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Sequencing-Related Papers of Note from the Last Two Weeks

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Next generation sequencing provides rapid access to the genome of Puccinia striiformis f. sp. tritici, the causal agent of wheat stripe rust.
Cantu D, Govindarajulu M, Kozik A, Wang M, et al.
PLoS One. 2011;6(8):e24230.


A partial genome assembly from a candidate division OP11 single cell from an anoxic spring (Zodletone spring, OK, USA) .
Youssef NH, Blainey PC, Quake SR, Elshahed MS.
Appl Environ Microbiol. 2011 Sep 9. [Epub ahead of print]


A rapid and cost-effective method for sequencing pooled cDNA clones by using a combination of transposon insertion and Gateway technology.
Morozumi T, Toki D, Eguchi-Ogawa T, Uenishi H.
Biotechniques. 2011 Sep;51(3):195-7.


Minor variant detection in amplicons using 454 massive parallel pyrosequencing: experiences and considerations for successful applications.
Vandenbroucke I, Marck HV, Verhasselt P, Thys K, et al.
Biotechniques. 2011 Sep;51(3):167-77.


Fragmentation of contaminant and endogenous DNA in ancient samples determined by shotgun sequencing; prospects for human palaeogenomics.
García-Garcerà M, Gigli E, Sanchez-Quinto F, Ramirez O, et al.
PLoS One. 2011;6(8):e24161.


DEB: A web interface for RNA-seq digital gene expression analysis.
Yao JQ, Yu F.
Bioinformation. 2011;7(1):44-5.


Differential expression in RNA-seq: A matter of depth.
Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A.
Genome Res. 2011 Sep 8. [Epub ahead of print]


FLASH: Fast Length Adjustment of Short Reads to improve genome assemblies.
Magoc T, Salzberg SL.
Bioinformatics. 2011 Sep 7. [Epub ahead of print]


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A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data.
Li H.
Bioinformatics. 2011 Sep 8. [Epub ahead of print]


SNIT: SNP identification for strain typing.
Vijaya Satya R, Zavaljevski N, Reifman J.
Source Code Biol Med. 2011 Sep 8;6(1):14.


Translocation of DNA molecules through nanopores with salt gradients: the role of osmotic flow.
Hatlo MM, Panja D, van Roij R.
Phys Rev Lett. 2011 Aug 5;107(6):068101.


Identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing.
Silva J, Scheffler B, Sanabria Y, De Guzman C, et al.
Theor Appl Genet. 2011 Sep 7. [Epub ahead of print]


Rapid mapping and identification of mutations in Caenorhabditis elegans by RAD mapping and genomic interval pull-down sequencing.
O'Rourke SM, Yochem J, Connolly AA, Price MH, et al.
Genetics. 2011 Sep 6. [Epub ahead of print]


SpliceTrap: a method to quantify alternative splicing under single cellular conditions.
Wu J, Akerman M, Sun S, McCombie WR, et al.
Bioinformatics. 2011 Sep 6. [Epub ahead of print]


wapRNA: a web-based application for the processing of RNA sequences.
Zhao W, Liu W, Tian D, Tang B, et al.
Bioinformatics. 2011 Sep 6. [Epub ahead of print]


Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.
Jayaprakash AD, Jabado O, Brown BD, Sachidanandam R.
Nucleic Acids Res. 2011 Sep 2. [Epub ahead of print]


Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing.
Sobreira NL, Gnanakkan V, Walsh M, Marosy B, et al.
Genome Res. 2011 Sep 2. [Epub ahead of print]


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Local and global factors affecting RNA sequencing analysis.
Sendler E, Johnson GD, Krawetz SA.
Anal Biochem. 2011 Aug 16. [Epub ahead of print]


Breadth by depth: Expanding our understanding of the repair of transposon-induced DNA double strand breaks via deep sequencing.
Huefner ND, Mizuno Y, Weil CF, Korf I, Britt AB.
DNA Repair. (Amst). 2011 Aug 31. [Epub ahead of print]


Assessment of nanomaterial cytotoxicity with SOLiD sequencing-based microRNA expression profiling.
Li S, Wang H, Qi Y, Tu J, et al.
Biomaterials. 2011 Aug 31. [Epub ahead of print]


A comprehensive map of mobile element insertion polymorphisms in humans.
Stewart C, Kural D, Strömberg MP, Walker JA, et al.
PLoS Genet. 2011 Aug;7(8):e1002236.


Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea.
Amselem J, Cuomo CA, van Kan JA, Viaud M, et al.
PLoS Genet. 2011 Aug;7(8):e1002230.


Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death.
Schuenemann VJ, Bos K, Dewitte S, Schmedes S, et al.
Proc Natl Acad Sci U S A. 2011 Aug 29. [Epub ahead of print]


Context-dependent individualization of nucleotides and virtual genomic hybridization allow the precise location of human SNPs.
Reyes J, Gómez-Romero L, Ibarra-Soria X, Palacios-Flores K, et al.
Proc Natl Acad Sci U S A. 2011 Aug 29. [Epub ahead of print]


MitoBamAnnotator: A web-based tool for detecting and annotating heteroplasmy in human mitochondrial DNA sequences.
Zhidkov I, Nagar T, Mishmar D, Rubin E.
Mitochondrion. 2011 Aug 22. [Epub ahead of print]


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Native molecular state of AAV vectors revealed by single molecule sequencing.
Xiao W.
Hum Gene Ther. 2011 Aug 29. [Epub ahead of print]


CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing.
Angiuoli SV, Matalka M, Gussman A, Galens K, et al.
BMC Bioinformatics. 2011 Aug 30;12(1):356.


The genome of the green anole lizard and a comparative analysis with birds and mammals.
Alföldi J, Di Palma F, Grabherr M, Williams C, et al.
Nature. 2011 Aug 31. [Epub ahead of print]


mirExplorer: Detecting microRNAs from genome and next generation sequencing data using the AdaBoost method with transition probability matrix and combined features.
Guan DG, Liao JY, Qu ZH, Zhang Y, Qu LH.
RNA Biol. 2011 Sep 1;8(5). [Epub ahead of print]


The human gut virome: Inter-individual variation and dynamic response to diet.
Minot S, Sinha R, Chen J, Li H, et al.
Genome Res. 2011 Aug 31. [Epub ahead of print]


Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens.
Mason VC, Li G, Helgen KM, Murphy WJ.
Genome Res. 2011 Aug 31. [Epub ahead of print]


Duplex-specific nuclease efficiently removes rRNA for prokaryotic RNA-seq.
Yi H, Cho YJ, Won S, Lee JE, et al.
Nucleic Acids Res. 2011 Aug 31. [Epub ahead of print]


rRNASelector: A computer program for selecting ribosomal RNA encoding sequences from metagenomic and metatranscriptomic shotgun libraries.
Lee JH, Yi H, Chun J.
J Microbiol. 2011 Aug;49(4):689-91.


Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and mammalian lung.
Zheng W, Wang Z, Collins JE, Andrews RM, et al.
PLoS One. 2011;6(8):e24019.


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Comparative analysis of bacterial communities in a potato field as determined by pyrosequencing.
Inceoğlu O, Al-Soud WA, Salles JF, Semenov AV, van Elsas JD.
PLoS One. 2011;6(8):e23321.


The disequilibrium of nucleosomes distribution along chromosomes plays a functional and evolutionarily role in regulating gene expression.
Cui P, Lin Q, Zhang L, Ding F, et al.
PLoS One. 2011;6(8):e23219.


Titration-free 454 sequencing using Y adapters.
Zheng Z, Advani A, Melefors O, Glavas S, et al.
Nat Protoc. 2011 Aug 18;6(9):1367-76.


Linking long-term dietary patterns with gut microbial enterotypes.
Wu GD, Chen J, Hoffmann C, Bittinger K, et al.
Science. 2011 Sep 1. [Epub ahead of print]


Nonspecific PCR amplification by high-fidelity polymerases: implications for next-generation sequencing of AFLP markers.
Brelsford A, Collin H, Perrin N, Fumagalli L.
Mol Ecol Resour. 2011 Sep 2. [Epub ahead of print]

The Scan

Shape of Them All

According to BBC News, researchers have developed a protein structure database that includes much of the human proteome.

For Flu and More

The Wall Street Journal reports that several vaccine developers are working on mRNA-based vaccines for influenza.

To Boost Women

China's Ministry of Science and Technology aims to boost the number of female researchers through a new policy, reports the South China Morning Post.

Science Papers Describe Approach to Predict Chemotherapeutic Response, Role of Transcriptional Noise

In Science this week: neural network to predict chemotherapeutic response in cancer patients, and more.