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Recent Sequencing-Related Papers of Note: Nov 11, 2014


Ulysses: Accurate detection of low-frequency structural variations in large insert-size sequencing libraries.
Gillet-Markowska A, Richard H, Fischer G, Lafontaine I.
Bioinformatics. 2014 Nov 7. [Epub ahead of print]

In silico pooling of ChIP-seq control experiments.
Sun G, Srinivasan R, Lopez-Anido C, Hung HA, et al.
PLOS One. 2014 Nov 7;9(11):e109691.

Genomic structure in Europeans dating back at least 36,200 years.
Seguin-Orlando A, Korneliussen TS, Sikora M, Malaspinas AS, et al.
Science. 2014 Nov 6. [Epub ahead of print]

DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.
Suzuki A, Wakaguri H, Yamashita R, Kawano S, et al.
Nucleic Acids Res. 2014 Nov 5. [Epub ahead of print]

RNA-seq-based toxicogenomic assessment of fresh frozen and formalin-fixed tissues yields similar mechanistic insights.
Auerbach SS, Phadke DP, Mav D, Holmgren S, et al.
J Appl Toxicol. 2014 Nov 6. [Epub ahead of print]

The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations.
Bai H, Guo X, Zhang D, Narisu N, et al.
Genome Biol Evol. 2014 Nov 5. [Epub ahead of print]

Comparison of genome sequencing technology and assembly methods for the analysis of a GC-rich bacterial genome.
Scott D, Ely B.
Curr Microbiol. 2014 Nov 7. [Epub ahead of print]

Assessment of quality control approaches for metagenomic data analysis.
Zhou Q, Su X, Ning K.
Sci Rep. 2014 Nov 7;4:6957.

Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa.
Alkan C, Kavak PN, Somel M, Gokcumen O, et al.
BMC Genomics. 2014 Nov 7;15(1):963.

Single haplotype assembly of the human genome from a hydatidiform mole.
Steinberg KM, Schneider VA, Graves-Lindsay TA, Fulton RS, et al.
Genome Res. 2014 Nov 4. [Epub ahead of print]

Large transcription units unify copy number variants and common fragile sites arising under replication stress.
Wilson TE, Arlt MF, Park SH, Rajendran S, et al.
Genome Res. 2014 Nov 4. [Epub ahead of print]

Design and synthesis of new acid cleavable linkers for DNA sequencing by synthesis.
Jiang M, Tang D, Zhao X, Li Q, et al.
Nucleosides Nucleotides Nucleic Acids. 2014 Dec 2;33(12):774-785.

Detecting differential peaks in ChIP-seq signals with ODIN.
Allhoff M, Seré K, Chauvistré H, Lin Q, et al.
Bioinformatics. 2014 Nov 3. [Epub ahead of print]

Next-generation sequencing studies guide the design of pyrrole-imidazole polyamides with improved binding specificity by the addition of β-alanine.
Anandhakumar C, Li Y, Kizaki S, Pandian GN, et al.
Chembiochem. 2014 Nov 4. [Epub ahead of print]

ARTIST: high-resolution genome-wide assessment of fitness using transposon-insertion sequencing.
Pritchard JR, Chao MC, Abel S, Davis BM, et al.
PLOS Genet. 2014 Nov 6;10(11):e1004782.

Polymer translocation through a nanopore driven by binding particles: influence of chain rigidity.
Yu W, Luo K.
Phys Rev E Stat Nonlin Soft Matter Phys. 2014 Oct;90(4-1):042708.

Methylated DNA is over-represented in whole-genome bisulfite sequencing data.
Ji L, Sasaki T, Sun X, Ma P, et al.
Front Genet. 2014 Oct 21;5:341.

RNAseqPS: a web tool for estimating sample size and power for RNA-seq experiment.
Guo Y, Zhao S, Li CI, Sheng Q, Shyr Y.
Cancer Inform. 2014 Oct 13;13(Suppl 6):1-5.

Quality Control for RNA-seq (QuaCRS): an integrated quality control pipeline.
Kroll KW, Mokaram NE, Pelletier AR, Frankhouser DE, et al.
Cancer Inform. 2014 Oct 15;13(Suppl 3):7-14.

Bayesian transcriptome assembly.
Maretty L, Sibbesen J, Krogh A.
Genome Biol. 2014 Oct 31;15(10):501.

MetaGeniE: Characterizing human clinical samples using deep metagenomic sequencing.
Rawat A, Engelthaler DM, Driebe EM, Keim P, Foster JT.
PLOS One. 2014 Nov 3;9(11):e110915.

High-throughput sequencing of human immunoglobulin variable regions with subtype identification.
Schanz M, Liechti T, Zagordi O, Miho E, et al.
PLOS One. 2014 Nov 3;9(11):e111726.

Probing solid-state nanopores with light for the detection of unlabeled analytes.
Anderson BN, Assad ON, Gilboa T, Squires AH, et al.
ACS Nano. 2014 Nov 2. [Epub ahead of print]
(See our coverage of this paper here.)

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history.
Zhou X, Wang B, Pan Q, Zhang J, et al.
Nat Genet. 2014 Nov 2. [Epub ahead of print]

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing.
Ziller MJ, Hansen KD, Meissner A, Aryee MJ.
Nat Methods. 2014 Nov 2. [Epub ahead of print]

Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing.
Wu H, Wu X, Shen L, Zhang Y.
Nat Biotechnol. 2014 Nov 2.[Epub ahead of print]