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In Print: Sequencing-Related Papers of Note of the Last Two Weeks: Sep 3, 2013


Theoretical electrical conductivity of hydrogen-bonded benzamide-derived molecules and single DNA bases.
Chen X.
J Biol Phys. 2013 Sep;39(4):607-24.

IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling.
Li S, Lefranc MP, Miles JJ, Alamyar E, et al.
Nat Commun. 2013 Sep 2;4:2333.

SAMstrt: Statistical test for differential expression in single-cell transcriptome with spike-in normalization.
Katayama S, Töhönen V, Linnarsson S, Kere J.
Bioinformatics. 2013 Aug 31. [Epub ahead of print]

PyroHMMvar: a sensitive and accurate method to call short INDELs and SNPs for Ion Torrent and 454 data.
Zeng F, Jiang R, Chen T.
Bioinformatics. 2013 Aug 31. [Epub ahead of print]

Consed: a graphical editor for next-generation sequencing.
Gordon D, Green P.
Bioinformatics. 2013 Aug 31. [Epub ahead of print]

Practical innovations for high-throughput amplicon sequencing.
Lundberg DS, Yourstone S, Mieczkowski P, Jones CD, Dangl JL.
Nat Methods. 2013 Sep 1. [Epub ahead of print]

Chemical fragmentation for massively parallel sequencing library preparation.
Gyarmati P, Song Y, Hällman J, Käller M.
J Biotechnol. 2013 Aug 27. [Epub ahead of print]

Optimization of de novo short read assembly of seabuckthorn (Hippophae rhamnoides L.) transcriptome.
Ghangal R, Chaudhary S, Jain M, Purty RS, Chand Sharma P.
PLoS One. 2013 Aug 21;8(8):e72516.

Genic intolerance to functional variation and the interpretation of personal genomes.
Petrovski S, Wang Q, Heinzen EL, Allen AS, Goldstein DB.
PLoS Genet. 2013 Aug;9(8):e1003709.

The MaSuRCA genome assembler.
Zimin A, Marçais G, Puiu D, Roberts M, et al.
Bioinformatics. 2013 Aug 29. [Epub ahead of print]

Spatial compartmentalization at the nuclear periphery characterized by genome-wide mapping.
Wu F, Yao J.
BMC Genomics. 2013 Aug 30;14(1):591.

Dietary intervention impact on gut microbial gene richness.
Cotillard A, Kennedy SP, Kong LC, Prifti E, et al.
Nature. 2013 Aug 29;500(7464):585-8.

The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions.
Johnson BR, Atallah J, Plachetzki DC.
BMC Genomics. 2013 Aug 28;14(1):586.

Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing.
Li YH, Zhao SC, Ma JX, Li D, et al.
BMC Genomics. 2013 Aug 28;14(1):579.

The Tarenaya Hassleriana genome provides insight into reproductive trait and genome evolution of crucifers.
Cheng S, van den Bergh E, Zeng P, Zhong X, et al.
Plant Cell. 2013 Aug 27. [Epub ahead of print]

Whole-genome sequencing reveals untapped genetic potential in Africa's indigenous cereal crop sorghum.
Mace ES, Tai S, Gilding EK, Li Y, et al.
Nat Commun. 2013 Aug 27;4:2320.

Inferring nucleosome positions with their histone mark annotation from ChIP data.
Mammana A, Vingron M, Chung HR.
Bioinformatics. 2013 Aug 26. [Epub ahead of print]

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data.
Bi Y, Davuluri RV.
BMC Bioinformatics. 2013 Aug 27;14(1):262.

MITIE: Simultaneous RNA-seq-based transcript identification and quantification in multiple samples.
Behr J, Kahles A, Zhong Y, Sreedharan VT, et al.
Bioinformatics. 2013 Aug 25. [Epub ahead of print]

Identification of transcription factor binding sites from ChIP-seq data at high-resolution.
Bardet AF, Steinmann J, Bafna S, Knoblich JA, et al.
Bioinformatics. 2013 Aug 24. [Epub ahead of print]

Quantifying population genetic differentiation from next-generation sequencing data.
Fumagalli M, Vieira FG, Korneliussen TS, Linderoth T, et al.
Genetics. 2013 Aug 26. [Epub ahead of print]

Automated analysis of immunoglobulin genes from high-throughput sequencing: life without a template.
Michaeli M, Barak M, Hazanov L, Noga H, Mehr R.
J Clin Bioinforma. 2013 Aug 27;3(1):15.

Impact of library preparation on downstream analysis and interpretation of RNA-seq data: comparison between Illumina polyA and NuGEN Ovation protocol.
Sun Z, Asmann YW, Nair A, Zhang Y, et al.
PLoS One. 2013 Aug 19;8(8):e71745.

The effect of primer choice and short read sequences on the outcome of 16S rRNA gene based diversity studies.
Ghyselinck J, Pfeiffer S, Heylen K, Sessitsch A, De Vos P.
PLoS One. 2013 Aug 19;8(8):e71360.

