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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]

The Scan

Not as High as Hoped

The Associated Press says initial results from a trial of CureVac's SARS-CoV-2 vaccine suggests low effectiveness in preventing COVID-19.

Finding Freshwater DNA

A new research project plans to use eDNA sampling to analyze freshwater rivers across the world, the Guardian reports.

Rise in Payments

Kaiser Health News investigates the rise of payments made by medical device companies to surgeons that could be in violation of anti-kickback laws.

Nature Papers Present Ginkgo Biloba Genome Assembly, Collection of Polygenic Indexes, More

In Nature this week: a nearly complete Ginkgo biloba genome assembly, polygenic indexes for dozens of phenotypes, and more.