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Papers of Note: Feb 9, 2010


Sequencing-Related Papers of Note, Jan. 2010

A map of open chromatin in human pancreatic islets.
Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, Fogarty MP, Panhuis TM, Mieczkowski P, et al.
Nat Genet. 2010 Jan 31. [Epub ahead of print]

Synchronous optical and electrical detection of biomolecules traversing through solid-state nanopores.
Soni GV, Singer A, Yu Z, Sun Y, McNally B, Meller A.
Rev Sci Instrum. 2010 Jan;81(1):014301.

BEDTools: A flexible suite of utilities for comparing genomic features.
Quinlan AR, Hall IM.
Bioinformatics. 2010 Jan 28. [Epub ahead of print]

Incorporating sequence quality data into alignment improves DNA read mapping.
Frith MC, Wan R, Horton P.
Nucleic Acids Res. 2010 Jan 27. [Epub ahead of print]

Monitoring the escape of DNA from a nanopore using an alternating current signal.
Lathrop DK, Ervin EN, Barrall GA, Keehan MG, Kawano R, Krupka MA, White HS, Hibbs AH.
J Am Chem Soc. 2010 Jan 25. [Epub ahead of print]

3'-end sequencing for expression quantification (3SEQ) from archival tumor samples.
Beck AH, Weng Z, Witten DM, Zhu S, Foley JW, Lacroute P, Smith CL, Tibshirani R, et al.
PLoS One. 2010 Jan 19;5(1):e8768.

Identical repeated backbone of the human genome.
Zepeda-Mendoza CJ, Lemus T, Yanez O, Garcia D, Valle-Garcia D, Meza-Sosa KF, et al.
BMC Genomics. 2010 Jan 23;11(1):60. [Epub ahead of print]

SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads.
Falgueras J, Lara AJ, Fernandez-Pozo N, Canton FR, Perez-Trabado G, Claros MG.
BMC Bioinformatics. 2010 Jan 20;11(1):38. [Epub ahead of print]

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Nanopore-based sequence specific detection of duplex DNA for genomic profiling.
Singer A, Wanunu M, Morrison W, Kuhn H, Frank-Kamenetskii M, Meller A.
Nano Lett. 2010 Jan 20. [Epub ahead of print]

Parallel, tag-directed assembly of locally derived short sequence reads.
Hiatt JB, Patwardhan RP, Turner EH, Lee C, Shendure J.
Nat Methods. 2010 Feb;7(2):119-22. Epub 2010 Jan 17.

FRT-seq: amplification-free, strand-specific transcriptome sequencing.
Mamanova L, Andrews RM, James KD, Sheridan EM, Ellis PD, Langford CF, Ost TW, Collins JE, Turner DJ.
Nat Methods. 2010 Feb;7(2):130-2. Epub 2010 Jan 17.

Accurate sodium bisulfite sequencing in plants.
Henderson IR, Chan SR, Cao X, Johnson L, Jacobsen SE.
Epigenetics. 2010 Jan 8;5(1). [Epub ahead of print]

Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment.
Gálvez S, Díaz D, Hernández P, Esteban FJ, Caballero JA, Dorado G.
Bioinformatics. 2010 Jan 16. [Epub ahead of print]

High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets.
Wang C, Sanders CM, Yang Q, Schroeder HW Jr, Wang E, Babrzadeh F, Gharizadeh B, et al.
Proc Natl Acad Sci U S A. 2010 Jan 4. [Epub ahead of print]

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life.
Hittinger CT, Johnston M, Tossberg JT, Rokas A.
Proc Natl Acad Sci U S A. 2010 Jan 4. [Epub ahead of print]

Fast and accurate long read alignment with Burrows-Wheeler transform.
Li H, Durbin R.
Bioinformatics. 2010 Jan 15. [Epub ahead of print]

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence.
Hyten DL, Cannon SB, Song Q, Weeks N, Fickus EW, Shoemaker RC, Specht JE, et al.
BMC Genomics. 2010 Jan 15;11(1):38. [Epub ahead of print]

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Improving sequence assembly using machine learning and comparative genomics for overlap correction.
Palmer LE, Dejori M, Bolanos R, Fasulo D.
BMC Bioinformatics. 2010 Jan 15;11(1):33. [Epub ahead of print]

Genome sequence of the palaeopolyploid soybean.
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, et al.
Nature. 2010 Jan 14;463(7278):178-83.

