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Papers of Note: Jan 25, 2011

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Last Week's Sequencing-Related Papers of Note

On optimal pooling designs to identify rare variants through massive resequencing.
Lee JS, Choi M, Yan X, Lifton RP, Zhao H.
Genet Epidemiol. 2011 Jan 19. doi: 10.1002/gepi.20561. [Epub ahead of print]


Exome sequencing allows for rapid gene identification in a Charcot-Marie-Tooth family.
Montenegro G, Powell E, Huang J, Speziani F, et al.
Ann Neurol. 2011 Jan 20. doi: 10.1002/ana.22235. [Epub ahead of print]


Genome-scale identification of resistance functions in Pseudomonas aeruginosa using Tn-seq.
Gallagher LA, Shendure J, Manoil C.
MBio. 2011 Jan 18;2(1). pii: e00315-10.


Integrated profiling of microRNAs and mRNAs: MicroRNAs located on Xq27.3 associate with clear cell renal cell carcinoma.
Zhou L, Chen J, Li Z, Li X, et al.
PLoS One. 2010 Dec 30;5(12):e15224.


Targeted next-generation sequencing detects point mutations, insertions,
deletions and balanced chromosomal rearrangements as well as identifies novel leukemia-specific fusion genes in a single procedure.

Grossmann V, Kohlmann A, Klein HU, Schindela S, et al.
Leukemia. 2011 Jan 21. [Epub ahead of print]


Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies.
Meder B, Haas J, Keller A, Heid C, et al.
Circ Cardiovasc Genet. 2011 Jan 20. [Epub ahead of print]


Length bias correction for RNA-seq data in gene set analyses.
Gao L, Fang Z, Zhang K, Zhi D, Cui X.
Bioinformatics. 2011 Jan 19. [Epub ahead of print]


Compression of genomic sequences in FASTQ format.
Deorowicz S, Grabowski S.
Bioinformatics. 2011 Jan 19. [Epub ahead of print]


TTC21B contributes both causal and modifying alleles across the ciliopathy spectrum.
Davis EE, Zhang Q, Liu Q, Diplas BH, et al.
Nat Genet. 2011 Jan 23. [Epub ahead of print]


Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3' UTRs.
Rosenberg BR, Hamilton CE, Mwangi MM, Dewell S, Papavasiliou FN.
Nat Struct Mol Biol. 2011 Jan 23. [Epub ahead of print]


Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs.
Leung AK, Young AG, Bhutkar A, Zheng GX, et al.
Nat Struct Mol Biol. 2011 Jan 23. [Epub ahead of print]


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Genomic screening by 454 pyrosequencing identifies a new human IGHV gene and sixteen other new IGHV allelic variants.
Wang Y, Jackson KJ, Gäeta B, Pomat W, et al.
Immunogenetics. 2011 Jan 20. [Epub ahead of print]


Nascent transcript sequencing visualizes transcription at nucleotide resolution.
Churchman LS, Weissman JS.
Nature. 2011 Jan 20;469(7330):368-73.


Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma.
Varela I, Tarpey P, Raine K, Huang D, et al.
Nature. 2011 Jan 19. [Epub ahead of print]


Identification of fusion genes in breast cancer by paired-end RNA-sequencing.
Edgren H, Murumaegi A, Kangaspeska S, Nicorici D, et al.
Genome Biol. 2011 Jan 19;12(1):R6.


Efficient storage of high throughput sequencing data using reference-based compression.
Hsi-Yang Fritz M, Leinonen R, Cochrane G, Birney E.
Genome Res. 2011 Jan 18. [Epub ahead of print]


BayesPeak — An R package for analyzing ChIP-seq data.
Cairns J, Spyrou C, Stark R, Smith ML, et al.
Bioinformatics. 2011 Jan 17. [Epub ahead of print]


Succinct data structures for assembling large genomes.
Conway TC, Bromage AJ.
Bioinformatics. 2011 Jan 17. [Epub ahead of print]


Next-generation sequencing for HLA typing of class I loci.
Erlich RL, Jia X, Anderson S, Banks E, et al.
BMC Genomics. 2011 Jan 18;12(1):42.


SeqWare Query Engine: storing and searching sequence data in the cloud.
O'Connor BD, Merriman B, Nelson SF.
BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S2.

The Scan

And Back

The New York Times reports that missing SARS-CoV-2 genome sequences are back in a different database.

Lacks Family Hires Attorney

A lawyer for the family of Henrietta Lacks plans to seek compensation from pharmaceutical companies that have used her cancer cells in product development, the Baltimore Sun reports.

For the Unknown

The Associated Press reports that family members are calling on the US military to use new DNA analysis techniques to identify unknown sailors and Marines who were on the USS Arizona.

PLOS Papers on Congenital Heart Disease, COVID-19 Infection Host MicroRNAs, Multiple Malformation Mutations

In PLOS this week: new genes linked to congenital heart disease, microRNAs with altered expression in COVID-19, and more.