinformatics. 2012 Oct 30;13(1):279.

Special features of RAD sequencing data: implications for genotyping.
Davey JW, Cezard T, Fuentes-Utrilla P, Eland C, et al.
Mol Ecol. 2012 Oct 30. [Epub ahead of print]

COPS: A sensitive and accurate tool for detecting somatic copy number alterations using short-read sequence data from paired samples.
Krishnan NM, Gaur P, Chaudhary R, Rao AA, Panda B.
PLoS One. 2012;7(10):e47812.

Sequencing the connectome.
Zador AM, Dubnau J, Oyibo HK, Zhan H, et al.
PLoS Biol. 2012 Oct;10(10):e1001411.

DNA sequencing and bar-coding using solid-state nanopores.
Atas E, Singer A, Meller A.
Electrophoresis. 2012 Sep 4. [Epub ahead of print]

Rare variant discovery and calling by sequencing pooled samples with overlaps.
Wang W, Yin X, Pyon YS, Hayes M, Li J.
Bioinformatics. 2012 Oct 27. [Epub ahead of print]

STAR: ultrafast universal RNA-seq aligner.
Dobin A, Davis CA, Schlesinger F, Drenkow J, et al.
Bioinformatics. 2012 Oct 25. [Epub ahead of print]

PriVar: a toolkit for prioritizing SNVs and indels from next generation sequencing data.
Zhang L, Zhang J, Yang J, Ying D, et al.
Bioinformatics. 2012 Oct 25. [Epub ahead of print]

Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates.
Lund SP, Nettleton D, McCarthy DJ, Smyth GK.
Stat Appl Genet Mol Biol. 2012 Oct 22;11(5).

Identification of an EMS-induced causal mutation in a gene required for boron-mediated root development by low-coverage genome re-sequencing in Arabidopsis.
Tabata R, Kamiya T, Shigenobu S, Yamaguchi K, et al.
Plant Signal Behav. 2012 Oct 26;8(1).

The GEM mapper: fast, accurate and versatile alignment by filtration.
Marco-Sola S, Sammeth M, Guigó R, Ribeca P.
Nat Methods. 2012 Oct 28. [Epub ahead of print]

The genomic landscape of species divergence in Ficedula flycatchers.
Ellegren H, Smeds L, Burri R, Olason PI, et al.
Nature. 2012 Oct 24. [Epub ahead of print]

Imputation of exome sequence variants into population-based samples and blood-cell trait-associated loci in African Americans: NHLBI GO exome sequencing project.
Auer PL, Johnsen JM, Johnson AD, Logsdon BA, et al.
Am J Hum Genet. 2012 Oct 24. [Epub ahead of print]

Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data.
Jun G, Flickinger M, Hetrick KN, Romm JM, et al.
Am J Hum Genet. 2012 Oct 23. [Epub ahead of print]

Single-neuron sequencing analysis of l1 retrotransposition and somatic mutation in the human brain.
Evrony GD, Cai X, Lee E, Hills LB, et al.
Cell. 2012 Oct 26;151(3):483-96.

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.