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In Print: Last Week's Sequencing-Related Papers of Note: Jul 17, 2012

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BROMOC-D: Brownian dynamics/Monte-Carlo program suite to study ion and DNA permeation in nanopores.
De Biase PM, Solano CJ, Markosyan S, Czapla L, Noskov SY.
J Chem Theory Comput. 2012 Jul 10;8(7):2540-2551.


Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.
Lam ET, Hastie A, Lin C, Ehrlich D, et al.
Nat Biotechnol. 2012 Jul 15. [Epub ahead of print]
(See our coverage of this paper here.)


A regression model for estimating DNA copy number data applied to capture sequencing data.
Rigaill GJ, Cadot S, Kluin RJ, Xue Z, et al.
Bioinformatics. 2012 Jul 13. [Epub ahead of print]


The cervical microbiome over 7 years and a comparison of methodologies for its characterization.
Smith BC, McAndrew T, Chen Z, Harari A, et al.
PLoS One. 2012;7(7):e40425.


IMG/M-HMP: a metagenome comparative analysis system for the human microbiome project.
Markowitz VM, Chen IM, Chu K, Szeto E, et al.
PLoS One. 2012;7(7):e40151.


Targeted recovery of novel phylogenetic diversity from next-generation sequence data.
Lynch MD, Bartram AK, Neufeld JD.
ISME J. 2012 Jul 12. [Epub ahead of print]


CBrowse: a SAM/BAM-based contig browser for transcriptome assembly visualization and analysis.
Li P, Ji G, Dong M, Schmidt E, et al.
Bioinformatics. 2012 Jul 12. [Epub ahead of print]


Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants.
Sellitto M, Bai G, Serena G, Fricke WF, et al.
PLoS One. 2012;7(3):e33387.


Single-molecule electrical random resequencing of DNA and RNA.
Ohshiro T, Matsubara K, Tsutsui M, Furuhashi M, et al.
Sci Rep. 2012;2:501.


Fast and automatic processing of multi-level events in nanopore translocation experiments.
Raillon C, Granjon P, Graf M, Steinbock LJ, Radenovic A.
Nanoscale. 2012 Jul 11. [Epub ahead of print]


NDesign: software for study design for the detection of rare variants from next-generation sequencing data.
Sugaya Y, Akazawa Y, Saito A, Kamitsuji S.
J Hum Genet. 2012 Jul 12. [Epub ahead of print]


Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells.
Peters BA, Kermani BG, Sparks AB, Alferov O, et al.
Nature. 2012 Jul 11;487(7406):190-5.
(See our coverage of this paper here.)


Bis-SNP: combined DNA methylation and SNP calling for bisulfite-seq data.
Liu Y, Siegmund KD, Laird PW, Berman BP.
Genome Biol. 2012 Jul 11;13(7):R61.


Efficient error correction for next-generation sequencing of viral amplicons.
Skums P, Dimitrova Z, Campo DS, Vaughan G, et al.
BMC Bioinformatics. 2012 Jun 25;13 Suppl 10:S6.


Improving genome assemblies by sequencing PCR products with PacBio.
Zhang X, Davenport KW, Gu W, Daligault HE, et al.
Biotechniques. 2012 Jul;53(1):61-2.


Assessing graphene nanopores for sequencing DNA.
Wells DB, Belkin M, Comer J, Aksimentiev A.
Nano Lett. 2012 Jul 10. [Epub ahead of print]


From sequencer to supercomputer: an automatic pipeline for managing and processing next generation sequencing data.
Camerlengo T, Ozer HG, Onti-Srinivasan R, Yan P, et al.
AMIA Summits Transl Sci Proc. 2012;2012:1-10.


Small RNA expression profiling by high-throughput sequencing: implications of enzymatic manipulation.
Zhuang F, Fuchs RT, Robb GB.
J Nucleic Acids. 2012;2012:360358.


Mixed sequence reader: a program for analyzing DNA sequences with heterozygous base calling.
Chang CT, Tsai CN, Tang CY, Chen CH, et al.
ScientificWorldJournal. 2012;2012:365104.

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