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Recent Sequencing-Related Papers of Note: Sep 30, 2014


Performance comparison of Illumina and Ion Torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling.
Salipante SJ, Kawashima T, Rosenthal C, Hoogestraat DR , et al.
Appl Environ Microbiol. 2014 Sep 26. [Epub ahead of print]

jChIP: a graphical environment for exploratory ChIP-Seq data analysis.
Chojnowski K, Goryca K, Rubel T, Mikula M.
BMC Res Notes. 2014 Sep 26;7(1):676.

HTSeq - A Python framework to work with high-throughput sequencing data.
Anders S, Pyl PT, Huber W.
Bioinformatics. 2014 Sep 25. [Epub ahead of print]

Statistical strategies for microRNAseq batch effect reduction.
Guo Y, Zhao S, Su PF, Li CI, et al.
Transl Cancer Res. 2014 Jun 1;3(3):260-265.

Large-scale identification of chemically induced mutations in Drosophila melanogaster.
Haelterman NA, Jiang L, Li Y, Bayat V, et al.
Genome Res. 2014 Sep 25. [Epub ahead of print]

From museums to genomics: old herbarium specimens shed light on a C3 to C4 transition.
Besnard G, Christin PA, Malé PJ, Lhuillier E, et al.
J Exp Bot. 2014 Sep 25. [Epub ahead of print]

Transcriptional diversity during lineage commitment of human blood progenitors.
Chen L, Kostadima M, Martens JH, Canu G, et al.
Science. 2014 Sep 26;345(6204):1251033.

Confirmation of the cellular targets of benomyl and rapamycin using next-generation sequencing of resistant mutants in S. cerevisiae.
Wride DA, Pourmand N, Bray WM, Kosarchuk JJ, et al.
Mol Biosyst. 2014 Sep 26. [Epub ahead of print]

Co-detection and sequencing of genes and transcripts from the same single cells facilitated by a microfluidics platform.
Han L, Zi X, Garmire LX, Wu Y, et al.
Sci Rep. 2014 Sep 26;4:6485.

Gibbon genome and the fast karyotype evolution of small apes.
Carbone L, Harris RA, Gnerre S, Veeramah KR, et al.
Nature. 2014 Sep 11;513(7517):195-201.

A Bayesian framework to identify methylcytosines from high-throughput bisulfite sequencing data.
Xie Q, Liu Q, Mao F, Cai W, et al.
PLOS Comput Biol. 2014 Sep 25;10(9):e1003853.

Whole-genome sequencing identifies genetic variances in culture-expanded human mesenchymal stem cells.
Cai J, Miao X, Li Y, Smith C, et al.
Stem Cell Reports. 2014 Aug 12;3(2):227-233.

SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores.
Meng J, Wang B, Wei Y, Feng S, Balaji P.
BMC Bioinformatics. 2014;15 Suppl 9:S2.

Detecting epigenetic motifs in low coverage and metagenomics settings.
Beckmann ND, Karri S, Fang G, Bashir A.
BMC Bioinformatics. 2014;15 Suppl 9:S16.

ProbeAlign: incorporating high-throughput sequencing-based structure probing information into ncRNA homology search.
Ge P, Zhong C, Zhang S.
BMC Bioinformatics. 2014;15 Suppl 9:S15.

A better sequence-read simulator program for metagenomics.
Johnson S, Trost B, Long JR, Pittet V, Kusalik A.
BMC Bioinformatics. 2014;15 Suppl 9:S14.

Ensemble analysis of adaptive compressed genome sequencing strategies.
Taghavi Z.
BMC Bioinformatics. 2014;15 Suppl 9:S13.

ARYANA: Aligning Reads by Yet Another Approach.
Gholami M, Arbabi A, Sharifi-Zarchi A, Chitsaz H, Sadeghi M .
BMC Bioinformatics. 2014;15 Suppl 9:S12.

BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-seq data.
Gu J, Wang X, Halakivi-Clarke L, Clarke R, Xuan J.
BMC Bioinformatics. 2014;15 Suppl 9:S6.

CASPER: context-aware scheme for paired-end reads from high-throughput amplicon sequencing.
Kwon S, Lee B, Yoon S.
BMC Bioinformatics. 2014;15 Suppl 9:S10.

Near-optimal assembly for shotgun sequencing with noisy reads.
Lam KK, Khalak A, Tse D.
BMC Bioinformatics. 2014;15 Suppl 9:S4.

Assembly-free genome comparison based on next-generation sequencing reads and variable length patterns.
Comin M, Schimd M.
BMC Bioinformatics. 2014;15 Suppl 9:S1.

