当前位置： SCI文献检索 > NATURE BIOTECHNOLOGY期刊下所有文献 > Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Full-length transcriptome assembly from RNA-Seq data without a reference genome.

Abstract：

:Massively parallel sequencing of cDNA has enabled deep and efficient probing of transcriptomes. Current approaches for transcript reconstruction from such data often rely on aligning reads to a reference genome, and are thus unsuitable for samples with a partial or missing reference genome. Here we present the Trinity method for de novo assembly of full-length transcripts and evaluate it on samples from fission yeast, mouse and whitefly, whose reference genome is not yet available. By efficiently constructing and analyzing sets of de Bruijn graphs, Trinity fully reconstructs a large fraction of transcripts, including alternatively spliced isoforms and transcripts from recently duplicated genes. Compared with other de novo transcriptome assemblers, Trinity recovers more full-length transcripts across a broad range of expression levels, with a sensitivity similar to methods that rely on genome alignments. Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome.

journal_name

Nat Biotechnol

journal_title

Nature biotechnology

authors

Grabherr MG,Haas BJ,Yassour M,Levin JZ,Thompson DA,Amit I,Adiconis X,Fan L,Raychowdhury R,Zeng Q,Chen Z,Mauceli E,Hacohen N,Gnirke A,Rhind N,di Palma F,Birren BW,Nusbaum C,Lindblad-Toh K,Friedman N,Regev A

doi

10.1038/nbt.1883

subject

Has Abstract

pub_date

2011-05-15 00:00:00

pages

644-52

issue

7

eissn

1087-0156

issn

1546-1696

pii

nbt.1883

journal_volume

29

pub_type

杂志文章

相关文献

NATURE BIOTECHNOLOGY文献大全
  • Human feeders support prolonged undifferentiated growth of human inner cell masses and embryonic stem cells.

    abstract：:Previous reports have demonstrated the growth of undifferentiated human embryonic stem (HES) cells on mouse embryonic fibroblast (MEF) feeders and on laminin- or Matrigel-coated plastic surfaces supplemented with MEF-conditioned medium. These xenosupport systems run the risk of cross-transfer of animal pathogens from ...

    journal_title：Nature biotechnology

    pub_type：

    doi：10.1038/nbt726

    authors： Richards M,Fong CY,Chan WK,Wong PC,Bongso A

    更新日期：2002-09-01 00:00:00

  • Phosphoramidate oligonucleotides as potent antisense molecules in cells and in vivo.

    abstract：:Antisense oligonucleotides are designed to specifically hybridize to a target messenger RNA (mRNA) and interfere with the synthesis of the encoded protein. Uniformly modified oligonucleotides containing N3'-P5' phosphoramidate linkages exhibit (NP) extremely high-affinity binding to single-stranded RNA, do not induce ...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/83489

    authors： Faria M,Spiller DG,Dubertret C,Nelson JS,White MR,Scherman D,Hélène C,Giovannangeli C

    更新日期：2001-01-01 00:00:00

  • Author Correction: Plants with genetically encoded autoluminescence.

    abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title：Nature biotechnology

    pub_type： 已发布勘误

    doi：10.1038/s41587-020-0578-0

    authors： Mitiouchkina T,Mishin AS,Somermeyer LG,Markina NM,Chepurnyh TV,Guglya EB,Karataeva TA,Palkina KA,Shakhova ES,Fakhranurova LI,Chekova SV,Tsarkova AS,Golubev YV,Negrebetsky VV,Dolgushin SA,Shalaev PV,Shlykov D,Melnik OA,

    更新日期：2020-08-01 00:00:00

  • Chaperones as thermodynamic sensors of drug-target interactions reveal kinase inhibitor specificities in living cells.

    abstract：:The interaction between the HSP90 chaperone and its client kinases is sensitive to the conformational status of the kinase, and stabilization of the kinase fold by small molecules strongly decreases chaperone interaction. Here we exploit this observation and assay small-molecule binding to kinases in living cells, usi...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.2620

    authors： Taipale M,Krykbaeva I,Whitesell L,Santagata S,Zhang J,Liu Q,Gray NS,Lindquist S

    更新日期：2013-07-01 00:00:00

  • Cell penetrating PNA constructs regulate galanin receptor levels and modify pain transmission in vivo.

    abstract：:Peptide nucleic acids (PNAs) form stable and tight complexes with complementary DNA and/or RNA and would be promising antisense reagents if their cellular delivery could be improved. We show that a 21-mer PNA, complementary to the human galanin receptor type 1 mRNA, coupled to the cellular transporter peptides, transp...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt0998-857

    authors： Pooga M,Soomets U,Hällbrink M,Valkna A,Saar K,Rezaei K,Kahl U,Hao JX,Xu XJ,Wiesenfeld-Hallin Z,Hökfelt T,Bartfai T,Langel U