Evaluation of MeDIP-Chip in the context of whole-genome bisulfite sequencing (WGBS-seq) in Arabidopsis.
Wardenaar R, Liu H, Colot V, Colomé-Tatché M, Johannes F.
Methods Mol Biol. 2013;1067:203-24.

Use of Bru-seq and BruChase-seq for genome-wide assessment of the synthesis and stability of RNA.
Paulsen MT, Veloso A, Prasad J, Bedi K, et al.
Methods. 2013 Aug 21. [Epub ahead of print]

MLML: Consistent simultaneous estimates of DNA methylation and hydroxymethylation.
Qu J, Zhou M, Song Q, Hong EE, Smith AD.
Bioinformatics. 2013 Aug 21. [Epub ahead of print]

Detecting association of rare variants by testing an optimally weighted combination of variants for quantitative traits in general families.
Fang S, Zhang S, Sha Q.
Hum Genet. 2013 Aug 22. [Epub ahead of print]

Whole transcriptome RNA-seq allelic expression in human brain.
Smith RM, Webb A, Papp AC, Newman LC, et al.
BMC Genomics. 2013 Aug 22;14(1):571.

MethyQA: a pipeline for bisulfite-treated methylation sequencing quality assessment.
Sun S, Noviski A, Yu X.
BMC Bioinformatics. 2013 Aug 23;14(1):259.

MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads.
Wu Y, Tian L, Pirastu M, Stambolian D, Li H.
Front Genet. 2013 Aug 16;4:157.

Assembler for de novo assembly of large genomes.
Chu TC, Lu CH, Liu T, Lee GC, et al.
Proc Natl Acad Sci U S A. 2013 Aug 21. [Epub ahead of print]

Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi.
Wasmund K, Schreiber L, Lloyd KG, Petersen DG, et al.
ISME J. 2013 Aug 22. [Epub ahead of print]

The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling.
Peng C, Fu LY, Dong PF, Deng ZL, et al.
Nucleic Acids Res. 2013 Aug 21. [Epub ahead of print]

De novo likelihood-based measures for comparing genome assemblies.
Ghodsi M, Hill CM, Astrovskaya I, Lin H, et al.
BMC Res Notes. 2013 Aug 22;6(1):334.

A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.
Esnaola M, Puig P, Gonzalez D, Castelo R, Gonzalez JR.
BMC Bioinformatics. 2013 Aug 21;14(1):254.

On the distribution of DNA translocation times in solid-state nanopores: an analysis using Schrödinger's first-passage-time theory.
Ling DY, Ling XS.
J Phys Condens Matter. 2013 Aug 21;25(37):375102.

Determination of genomic copy number alteration emphasizing a restriction-site based strategy of genome re-sequencing.
Zheng C, Miao X, Li Y, Huang Y, et al.
Bioinformatics. 2013 Aug 20. [Epub ahead of print]

Calculating sample size estimates for RNA sequencing data.
Hart SN, Therneau TM, Zhang Y, Poland GA, Kocher JP.
J Comput Biol. 2013 Aug 20. [Epub ahead of print]

A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes.
Piñol J, San Andrés V, Clare EL, Mir G, Symondson WO.
Mol Ecol Resour. 2013 Aug 20. [Epub ahead of print]

Automated serial extraction of DNA and RNA from biobanked tissue specimens.
Mathot L, Wallin M, Sjöblom T.
BMC Biotechnol. 2013 Aug 19;13(1):66.

Fine mapping of V(D)J recombinase mediated rearrangements in human lymphoid malignancies.
Halper-Stromberg E, Steranka J, Giraldo-Castillo N, Fuller T, et al.
BMC Genomics. 2013 Aug 19;14(1):565.

Imputation of coding variants in African Americans: better performance using data from the exome sequencing project.
Duan Q, Liu EY, Auer PL, Zhang G, et al.
Bioinformatics. 2013 Aug 16. [Epub ahead of print]

A local Poisson graphical model for inferring networks from sequencing data.
Allen G, Liu Z.
IEEE Trans Nanobioscience. 2013 Aug 15. [Epub ahead of print]

The sacred lotus genome provides insights into the evolution of flowering plants.
Wang Y, Fan G, Liu Y, Sun F, et al.
Plant J. 2013 Aug 16. [Epub ahead of print]

Time- and cost-efficient identification of T-DNA insertion sites through targeted genomic sequencing.
Lepage E, Zampini E, Boyle B, Brisson N.
PLOS One. 2013 Aug 12;8(8):e70912.

Comprehensive characterization of 10,571 mouse large intergenic noncoding RNAs from whole transcriptome sequencing.
Luo H, Sun S, Li P, Bu D, et al.
PLOS One. 2013 Aug 12;8(8):e70835.

Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation.
Vieira FG, Fumagalli M, Albrechtsen A, Nielsen R.
Genome Res. 2013 Aug 15. [Epub ahead of print]

Evaluation of next generation mtGenome sequencing using the Ion Torrent Personal Genome Machine (PGM).
Parson W, Strobl C, Huber G, Zimmermann B, et al.
Forensic Sci Int Genet. 2013 Sep;7(5):543-9.