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：
Inanc Birol
金额：
$ 19.13万
依托单位：
PROVINCIAL HEALTH SERVICES AUTHORITY
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：
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

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.

概括该赠款更新提案是关于开发创新的新软件，该软件允许健康研究人员利用DNA测序的新进展。在过去的十年中，技术的进步使DNA测序了常规和成本 - 生命科学研究领域的有效方法。一开始的主要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（构成DNA序列的“字母”）。这些简短的“读取”必须在正确的命令以理解数据。 Birol博士和他的团队是基因组的世界领导人组装和他们开发的屡获殊荣的软件（在他们的支持下现有的NIH赠款和其他资金）已用于潜水DNA测序项目，包括癌症基因组图集项目。现在可以使用较新的技术，可以在更长的时间内生成信息输入DNA作为长或链接的读取。长读平台可以序列超过100,000个基对每读，尽管错误率相对较高。链接的读取平台可以关联多个读取相似的长度，尽管数据包含许多差距。不过，当与这些新测序的生物信息学工具可以利用它们提供的丰富信息平台开放了健康研究的新领域。 Birol博士正在寻求扩大他的NIH资金支持，以便他和他的团队可以成为维护以继续开发专门的软件，以迅速，准确，高效组装和分析较长的链接序列读取。这些工具提供了高级使用遗传信息以选择治疗个体患者癌症的最佳药物，以及其他申请。新工具可在线免费提供，供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进展健康研究。

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：
F1000Research
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：
ArXiv
影响因子：
0
作者：
Warren,RenéL;Birol,Inanç
通讯作者：
Birol,Inanç

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

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

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