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In Print: Last Week's Sequencing-Related Papers of Note: Aug 28, 2012

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Dynamic regulation of HIV-1 mRNA populations analyzed by single-molecule enrichment and long-read sequencing.
Ocwieja KE, Sherrill-Mix S, Mukherjee R, Custers-Allen R, et al.
Nucleic Acids Res. 2012 Aug 25. [Epub ahead of print]


Chromatin accessibility, p300 and histone acetylation define PML-RARα and AML1-ETO binding sites in acute myeloid leukemia.
Saeed S, Logie C, Francoijs KJ, Frigè G, Romanenghi M, et al.
Blood. 2012 Aug 24. [Epub ahead of print]


Genomic and transcriptomic studies of an RDX-degrading actinobacterium.
Chen HP, Zhu SH, Casabon I, Hallam SJ, Crocker FH, Mohn WW, Indest KJ, Eltis LD.
Appl Environ Microbiol. 2012 Aug 24. [Epub ahead of print]


Next-generation sequencing of microbial communities in the Athabasca River and its tributaries in relation to oil sands mining activities.
Yergeau E, Lawrence JR, Sanschagrin S, Waiser MJ, Korber DR, Greer CW.
Appl Environ Microbiol. 2012 Aug 24. [Epub ahead of print]


GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data.
Feng J, Meyer CA, Wang Q, Liu JS, Liu XS, Zhang Y.
Bioinformatics. 2012 Aug 24. [Epub ahead of print]


Transcriptome sequencing and annotation of the predatory mite Metaseiulus occidentalis (Acari: Phytoseiidae): a cautionary tale about possible contamination by prey sequences.
Hoy MA, Yu F, Meyer JM, Tarazona OA, Jeyaprakash A, Wu K.
Exp Appl Acarol. 2012 Aug 25. [Epub ahead of print]


The draft genome of a diploid cotton Gossypium raimondii.
Wang K, Wang Z, Li F, Ye W, Wang J, Song G, Yue Z, Cong L, et al.
Nat Genet. 2012 Aug 26. [Epub ahead of print]


Yellow lupin (Lupinus luteus L. ) transcriptome sequencing: molecular marker development and comparative studies.
Parra-Gonzalez LB, Aravena-Abarzua GA, Navarro-Navarro CS, et al.
BMC Genomics. 2012 Aug 24;13(1):425.


Human-specific transcriptional networks in the brain.
Konopka G, Friedrich T, Davis-Turak J, Winden K, Oldham MC, et al.
Neuron. 2012 Aug 23;75(4):601-17.


Full genomic sequence of an African Avian Paramyxovirus Type 4 strain isolated from a wild duck.
Abolnik C, de Castro M, Rees J.
Virus Genes. 2012 Aug 24. [Epub ahead of print]


Sequencing and characterisation of the FVB/NJ mouse genome.
Wong K, Bumpstead S, van der Weyden L, Reinholdt LG, et al.
Genome Biol. 2012 Aug 23;13(8):R72.


An Empirical Bayes Mixture Model for SNP Detection in Pooled Sequencing Data.
Zhou B.
Bioinformatics. 2012 Aug 22. [Epub ahead of print]


Qualimap: evaluating next generation sequencing alignment data.
García-Alcalde F, Okonechnikov K, Carbonell J, et al.
Bioinformatics. 2012 Aug 22. [Epub ahead of print]


Improving mapping and SNP-calling performance in multiplexed targeted next-generation sequencing.
Elsharawy A, Forster M, Schracke N, Keller A, Thomsen I, et al.
BMC Genomics. 2012 Aug 22;13(1):417.
(see related story, this issue).

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