Piecing the puzzle together: a revisit to transcript reconstruction problem in RNA-seq.
Huang Y, Hu Y, Liu J.
BMC Bioinformatics. 2014;15 Suppl 9:S3.

Shape-based retrieval of CNV regions in read coverage data.
Hong S, Yoon J, Hong D, Lee U, et al.
Int J Data Min Bioinform. 2014;9(3):254-76.

A distributed amplifier system for bilayer lipid membrane (BLM) arrays with noise and individual offset cancellation.
Crescentini M, Thei F, Bennati M, Saha S, et al.
IEEE Trans Biomed Circuits Syst. 2014 Sep 19. [Epub ahead of print]

High-resolution transcriptome analysis with long-read RNA sequencing.
Cho H, Davis J, Li X, Smith KS, et al.
PLOS One. 2014 Sep 24;9(9):e108095.

MACE: model based analysis of ChIP-exo.
Wang L, Chen J, Wang C, Uusküla-Reimand L, et al.
Nucleic Acids Res. 2014 Sep 23. [Epub ahead of print]

RRHP: a tag-based approach for 5-hydroxymethylcytosine mapping at single-site resolution.
Petterson A, Chung T, Tan D, Sun X, Jia XY.
Genome Biol. 2014 Sep 24;15(9):456.

Power analysis and sample size estimation for RNA-seq differential expression.
Ching T, Huang S, Garmire LX.
RNA. 2014 Sep 22. [Epub ahead of print]

Multistep hierarchical self-assembly of chiral nanopore arrays.
Kim H, Lee S, Shin TJ, Korblova E, et al.
Proc Natl Acad Sci U S A. 2014 Sep 22. [Epub ahead of print]

Rule-based integration of RNA-seq analyses tools for identification of novel transcripts.
Inamdar H, Datta A, Manjari K S, Joshi R.
J Bioinform Comput Biol. 2014 Aug 20 [Epub ahead of print]

Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi.
Jiang X, Peery A, Hall A, Sharma A, et al.
Genome Biol. 2014 Sep 23;15(9):459.

Family-based association test using both common and rare variants and accounting for directions of effects for sequencing data.
Chung RH, Tsai WY, Martin ER.
PLOS One. 2014 Sep 22;9(9):e107800.

Quality control method for RNA-seq using single nucleotide polymorphism allele frequency.
Endo TA.
Genes Cells. 2014 Sep 21. [Epub ahead of print]

Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases.
Li W, Freudenberg J.
Comput Biol Chem. 2014 Aug 20. [Epub ahead of print]

nRIP-seq: a technique to identify RNA targets of an RNA binding protein on a genome-wide scale.
Zhao JC.
Methods Mol Biol. 2015;1206:97-106.

Genome sequence and genetic diversity of the common carp, Cyprinus carpio.
Xu P, Zhang X, Wang X, Li J, et al.
Nat Genet. 2014 Sep 21. [Epub ahead of print]

Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies.
Panousis NI, Gutierrez-Arcelus M, Dermitzakis ET, Lappalainen T.
Genome Biol. 2014 Sep 20;15(9):467.

PLEK: a tool for predicting long non-coding RNAs and messenger RNAs based on an improved k-mer scheme.
Li A, Zhang J, Zhou Z.
BMC Bioinformatics. 2014 Sep 19;15(1):311.

SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data.
Steyaert S, Van Criekinge W, De Paepe A, Denil S, et al.
Nucleic Acids Res. 2014 Sep 18. [Epub ahead of print]

Programmed synthesis of freestanding graphene nanomembrane arrays.
Waduge P, Larkin J, Upmanyu M, Kar S, Wanunu M.
Small. 2014 Sep 18. [Epub ahead of print]

DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly.
Scheinin I, Sie D, Bengtsson H, van de Wiel MA, et al.
Genome Res. 2014 Sep 18. [Epub ahead of print]

Using population data for assessing next generation sequencing performance.
Houniet DT, Rahman TJ, Al Turki S, Hurles ME, et al.
Bioinformatics. 2014 Sep 17. [Epub ahead of print]

RNA-seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations.
Munger SC, Raghupathy N, Choi K, Simons AK, et al.
Genetics. 2014 Sep;198(1):59-73.

The effects of demography and long term selection on the accuracy of genomic prediction with sequence data.
MacLeod IM, Hayes BJ, Goddard ME.
Genetics. 2014 Sep 18. [Epub ahead of print]

Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world.
Hirakawa H, Shirasawa K, Miyatake K, Nunome T, et al.
DNA Res. 2014 Sep 18. [Epub ahead of print]