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Papers of Note: Sep 7, 2010


Rapid identification of genetic modifications in Bacillus anthracis using whole genome draft sequences generated by 454 pyrosequencing.
Chen PE, Willner KM, Butani A, Dorsey S, et al.
PLoS One. 2010 Aug 25;5(8). pii: e12397.

Integrating common and rare genetic variation in diverse human populations.
The International HapMap 3 Consortium
Nature. 2010 Sep 2;467(7311):52-58.

Overlap and effective size of the human CD8+ T cell receptor repertoire.
Robins HS, Srivastava SK, Campregher PV, Turtle CJ, et al.
Sci Transl Med. 2010 Sep 1;2(47):47ra64.

Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing.
Teer JK, Bonnycastle LL, Chines PS, Hansen NF, et al.
Genome Res. 2010 Sep 1. [Epub ahead of print]

Simple copy number determination with Reference Query Pyrosequencing (RQPS).
Liu Z, Schneider DL, Kornfeld K, Kopan R.
Cold Spring Harb Protoc. 2010 Sep 1;2010

The sheep genome reference sequence: a work in progress.
The International Sheep Genomics Consortium
Anim Genet
. 2010 Aug 31. [Epub ahead of print]

Mitochondrial DNA variant discovery and evaluation in human cardiomyopathies through next-generation sequencing.
Zaragoza MV, Fass J, Diegoli M, Lin D, Arbustini E.
PLoS One. 2010 Aug 20;5(8). pii: e12295.

Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing.
Fischer W, Ganusov VV, Giorgi EE, Hraber PT, et al.
PLoS One. 2010 Aug 20;5(8). pii: e12303.

Comparison between NuGEN's WT-Ovation Pico and One-Direct amplification systems.
Morse AM, Carballo V, Baldwin DA, Taylor CG, McIntyre LM.
J Biomol Tech. 2010 Sep;21(3):141-7.

Multi-sample pooling and Illumina Genome Analyzer sequencing methods to determine gene sequence variation for database development.
Margraf RL, Durtschi JD, Dames S, Pattison DC, et al.
J Biomol Tech. 2010 Sep;21(3):126-40.

Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix.
Mirsaidov U, Comer J, Dimitrov V, Aksimentiev A, Timp G.
Nanotechnology. 2010 Sep 1;21(39):395501.

Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes.
Sahota G, Stormo GD.
Bioinformatics. 2010 Aug 31.

Does large scale DNA sequencing of patient and tumor DNA yet provide clinically actionable information?
Harris T.
Discov Med. 2010 Aug;10(51):144-50.

Design of 16S rRNA gene primers for 454 pyrosequencing of the human foregut microbiome.
Nossa CW, Oberdorf WE, Yang L, Aas JA, et al.
World J Gastroenterol. 2010 Sep 7;16(33):4135-44.

PeakRegressor identifies composite sequence motifs responsible for STAT1 binding sites and their potential rSNPs.
Pessiot JF, Chiba H, Hyakkoku H, Taniguchi T, Fujibuchi W.
PLoS One. 2010 Aug 27;5(8). pii: e11881.

Gut microbial gene expression in mother-fed and formula-fed piglets.
Poroyko V, White JR, Wang M, Donovan S, et al.
PLoS One. 2010 Aug 27;5(8). pii: e12459.

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions.
Reeder J, Knight R.
Nat Methods. 2010 Sep;7(9):668-9.

Next-generation sequencing for clinical diagnostics-principles and application to targeted resequencing for hypertrophic cardiomyopathy: a paper from the 2009 William Beaumont hospital symposium on molecular pathology.
Voelkerding KV, Dames S, Durtschi JD.
J Mol Diagn. 2010 Sep;12(5):539-51.

Preference of RIG-I for short viral RNA molecules in infected cells revealed by next-generation sequencing.
Baum A, Sachidanandam R, García-Sastre A.
Proc Natl Acad Sci U S A. 2010 Aug 30. [Epub ahead of print]

Detecting copy number variation with mated short reads.
Medvedev P, Fiume M, Dzamba M, Smith T, Brudno M.
Genome Res. 2010 Aug 30. [Epub ahead of print]

FragGeneScan: predicting genes in short and error-prone reads.
Rho M, Tang H, Ye Y.
Nucleic Acids Res. 2010 Aug 30. [Epub ahead of print]

Loss-of-function variants in the genomes of healthy humans.
MacArthur DG, Tyler-Smith C.
Hum Mol Genet. 2010 Aug 30. [Epub ahead of print]

The missing graphical user interface for genomics.
Schatz MC.
Genome Biol. 2010 Aug 25;11(8):128.

HIV-1 V3 envelope deep sequencing for clinical plasma specimens failing in phenotypic tropism assays.
Vandenbroucke I, Van Marck H, Mostmans W, Van Eygen V, et al.
AIDS Res Ther. 2010 Feb 15;7:4.

Field effect regulation of DNA translocation through a nanopore.
Ai Y, Liu J, Zhang B, Qian S.
Anal Chem. 2010 Aug 30. [Epub ahead of print]

The Scan

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.