    更新日期：1998-09-01 00:00:00

  • High-throughput measurement of single-cell growth rates using serial microfluidic mass sensor arrays.

    abstract：:Methods to rapidly assess cell growth would be useful for many applications, including drug susceptibility testing, but current technologies have limited sensitivity or throughput. Here we present an approach to precisely and rapidly measure growth rates of many individual cells simultaneously. We flow cells in suspen...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.3666

    authors： Cermak N,Olcum S,Delgado FF,Wasserman SC,Payer KR,A Murakami M,Knudsen SM,Kimmerling RJ,Stevens MM,Kikuchi Y,Sandikci A,Ogawa M,Agache V,Baléras F,Weinstock DM,Manalis SR

    更新日期：2016-10-01 00:00:00

  • Genome architectures revealed by tethered chromosome conformation capture and population-based modeling.

    abstract：:We describe tethered conformation capture (TCC), a method for genome-wide mapping of chromatin interactions. By performing ligations on solid substrates rather than in solution, TCC substantially enhances the signal-to-noise ratio, thereby facilitating a detailed analysis of interactions within and between chromosomes...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.2057

    authors： Kalhor R,Tjong H,Jayathilaka N,Alber F,Chen L

    更新日期：2011-12-25 00:00:00

  • Recombinant Dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing.

    abstract：:RNA interference (RNAi) is a powerful method for specifically silencing gene expression in diverse cell types. RNAi is mediated by approximately 21-nucleotide small interfering RNAs (siRNAs), which are produced from larger double-stranded RNAs (dsRNAs) in vivo through the action of Dicer, an RNase III-family enzyme. T...

    journal_title：Nature biotechnology

    pub_type：

    doi：10.1038/nbt792

    authors： Myers JW,Jones JT,Meyer T,Ferrell JE Jr

    更新日期：2003-03-01 00:00:00

  • Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays.

    abstract：:We describe a novel sequencing approach that combines non-gel-based signature sequencing with in vitro cloning of millions of templates on separate 5 microm diameter microbeads. After constructing a microbead library of DNA templates by in vitro cloning, we assembled a planar array of a million template-containing mic...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/76469

    authors： Brenner S,Johnson M,Bridgham J,Golda G,Lloyd DH,Johnson D,Luo S,McCurdy S,Foy M,Ewan M,Roth R,George D,Eletr S,Albrecht G,Vermaas E,Williams SR,Moon K,Burcham T,Pallas M,DuBridge RB,Kirchner J,Fearon K,Mao J,

    更新日期：2000-06-01 00:00:00

  • Author Correction: Brain leaks and consumer neurotechnology.

    abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title：Nature biotechnology

    pub_type： 已发布勘误

    doi：10.1038/s41587-019-0167-2

    authors： Ienca M,Haselager P,Emanuel EJ

    更新日期：2019-07-01 00:00:00

  • Metalloenzyme nitrile hydratase: structure, regulation, and application to biotechnology.

    abstract：:Nitrile hydratase (NHase), which catalyzes the hydration of nitriles to amides, has been used in the industrial production of acrylamide and nicotinamide. Recent studies on NHases, which are roughly classified into iron and cobalt types according to the metal involved, have clarified the photoactivation mechanism, the...

    journal_title：Nature biotechnology

    pub_type： 杂志文章,评审

    doi：10.1038/nbt0898-733

    authors： Kobayashi M,Shimizu S

    更新日期：1998-08-01 00:00:00

  • Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis.

    abstract：:Epigenetic mechanisms integrate genetic and environmental causes of disease, but comprehensive genome-wide analyses of epigenetic modifications have not yet demonstrated robust association with common diseases. Using Illumina HumanMethylation450 arrays on 354 anti-citrullinated protein antibody-associated rheumatoid a...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.2487

    authors： Liu Y,Aryee MJ,Padyukov L,Fallin MD,Hesselberg E,Runarsson A,Reinius L,Acevedo N,Taub M,Ronninger M,Shchetynsky K,Scheynius A,Kere J,Alfredsson L,Klareskog L,Ekström TJ,Feinberg AP

    更新日期：2013-02-01 00:00:00

  • Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.

    abstract：:The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single ce...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.3880

    authors： Lan F,Demaree B,Ahmed N,Abate AR

    更新日期：2017-07-01 00:00:00

  • A bacterial glycosidase enables mannose-6-phosphate modification and improved cellular uptake of yeast-produced recombinant human lysosomal enzymes.

