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Papers of Note: Jul 6, 2010

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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.


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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]


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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.


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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]


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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.


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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]


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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]

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