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Papers of Note: Jul 6, 2010


Sequencing-Related Papers of Note, June 2010

High resolution typing by integration of genome sequencing data in a large tuberculosis cluster.
Schürch AC, Kremer K, Daviena O, Kiers A, et al.
J Clin Microbiol. 2010 Jun 30. [Epub ahead of print]

MIReNA: finding microRNAs with high accuracy and no learning at genome scale and from deep sequencing data.
Mathelier A, Carbone A.
Bioinformatics. 2010 Jun 30. [Epub ahead of print]

A myriad of miRNA variants in control and Huntington's disease brain regions detected by massively parallel sequencing.
Martí E, Pantano L, Bañez-Coronel M, Llorens F, et al.
Nucleic Acids Res. 2010 Jun 30. [Epub ahead of print]

Mobile element scanning (ME-Scan) by targeted high-throughput sequencing.
Witherspoon DJ, Xing J, Zhang Y, Watkins WS, et al.
BMC Genomics. 2010 Jun 30;11(1):410. [Epub ahead of print]

Comprehensive survey of human brain microRNA by deep sequencing.
Shao NY, Hu HY, Yan Z, Xu Y, et al.
BMC Genomics. 2010 Jun 30;11(1):409. [Epub ahead of print]

Nanopores: fabrication of metallized nanopores in silicon nitride membranes for single-molecule sensing.
Wei R, Pedone D, Zürner A, Döblinger M, Rant U.
Small. 2010 Jun 29;6(13). [Epub ahead of print]

Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer.
Chmielecki J, Peifer M, Jia P, Socci ND, et al.
Nucleic Acids Res. 2010 Jun 29. [Epub ahead of print]

Targeted genome-wide enrichment of functional regions.
Senapathy P, Bhasi A, Mattox J, Dhandapany PS, Sadayappan S.
PLoS One. 2010 Jun 16;5(6):e11138.


Estimating enrichment of repetitive elements from high-throughput sequence data.
Day DS, Luquette LJ, Park PJ, Kharchenko PV.
Genome Biol. 2010 Jun 28;11(6):R69. [Epub ahead of print]

Ionic memcapacitive effects in nanopores.
Krems M, Pershin YV, Di Ventra M.
Nano Lett. 2010 Jun 28. [Epub ahead of print]

Integrative genomic profiling of human prostate cancer.
Taylor BS, Schultz N, Hieronymus H, Gopalan A, et al.
Cancer Cell. 2010 Jun 23. [Epub ahead of print]

Whole-genome sequencing of a single proband together with linkage analysis identifies a Mendelian disease gene.
Sobreira NL, Cirulli ET, Avramopoulos D, Wohler E, et al.
PLoS Genet. 2010 Jun 17;6(6):e1000991.

A probabilistic framework for aligning paired-end RNA-seq data.
Hu Y, Wang K, He X, Chiang DY, et al.
Bioinformatics. 2010 Jun 23. [Epub ahead of print]

Local alignment of generalized k-base encoded DNA sequence.
Homer N, Nelson SF, Merriman B.
BMC Bioinformatics. 2010 Jun 24;11(1):347. [Epub ahead of print]

SOPRA: Scaffolding algorithm for paired reads via statistical optimization.
Dayarian A, Michael TP, Sengupta AM.
BMC Bioinformatics. 2010 Jun 24;11(1):345. [Epub ahead of print]

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets.
Schmieder R, Lim YW, Rohwer F, Edwards R.
BMC Bioinformatics. 2010 Jun 23;11(1):341. [Epub ahead of print]


Identification of novel SNPs by next-generation sequencing of the genomic region containing the APC gene in colorectal cancer patients in China.
Cheng Y, Wang J, Shao J, Chen Q, et al.
OMICS. 2010 Jun;14(3):315-25.

