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In Print: Last Week's Sequencing-Related Papers of Note: Mar 12, 2013


Evaluation of allele frequency estimation using pooled sequencing data simulation.
Guo Y, Samuels DC, Li J, Clark T, et al.
ScientificWorldJournal. 2013;2013:895496. Epub 2013 Feb 7.

Investigation of the bacterial retting community of kenaf (Hibiscus cannabinus) under different conditions using next-generation semiconductor sequencing.
Visi DK, D'Souza N, Ayre BG, Webber Iii CL, Allen MS.
J Ind Microbiol Biotechnol. 2013 Mar 10. [Epub ahead of print]

Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers.
Nordström KJ, Albani MC, James GV, Gutjahr C, et al.
Nat Biotechnol. 2013 Mar 10. [Epub ahead of print]

Detection and quantification of methylation in DNA using solid-state nanopores.
Shim J, Humphreys GI, Venkatesan BM, Munz JM, et al.
Sci Rep. 2013 Mar 11;3:1389.

MitoSeek: extracting mitochondria information and performing high throughput mitochondria sequencing analysis.
Guo Y, Li J, Li CI, Shyr Y, Samuels DC.
Bioinformatics. 2013 Mar 6. [Epub ahead of print]

freeIbis: an efficient basecaller with calibrated quality scores for Illumina sequencers.
Renaud G, Kircher M, Stenzel U, Kelso J.
Bioinformatics. 2013 Mar 6. [Epub ahead of print]

A high-throughput and quantitative method to assess the mutagenic potential of translesion DNA synthesis.
Taggart DJ, Camerlengo TL, Harrison JK, Sherrer SM, et al.
Nucleic Acids Res. 2013 Mar 6. [Epub ahead of print]

Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.
Lundin S, Gruselius J, Nystedt B, Lexow P, et al.
Sci Rep. 2013 Mar 8;3:1186.

Digging the New York City skyline: soil fungal communities in green roofs and city parks.
McGuire KL, Payne SG, Palmer MI, Gillikin CM, et al.
PLoS One. 2013;8(3):e58020.

TagGD: fast and accurate software for DNA tag generation and demultiplexing.
Costea PI, Lundeberg J, Akan P.
PLoS One. 2013;8(3):e57521.

Genome wide allele frequency fingerprints (GWAFFs) of populations via genotyping by sequencing.
Byrne S, Czaban A, Studer B, Panitz F, et al.
PLoS One. 2013;8(3):e57438.

De novo assembly, gene annotation and marker development using Illumina paired-end transcriptome sequences in celery (Apium graveolens L.).
Fu N, Wang Q, Shen HL.
PLoS One. 2013;8(2):e57686.

The poultry-associated microbiome: network analysis and farm-to-fork characterizations.
Oakley BB, Morales CA, Line J, Berrang ME, et al.
PLoS One. 2013;8(2):e57190.

De novo transcriptome assembly (NGS) of Curcuma longa L. rhizome reveals novel transcripts related to anticancer and antimalarial terpenoids.
Annadurai RS, Neethiraj R, Jayakumar V, Damodaran AC, et al.
PLoS One. 2013;8(2):e56217.

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci.
Schardl CL, Young CA, Hesse U, Amyotte SG, et al.
PLoS Genet. 2013 Feb;9(2):e1003323.

Patterns of population epigenomic diversity.
Schmitz RJ, Schultz MD, Urich MA, Nery JR, et al.
Nature. 2013 Mar 6. [Epub ahead of print]

Differential gene expression analysis between anagen and telogen of Capra hircus skin based on the de novo assembled transcriptome sequence.
Xu T, Guo X, Wang H, Hao F, et al.
Gene. 2013 Mar 2. pii: S0378-1119(13)00194-7.

Polymer translocation through a nanopore: DPD study.
Yang K, Vishnyakov A, Neimark AV.
J Phys Chem B. 2013 Mar 6. [Epub ahead of print]

Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua.
Carlsson J, Gauthier DT, Carlsson JE, Coughlan JP, et al.
J Fish Biol. 2013 Mar;82(3):944-58.

Sex differences in the gut microbiome drive hormone-dependent regulation of autoimmunity.
Markle JG, Frank DN, Mortin-Toth S, Robertson CE, et al.
Science. 2013 Mar 1;339(6123):1084-8.

A robust method for transcript quantification with RNA-seq data.
Huang Y, Hu Y, Jones CD, Macleod JN, et al.
J Comput Biol. 2013 Mar;20(3):167-87.

Canonical correlation analysis for RNA-seq co-expression networks.
Hong S, Chen X, Jin L, Xiong M.
Nucleic Acids Res. 2013 Mar 4. [Epub ahead of print]

Comparison of analysis tools for miRNA high throughput sequencing using nerve crush as a model.
Metpally RP, Nasser S, Malenica I, Courtright A, et al.
Front Genet. 2013;4:20.

A highly accurate heuristic algorithm for the haplotype assembly problem.
Deng F, Cui W, Wang L.
BMC Genomics. 2013;14 Suppl 2:S2.