    abstract：:Lysosomal storage diseases are treated with human lysosomal enzymes produced in mammalian cells. Such enzyme therapeutics contain relatively low levels of mannose-6-phosphate, which is required to target them to the lysosomes of patient cells. Here we describe a method for increasing mannose-6-phosphate modification o...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.2427

    authors： Tiels P,Baranova E,Piens K,De Visscher C,Pynaert G,Nerinckx W,Stout J,Fudalej F,Hulpiau P,Tännler S,Geysens S,Van Hecke A,Valevska A,Vervecken W,Remaut H,Callewaert N

    更新日期：2012-12-01 00:00:00

  • Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs.

    abstract：:Current tools for targeted RNA editing rely on the delivery of exogenous proteins or chemically modified guide RNAs, which may lead to aberrant effector activity, delivery barrier or immunogenicity. Here, we present an approach, called leveraging endogenous ADAR for programmable editing of RNA (LEAPER), that employs s...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/s41587-019-0178-z

    authors： Qu L,Yi Z,Zhu S,Wang C,Cao Z,Zhou Z,Yuan P,Yu Y,Tian F,Liu Z,Bao Y,Zhao Y,Wei W

    更新日期：2019-09-01 00:00:00

  • Pancreatic endoderm derived from human embryonic stem cells generates glucose-responsive insulin-secreting cells in vivo.

    abstract：:Development of a cell therapy for diabetes would be greatly aided by a renewable supply of human beta-cells. Here we show that pancreatic endoderm derived from human embryonic stem (hES) cells efficiently generates glucose-responsive endocrine cells after implantation into mice. Upon glucose stimulation of the implant...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt1393

    authors： Kroon E,Martinson LA,Kadoya K,Bang AG,Kelly OG,Eliazer S,Young H,Richardson M,Smart NG,Cunningham J,Agulnick AD,D'Amour KA,Carpenter MK,Baetge EE

    更新日期：2008-04-01 00:00:00

  • A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments.

    abstract：:Thermostable enzymes combine catalytic specificity with the toughness required to withstand industrial reaction conditions. Stabilized enzymes also provide robust starting points for evolutionary improvement of other protein properties. We recently created a library of at least 2,300 new active chimeras of the biotech...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt1333

    authors： Li Y,Drummond DA,Sawayama AM,Snow CD,Bloom JD,Arnold FH

    更新日期：2007-09-01 00:00:00

  • Large-scale detection of antigen-specific T cells using peptide-MHC-I multimers labeled with DNA barcodes.

    abstract：:Identification of the peptides recognized by individual T cells is important for understanding and treating immune-related diseases. Current cytometry-based approaches are limited to the simultaneous screening of 10-100 distinct T-cell specificities in one sample. Here we use peptide-major histocompatibility complex (...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.3662

    authors： Bentzen AK,Marquard AM,Lyngaa R,Saini SK,Ramskov S,Donia M,Such L,Furness AJ,McGranahan N,Rosenthal R,Straten PT,Szallasi Z,Svane IM,Swanton C,Quezada SA,Jakobsen SN,Eklund AC,Hadrup SR

    更新日期：2016-10-01 00:00:00

  • Expression monitoring by hybridization to high-density oligonucleotide arrays.

    abstract：:The human genome encodes approximately 100,000 different genes, and at least partial sequence information for nearly all will be available soon. Sequence information alone, however, is insufficient for a full understanding of gene function, expression, regulation, and splice-site variation. Because cellular processes ...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt1296-1675

    authors： Lockhart DJ,Dong H,Byrne MC,Follettie MT,Gallo MV,Chee MS,Mittmann M,Wang C,Kobayashi M,Horton H,Brown EL

    更新日期：1996-12-01 00:00:00

  • RNAi modulation of placental sFLT1 for the treatment of preeclampsia.

    abstract：:Preeclampsia is a placentally induced hypertensive disorder of pregnancy that is associated with substantial morbidity and mortality to mothers and fetuses. Clinical manifestations of preterm preeclampsia result from excess circulating soluble vascular endothelial growth factor receptor FLT1 (sFLT1 or sVEGFR1) of plac...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.4297

    authors： Turanov AA,Lo A,Hassler MR,Makris A,Ashar-Patel A,Alterman JF,Coles AH,Haraszti RA,Roux L,Godinho BMDC,Echeverria D,Pears S,Iliopoulos J,Shanmugalingam R,Ogle R,Zsengeller ZK,Hennessy A,Karumanchi SA,Moore MJ,Khvoro

    更新日期：2018-11-19 00:00:00

  • Designing around patents: a guideline.

    abstract：:An analysis of US Federal Circuit decisions shows strategies for designing around patents. ...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt0508-519

    authors： Wang SJ

    更新日期：2008-05-01 00:00:00

  • Inovio.

    abstract：:A Pennsylvania company hopes to turn synthetic DNA vaccines into rapid response agents against flu epidemics and cancer. ...