Theory for polymer analysis using nanopore-based single-molecule mass spectrometry.
Reiner JE, Kasianowicz JJ, Nablo BJ, Robertson JW.
Proc Natl Acad Sci U S A. 2010 Jun 21. [Epub ahead of print]

Designing deep sequencing experiments: structural variation, haplotype assembly, and transcript abundance.
Bashir A, Bansal V, Bafna V.
BMC Genomics. 2010 Jun 18;11(1):385. [Epub ahead of print]

Whole exome capture in solution with 3Gbp of data.
Bainbridge MN, Wang M, Burgess DL, Kovar C, et al.
Genome Biol. 2010 Jun 17;11(6):R62. [Epub ahead of print]

Comparison and calibration of transcriptome data from RNA-seq and tiling arrays.
Agarwal A, Koppstein D, Rozowsky J, Sboner A, et al.
BMC Genomics. 2010 Jun 17;11(1):383. [Epub ahead of print]

Savant: Genome browser for high-throughput sequencing data.
Fiume M, Williams V, Brudno M.
Bioinformatics. 2010 Jun 20. [Epub ahead of print]

An alignment algorithm for bisulfite sequencing using the Applied Biosystems SOLiD System.
Ondov BD, Cochran C, Landers M, Meredith GD, et al.
Bioinformatics. 2010 Jun 18. [Epub ahead of print]

Manipulation of FASTQ data with Galaxy.
Blankenberg D, Gordon A, Von Kuster G, Coraor N, et al.
Bioinformatics. 2010 Jul 15;26(14):1783-5. Epub 2010 Jun 18.

Iterative correction of reference nucleotides (iCORN) using second generation sequencing technology.
Otto TD, Sanders M, Berriman M, Newbold C.
Bioinformatics. 2010 Jul 15;26(14):1704-7. Epub 2010 Jun 18.


Evaluation of oligonucleotide sequence capture arrays and comparison of next-generation sequencing platforms for use in molecular diagnostics.
Hoppman-Chaney N, Peterson LM, Klee EW, Middha S, et al.
Clin Chem. 2010 Jun 18. [Epub ahead of print]

Analysis of the size distributions of fetal and maternal cell-free DNA by paired-end sequencing.
Fan HC, Blumenfeld YJ, Chitkara U, Hudgins L, Quake SR.
Clin Chem. 2010 Jun 17. [Epub ahead of print]

Sequencing the multiple sclerosis genome: more questions than answers.
Ramagopalan SV, Ebers GC.
Lancet Neurol. 2010 Jun 15. [Epub ahead of print]

Pore fabrication in various silica-based nanoparticles by controlled etching.
Zhao L, Zhao Y, Han Y.
Langmuir. 2010 Jun 17. [Epub ahead of print]

Statistical comparison of methods to estimate the error probability in short-read Illumina sequencing.
Abnizova I, Skelly T, Naumenko F, Whiteford N, et al.
J Bioinform Comput Biol. 2010 Jun;8(3):579-91.

rQuant.web: a tool for RNA-Seq-based transcript quantitation.
Bohnert R, Rätsch G.
Nucleic Acids Res. 2010 Jul 1;38 Suppl:W348-51. Epub 2010 Jun 15.

Genome-wide searching of rare genetic variants in WTCCC data.
Feng T, Zhu X.
Hum Genet. 2010 Jun 13. [Epub ahead of print]

High-throughput sequencing identifies STAT3 as the DNA-associated factor for p53 - NF-kappaB - complex-dependent gene expression in human heart failure.
Choy MK, Movassagh M, Siggens L, Vujic A, et al.
Genome Med. 2010 Jun 14;2(6):37. [Epub ahead of print]


De novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
Nagarajan H, Butler JE, Klimes A, Qiu Y, et al.
PLoS One. 2010 Jun 8;5(6):e10922.

Utilizing genotype imputation for the augmentation of sequence data.
Fridley BL, Jenkins G, Deyo-Svendsen ME, Hebbring S, Freimuth R.
PLoS One. 2010 Jun 8;5(6):e11018.

Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan.
Plessy C, Bertin N, Takahashi H, Simone R, et al.
Nat Methods. 2010 Jul;7(7):528-34. Epub 2010 Jun 13.

