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Papers of Note: Jun 1, 2010


Sequencing-Related Papers of Note, April 2010

Towards reliable isoform quantification using RNA-Seq data.
Howard BE, Heber S.
BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S6.

On the feasibility of using the intrinsic fluorescence of nucleotides for DNA sequencing.
Chowdhury MH, Ray K, Johnson ML, Gray SK, Pond J, Lakowicz JR.
J Phys Chem C Nanomater Interfaces. 2010 Apr 29;114(16):7448-7461.

Titration-free massively parallel pyrosequencing using trace amounts of starting material.
Zheng Z, Advani A, Melefors O, Glavas S, Nordström H, Ye W, et al.
Nucleic Acids Res. 2010 Apr 30. [Epub ahead of print]

Challenges in the clinical application of whole-genome sequencing.
Ormond KE, Wheeler MT, Hudgins L, Klein TE, Butte AJ, Altman RB, et al.
Lancet. 2010 May 15;375(9727):1749-51. Epub 2010 Apr 29.

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
Atanur SS, Birol I, Guryev V, Hirst M, Hummel O, Morrissey C, et al.
Genome Res. 2010 Apr 29. [Epub ahead of print]

Whole genome DNA methylation analysis based on high throughput sequencing technology.
Li N, Ye M, Li Y, Yan Z, Butcher LM, Sun J, et al.
Methods. 2010 Apr 27. [Epub ahead of print]

One bacterial cell, one complete genome.
Woyke T, Tighe D, Mavromatis K, Clum A, Copeland A, Schackwitz W, et al.
PLoS One. 2010 Apr 23;5(4):e10314.

A parallel algorithm for error correction in high-throughput short-read data on CUDA-enabled graphics hardware.
Shi H, Schmidt B, Liu W, Müller-Wittig W.
J Comput Biol. 2010 Apr;17(4):603-15.

Metagenomic sequencing of an in vitro-simulated microbial community.
Morgan JL, Darling AE, Eisen JA.
PLoS One. 2010 Apr 16;5(4):e10209.

Massively parallel signature sequencing and bioinformatics analysis identifies up-regulation of TGFBI and SOX4 in human glioblastoma.
Lin B, Madan A, Yoon JG, Fang X, Yan X, Kim TK, et al.
PLoS One. 2010 Apr 19;5(4):e10210.

Comparison of normalization methods for construction of large multiplex amplicon pools for next-generation sequencing.
Harris JK, Sahl JW, Castoe TA, Wagner BD, Pollock DD, Spear JR.
Appl Environ Microbiol. 2010 Apr 23. [Epub ahead of print]

BS Seeker: precise mapping for bisulfite sequencing.
Chen PY, Cokus SJ, Pellegrini M.
BMC Bioinformatics. 2010 Apr 23;11:203.

Mammalian microRNAs: experimental evaluation of novel and previously annotated genes.
Chiang HR, Schoenfeld LW, Ruby JG, Auyeung VC, Spies N, Baek D, et al.
Genes Dev. 2010 May 15;24(10):992-1009. Epub 2010 Apr 22.

Direct pathogen detection from swab samples using a new high-throughput sequencing technology.
Yongfeng H, Fan Y, Jie D, Jian Y, Ting Z, Lilian S, Jin Q.
Clin Microbiol Infect. 2010 Apr 15. [Epub ahead of print]

Supersplat — spliced RNA-seq alignment.
Bryant DW Jr, Shen R, Priest HD, Wong WK, Mockler TC.
Bioinformatics. 2010 Apr 21. [Epub ahead of print]

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Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer.
Sathira N, Yamashita R, Tanimoto K, Kanai A, Arauchi T, Kanematsu S, et al.
DNA Res. 2010 Apr 17. [Epub ahead of print]

Molecular bases of cyclodextrin adapter interactions with engineered protein nanopores.
Banerjee A, Mikhailova E, Cheley S, Gu LQ, Montoya M, Nagaoka Y, et al.
Proc Natl Acad Sci U S A. 2010 May 4;107(18):8165-70. Epub 2010 Apr 16.

DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing.
Castle JC, Biery M, Bouzek H, Xie T, Chen R, Misura K, et al.
BMC Genomics. 2010 Apr 16;11:244.

Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data.
Nishito Y, Osana Y, Hachiya T, Popendorf K, Toyoda A, Fujiyama A, et al.
BMC Genomics. 2010 Apr 16;11:243.

Finishing genomes with limited resources: lessons from an ensemble of microbial genomes.
Nagarajan N, Cook C, Di Bonaventura M, Ge H, Richards A, Bishop-Lilly KA, et al.
BMC Genomics. 2010 Apr 16;11:242.

Biases in Illumina transcriptome sequencing caused by random hexamer priming.
Hansen KD, Brenner SE, Dudoit S.
Nucleic Acids Res. 2010 Apr 14. [Epub ahead of print]

Genome remodelling in a basal-like breast cancer metastasis and xenograft.
Ding L, Ellis MJ, Li S, Larson DE, Chen K, Wallis JW, et al.
Nature. 2010 Apr 15;464(7291):999-1005.

Artificial and natural duplicates in pyrosequencing reads of metagenomic data.
Niu B, Fu L, Sun S, Li W.
BMC Bioinformatics. 2010 Apr 13;11:187.

