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In Print: Last Week's Sequencing-Related Papers of Note: Jul 23, 2013


Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes.
Farkas MH, Grant GR, White JA, Sousa ME, et al.
BMC Genomics. 2013 Jul 18;14(1):486.

Metagenomic analysis of tuberculosis in a mummy.
Chan JZ, Sergeant MJ, Lee OY, Minnikin DE, et al.
N Engl J Med. 2013 Jul 18;369(3):289-90.

Silicon nitride nanopores for nanoparticle sensing.
Kong J, Wu H, Liu L, Xie X, et al.
J Nanosci Nanotechnol. 2013 Jun;13(6):4010-6.

Fine-scale patterns of population stratification confound rare variant association tests.
O'Connor TD, Kiezun A, Bamshad M, Rich SS, et al.
PLoS One. 2013 Jul 4;8(7):e65834.

A versatile microsatellite instability reporter system in human cells.
Koole W, Schäfer HS, Agami R, van Haaften G, Tijsterman M.
Nucleic Acids Res. 2013 Jul 16. [Epub ahead of print]

Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins.
Mesner LD, Valsakumar V, Cieslik M, Pickin R, et al.
Genome Res. 2013 Jul 16. [Epub ahead of print]

A fast and accurate algorithm for diploid individual haplotype reconstruction.
Wu J, Liang B.
J Bioinform Comput Biol. 2013 Aug;11(4):1350010.

Comparison of the respiratory microbiome in healthy nonsmokers and smokers.
Morris A, Beck JM, Schloss PD, Campbell TB, et al.
Am J Respir Crit Care Med. 2013 May 15;187(10):1067-75.

SNVHMM: predicting single nucleotide variants from next generation sequencing.
Bian J, Liu C, Wang H, Xing J, et al.
BMC Bioinformatics. 2013 Jul 15;14(1):225.

Mass production of SNP markers in a nonmodel passerine bird through RAD sequencing and contig mapping to the zebra finch genome.
Bourgeois YX, Lhuillier E, Cézard T, Bertrand JA, et al.
Mol Ecol Resour. 2013 Jul 16. [Epub ahead of print]

BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge.
Moore CB, Wallace JR, Frase AT, Pendergrass SA, Ritchie MD.
BMC Med Genomics. 2013;6 Suppl 2:S6. Epub 2013 May 7.

GAM-NGS: genomic assemblies merger for next generation sequencing.
Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A.
BMC Bioinformatics. 2013 Apr 22;14 Suppl 7:S6.

State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?
Carrara M, Beccuti M, Cavallo F, Donatelli S, et al.
BMC Bioinformatics. 2013 Apr 22;14 Suppl 7:S2.

WEP: a high-performance analysis pipeline for whole-exome data.
D'Antonio M, D'Onorio De Meo P, Paoletti D, Elmi B, et al.
BMC Bioinformatics. 2013 Apr 22;14 Suppl 7:S11.

NGS-Trex: Next generation sequencing transcriptome profile explorer.
Boria I, Boatti L, Pesole G, Mignone F.
BMC Bioinformatics. 2013 Apr 22;14 Suppl 7:S10.

A patch-clamp ASIC for nanopore-based DNA analysis.
Kim J, Maitra R, Pedrotti KD, Dunbar WB.
IEEE Trans Biomed Circuits Syst. 2013 Jun;7(3):285-295.

RACER: Rapid and Accurate Correction of Errors in Reads.
Ilie L, Molnar M.
Bioinformatics. 2013 Jul 12. [Epub ahead of print]

In situ sequencing for RNA analysis in preserved tissue and cells.
Ke R, Mignardi M, Pacureanu A, Svedlund J, et al.
Nat Methods. 2013 Jul 14. [Epub ahead of print]

A new system for comparative functional genomics of Saccharomyces yeasts.
Caudy AA, Guan Y, Jia Y, Hansen C, et al.
Genetics. 2013 Jul 12. [Epub ahead of print]

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph.
Wicker T, Oberhaensli S, Parlange F, Buchmann JP, et al.
Nat Genet. 2013 Jul 14. [Epub ahead of print]

Insights into the phylogeny and coding potential of microbial dark matter.
Rinke C, Schwientek P, Sczyrba A, Ivanova NN, et al.
Nature. 2013 Jul 14. [Epub ahead of print]

CoLIde: A bioinformatics tool for CO-expression based small RNA loci Identification using high-throughput sequencing data.
Mohorianu I, Stocks MB, Wood J, Dalmay T, Moulton V.
RNA Biol. 2013 Jun 28;10(7).

Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure.
Shoguchi E, Shinzato C, Kawashima T, Gyoja F, et al.
Curr Biol. 2013 Jul 9. [Epub ahead of print]

FGF Signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency.
Ficz G, Hore TA, Santos F, Lee HJ, et al.
Cell Stem Cell. 2013 Jul 10. [Epub ahead of print]

Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells.
Habibi E, Brinkman AB, Arand J, Kroeze LI, et al.
Cell Stem Cell. 2013 Jul 10. [Epub ahead of print]

Opposite translocation of long and short oligomers through a nanopore.
Getfert S, Töws T, Reimann P.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jun;87(6-1):062710.

Molecular dynamics study of DNA translocation through graphene nanopores.
Li J, Zhang Y, Yang J, Bi K, et al.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Jun;87(6-1):062707.

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.