Whole-genome DNA methylation profiling using MethylCap-seq.
Brinkman AB, Simmer F, Ma K, Kaan A, et al.
Methods. 2010 Jun 11. [Epub ahead of print]

LOX: inferring level of expression from diverse methods of census sequencing.
Zhang Z, Lopez-Giraldez F, Townsend JP.
Bioinformatics. 2010 Jun 10. [Epub ahead of print]

ZOOM Lite: next-generation sequencing data mapping and visualization software.
Zhang Z, Lin H, Ma B.
Nucleic Acids Res. 2010 Jul 1;38 Suppl:W743-8. Epub 2010 Jun 8.

Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery.
Hormozdiari F, Hajirasouliha I, Dao P, Hach F, et al.
Bioinformatics. 2010 Jun 15;26(12):i350-7.

VARiD: a variation detection framework for color-space and letter-space platforms.
Dalca AV, Rumble SM, Levy S, Brudno M.
Bioinformatics. 2010 Jun 15;26(12):i343-9.

A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data.
Chen X, Hoffman MM, Bilmes JA, Hesselberth JR, Noble WS.
Bioinformatics. 2010 Jun 15;26(12):i334-42.


A statistical method for the detection of variants from next-generation resequencing of DNA pools.
Bansal V.
Bioinformatics. 2010 Jun 15;26(12):i318-24.

Optimal algorithms for haplotype assembly from whole-genome sequence data.
He D, Choi A, Pipatsrisawat K, Darwiche A, Eskin E.
Bioinformatics. 2010 Jun 15;26(12):i183-90.

Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma.
Palanisamy N, Ateeq B, Kalyana-Sundaram S, Pflueger D, et al.
Nat Med. 2010 Jun 6. [Epub ahead of print]

Using next-generation sequencing for high-resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens.
Wood HM, Belvedere O, Conway C, Daly C, et al.
Nucleic Acids Res. 2010 Jun 4. [Epub ahead of print]

ChIP-PaM: an algorithm to identify protein-DNA interaction using ChIP-seq data.
Wu S, Wang J, Zhao W, Pounds S, Cheng C.
Theor Biol Med Model
. 2010 Jun 3;7:18.

PEACE: Parallel Environment for Assembly and Clustering of Gene Expression.
Rao DM, Moler JC, Ozden M, Zhang Y, et al.
Nucleic Acids Res. 2010 Jul 1;38 Suppl:W737-42. Epub 2010 Jun 3.

Strand-specific deep sequencing of the transcriptome.
Vivancos AP, Güell M, Dohm JC, Serrano L, Himmelbauer H.
Genome Res. 2010 Jul;20(7):989-99. Epub 2010 Jun 2.

A computational genomics pipeline for prokaryotic sequencing projects.
Kislyuk AO, Katz LS, Agrawal S, Hagen MS, et al.
Bioinformatics. 2010 Jun 2. [Epub ahead of print]


Unexpected allelic heterogeneity and spectrum of mutations in Fowler syndrome revealed by next-generation exome sequencing.
Lalonde E, Albrecht S, Ha KC, Jacob K, et al.
Hum Mutat. 2010 Jun 1. [Epub ahead of print]

Illumina sequencing library preparation for highly multiplexed target capture and sequencing.
Meyer M, Kircher M.
Cold Spring Harb Protoc. 2010 Jun 1;2010(6):pdb.prot5448.

Assembly of large genomes using second-generation sequencing.
Schatz MC, Delcher AL, Salzberg SL.
Genome Res. 2010 Jun 21. [Epub ahead of print]

The Scan

Booster for At-Risk

The New York Times reports that the US Food and Drug Administration has authorized a third dose of the Pfizer-BioNTech SARS-CoV-2 vaccine for people over 65 or at increased risk.

Preprints OK to Mention Again

Nature News reports the Australian Research Council has changed its new policy and now allows preprints to be cited in grant applications.

Hundreds of Millions More to Share

The US plans to purchase and donate 500 million additional SARS-CoV-2 vaccine doses, according to the Washington Post.

Nature Papers Examine Molecular Program Differences Influencing Neural Cells, Population History of Polynesia

In Nature this week: changes in molecular program during embryonic development leads to different neural cell types, and more.