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Recent Sequencing Papers of Note: Sep 16, 2014


JBP1-seq: A fast and efficient method for genome-wide profiling of 5hmC.
Cui L, Chung TH, Tan D, Sun X, Jia XY.
Genomics. 2014 Sep 10. [Epub ahead of print]

De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.
Li YH, Zhou G, Ma J, Jiang W, et al.
Nat Biotechnol. 2014 Sep 14. [Epub ahead of print]

Binning metagenomic contigs by coverage and composition.
Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, et al.
Nat Methods. 2014 Sep 14. [Epub ahead of print]

Improved rat genome gene prediction by integration of ESTs with RNA-seq information.
Li L, Chen E, Yang C, Zhu J, et al.
Bioinformatics. 2014 Sep 12. [Epub ahead of print]

Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis.
Tallon LJ, Liu X, Bennuru S, Chibucos MC, et al.
BMC Genomics. 2014 Sep 12;15(1):788.

Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge.
Gusev O, Suetsugu Y, Cornette R, Kawashima T, et al.
Nat Commun. 2014 Sep 12;5:4784.

Comparison of hepatocellular carcinoma miRNA expression profiling as evaluated by next generation sequencing and microarray.
Murakami Y, Tanahashi T, Okada R, Toyoda H, et al.
PLOS One. 2014 Sep 12;9(9):e106314.

Determination and inference of eukaryotic transcription factor sequence specificity.
Weirauch MT, Yang A, Albu M, Cote AG, et al.
Cell. 2014 Sep 11;158(6):1431-1443.

Genome-wide profiling of untranslated regions by paired-end ditag sequencing reveals unexpected transcriptome complexity in yeast.
Kang YN, Lai DP, Ooi HS, Shen TT, et al.
Mol Genet Genomics. 2014 Sep 12. [Epub ahead of print]

GSAASeqSP: a toolset for gene set association analysis of RNA-seq data.
Xiong Q, Mukherjee S, Furey TS.
Sci Rep. 2014 Sep 12;4:6347.

De novo genome assembly of the economically-important weed Conyza Canadensis using integrated data from multiple sequencing platforms.
Peng Y, Lai Z, Lane T, Rao M, et al.
Plant Physiol. 2014 Sep 10. [Epub ahead of print]

Gibbon genome and the fast karyotype evolution of small apes.
Carbone L, Harris RA, Gnerre S, Veeramah KR, et al.
Nature. 2014 Sep 11;513(7517):195-201.

Reversible positioning of single molecules inside zero-mode waveguides.
Larkin J, Foquet M, Turner SW, Korlach J, Wanunu M.
Nano Lett. 2014 Sep 11. [Epub ahead of print]

Ribosomal DNA copy number is coupled with gene expression variation and mitochondrial abundance in humans.
Gibbons JG, Branco AT, Yu S, Lemos B.
Nat Commun. 2014 Sep 11;5:4850.

Paleomicrobiology: revealing fecal microbiomes of ancient indigenous cultures.
Cano RJ, Rivera-Perez J, Toranzos GA, Santiago-Rodriguez TM, et al.
PLOS One. 2014 Sep 10;9(9):e106833.

Single-molecule correlated chemical probing of RNA.
Homan PJ, Favorov OV, Lavender CA, Kursun O, et al.
Proc Natl Acad Sci U S A. 2014 Sep 9. [Epub ahead of print]

RNA-seq of the nucleolus reveals abundant SNORD44-derived small RNAs.
Bai B, Yegnasubramanian S, Wheelan SJ, Laiho M.
PLOS One. 2014 Sep 9;9(9):e107519.

Partition enrichment of nucleotide sequences (PINS) − a generally applicable, sequence based method for enrichment of complex DNA samples.
Kvist T, Sondt-Marcussen L, Mikkelsen MJ.
PLOS One. 2014 Sep 9;9(9):e106817.

Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins.
Carmi S, Hui KY, Kochav E, Liu X, et al.
Nat Commun. 2014 Sep 9;5:4835.

Reading single DNA with DNA polymerase followed by atomic force microscopy.
Kim Y, Kim ES, Lee Y, Kim JH, et al.
J Am Chem Soc. 2014 Sep 9. [Epub ahead of print]

Genome sequencing of chimpanzee malaria parasites reveals possible pathways of adaptation to human hosts.
Otto TD, Rayner JC, Böhme U, Pain A, et al.
Nat Commun. 2014 Sep 9;5:4754.

Graphene nanopore with a self-integrated optical antenna.
Nam S, Choi I, Fu CC, Kim K, et al.
Nano Lett. 2014 Sep 9. [Epub ahead of print]

A long PCR-based approach for DNA enrichment prior to next-generation sequencing for systematic studies.
Uribe-Convers S, Duke JR, Moore MJ, Tank DC.
Appl Plant Sci. 2014 Jan 7;2(1).

A method for extracting high-quality RNA from diverse plants for next-generation sequencing and gene expression analyses.
Yockteng R, Almeida AM, Yee S, Andre T, et al.
Appl Plant Sci. 2013 Dec 9;1(12).

Towards accurate characterization of clonal heterogeneity based on structural variation.
Fan X, Zhou W, Chong Z, Nakhleh L, Chen K.
BMC Bioinformatics. 2014 Sep 8;15(1):299.

SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets.
Sarovich DS, Price EP.
BMC Res Notes. 2014 Sep 8;7(1):618.

Next-generation RNA sequencing of archival formalin-fixed paraffin-embedded urothelial bladder cancer.
Liu Y, Noon AP, Aguiar Cabeza E, Shen J, et al.
Eur Urol. 2014 Sep 5. [Epub ahead of print]

GABenchToB: a genome assembly benchmark tuned on bacteria and benchtop sequencers.
Jünemann S, Prior K, Albersmeier A, Albaum S, et al.
PLOS One. 2014 Sep 8;9(9):e107014.

Single cell sequencing reveals low levels of aneuploidy across mammalian tissues.
Knouse KA, Wu J, Whittaker CA, Amon A.
Proc Natl Acad Sci U S A. 2014 Sep 2. [Epub ahead of print]

Vanno: a visualization-aided variant annotation tool.
Huang PJ, Lee CC, Tan BC, Yeh YM, et al.
Hum Mutat. 2014 Sep 4. [Epub ahead of print]