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In Print: Last Week's Sequencing-Related Papers of Note: Apr 17, 2012


Forensic STR analysis using massive parallel sequencing.
Van Neste C, Van Nieuwerburgh F, Van Hoofstat D, Deforce D.
Forensic Sci Int Genet. 2012 Apr 12. [Epub ahead of print]

Molecular dissection of atrazine-responsive transcriptome and gene networks in rice by high-throughput sequencing.
Zhang JJ, Zhou ZS, Song JB, Liu ZP, Yang H.
J Hazard Mater. 2012 Mar 22. [Epub ahead of print]

Dynamic transformations of genome-wide epigenetic marking and transcriptional control establish T cell identity.
Zhang JA, Mortazavi A, Williams BA, Wold BJ, Rothenberg EV.
Cell. 2012 Apr 13;149(2):467-82.

Normalization, bias correction, and peak calling for ChIP-seq.
Diaz A, Park K, Lim DA, Song JS.
Stat Appl Genet Mol Biol. 2012 Mar 31;11(3).

A new approach for the joint analysis of multiple ChIP-seq libraries with application to histone modification.
Ferguson JP, Cho JH, Zhao H.
Stat Appl Genet Mol Biol. 2012 Feb 10;11(3).

A family-based probabilistic method for capturing de novo mutations from high-throughput short-read sequencing data.
Cartwright RA, Hussin J, Keebler JE, Stone EA, Awadalla P.
Stat Appl Genet Mol Biol. 2012 Jan 6;11(2).

Systematic identification of edited microRNAs in the human brain.
Alon S, Mor E, Vigneault F, Church G, et al.
Genome Res. 2012 Apr 12. [Epub ahead of print]

Fast homozygosity mapping and identification of a zebrafish ENU-induced mutation by whole-genome sequencing.
Voz ML, Coppieters W, Manfroid I, Baudhuin A, et al.
PLoS One. 2012;7(4):e34671.

Fast and accurate taxonomic assignments of metagenomic sequences using MetaBin.
Sharma VK, Kumar N, Prakash T, Taylor TD.
PLoS One. 2012;7(4):e34030.

Spatial proximity and similarity of the epigenetic state of genome domains.
Khrameeva EE, Mironov AA, Fedonin GG, Khaitovich P, Gelfand MS.
PLoS One. 2012;7(4):e33947.

RNA-seq mapping and detection of gene fusions with a suffix array algorithm.
Sakarya O, Breu H, Radovich M, Chen Y, et al.
PLoS Comput Biol. 2012 Apr;8(4):e1002464.

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth.
Peng Y, Leung HC, Yiu SM, Chin FY.
Bioinformatics. 2012 Apr 11. [Epub ahead of print]

CistromeMap: A knowledgebase and web server for ChIP-seq and DNase-seq studies in mouse and human.
Qin B, Zhou M, Ge Y, Taing L, et al.
Bioinformatics. 2012 Apr 11. [Epub ahead of print]

A de novo metagenomic assembly program for shotgun DNA reads.
Lai B, Ding R, Li Y, Duan L, Zhu H.
Bioinformatics. 2012 Apr 11. [Epub ahead of print]

De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode.
Xu DL, Long H, Liang JJ, Zhang J, et al.
BMC Genomics. 2012 Apr 11;13(1):133.

Discovery of potential piRNAs from next generation sequences of the sexually mature porcine testes.
Liu G, Lei B, Li Y, Tong K, et al.
PLoS One. 2012;7(4):e34770.

Atom-by-atom nucleation and growth of graphene nanopores.
Russo CJ, Golovchenko JA.
Proc Natl Acad Sci U S A. 2012 Apr 6. [Epub ahead of print]

Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs.
Li Z, Ender C, Meister G, Moore PS, et al.
Nucleic Acids Res. 2012 Apr 9. [Epub ahead of print]

GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies.
Gritsenko AA, Nijkamp JF, Reinders MJ, Ridder DD.
Bioinformatics. 2012 Apr 6. [Epub ahead of print]

PaGeFinder: quantitative identification of spatiotemporal pattern genes.
Pan JB, Hu SC, Wang H, Zou Q, Ji ZL.
Bioinformatics. 2012 Apr 6. [Epub ahead of print]

SAVoR: a server for sequencing annotation and visualization of RNA structures.
Li F, Ryvkin P, Childress DM, Valladares O, et al.
Nucleic Acids Res. 2012 Apr 6. [Epub ahead of print]

Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes using DNA microarray and next generation sequencing technologies.
Leimena MM, Wels MW, Bongers RS, Smid EJ, et al.
Appl Environ Microbiol. 2012 Apr 6. [Epub ahead of print]

Eoulsan: a cloud computing-based framework facilitating high throughput sequencing analyses.
Jourdren L, Bernard M, Dillies MA, Le Crom S.
Bioinformatics. 2012 Apr 5. [Epub ahead of print]

A survey of error-correction methods for next-generation sequencing.
Yang X, Chockalingam SP, Aluru S.
Brief Bioinform. 2012 Apr 6. [Epub ahead of print]

A tailed PCR procedure for cost-effective, two-order multiplex sequencing of candidate genes in polyploid plants.
Gholami M, Bekele WA, Schondelmaier J, Snowdon RJ.
Plant Biotechnol J. 2012 Apr 11. [Epub ahead of print]

Microsatellite development for an endangered bream Megalobrama pellegrini (teleostei, cyprinidae) using 454 sequencing.
Wang J, Yu X, Zhao K, Zhang Y, et al.
Int J Mol Sci. 2012;13(3):3009-21.

Identification and characterization of microRNAs from barley (Hordeum vulgare L.) by high-throughput sequencing.
Lv S, Nie X, Wang L, Du X, et al.
Int J Mol Sci. 2012;13(3):2973-84.

DNA origami gatekeepers for solid-state nanopores.
Wei R, Martin TG, Rant U, Dietz H.
Angew Chem Int Ed Engl. 2012 Apr 4. [Epub ahead of print]

Towards next-generation biodiversity assessment using DNA metabarcoding.
Taberlet P, Coissac E, Pompanon F, Brochmann C, Willerslev E.
Mol Ecol. 2012 Apr;21(8):2045-50.

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