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In Print: Last Week's Sequencing-Related Papers of Note: Dec 20, 2011


A chemically synthesized peptoid-based drag-tag enhances free-solution DNA sequencing by capillary electrophoresis.
Haynes RD, Meagher RJ, Barron AE.
Biopolymers. 2011;96(5):702-7.

ClaMS: A Classifier for Metagenomic Sequences.
Pati A, Heath LS, Kyrpides NC, Ivanova N.
Stand Genomic Sci. 2011 Nov 30;5(2):248-53.

Solving the problem: genome annotation standards before the data deluge.
Klimke W, O'Donovan C, White O, Brister JR, et al.
Stand Genomic Sci. 2011 Oct 15;5(1):168-93.

A deep sequencing approach to comparatively analyze the transcriptome of lifecycle stages of the filarial worm, Brugia malayi.
Choi YJ, Ghedin E, Berriman M, McQuillan J, et al.
PLoS Negl Trop Dis. 2011 Dec;5(12):e1409.

Condensin dysfunction in human cells induces nonrandom chromosomal breaks in anaphase, with distinct patterns for both unique and repeated genomic regions.
Samoshkin A, Dulev S, Loukinov D, Rosenfeld JA, Strunnikov AV.
Chromosoma. 2011 Dec 17. [Epub ahead of print]

A computational pipeline for comparative ChIP-seq analyses.
Bardet AF, He Q, Zeitlinger J, Stark A.
Nat Protoc. 2011 Dec 15;7(1):45-61.

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing.
Reumers J, De Rijk P, Zhao H, Liekens A, et al.
Nat Biotechnol. 2011 Dec 18. [Epub ahead of print]

Performance comparison of whole-genome sequencing platforms.
Lam HY, Clark MJ, Chen R, Chen R, et al.
Nat Biotechnol. 2011 Dec 18. [Epub ahead of print]
(see our coverage of this paper in this issue)

GC-content normalization for RNA-seq data.
Risso D, Schwartz K, Sherlock G, Dudoit S.
BMC Bioinformatics. 2011 Dec 17;12(1):480.

Computational techniques for human genome resequencing using mated gapped reads.
Carnevali P, Baccash J, Halpern AL, Nazarenko I, et al.
J Comput Biol. 2011 Dec 16. [Epub ahead of print]

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics.
Straub SC, Parks M, Weitemier K, Fishbein M, et al.
Am J Bot. 2011 Dec 14. [Epub ahead of print]

Artificial functional difference between microbial communities caused by length difference of sequencing reads.
Zhang Q, Doak TG, Ye Y.
Pac Symp Biocomput. 2012:259-70.

Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data.
McMurdie PJ, Holmes S.
Pac Symp Biocomput. 2012:235-46.

Efficient mapping and cloning of mutations in zebrafish by low coverage whole genome sequencing.
Bowen ME, Henke K, Siegfried KR, Warman ML, Harris MP.
Genetics. 2011 Dec 14. [Epub ahead of print]

CrossQuery: a web tool for easy associative querying of transcriptome data.
Wagner TU, Fischer A, Thoma EC, Schartl M.
PLoS One. 2011;6(12):e28990.

Plantagora: modeling whole genome sequencing and assembly of plant genomes.
Barthe lson R, McFarlin AJ, Rounsley SD, Young S.
PLoS One. 2011;6(12):e28436.

Genome characterization of the oleaginous fungus Mortierella alpina.
Wang L, Chen W, Feng Y, Ren Y, et al.
PLoS One. 2011;6(12):e28319.

Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery.
Jung H, Lyons RE, Dinh H, Hurwood DA, et al.
PLoS One. 2011;6(12):e27938.

Detection of microRNAs in color-space.
Marco A, Griffiths-Jones S.
Bioinformatics. 2011 Dec 9. [Epub ahead of print]

Identifying small interfering RNA loci from high-throughput sequencing data.
Hardcastle TJ, Kelly KA, Baulcombe DC.
Bioinformatics. 2011 Dec 9. [Epub ahead of print]

Transformations for the compression of FASTQ quality scores of next generation sequencing data.
Wan R, Anh VN, Asai K.
Bioinformatics. 2011 Dec 13. [Epub ahead of print]

454 pyrosequencing reveals bacterial diversity of activated sludge from 14 sewage treatment plants.
Zhang T, Shao MF, Ye L.
ISME J. 2011 Dec 15. [Epub ahead of print]

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys.
Werner JJ, Zhou D, Caporaso JG, Knight R, Angenent LT.
ISME J. 2011 Dec 15. [Epub ahead of print]

Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows.
Barriuso J, Valverde JR, Mellado RP.
BMC Bioinformatics. 2011 Dec 14;12(1):473.

Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing.
Hiiesalu I, Opik M, Metsis M, Lilje L, et al.
Mol Ecol. 2011 Dec 14. [Epub ahead of print]

A single-step competitive binding assay for mapping of single DNA molecules.
Nyberg LK, Persson F, Berg J, Bergström J, et al.
Biochem Biophys Res Commun. 2011 Dec 7. [Epub ahead of print]

Stacked graphene-Al2O3 nanopore sensors for sensitive detection of DNA and DNA-protein complexes.
Venkatesan BM, Estrada D, Banerjee S, Jin X, et al.
ACS Nano. 2011 Dec 13. [Epub ahead of print]

One-way sequencing of multiple amplicons from tandem repetitive mitochondrial DNA control region.
Xu J, Fonseca DM.
Mitochondrial DNA. 2011 Oct;22(5-6):155-8.

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.