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In Print: Last Week's Sequencing-Related Papers of Note: Nov 5, 2013


Optoelectronic control of surface charge and translocation dynamics in solid-state nanopores.
Di Fiori N, Squires A, Bar D, Gilboa T, et al.
Nat Nanotechnol. 2013 Nov 3. [Epub ahead of print]

Assessment of transcript reconstruction methods for RNA-seq.
Steijger T, Abril JF, Engström PG, Kokocinski F et al.
Nat Methods. 2013 Nov 3. [Epub ahead of print]

Systematic evaluation of spliced alignment programs for RNA-seq data.
Engström PG, Steijger T, Sipos B, Grant GR, et al.
Nat Methods. 2013 Nov 3. [Epub ahead of print]

GWIPS-viz: development of a ribo-seq genome browser.
Michel AM, Fox G, M Kiran A, De Bo C, et al.
Nucleic Acids Res. 2013 Oct 31. [Epub ahead of print]

Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing.
Selvaraj S, R Dixon J, Bansal V, Ren B.
Nat Biotechnol. 2013 Nov 3. [Epub ahead of print]

Probabilistic model based error correction in a set of various mutant sequences analyzed by next-generation sequencing.
Aita T, Ichihashi N, Yomo T.
Comput Biol Chem. 2013 Oct 10;47C:221-230. [Epub ahead of print]

Mapping of mitochondrial RNA-protein interactions by digital RNase footprinting.
Liu G, Mercer TR, Shearwood AM, Siira SJ, et al.
Cell Rep. 2013 Oct 29. [Epub ahead of print]

A benchmark study on error assessment and quality control of CCS reads derived from the PacBio RS.
Jiao X, Zheng X, Ma L, Kutty G, et al.
J Data Mining Genomics Proteomics. 2013 Jul 31;4(3).

Mosaic copy number variation in human neurons.
McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, et al.
Science. 2013 Nov 1;342(6158):632-7.

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.
Guo H, Zhu P, Wu X, Li X, et al.
Genome Res. 2013 Oct 31. [Epub ahead of print]

Non-equilibrium folding of individual DNA molecules recaptured up to 1000 times in a solid state nanopore.
Plesa C, Cornelissen L, Tuijtel MW, Dekker C.
Nanotechnology. 2013 Oct 31;24(47):475101.

HapFABIA: Identification of very short segments of identity by descent characterized by rare variants in large sequencing data.
Hochreiter S.
Nucleic Acids Res. 2013 Oct 29. [Epub ahead of print]

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins.
Teytelman L, Thurtle DM, Rine J, van Oudenaarden A.
Proc Natl Acad Sci U S A. 2013 Oct 30. [Epub ahead of print]

EXCAVATOR: detecting copy number variants from whole-exome sequencing data.
Magi A, Tattini L, Cifola I, D'Aurizio R, et al.
Genome Biol. 2013 Oct 30;14(10):R120.

Nanopore-based identification of individual nucleotides for direct RNA sequencing.
Ayub M, Hardwick SW, Luisi BF, Bayley H.
Nano Lett. 2013 Oct 31. [Epub ahead of print]

Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations.
Zhou X, Sun F, Xu S, Fan G, et al.
Nat Commun. 2013 Oct 29;4:2708.

Identification of novel viruses using VirusHunter — an automated data analysis pipeline.
Zhao G, Krishnamurthy S, Cai Z, Popov VL, et al.
PLOS One. 2013 Oct 22;8(10):e78470.

Experimental design-based functional mining and characterization of high-throughput sequencing data in the sequence read archive.
Nakazato T, Ohta T, Bono H.
PLOS One. 2013 Oct 22;8(10):e77910.

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands.
Schreiber J, Wescoe ZL, Abu-Shumays R, Vivian JT, et al.
Proc Natl Acad Sci U S A. 2013 Oct 28. [Epub ahead of print]

Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA.
Laszlo AH, Derrington IM, Brinkerhoff H, Langford KW, et al.
Proc Natl Acad Sci U S A. 2013 Oct 28. [Epub ahead of print]

Identifying rare variants with optimal depth of coverage and cost-effective overlapping pool sequencing.
Cao CC, Li C, Huang Z, Ma X, Sun X.
Genet Epidemiol. 2013 Oct 28. [Epub ahead of print]

Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing.
Elliott CP, Enright NJ, Allcock RJ, Gardner MG, et al.
Mol Ecol Resour. 2013 Oct 24. [Epub ahead of print]

Modeling, simulation and analysis of methylation profiles from reduced representation bisulfite sequencing experiments.
Lacey MR, Baribault C, Ehrlich M.
Stat Appl Genet Mol Biol. 2013 Oct 25:1-20. [Epub ahead of print]

Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars.
Li M, Tian S, Jin L, Zhou G, et al.
Nat Genet. 2013 Oct 27. [Epub ahead of print]

The microglial sensome revealed by direct RNA sequencing.
Hickman SE, Kingery ND, Ohsumi TK, Borowsky ML, et al.
Nat Neurosci. 2013 Oct 27. [Epub ahead of print]

SSP: An interval integer linear programming for de novo transcriptome assembly and isoform discovery of RNA-seq reads.
Safikhani Z, Sadeghi M, Pezeshk H, Eslahchi C.
Genomics. 2013 Oct 23. [Epub ahead of print]

Slowing DNA translocation through a nanopore using a functionalized electrode.
Krishnakumar P, Gyarfas B, Song W, Sen S, et al.
ACS Nano. 2013 Oct 28. [Epub ahead of print]