De Novo Assembly Tools: Research with Unbiased Engines - Renewal (DNA-TRUER)
从头组装工具:使用无偏差引擎进行研究 - 更新 (DNA-TRUER)
基本信息
- 批准号:10589632
- 负责人:
- 金额:$ 19.13万
- 依托单位:
- 依托单位国家:美国
- 项目类别:
- 财政年份:2022
- 资助国家:美国
- 起止时间:2022-03-10 至 2023-03-31
- 项目状态:已结题
- 来源:
- 关键词:AlgorithmsAmericasAwardBase PairingBasic ScienceBioinformaticsBiological PhenomenaBiological SciencesCancer PatientCategoriesCohort StudiesCollaborationsCommunicable DiseasesComputer softwareConsensusCoupledDNADNA SequenceDNA Sequence AnalysisDNA sequencingDataDetectionDevelopmentDiseaseDisease OutbreaksDisease SurveillanceFundingGenomeGenomicsGrantGuidelinesHealthHigh-Throughput Nucleotide SequencingLengthLettersLinkMalignant NeoplasmsMethodsModelingPharmaceutical PreparationsProcessProtein IsoformsProtocols documentationPublicationsPublishingQuality ControlRNAReagentResearchResearch PersonnelSequence AlignmentSoftware ToolsStretchingSystemTechnologyThe Cancer Genome AtlasTranscriptUnited States National Institutes of Healthbasebioinformatics toolcostcost effectivedesignexperimental studyfield studyfrontiergenetic analysisgenetic informationhuman genomicsindexingindividual patientinnovationinstrumentmicrobialmicrobial genomicsnanoporenew technologypersonalized medicineprecision medicinereconstructionresponsesequencing platformsymposiumtooltranscriptome sequencingusability
项目摘要
Summary
This grant renewal proposal is about developing innovative new software that allow health
researchers to take advantage of new advances in DNA sequencing.
Over the last decade, technology advances have made DNA sequencing a routine and cost-
effective method in many fields of life sciences research. The dominant technology at the start
of our project generated millions of short sequences, consisting of 75-300 base pairs (the
“letters” that make up the DNA sequence). These short “reads” have to be assembled in the
right order to make sense of the data. Dr. Birol and his team are world leaders in genome
assembly, and the award-winning software they have developed (with support from their
existing NIH grant and other funding) has been used in diverse DNA sequencing projects,
including The Cancer Genome Atlas project.
Newer technologies are now available that generate information on much longer stretches of the
input DNA as long or linked reads. Long read platforms can sequence over 100,000 base pairs
per read, though with a relatively high error rate. Linked read platforms can associate multiple
reads over similar lengths, although the data contains many gaps. Still, when coupled with
bioinformatics tools that can leverage the rich information they provide, these new sequencing
platforms open new frontiers in health research.
Dr. Birol is seeking to extend his NIH funding support so that he and his team can be
maintained to continue developing specialized software that quickly, accurately, and efficiently
assemble and analyse long and linked sequence reads. These tools provide advanced
capabilities in a range of projects, such as tracking infectious disease outbreaks, using genetic
information to select the best drugs to treat an individual patient's cancer, and other
applications.
The new tools are being made available online free for other non-profit researchers to use in
their own sequencing projects, allowing teams around the world to make faster progress in
health research.
摘要
这项拨款续期提案是关于开发创新的新软件,使健康
研究人员将利用DNA测序方面的新进展。
在过去的十年里,技术的进步使DNA测序成为例行公事和成本-
在生命科学研究的许多领域都是有效的方法。一开始的主导技术
产生了数百万个短序列,由75-300个碱基对(
组成DNA序列的“字母”)。这些短小的“读数”必须在
正确的顺序来理解数据。比罗尔博士和他的团队是基因组领域的世界领先者
汇编和他们开发的获奖软件(在他们的支持下
现有的NIH拨款和其他资金)已用于各种DNA测序项目,
包括癌症基因组图谱项目。
现在有了更新的技术,可以在更长的范围内生成信息
以长读或链接读的形式输入DNA。长阅读平台可以测序超过100,000个碱基对
每次读取,尽管具有相对较高的错误率。链接阅读平台可以关联多个
阅读的长度相似,尽管数据包含许多差距。尽管如此,当与
生物信息学工具可以利用它们提供的丰富信息,这些新的测序
平台开辟了健康研究的新领域。
比罗尔博士正在寻求延长他的NIH资金支持,这样他和他的团队就可以
维护以继续快速、准确和高效地开发专门的软件
组装和分析长的和相连的序列读数。这些工具提供高级
在一系列项目中的能力,如跟踪传染病暴发,使用基因
选择治疗个别患者癌症的最佳药物的信息,以及其他
申请。
这些新工具正在网上免费提供给其他非营利性研究人员使用
他们自己的测序项目,使世界各地的团队在
健康研究。
项目成果
期刊论文数量(45)
专著数量(0)
科研奖励数量(0)
会议论文数量(0)
专利数量(0)
Interactive SARS-CoV-2 mutation timemaps.