    journal_title：Nature biotechnology

    pub_type： 新闻

    doi：10.1038/nbt0213-98

    authors： Rohn J

    更新日期：2013-02-01 00:00:00

  • Low probability of chloroplast movement from oilseed rape (Brassica napus) into wild Brassica rapa.

    abstract：:Pollen-mediated movement of transgenes from transplastomic oilseed rape (Brassica napus) into wild relatives will be avoided if chloroplasts are maternally transmitted. We assess the probability of chloroplast exchange between conventional oilseed rape and wild Brassica rapa to model the future behavior of transplasto...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/7952

    authors： Scott SE,Wilkinson MJ

    更新日期：1999-04-01 00:00:00

  • Label-free, normalized quantification of complex mass spectrometry data for proteomic analysis.

    abstract：:Replicate mass spectrometry (MS) measurements and the use of multiple analytical methods can greatly expand the comprehensiveness of shotgun proteomic profiling of biological samples. However, the inherent biases and variations in such data create computational and statistical challenges for quantitative comparative a...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.1592

    authors： Griffin NM,Yu J,Long F,Oh P,Shore S,Li Y,Koziol JA,Schnitzer JE

    更新日期：2010-01-01 00:00:00

  • Integration and expression of the high-molecular-weight glutenin subunit 1Ax1 gene into wheat.

    abstract：:The unique bread-making characteristic of wheat flour is closely related to the elasticity and extensibility of the gluten proteins stored in the starchy endosperm, particularly the high-molecular-weight glutenin subunits (HMW-GS), which are important in determining gluten and dough elasticity. The quality of wheat cu...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt0996-1155

    authors： Altpeter F,Vasil V,Srivastava V,Vasil IK

    更新日期：1996-09-01 00:00:00

  • Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues.

    abstract：:The biology of multicellular organisms is coordinated across multiple size scales, from the subnanoscale of molecules to the macroscale, tissue-wide interconnectivity of cell populations. Here we introduce a method for super-resolution imaging of the multiscale organization of intact tissues. The method, called magnif...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt.3641

    authors： Ku T,Swaney J,Park JY,Albanese A,Murray E,Cho JH,Park YG,Mangena V,Chen J,Chung K

    更新日期：2016-09-01 00:00:00

  • Molecular goniometers for single-particle cryo-electron microscopy of DNA-binding proteins.

    abstract：:Correct reconstruction of macromolecular structure by cryo-electron microscopy (cryo-EM) relies on accurate determination of the orientation of single-particle images. For small (<100 kDa) DNA-binding proteins, obtaining particle images with sufficiently asymmetric features to correctly guide alignment is challenging....

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/s41587-020-0716-8

    authors： Aksel T,Yu Z,Cheng Y,Douglas SM

    更新日期：2020-10-19 00:00:00

  • Author Correction: Programmable RNA editing by recruiting endogenous ADAR using engineered RNAs.

    abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

    journal_title：Nature biotechnology

    pub_type： 已发布勘误

    doi：10.1038/s41587-019-0292-y

    authors： Qu L,Yi Z,Zhu S,Wang C,Cao Z,Zhou Z,Yuan P,Yu Y,Tian F,Liu Z,Bao Y,Zhao Y,Wei W

    更新日期：2019-11-01 00:00:00

  • Biomagnetic isolation of antigen-specific CD8+ T cells usable in immunotherapy.

    abstract：:Isolating antigen-specific T lymphocytes is hampered by the low frequency of the cells and the low affinity between T-cell receptors (TCR) and antigen. We describe the isolation and purification of antigen-specific CD8+ T lymphocytes from mixed T-cell populations. Magnetic beads coated with major histocompatibility co...

    journal_title：Nature biotechnology

    pub_type： 杂志文章

    doi：10.1038/nbt0398-281

    authors： Luxembourg AT,Borrow P,Teyton L,Brunmark AB,Peterson PA,Jackson MR

    更新日期：1998-03-01 00:00:00

  • Publisher Correction: Federated discovery and sharing of genomic data using Beacons.

    abstract：:In the version of this article initially published, Lena Dolman's second affiliation was given as Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK. The correct second affiliation is Ontario Institute for Cancer Research, Toronto, Ontario, Canada. The error has been corrected in the HTML ...

    journal_title：Nature biotechnology

    pub_type： 杂志文章,已发布勘误

    doi：10.1038/s41587-019-0094-2

    authors： Fiume M,Cupak M,Keenan S,Rambla J,de la Torre S,Dyke SOM,Brookes AJ,Carey K,Lloyd D,Goodhand P,Haeussler M,Baudis M,Stockinger H,Dolman L,Lappalainen I,Törnroos J,Linden M,Spalding JD,Ur-Rehman S,Page A,Flicek P,

    更新日期：2019-04-01 00:00:00