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In Print: Last Week's Sequencing-Related Papers of Note: Jun 18, 2013


Fungal High-throughput Taxonomic Identification tool for use with Next-Generation Sequencing (FHiTINGS).
Dannemiller KC, Reeves D, Bibby K, Yamamoto N, Peccia J.
J Basic Microbiol. 2013 Jun 14. [Epub ahead of print]

Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae.
Schuenemann VJ, Singh P, Mendum TA, Krause-Kyora B, et al.
Science.2013 Jun 13. [Epub ahead of print]

Deep mutational scanning of an antibody against epidermal growth factor receptor using mammalian cell display and massively parallel pyrosequencing.
Forsyth CM, Juan V, Akamatsu Y, Dubridge RB, et al.
MAbs. 2013 May 29;5(4).

Genome-wide measurement of protein-DNA binding dynamics using competition ChIP.
Lickwar CR, Mueller F, Lieb JD.
Nat Protoc. 2013 Jun 13;8(7):1337-53.

Characterization of tetracycline resistant bacterial community in saline activated sludge using batch stress incubation with high-throughput sequencing analysis.
Li B, Zhang X, Guo F, Wu W, Zhang T.
Water Res. 2013 May 3;47(13):4207-4216.

A Modified RNA-Seq Approach for Whole Genome Sequencing of RNA Viruses from Faecal and Blood Samples.
Batty EM, Wong TH, Trebes A, Argoud K, et al.
PLoS One. 2013 Jun 10;8(6):e66129.

diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates.
Shen L, Shao NY, Liu X, Maze I, et al.
PLoS One. 2013 Jun 10;8(6):e65598.

Case-control association testing of common variants from sequencing of DNA pools.
McRae AF, Richter MM, Lind PA.
PLoS One. 2013 Jun 7;8(6):e65410.

DNA qualification workflow for next generation sequencing of histopathological samples.
Simbolo M, Gottardi M, Corbo V, Fassan M, et al.
PLoS One. 2013 Jun 6;8(6):e62692.

The Genome of Anopheles darlingi, the main neotropical malaria vector.
Marinotti O, Cerqueira GC, de Almeida LG, Ferro MI, et al.
Nucleic Acids Res. 013 Jun 12. [Epub ahead of print]

Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?
Lundin D, Severin I, Logue JB, Ostman O, et al.
Environ Microbiol Rep. 2012 Jun;4(3):367-72.

COVER: a priori estimation of coverage for metagenomic sequencing.
Tamames J, de la Peña S, de Lorenzo V.
Environ Microbiol Rep. 2012 Jun;4(3):335-41.

Dynamics of 5-hydroxymethylcytosine during mouse spermatogenesis.
Gan H, Wen L, Liao S, Lin X, et al.
Nat Commun. 2013 Jun 13;4:1995.

Comprehensive genotyping of the USA national maize inbred seed bank.
Romay MC, Millard MJ, Glaubitz JC, Peiffer JA, et al.
Genome Biol. 2013 Jun 11;14(6):R55.

Skin transcriptome profiles associated with coat color in sheep.
Fan R, Xie J, Bai J, Wang H, et al.
BMC Genomics. 2013 Jun 10;14(1):389.

ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking.
Wu G, Ji H.
BMC Bioinformatics. 2013 Jun 10;14(1):188.

QualComp: a new lossy compressor for quality scores based on rate distortion theory.
Ochoa I, Asnani H, Bharadia D, Chowdhury M, et al.
BMC Bioinformatics. 2013 Jun 8;14(1):187.

Benchmarking short sequence mapping tools.
Hatem A, Bozda D, Toland AE, Catalyürek UV.
BMC Bioinformatics. 2013 Jun 7;14(1):184.

Chemical Modification-Assisted Bisulfite Sequencing (CAB-Seq) for 5-Carboxylcytosine Detection in DNA.
Lu X, Song CX, Szulwach K, Wang Z, et al.
J Am Chem Soc. 2013 Jun 17. [Epub ahead of print]

Capturing protein-coding genes across highly divergent species.
Li C, Hofreiter M, Straube N, Corrigan S, Naylor GJ.
Biotechniques. 2013 Jun;54(6):321-6.

Threading Immobilized DNA Molecules through a Solid-State Nanopore at >100 μs per Base Rate.
Hyun C, Kaur H, Rollings R, Xiao M, Li J.
ACS Nano. 2013 Jun 11. [Epub ahead of print]

A mixture model for expression deconvolution from RNA-seq in heterogeneous tissues.
Li Y, Xie X.
BMC Bioinformatics. 2013;14 Suppl 5:S11.