- DOI:10.12688/f1000research.50857.2
- 发表时间:2021
- 期刊:
- 影响因子:0
- 作者:Warren RL;Birol I
- 通讯作者:Birol I
HLA predictions from the bronchoalveolar lavage fluid samples of five patients at the early stage of the wuhan seafood market COVID-19 outbreak.
对武汉海鲜市场 COVID-19 疫情早期 5 名患者的支气管肺泡灌洗液样本进行 HLA 预测。
- DOI:
- 发表时间:2020
- 期刊:
- 影响因子:0
- 作者:Warren,RenéL;Birol,Inanç
- 通讯作者:Birol,Inanç
LongStitch: high-quality genome assembly correction and scaffolding using long reads.
- DOI:10.1186/s12859-021-04451-7
- 发表时间:2021-10-30
- 期刊:
- 影响因子:3
- 作者:Coombe L;Li JX;Lo T;Wong J;Nikolic V;Warren RL;Birol I
- 通讯作者:Birol I
Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2.
- DOI:10.1038/s41467-023-38553-y
- 发表时间:2023-05-22
- 期刊:
- 影响因子:16.6
- 作者:Nip, Ka Ming;Hafezqorani, Saber;Gagalova, Kristina K.;Chiu, Readman;Yang, Chen;Warren, Rene L.;Birol, Inanc
- 通讯作者:Birol, Inanc
LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads.
- DOI:10.1186/s13742-015-0076-3
- 发表时间:2015
- 期刊:
- 影响因子:9.2
- 作者:Warren RL;Yang C;Vandervalk BP;Behsaz B;Lagman A;Jones SJ;Birol I
- 通讯作者:Birol I
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{{ truncateString('Inanc Birol', 18)}}的其他基金
De Novo Assembly Tools: Research with Unbiased Engines - Renewal (DNA-TRUER)
从头组装工具:使用无偏差引擎进行研究 - 更新 (DNA-TRUER)
- 批准号:
9552251 - 财政年份:2014
- 资助金额:
$ 19.13万 - 项目类别:
De Novo Assembly Tools: Research with Unbiased Engines (DNA-TRUE)
从头组装工具:使用无偏差引擎进行研究 (DNA-TRUE)
- 批准号:
8631896 - 财政年份:2014
- 资助金额:
$ 19.13万 - 项目类别:
De Novo Assembly Tools: Research with Unbiased Engines - Renewal (DNA-TRUER)
从头组装工具:使用无偏差引擎进行研究 - 更新 (DNA-TRUER)
- 批准号:
9382151 - 财政年份:2014
- 资助金额:
$ 19.13万 - 项目类别:
De Novo Assembly Tools: Research with Unbiased Engines (DNA-TRUE)
从头组装工具:使用无偏差引擎进行研究 (DNA-TRUE)
- 批准号:
8816112 - 财政年份:2014
- 资助金额:
$ 19.13万 - 项目类别:
De Novo Assembly Tools: Research with Unbiased Engines - Renewal (DNA-TRUER)
从头组装工具:使用无偏差引擎进行研究 - 更新 (DNA-TRUER)
- 批准号:
9791194 - 财政年份:2014
- 资助金额:
$ 19.13万 - 项目类别:
De Novo Assembly Tools: Research with Unbiased Engines (DNA-TRUE)
从头组装工具:使用无偏差引擎进行研究 (DNA-TRUE)
- 批准号:
9002847 - 财政年份:2014
- 资助金额:
$ 19.13万 - 项目类别:
Identification and annotation of 3' UTR ends using RNA-seq data
使用 RNA-seq 数据识别和注释 3 UTR 末端
- 批准号:
8751765 - 财政年份:2014
- 资助金额:
$ 19.13万 - 项目类别:
De Novo Assembly Tools: Research with Unbiased Engines - Renewal (DNA-TRUER)
从头组装工具:使用无偏差引擎进行研究 - 更新 (DNA-TRUER)
- 批准号:
9976547 - 财政年份:2014
- 资助金额:
$ 19.13万 - 项目类别:
Pan-cancer survey of candidate non-coding RNA transcripts on the cloud using a targeted de novo assembly approach
使用靶向从头组装方法在云上对候选非编码 RNA 转录本进行泛癌调查
- 批准号:
9167382 - 财政年份:2014
- 资助金额:
$ 19.13万 - 项目类别:
Neuroinformatics for gene expression: networks, function and meta-analysis
基因表达的神经信息学:网络、功能和荟萃分析
- 批准号:
8502624 - 财政年份:2005
- 资助金额:
$ 19.13万 - 项目类别:
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