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In Print: Last Week's Sequencing-Related Papers of Note: Nov 8, 2011


959 Nematode Genomes: a semantic wiki for coordinating sequencing projects.
Kumar S, Schiffer PH, Blaxter M.
Nucleic Acids Res. 2011 Nov 3. [Epub ahead of print]

pre-miRNA profiles obtained through application of locked nucleic acids and deep sequencing reveals complex 5'/3' arm variation including concomitant cleavage and polyuridylation patterns.
Burroughs AM, Kawano M, Ando Y, Daub CO, Hayashizaki Y.
Nucleic Acids Res. 2011 Nov 3. [Epub ahead of print]

Detecting differential binding of transcription factors with ChIP-seq.
Liang K, Keles S.
Bioinformatics. 2011 Nov 3. [Epub ahead of print]

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers.
Varshney RK, Chen W, Li Y, Bharti AK, et al.
Nat Biotechnol. 2011 Nov 6. [Epub ahead of print]

Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw.
Mackelprang R, Waldrop MP, Deangelis KM, David MM, et al.
Nature. 2011 Nov 6. [Epub ahead of print]

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.
Ameur A, Zaghlool A, Halvardson J, Wetterbom A, et al.
Nat Struct Mol Biol. 2011 Nov 6. [Epub ahead of print]

deepBlockAlign: A tool for aligning RNA-seq profiles of read block patterns.
Langenberger D, Pundhir S, Ekstrøm CT, Stadler PF, et al.
Bioinformatics. 2011 Nov 3. [Epub ahead of print]

Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing.
Harakalova M, Mokry M, Hrdlickova B, Renkens I, et al.
Nat Protoc. 2011 Nov 3;6(12):1870-86.

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.
Thomas-Chollier M, Hufton A, Heinig M, O'Keeffe S, et al.
Nat Protoc. 2011 Nov 3;6(12):1860-9.

Simultaneous structural variation discovery among multiple paired-end sequenced genomes.
Hormozdiari F, Hajirasouliha I, McPherson A, Eichler EE, Sahinalp SC.
Genome Res. 2011 Nov 2. [Epub ahead of print]

RNA-seq improves annotation of protein-coding genes in the cucumber genome.
Li Z, Zhang Z, Yan P, Huang S, et al.
BMC Genomics. 2011 Nov 2;12(1):540.

Assessing diversity of the female urine microbiota by high throughput sequencing of 16S rDNA amplicons.
Siddiqui H, Nederbragt AJ, Lagesen K, Jeansson SL, Jakobsen KS.
BMC Microbiol. 2011 Nov 2;11(1):244.

RNA-seq reveals an integrated immune response in nucleated erythrocytes.
Morera D, Roher N, Ribas L, Balasch JC, et al.
PLoS One. 2011;6(10):e26998.

Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing.
Van Nieuwerburgh F, Soetaert S, Podshivalova K, Ay-Lin Wang E, et al.
PLoS One. 2011;6(10):e26969.

ReCombine: A suite of programs for detection and analysis of meiotic recombination in whole-genome datasets.
Anderson CM, Chen SY, Dimon MT, Oke A, et al.
PLoS One. 2011;6(10):e25509.

Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells.
Kolle G, Shepherd JL, Gardiner B, Kassahn KS, et al.
Genome Res. 2011 Oct 31. [Epub ahead of print]

Deep sequencing the transcriptome reveals seasonal adaptive mechanisms in a hibernating mammal.
Hampton M, Melvin RG, Kendall AH, Kirkpatrick BR, et al.
PLoS One. 2011;6(10):e27021.

The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.