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: 10589632
• 负责人: Inanc Birol
• 金额: $ 19.13万
• 依托单位: PROVINCIAL HEALTH SERVICES AUTHORITY
• 依托单位国家: 美国
• 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: https://reporter.nih.gov/project-details/10589632
• 关键词: Algorithms; Americas; Award; Base Pairing; Basic Science; Bioinformatics; Biological Phenomena; Biological Sciences; Cancer Patient; Categories; Cohort Studies; Collaborations; Communicable Diseases; Computer software; Consensus; Coupled; DNA; DNA Sequence; DNA Sequence Analysis; DNA sequencing; Data; Detection; Development; Disease; Disease Outbreaks; Disease Surveillance; Funding; Genome; Genomics; Grant; Guidelines; Health; High-Throughput Nucleotide Sequencing; Length; Letters; Link; Malignant Neoplasms; Methods; Modeling; Pharmaceutical Preparations; Process; Protein Isoforms; Protocols documentation; Publications; Publishing; Quality Control; RNA; Reagent; Research; Research Personnel; Sequence Alignment; Software Tools; Stretching; System; Technology; The Cancer Genome Atlas; Transcript; United States National Institutes of Health; base; bioinformatics tool; cost; cost effective; design; experimental study; field study; frontier; genetic analysis; genetic information; human genomics; indexing; individual patient; innovation; instrument; microbial; microbial genomics; nanopore; new technology; personalized medicine; precision medicine; reconstruction; response; sequencing platform; symposium; tool; transcriptome sequencing; usability

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.

总结 这项拨款更新提案是关于开发创新的新软件， 研究人员利用DNA测序的新进展。 在过去的十年中，技术进步已经使DNA测序成为一种常规和成本- 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 我们的项目产生了数百万个短序列，由75-300个碱基对组成（ 组成DNA序列的“字母”）。这些简短的“读取”必须在 正确的顺序来理解数据。比罗尔博士和他的团队是世界基因组研究的领导者 他们开发的获奖软件（在他们的支持下） 现有的NIH赠款和其他资金）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，可以生成关于更长时间的信息。 输入DNA作为长或连接的读段。长读段平台可以测序超过100，000个碱基对 虽然具有相对较高的错误率。链接读取平台可以将多个 读取类似的长度，尽管数据包含许多间隙。不过，当加上 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 这些平台开辟了健康研究的新领域。 博士Birol正在寻求扩大他的NIH资金支持，以便他和他的团队能够 继续开发快速、准确、高效的专业软件， 组装和分析长的和连接的序列读段。这些工具提供了先进的 在一系列项目中的能力，如跟踪传染病爆发，使用基因 选择最好的药物来治疗个别患者的癌症，以及其他 应用. 这些新工具将在网上免费提供给其他非营利研究人员使用， 他们自己的测序项目，使世界各地的团队能够更快地取得进展， 健康研究。

项目成果

Interactive SARS-CoV-2 mutation timemaps.

• DOI: 10.12688/f1000research.50857.2
• 发表时间: 2021
• 期刊: F1000Research
• 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。

• 发表时间: 2020
• 期刊: ArXiv
• 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: BMC bioinformatics
• 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

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: GigaScience
• 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

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: NATURE COMMUNICATIONS
• 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