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.

概括 该赠款续订提案旨在开发创新的新软件，以促进健康 研究人员利用 DNA 测序的新进展。 在过去的十年中，技术进步使 DNA 测序成为一种常规且成本低廉的方法。 是生命科学研究许多领域的有效方法。 我们的项目生成了数百万个短序列，由 75-300 个碱基对组成（ 组成 DNA 序列的“字母”）必须组装在这些短“读数”中。 比罗尔博士和他的团队是基因组领域的世界领导者。 大会，以及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。 现在可以使用更新的技术来生成更长距离的信息 输入 DNA 作为长读或链接读长平台可以对超过 100,000 个碱基对进行测序。 每次读取，虽然错误率相对较高，但链接读取平台可以关联多个。 尽管数据仍然包含许多间隙，但读取的长度相似。 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 这些工具提供先进的组装和分析长链接序列读取。 一系列项目的能力，例如跟踪传染病爆发、利用基因 选择治疗个体患者癌症的最佳药物的信息，以及其他 应用程序。 这些新工具免费在线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

ARKS: chromosome-scale scaffolding of human genome drafts with linked read kmers.

ARKS：人类基因组草图的染色体规模支架，具有链接的读取公里数。

• 发表时间: 2018-06-20
• 影响因子: 3
• 作者: Coombe, Lauren;Zhang, Jessica;Vandervalk, Benjamin P;Chu, Justin;Jackman, Shaun D;Birol, Inanc;Warren, René L
• 通讯作者: Warren, René L

HLA alleles measured from COVID-19 patient transcriptomes reveal associations with disease prognosis in a New York cohort.

从 COVID-19 患者转录组中测量的 HLA 等位基因揭示了纽约队列中疾病预后的相关性。

• 发表时间: 2021
• 影响因子: 2.7
• 作者: Warren, René L;Birol, Inanc
• 通讯作者: Birol, Inanc

ntEdit+Sealer: Efficient Targeted Error Resolution and Automated Finishing of Long-Read Genome Assemblies.

ntEdit Sealer：高效的目标错误解决和长读长基因组组装的自动完成。

• 发表时间: 2022-05
• 作者: Li, Janet X;Coombe, Lauren;Wong, Johnathan;Birol, Inanç;Warren, René L
• 通讯作者: Warren, René L

RResolver: efficient short-read repeat resolution within ABySS.

RResolver：ABySS 内高效的短读重复分辨率。

• 发表时间: 2022-06-21
• 影响因子: 3
• 作者: Nikolić, Vladimir;Afshinfard, Amirhossein;Chu, Justin;Wong, Johnathan;Coombe, Lauren;Nip, Ka Ming;Warren, René L;Birol, Inanç
• 通讯作者: Birol, Inanç

Linear time complexity de novo long read genome assembly with GoldRush.

使用 GoldRush 进行线性时间复杂度的从头长读基因组组装。

• 发表时间: 2023-05-22
• 影响因子: 16.6
• 作者: Wong, Johnathan;Coombe, Lauren;Nikolić, Vladimir;Zhang, Emily;Nip, Ka Ming;Sidhu, Puneet;Warren, René L;Birol, Inanç
• 通讯作者: Birol, Inanç