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Papers of Note: May 3, 2011

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Bisulfite sequencing for cytosine-methylation analysis in plants.
Haque N, Nishiguchi M.
Methods Mol Biol. 2011;744:187-97.


Large-scale sequencing of plant small RNAs.
Donovan WP, Zhang Y, Howell MD.
Methods Mol Biol. 2011;744:159-73.


Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos.
Hajibabaei M, Shokralla S, Zhou X, Singer GA, Baird DJ.
PLoS One. 2011 Apr 13;6(4):e17497.


Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage.
Grindberg RV, Ishoey T, Brinza D, et al.
PLoS One. 2011 Apr 12;6(4):e18565.


A ChIP-seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites.
Håndstad T, Rye MB, Drabløs F, Sætrom P.
PLoS One. 2011 Apr 14;6(4):e18430.


Epigenetic regulation of cell type-specific expression patterns in the human mammary epithelium.
Maruyama R, Choudhury S, Kowalczyk A, et al.
PLoS Genet. 2011 Apr;7(4):e1001369.


Discovery of rare mutations in populations: TILLING by sequencing.
Tsai H, Howell T, Nitcher R, et al.
Plant Physiol. 2011 Apr 29. [Epub ahead of print]


Immunoprecipitation of piRNPs and directional, next-generation sequencing of piRNAs.
Kirino Y, Vourekas A, Khandros E, Mourelatos Z.
Methods Mol Biol. 2011;725:281-293.


Mapping meiotic breaks: Spo11 oligonucleotides precisely mark the spots.
Hwang PY, Hunter N.
Genome Biol. 2011 Apr 28;12(4):111. [Epub ahead of print]


Coarse-grained molecular dynamics simulation of DNA translocation in chemically modified nanopores.
Ramachandran A, Guo Q, Iqbal SM, Liu Y.
J Phys Chem B. 2011 Apr 28. [Epub ahead of print]


The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist.
Suen G, Weimer PJ, Stevenson DM, et al.
PLoS One. 2011 Apr 19;6(4):e18814.


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Evaluation of next-generation sequencing software in mapping and assembly.
Bao S, Jiang R, Kwan W, Wang B, Ma X, Song YQ.
J Hum Genet. 2011 Apr 28. [Epub ahead of print]


Single-molecule analysis of genome rearrangements in cancer.
Pole JC, McCaughan F, Newman S, Howarth KD, Dear PH, Edwards PA.
Nucleic Acids Res. 2011 Apr 27. [Epub ahead of print]


Targeted sequencing of the human X chromosome exome.
Mondal K, Shetty AC, Patel V, Cutler DJ, Zwick ME.
Genomics. 2011 Apr 16. [Epub ahead of print]


Sequence characteristics of T4-like bacteriophage IME08 genome termini revealed by high throughput sequencing.
Jiang X, Jiang H, Li C, Wang S, Mi Z, An X, Chen J, Tong Y.
Virol J. 2011 Apr 27;8(1):194.


Association studies for next-generation sequencing.
Luo L, Boerwinkle E, Xiong M.
Genome Res. 2011 Apr 26. [Epub ahead of print]


ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data.
Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N.
BMC Bioinformatics. 2011 Apr 26;12(1):119.


dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions.
Liu X, Jian X, Boerwinkle E.
Hum Mutat. 2011 Apr 21. doi: 10.1002/humu.21517.


Next-generation mapping of Arabidopsis genes.
Austin RS, Vidaurre D, Stamatiou G, et al.
Plant J. 2011 Apr 23. doi: 10.1111/j.1365-313X.2011.04619.x. [Epub ahead of print]


BM-Map: Bayesian mapping of multireads for next-generation sequencing data.
Ji Y, Xu Y, Zhang Q, Tsui KW, et al.
Biometrics. 2011 Apr 22. doi: 10.1111/j.1541-0420.2011.01605.x. [Epub ahead of print]


Comparing multiple ChIP-sequencing experiments.
Ozer HG, Huang YW, Wu J, Parvin JD, Huang TH, Huang K.
J Bioinform Comput Biol. 2011 Apr;9(2):269-82.

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