Improving draft assemblies by iterative mapping and assembly of short reads to eliminate gaps.
Tsai IJ, Otto TD, Berriman M.
Genome Biol. 2010 Apr 13;11(4):R41. [Epub ahead of print]

De novo assembly of a 40 Mb eukaryotic genome from short sequence reads: Sordaria macrospora, a model organism for fungal morphogenesis.
Nowrousian M, Stajich JE, Chu M, Engh I, Espagne E, Halliday K, et al.
PLoS Genet. 2010 Apr 8;6(4):e1000891.

Increased throughput by parallelization of library preparation for massive sequencing.
Lundin S, Stranneheim H, Pettersson E, Klevebring D, Lundeberg J.
PLoS One. 2010 Apr 6;5(4):e10029.

Detection and characterization of novel sequence insertions using paired-end next-generation sequencing.
Hajirasouliha I, Hormozdiari F, Alkan C, Kidd JM, Birol I, Eichler EE, Sahinalp SC.
Bioinformatics. 2010 May 15;26(10):1277-83. Epub 2010 Apr 12.

AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay.
Butcher LM, Beck S.
Methods. 2010 Apr 10. [Epub ahead of print]

QIIME allows analysis of high-throughput community sequencing data.
Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, et al.
Nat Methods. 2010 May;7(5):335-6. Epub 2010 Apr 11. No abstract available.

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.
Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, et al.
Genome Res. 2010 Apr 28. [Epub ahead of print]

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Correction of sequencing errors in a mixed set of reads.
Salmela L.
Bioinformatics. 2010 May 15;26(10):1284-90. Epub 2010 Apr 8.

Structural variation analysis with strobe reads.
Ritz A, Bashir A, Raphael BJ.
Bioinformatics. 2010 May 15;26(10):1291-8. Epub 2010 Apr 8.

Gene set enrichment meta-learning analysis: next-generation sequencing versus microarrays.
Stiglic G, Bajgot M, Kokol P.
BMC Bioinformatics. 2010 Apr 8;11:176.

Digital gene expression by tag sequencing on the Illumina Genome Analyzer.
Morrissy S, Zhao Y, Delaney A, Asano J, Dhalla N, Li I, McDonald H, et al.
Curr Protoc Hum Genet. 2010 Apr;Chapter 11:Unit 11.11.1-36.

Detection of splice junctions from paired-end RNA-seq data by SpliceMap.
Au KF, Jiang H, Lin L, Xing Y, Wong WH.
Nucleic Acids Res. 2010 Apr 5. [Epub ahead of print]

A signal-noise model for significance analysis of ChIP-seq with negative control.
Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK.
Bioinformatics. 2010 May 1;26(9):1199-204. Epub 2010 Apr 5.

miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data.
Hendrix D, Levine M, Shi W.
Genome Biol. 2010 Apr 6;11(4):R39. [Epub ahead of print]

Deep sequencing of target linkage assay-identified regions in familial breast cancer: methods, analysis pipeline and troubleshooting.
Rosa-Rosa JM, Gracia-Aznárez FJ, Hodges E, Pita G, Rooks M, Xuan Z, et al.
PLoS One. 2010 Apr 2;5(4):e9976.

Function-based gene identification using enzymatically generated normalized shRNA library and massive parallel sequencing.
Shtutman M, Maliyekkel A, Shao Y, Carmack CS, Baig M, Warholic N, et al.
Proc Natl Acad Sci U S A. 2010 Apr 20;107(16):7377-82. Epub 2010 Apr 5.

Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing.
Park H, Kim JI, Ju YS, Gokcumen O, Mills RE, Kim S, et al.
Nat Genet. 2010 May;42(5):400-5. Epub 2010 Apr 4.

Mutation spectrum revealed by breakpoint sequencing of human germline CNVs.
Conrad DF, Bird C, Blackburne B, Lindsay S, Mamanova L, Lee C, et al.
Nat Genet. 2010 May;42(5):385-91. Epub 2010 Apr 4.

ACCUSA — accurate SNP calling on draft genomes.
Fröhler S, Dieterich C.
Bioinformatics. 2010 May 15;26(10):1364-5. Epub 2010 Apr 1.

The genome of a songbird.
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Künstner A, et al.
Nature. 2010 Apr 1;464(7289):757-62.

Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression.
Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, et al.
RNA. 2010 May;16(5):991-1006. Epub 2010 Apr 1.

Identifying and removing artificial replicates from 454 pyrosequencing data.
Teal TK, Schmidt TM.
Cold Spring Harb Protoc. 2010 Apr;2010(4):pdb.prot5409.

Optimized design and data analysis of tag-based cytosine methylation assays.
Suzuki M, Jing Q, Lia D, Pascual M, McLellan A, Greally JM.
Genome Biol. 2010 Apr 1;11(4):R36. [Epub ahead of print]

Unraveling single-stranded DNA in a solid-state nanopore.
Kowalczyk SW, Tuijtel MW, Donkers SP, Dekker C.
Nano Lett. 2010 Apr 14;10(4):1414-20.

The Scan

Dropped Charges

The US Justice Department has dropped visa fraud charges against five Chinese researchers, according to the Wall Street Journal.

More Kids

The Associated Press says Moderna is expanding its SARS-CoV-2 vaccine study to included additional children and may include even younger children.

PNAS Papers on Rat Clues to Human Migration, Thyroid Cancer, PolyG-DS

In PNAS this week: ancient rat genome analysis gives hints to human migrations, WDR77 gene mutations in thyroid cancer, and more.

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.