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Last Week's Sequencing-Related Papers of Note: Apr 15, 2014


A Model-Based Approach to Identify Binding Sites in CLIP-Seq Data.
Wang T1, Chen B2, Kim M2, Xie Y2, Xiao G1.
PLoS One. 2014 Apr 8;9(4):e93248.

Genome alignment with graph data structures: a comparison.
Kehr B, Trappe K, Holtgrewe M, Reinert K.
BMC Bioinformatics. 2014 Apr 9;15(1):99.

TraV: A Genome Context Sensitive Transcriptome Browser.
Dietrich S, Wiegand S, Liesegang H.
PLoS One. 2014 Apr 7;9(4):e93677.

An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3.
Schifano JM1, Vvedenskaya IO2, Knoblauch JG2, Ouyang M3, Nickels BE2, Woychik NA1.
Nat Commun. 2014 Apr 8;5:3538.

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization.
Bonhoure N1, Bounova G, Bernasconi D, Praz V, Lammers F, et al.
Genome Res. 2014 Apr 7. [Epub ahead of print]

LaSSO, a strategy for genome-wide mapping of intronic lariats and branch-points using RNA-seq.
Bitton DA1, Rallis C, Jeffares DC, Smith GC, Chen YY, Codlin S, Marguerat S, Bahler J.
Genome Res. 2014 Apr 7. [Epub ahead of print]

A detailed analysis of next generation sequencing reads of microRNA expression in Barrett's Esophagus: absolute versus relative quantification.
Lee IH, Hong X, Mathur SC, Sharma M, Rastogi A, Sharma P, Christenson LK, Bansal A.
BMC Res Notes. 2014 Apr 4;7(1):212.

VCGDB: a dynamic genome database of the Chinese population.
Ling Y, Jin Z, Su M, Zhong J, Zhao Y, Yu J, Wu J, Xiao J.
BMC Genomics. 2014 Apr 5;15(1):265.

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data.
Caboche S, Audebert C, Lemoine Y, Hot D.
BMC Genomics. 2014 Apr 5;15(1):264.

Exome capture from saliva produces high quality genomic and metagenomic data.
Kidd JM, Sharpton TJ, Bobo D, Norman PJ, Martin AR, et al.
BMC Genomics. 2014 Apr 4;15(1):262.

Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS.
Tosar JP, Rovira C, Naya H, Cayota A.
RNA. 2014 Apr 11. [Epub ahead of print]

A change-point model for identifying 3'UTR switching by next-generation RNA sequencing.
Wang W, Wei Z, Li H.
Bioinformatics. 2014 Apr 11. [Epub ahead of print]

Deep-Sequencing Method for Quantifying Background Abundances of Symbiodinium Types: Exploring the Rare Symbiodinium Biosphere in Reef-Building Corals.
Quigley KM, Davies SW, Kenkel CD, Willis BL, Matz MV, Bay LK.
PLoS One. 2014 Apr 11;9(4):e94297.

A Two-Dimensional Pooling Strategy for Rare Variant Detection on Next-Generation Sequencing Platforms.
Zuzarte PC, Denroche RE, Fehringer G, Katzov-Eckert H, Hung RJ, McPherson JD.
PLoS One. 2014 Apr 11;9(4):e93455.

Amplicon -Based Metagenomic Analysis of Mixed Fungal Samples Using Proton Release Amplicon Sequencing.
Tonge DP, Pashley CH, Gant TW.
PLoS One. 2014 Apr 11;9(4):e93849.

Isolation and characterization of novel lipase gene LipHim1 from the DNA isolated from soil samples.
Pindi PK, Raja SR, Pavankumar TL.
J Microbiol. 2014 Apr 11. [Epub ahead of print]

Charged particle separation by an electrically tunable nanoporous membrane.
Jou IA, Melnikov DV, Nadtochiy A, Gracheva ME.
Nanotechnology. 2014 Apr 11;25(14):145201.

Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome.
Zuo Y, Zhang P, Liu L, Li T, Peng Y, Li G, Li Q.
Chromosome Res. 2014 Apr 12. [Epub ahead of print]

Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication.
Li M, Tian S, Yeung CK, Meng X, Tang Q, Niu L, Wang X, et al.
Sci Rep. 2014 Apr 14;4:4678.

Next-generation sequencing and bioinformatic approaches to detect and analyze influenza virus in ferrets.
Lin Z, Farooqui A, Li G, Wong GK, Mason AL, Banner D, Kelvin AA, Kelvin DJ, Leon AJ.
J Infect Dev Ctries. 2014 Apr 15;8(4):498-509.

Single-Cell and Deep Sequencing of IgG-Switched Macaque B Cells Reveal a Diverse Ig Repertoire following Immunization.
Sundling C, Zhang Z, Phad GE, Sheng Z, Wang Y, Mascola JR, Li Y, Wyatt RT, Shapiro L, Karlsson Hedestam GB.
J Immunol. 2014 Apr 15;192(8):3637-44.