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Recent Sequencing-Related Papers of Note: Jun 17, 2014

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Evaluation and validation of de novo and hybrid assembly techniques to derive high quality genome sequences.
Utturkar SM, Klingeman DM, Land ML, Schadt CW, et al.
Bioinformatics. 2014 Jun 14. [Epub ahead of print]


An integrative method to normalize RNA-seq data.
Filloux C, Meersseman C, Philippe R, Forestier L, et al.
BMC Bioinformatics. 2014 Jun 14;15(1):188.


Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.
Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, et al.
Nat Genet. 2014 Jun 15. [Epub ahead of print]


Genome and transcriptome of the porcine whipworm Trichuris suis.
Jex AR, Nejsum P, Schwarz EM, Hu L, et al.
Nat Genet. 2014 Jun 15. [Epub ahead of print]


Methylation-capture and next-generation sequencing of free circulating DNA from human plasma.
Warton K, Lin V, Navin T, Armstrong NJ, et al.
BMC Genomics. 2014 Jun 15;15(1):476.


Automatic analysis pipeline of next-generation sequencing data.
Wenke L, Fengyu L, Siyao Z, Bin C, et al.
Yi Chuan. 2014 Jun 20;36(6):618-624.


DNA sequence analysis with droplet-based microfluidics.
Abate AR, Hung T, Sperling RA, Mary P, et al.
Lab Chip. 2013 Dec 21;13(24):4864-9.


Antibody repertoire deep sequencing reveals antigen-independent selection in maturing B cells.
Kaplinsky J, Li A, Sun A, Coffre M, et al.
Proc Natl Acad Sci U S A. 2014 Jun 9. [Epub ahead of print]


Draft genome sequence of a rare smut relative, Tilletiaria anomala UBC 951.
Toome M, Kuo A, Henrissat B, Lipzen A, et al.
Genome Announc. 2014 Jun 12;2(3).


Interactions between RNA polymerase and the "core recognition element" counteract pausing.
Vvedenskaya IO, Vahedian-Movahed H, Bird JG, Knoblauch JG, et al.
Science. 2014 Jun 13;344(6189):1285-1289.


Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads.
Jiang H, Lei R, Ding SW, Zhu S.
BMC Bioinformatics. 2014 Jun 12;15(1):182.


Library construction for ancient genomics: Single strand or double strand?
Bennett EA, Massilani D, Lizzo G, Daligault J, et al.
Biotechniques. 2014 Jun 1;56(6):289-300.


Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.
Ekblom R, Smeds L, Ellegren H.
BMC Genomics. 2014 Jun 12;15(1):467.


The bias associated with amplicon sequencing does not affect the quantitative assessment of bacterial community dynamics.
Ibarbalz FM, Pérez MV, Figuerola EL, Erijman L.
PLOS One. 2014 Jun 12;9(6):e99722.


Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens.
Jin C, Yang L, Xie M, Lin C, et al.
Proc Natl Acad Sci U S A. 2014 Jun 13. [Epub ahead of print]


Improving analysis of transcription factor binding sites within ChIP-seq data based on topological motif enrichment.
Worsley Hunt R, Mathelier A, Del Peso L, Wasserman WW.
BMC Genomics. 2014 Jun 13;15(1):472.


Capture and amplification by tailing and switching (CATS): an ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA.
Turchinovich A, Surowy H, Serva A, Zapatka M, et al.
RNA Biol. 2014 Jun 12;11(7).


ARH-seq: identification of differential splicing in RNA-seq data.
Rasche A, Lienhard M, Yaspo ML, Lehrach H, Herwig R.
Nucleic Acids Res. 2014 Jun 11. [Epub ahead of print]


Controlling the motion of DNA in a nanochannel with transversal alternating electric voltages.
Luan B, Wang C, Royyuru A, Stolovitzky G.
Nanotechnology. 2014 Jun 12;25(26):265101.


Blue: correcting sequencing errors using consensus and context.
Greenfield P, Duesing K, Papanicolaou A, Bauer DC.
Bioinformatics. 2014 Jun 11. [Epub ahead of print]


Comparison of the performance of Ion Torrent chips in noninvasive prenatal trisomy detection.
Wang Y, Wen Z, Shen J, Cheng W, et al.
J Hum Genet. 2014 Jun 12. [Epub ahead of print]


Fully automated high-throughput chromatin immunoprecipitation for ChIP-seq: Identifying ChIP-quality p300 monoclonal antibodies.
Gasper WC, Marinov GK, Pauli-Behn F, Scott MT, et al.
Sci Rep. 2014 Jun 12;4:5152.


Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.
Shalek AK, Satija R, Shuga J, Trombetta JJ, et al.
Nature. 2014 Jun 11. [Epub ahead of print]


The genome of Eucalyptus grandis.
Myburg AA, Grattapaglia D, Tuskan GA, Hellsten U, et al.
Nature. 2014 Jun 11. [Epub ahead of print]


HIVE-Hexagon: High-performance, parallelized sequence alignment for next-generation sequencing data analysis.
Santana-Quintero L, Dingerdissen H, Thierry-Mieg J, Mazumder R, Simonyan V.
PLOS One. 2014 Jun 11;9(6):e99033.


Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products.
Beitel CW, Froenicke L, Lang JM, Korf IF, et al.
PeerJ. 2014 May 27;2:e415.


PBHoney: Identifying genomic variants via long-read discordance and interrupted mapping.
English AC, Salerno WJ Dr, Reid JG.
BMC Bioinformatics. 2014 Jun 10;15(1):180.


Performance comparison of four exome capture systems for deep sequencing.
Chilamakuri CS, Lorenz S, Madoui MA, Vodák D, et al.
BMC Genomics. 2014 Jun 9;15(1):449.


Analysis of run-to-run variation of bar-coded pyrosequencing for evaluating bacterial community shifts and individual taxa dynamics.
Ge Y, Schimel JP, Holden PA.
PLOS One. 2014 Jun 9;9(6):e99414.


Evaluation of a pooled strategy for high-throughput sequencing of cosmid clones from metagenomic libraries.
Lam KN, Hall MW, Engel K, Vey G, et al.
PLOS One. 2014 Jun 9;9(6):e98968.


Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis.
Fernandes AD, Reid JN, Macklaim JM, McMurrough TA, et al.
Microbiome. 2014 May 5;2:15.

The Scan

WHO Seeks Booster Pause

According to CNN, the World Health Organization is calling for a moratorium on administering SARS-CoV-2 vaccine boosters until more of the world has received initial doses.

For Those Long Legs

With its genome sequence and subsequent RNAi analyses, researchers have examined the genes that give long legs to daddy longlegs, New Scientist says.

September Plans

The New York Times reports that the US Food and Drug Administration is aiming for early September for full approval of the Pfizer-BioNTech SARS-CoV-2 vaccine.

Nucleic Acids Research Papers on Targeting DNA Damage Response, TSMiner, VarSAn

In Nucleic Acids Research this week: genetic changes affecting DNA damage response inhibitor response, "time-series miner" approach, and more.