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In Print: Sequencing-Related Papers of Note from the Last Two Weeks


Characterizing bias in population genetic inferences from low coverage sequencing data.
Han E, Sinsheimer JS, Novembre J.
Mol Biol Evol. 2013 Nov 27. [Epub ahead of print]

Scrapheap Challenge: A novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages.
Murray DC, Haile J, Dortch J, White NE, et al.
Sci Rep. 2013 Nov 28;3:3371.

Efficiency of whole genome amplification of single circulating tumor cells enriched by CellSearch and sorted by FACS.
Swennenhuis JF, Reumers J, Thys K, Aerssens J, Terstappen LW.
Genome Med. 2013 Nov 29;5(11):106.

Mutational and fitness landscapes of an RNA virus revealed through population sequencing.
Acevedo A, Brodsky L, Andino R.
Nature. 2013 Nov 27. [Epub ahead of print]

ezRAD: a simplified method for genomic genotyping in non-model organisms.
Toonen RJ, Puritz JB, Forsman ZH, Whitney JL, et al.
PeerJ. 2013 Nov 19;1:e203.

DNA-COMPACT: DNA COMpression Based on a Pattern-Aware Contextual Modeling Technique.
Li P, Wang S, Kim J, Xiong H, et al.
PLoS One. 2013 Nov 25;8(11):e80377.

Characterization of the human ESC transcriptome by hybrid sequencing.
Au KF, Sebastiano V, Afshar PT, Durruthy JD, et al.
Proc Natl Acad Sci U S A. 2013 Nov 26. [Epub ahead of print]

Dissection of the octoploid strawberry genome by deep sequencing of the genomes of fragaria species.
Hirakawa H, Shirasawa K, Kosugi S, Tashiro K, et al.
DNA Res. 2013 Nov 26. [Epub ahead of print]

Flexible analysis of RNA-seq data using mixed effects models.
Turro E, Astle WJ, Tavaré S.
Bioinformatics. 2013 Nov 26. [Epub ahead of print]

An extended genovo metagenomic assembler by incorporating paired-end information.
Afiahayati, Sato K, Sakakibara Y.
PeerJ. 2013 Oct 31;1:e196.

Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data.
Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, et al.
Rice. 2013 Feb 6;6(1):4.

Mapping genome-wide transcription factor binding sites in frozen tissues.
Savic D, Gertz J, Jain P, Cooper GM, Myers RM.
Epigenetics Chromatin. 2013 Sep 16;6(1):30.

Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing.
Masser DR, Berg AS, Freeman WM.
Epigenetics Chromatin. 2013 Oct 11;6(1):33.

Assessing computational methods for transcription factor target gene identification based on ChIP-seq data.
Sikora-Wohlfeld W, Ackermann M, Christodoulou EG, et al.
PLoS Comput Biol. 2013 Nov;9(11):e1003342.

Grouped false-discovery rate for removing the gene-set-level bias of RNA-seq.
Yang TY, Jeong S.
Evol Bioinform Online. 2013 Nov 13;9:467-478.

DNA translocation through low-noise glass nanopores.
Steinbock LJ, Bulushev RD, Krishnan S, et al.
ACS Nano. 2013 Nov 26. [Epub ahead of print]

A classification approach for DNA methylation profiling with bisulphite next-generation sequencing data.
Cheng L, Zhu Y.
Bioinformatics. 2013 Nov 21. [Epub ahead of print]

NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes.
Geisen S, Barturen G, Alganza AM, et al.
Nucleic Acids Res. 2013 Nov 22. [Epub ahead of print]

High-throughput genome scaffolding from in vivo DNA interaction frequency.
Kaplan N, Dekker J.
Nat Biotechnol. 2013 Nov 24. [Epub ahead of print]

Rapid electrokinetic isolation of cancer-related circulating cell-free DNA directly from blood.
Sonnenberg A, Marciniak JY, Rassenti L, Ghia EM, et al.
Clin Chem. 2013 Nov 22. [Epub ahead of print]

Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing.
Zhang R, Li X, Ramaswami G, Smith KS, et al.
Nat Methods. 2013 Nov 24. [Epub ahead of print]

Minke whale genome and aquatic adaptation in cetaceans.
Yim HS, Cho YS, Guang X, Kang SG, et al.
Nat Genet. 2013 Nov 24. [Epub ahead of print]

MMDiff: quantitative testing for shape changes in ChIP-seq data sets.
Schweikert G, Cseke B, Clouaire T, et al.
BMC Genomics. 2013 Nov 24;14(1):826.

Combining de novo and reference-guided assembly with scaffold_builder.
Silva GG, Dutilh BE, Matthews TD, et al.
Source Code Biol Med. 2013 Nov 22;8(1):23.

SomatiCA: identifying, characterizing and quantifying somatic copy number aberrations from cancer genome sequencing data.
Chen M, Gunel M, Zhao H.
PLoS One. 2013 Nov 12;8(11):e78143.