An optimized algorithm for detecting and annotating regional differential methylation.
Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, et al.
BMC Bioinformatics. 2013;14 Suppl 5:S10.

Discovering motifs that induce sequencing errors.
Allhoff M, Schönhuth A, Martin M, Costa IG, et al.
BMC Bioinformatics. 2013;14 Suppl 5:S1.

Assembling contigs in draft genomes using reversals and block-interchanges.
Li CL, Chen KT, Lu CL.
BMC Bioinformatics. 2013;14 Suppl 5:S9.

A random-permutations-based approach to fast read alignment.
Lederman R.
BMC Bioinformatics. 2013;14 Suppl 5:S8.

Bellerophon: a hybrid method for detecting interchromo-somal rearrangements at base pair resolution using next-generation sequencing data.
Hayes M, Li J.
BMC Bioinformatics. 2013;14 Suppl 5:S6.

Joint genotype inference with germline and somatic mutations.
Bareke E, Saillour V, Spinella JF, Vidal R, et al.
BMC Bioinformatics. 2013;14 Suppl 5:S3.

metaBEETL: high-throughput analysis of heterogeneous microbial populations from shotgun DNA sequences.
Ander C, Schulz-Trieglaff OB, Stoye J, Cox AJ.
BMC Bioinformatics. 2013;14 Suppl 5:S2.

De novo inference of stratification and local admixture in sequencing studies.
Zhang Y.
BMC Bioinformatics. 2013;14 Suppl 5:S17.

Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing.
Wang X, Cairns MJ.
BMC Bioinformatics. 2013;14 Suppl 5:S16.

A novel min-cost flow method for estimating transcript expression with RNA-Seq.
Tomescu AI, Kuosmanen A, Rizzi R, Mäkinen V.
BMC Bioinformatics. 2013;14 Suppl 5:S15.

CLASS: constrained transcript assembly of RNA-seq reads.
Song L, Florea L.
BMC Bioinformatics. 2013;14 Suppl 5:S14.

Evaluating genome architecture of a complex region via generalized bipartite matching.
Lo C, Kim S, Zakov S, Bafna V.
BMC Bioinformatics. 2013;14 Suppl 5:S13.

The new sequencer on the block: comparison of Life Technology's Proton sequencer to an Illumina HiSeq for whole-exome sequencing.
Boland JF, Chung CC, Roberson D, Mitchell J, et al.
Hum Genet. 2013 Jun 12. [Epub ahead of print]

How much metagenomic sequencing is enough to achieve a given goal?
Ni J, Yan Q, Yu Y.
Sci Rep. 2013 Jun 11;3:1968.

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing.
Fang G, Munera D, Friedman DI, Mandlik A, et al.
Nat Biotechnol. 2013 Jun;31(6):566.

Using Genome Query Language to uncover genetic variation.
Kozanitis C, Heiberg A, Varghese G, Bafna V.
Bioinformatics. 2013 Jun 10. [Epub ahead of print]

Characterization of the DNA methylome and its interindividual variation in human peripheral blood monocytes.
Shen H, Qiu C, Li J, Tian Q, Deng HW.
Epigenomics. 2013 Jun;5(3):255-69.

A genome-wide survey of genetic variation in gorillas using reduced representation sequencing.
Scally A, Yngvadottir B, Xue Y, Ayub Q, et al.
PLoS One. 2013 Jun 4;8(6):e65066.

DMEAS: DNA Methylation Entropy Analysis Software.
He J, Sun X, Shao X, Liang L, Xie H.
Bioinformatics. 2013 Jun 8. [Epub ahead of print]

TASUKE: a web-based visualization program for large-scale resequencing data.
Kumagai M, Kim J, Itoh R, Itoh T.
Bioinformatics. 2013 Jun 11. [Epub ahead of print]

PurBayes: estimating tumor cellularity and subclonality in next-generation sequencing data.
Larson NB, Fridley BL.
Bioinformatics. 2013 Jun 14. [Epub ahead of print]

The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing.
Pechal JL, Crippen TL, Benbow ME, Tarone AM, et al.
Int J Legal Med. 2013 Jun 10. [Epub ahead of print]

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments.
Zambelli F, Pesole G, Pavesi G.
Nucleic Acids Res. 2013 Jun 7. [Epub ahead of print]