A statistical method for the detection of alternative splicing using RNA-seq.
Wang L, Xi Y, Yu J, Dong L, Yen L, Li W.
PLoS One. 2010 Jan 8;5(1):e8529.

Current blockade in nanopores in the presence of double-stranded DNA and the microscopic mechanisms.
Cui S.
J Phys Chem B. 2010 Jan 13. [Epub ahead of print]

Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates.
Blakesley RW, Hansen NF, Gupta J, McDowell JC, Maskeri B, Barnabas BB, Brooks SY, et al.
BMC Genomics. 2010 Jan 11;11(1):21. [Epub ahead of print]

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution.
Gu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, Tomazou E, Gnirke A, Lander ES, Meissner A.
Nat Methods. 2010 Feb;7(2):133-6. Epub 2010 Jan 10.

Nanopores in solid-state membranes engineered for single molecule detection.
Dimitrov V, Mirsaidov U, Wang D, Sorsch T, Mansfield W, Miner J, Klemens F, Cirelli R, et al.
Nanotechnology. 2010 Feb 10;21(6):065502. Epub 2010 Jan 11.

On the detection and refinement of transcription factor binding sites using ChIP-seq data.
Hu M, Yu J, Taylor JM, Chinnaiyan AM, Qin ZS.
Nucleic Acids Res. 2010 Jan 6. [Epub ahead of print]

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Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes.
Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, Butler A, Davies H, Edkins S, Hardy C, et al.
Nature. 2010 Jan 21;463(7279):360-3. Epub 2010 Jan 6.

Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability.
De Grassi A, Segala C, Iannelli F, Volorio S, Bertario L, Radice P, Bernard L, Ciccarelli FD.
PLoS Biol. 2010 Jan;8(1):e1000275. Epub 2010 Jan 5.

Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries.
de Hoon MJ, Taft RJ, Hashimoto T, Kanamori-Katayama M, Kawaji H, Kawano M, Kishima M, et al.
Genome Res. 2010 Jan 5. [Epub ahead of print]

Direct force measurements on double-stranded RNA in solid-state nanopores.
van den Hout M, Vilfan ID, Hage S, Dekker NH.
Nano Lett. 2010 Jan 5. [Epub ahead of print]

Rapid sequencing of individual DNA molecules in graphene nanogaps.
Postma HW.
Nano Lett. 2010 Jan 4. [Epub ahead of print]

Translocation of single-stranded DNA through single-walled carbon nanotubes.
Liu H, He J, Tang J, Liu H, Pang P, Cao D, Krstic P, Joseph S, Lindsay S, Nuckolls C.
Science. 2010 Jan 1;327(5961):64-7.

Entrapment of individual DNA molecules and nanoparticles in porous alumina membranes.
Ma C, Yeung ES.

Anal Chem. 2010 Jan 15;82(2):654-7.

The Scan

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.

Coronary Artery Disease Risk Loci, Candidate Genes Identified in GWAS Meta-Analysis

A GWAS in Nature Genetics of nearly 1.4 million coronary artery disease cases and controls focused in on more than 200 candidate causal genes, including the cell motility-related myosin gene MYO9B.

Multiple Sclerosis Contributors Found in Proteome-Wide Association Study

With a combination of genome-wide association and brain proteome data, researchers in the Annals of Clinical and Translational Neurology tracked down dozens of potential multiple sclerosis risk proteins.

Quality Improvement Study Compares Molecular Tumor Boards, Central Consensus Recommendations

With 50 simulated cancer cases, researchers in JAMA Network Open compared molecular tumor board recommendations with central consensus plans at a dozen centers in Japan.