Quick, sensitive and specific detection and evaluation of quantification of minor variants by high-throughput sequencing.
Leung RK, Dong ZQ, Sa F, et al.
Mol Biosyst. 2013 Nov 22. [Epub ahead of print]

Target analysis by integration of transcriptome and ChIP-seq data with BETA.
Wang S, Sun H, Ma J, et al.
Nat Protoc. 2013 Dec;8(12):2502-2515.

Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.
Hong C, Clement NL, Clement S, et al.
BMC Bioinformatics. 2013 Nov 21;14(1):337.

Detecting a single molecule using a micropore-nanopore hybrid chip.
Liu L, Zhu L, Ni Z, Chen Y.
Nanoscale Res Lett. 2013 Nov 21;8(1):498.

Compression of structured high-throughput sequencing data.
Campagne F, Dorff KC, Chambwe N, et al.
PLoS One. 2013 Nov 18;8(11):e79871.

Assessing the effect of sequencing depth and sample size in population genetics inferences.
Fumagalli M.
PLoS One. 2013 Nov 18;8(11):e79667.

rSeqDiff: detecting differential isoform expression from RNA-seq data using hierarchical likelihood ratio test.
Shi Y, Jiang H.
PLoS One. 2013 Nov 18;8(11):e79448.

UnSplicer: mapping spliced RNA-seq reads in compact genomes and filtering noisy splicing.
Burns PD, Li Y, Ma J, Borodovsky M.
Nucleic Acids Res. 2013 Nov 19. [Epub ahead of print]

Whole-exome resequencing distinguishes cystic kidney diseases from phenocopies in renal ciliopathies.
Gee HY, Otto EA, Hurd TW, Ashraf S, et al.
Kidney Int. 2013 Nov 20. [Epub ahead of print]

Improved workflows for high throughput library preparation using the transposome-based nextera system.
Lamble S, Batty E, Attar M, Buck D, et al.
BMC Biotechnol. 2013 Nov 20;13(1):104.

Upper palaeolithic Siberian genome reveals dual ancestry of Native Americans.
Raghavan M, Skoglund P, Graf KE, Metspalu M, et al.
Nature. 2013 Nov 20. [Epub ahead of print]

DNA translocation through hydrophilic nanopore in hexagonal boron nitride.
Zhou Z, Hu Y, Wang H, Xu Z, et al.
Sci Rep. 2013 Nov 21;3:3287.

Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.
Waszak SM, Kilpinen H, Gschwind AR, Orioli A, et al.
Bioinformatics. 2013 Nov 18. [Epub ahead of print]

SNPAAMapper: An efficient genome-wide SNP variant analysis pipeline for next-generation sequencing data.
Bai Y, Cavalcoli J.
Bioinformation. 2013 Oct 16;9(17):870-2.

Exploring the transcriptome space of a recombinant BHK cell line through next generation sequencing.
Johnson KC, Yongky A, Vishwanathan N, Jacob NM, et al.
Biotechnol Bioeng. 2013 Oct 12. [Epub ahead of print]

RNA-sequencing from single nuclei.
Grindberg RV, Yee-Greenbaum JL, McConnell MJ, Novotny M, et al.
Proc Natl Acad Sci U S A. 2013 Nov 18. [Epub ahead of print]

snp-search: simple processing, manipulation and searching of SNPs from high-throughput sequencing.
Al-Shahib A, Underwood A.
BMC Bioinformatics. 2013 Nov 19;14(1):326. [Epub ahead of print]

CNVannotator: a comprehensive annotation server for copy number variation in the human genome.
Zhao M, Zhao Z.
PLoS One. 2013 Nov 14;8(11):e80170.

Practical guidelines for the comprehensive analysis of ChIP-seq data.
Bailey T, Krajewski P, Ladunga I, Lefebvre C, et al.
PLoS Comput Biol. 2013 Nov;9(11):e1003326.

Systematically differentiating functions for alternatively spliced isoforms through integrating RNA-seq data.
Eksi R, Li HD, Menon R, Wen Y, et al.
PLoS Comput Biol. 2013 Nov;9(11):e1003314.

High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing.
Lou DI, Hussmann JA, McBee RM, Acevedo A, et al.
Proc Natl Acad Sci U S A. 2013 Nov 15. [Epub ahead of print]
(See our coverage of this paper here.)

Detecting the translocation of DNA through a nanopore using graphene nanoribbons.
Traversi F, Raillon C, Benameur SM, Liu K, et al.
Nat Nanotechnol. 2013 Nov 17. [Epub ahead of print]
(See our coverage of this paper here.)

Noise and its reduction in graphene based nanopore devices.
Kumar A, Park KB, Kim HM, Kim KB.
Nanotechnology. 2013 Nov 15;24(49):495503.

DPS - A rapid method for genome sequencing of DNA-containing bacteriophages directly from a single plaque.
Kot W, Vogensen FK, Sørensen SJ, Hansen LH.
J Virol Methods. 2013 Nov 14. pii: S0166-0934(13)00454-0.