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Papers of Note: Mar 1, 2011


Strategy for Robust detection of insertions, deletions, and point mutations in CEBPA, a GC-rich content gene, using 454 next-generation deep-sequencing technology.
Grossmann V, Schnittger S, Schindela S, Klein HU, et al.
J Mol Diagn. 2011 Mar;13(2):129-36.

Exome sequencing identifies truncating mutations in human SERPINF1 in autosomal-recessive osteogenesis imperfecta.
Becker J, Semler O, Gilissen C, Li Y, et al.
Am J Hum Genet. 2011 Feb 23. [Epub ahead of print]

Genome-wide studies of copy number variation and exome sequencing identify rare variants in BAG3 as a cause of dilated cardiomyopathy.
Norton N, Li D, Rieder MJ, Siegfried JD, et al.
Am J Hum Genet. 2011 Feb 23. [Epub ahead of print]

Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes.
Warren RL, Freeman JD, Zeng T, Choe G, et al.
Genome Res. 2011 Feb 24. [Epub ahead of print]

R453Plus1toolbox: an R/Bioconductor package for analyzing Roche 454 sequencing data.
Klein HU, Bartenhagen C, Kohlmann A, Grossmann V, et al.
Bioinformatics. 2011 Feb 23. [Epub ahead of print]

Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.
Kiialainen A, Karlberg O, Ahlford A, Sigurdsson S, et al.
PLoS One. 2011 Feb 9;6(2):e16486.

Characterization of bacteria in biopsies of colon and stools by high throughput sequencing of the V2 region of bacterial 16S rRNA gene in human.

Momozawa Y, Deffontaine V, Louis E, Medrano JF.
PLoS One. 2011 Feb 10;6(2):e16952.

PositionMatcher: A fast custom-annotation tool for short DNA sequences.
Pitzer E, Kim J, Patel K, Galante PA, Ohno-Machado L.
AMIA Summits Transl Sci Proc. 2010 Mar 1;2010:25-9.

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Discovery of novel human breast cancer microRNAs from deep sequencing data by analysis of pri-microRNA secondary structures.

Ryu S, Joshi N, McDonnell K, Woo J, et al.
PLoS One. 2011 Feb 8;6(2):e16403.

Reproducibility and quantitation of amplicon sequencing-based detection.
Zhou J, Wu L, Deng Y, Zhi X, et al.
ISME J. 2011 Feb 24. [Epub ahead of print]

Breast cancer genome heterogeneity: a challenge to personalised medicine?
Swanton C, Burrell RA, Futreal PA.
Breast Cancer Res. 2011 Feb 1;13(1):104. [Epub ahead of print]

Traces of post-transcriptional RNA modifications in deep sequencing data.
Findeiß S, Langenberger D, Stadler PF, Hoffmann S.
Biol Chem. 2011 Feb 24. [Epub ahead of print]

Whole-genome sequencing and social-network analysis of a tuberculosis outbreak.
Gardy JL, Johnston JC, Sui SJ, Cook VJ, et al.
N Engl J Med. 2011 Feb 24;364(8):730-9.

Identification of a salmonellosis outbreak by means of molecular sequencing.
Lienau EK, Strain E, Wang C, Zheng J, et al.
N Engl J Med. 2011 Feb 23. [Epub ahead of print]

Detection of IDH1 mutation in human gliomas: comparison of immunohistochemistry and sequencing.
Takano S, Tian W, Matsuda M, Yamamoto T, et al.
Brain Tumor Pathol. 2011 Feb 23. [Epub ahead of print]

Technology-specific error signatures in the 1000 Genomes Project data.
Nothnagel M, Herrmann A, Wolf A, Schreiber S, et al.
Hum Genet. 2011 Feb 23. [Epub ahead of print]

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Comparative genome sequencing of an isogenic pair of USA800 clinical MRSA isolates obtained before and after daptomycin treatment failure.
Boyle-Vavra S, Jones M, Gourley BL, Holmes M, et al.
Antimicrob Agents Chemother. 2011 Feb 22. [Epub ahead of print]

Complex and dynamic landscape of RNA polyadenylation revealed by PAS-seq.
Shepard PJ, Choi EA, Lu J, Flanagan LA, et al.
RNA. 2011 Feb 22. [Epub ahead of print]

Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in myelodysplastic syndromes.
Beck D, Ayers S, Wen J, Brandl MB, et al.
BMC Med Genomics. 2011 Feb 23;4(1):19.

Error and error mitigation in low-coverage genome assemblies.
Hubisz MJ, Lin MF, Kellis M, Siepel A.
PLoS One. 2011 Feb 14;6(2):e17034.

Identification of recurring tumor-specific somatic mutations in acute myeloid leukemia by transcriptome sequencing.
Greif PA, Eck SH, Konstandin NP, Benet-Pagès A, et al.
Leukemia. 2011 Feb 22. [Epub ahead of print]

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries.
Aird D, Ross MG, Chen WS, Danielsson M, et al.
Genome Biol. 2011 Feb 21;12(2):R18.

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Also Subvariants

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