NIGMS Administrative Supplements to Support Undergraduate Summer Research

NIGMS 支持本科生暑期研究的行政补充

• 批准号: 10393964
• 负责人: MARK BORODOVSKY
• 金额: $ 0.53万
• 依托单位: GEORGIA INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10393964
• 关键词: Address; Administrative Supplement; Algorithm Design; Algorithms; Area; Attention; Code; Complex; Computational Biology; Computational algorithm; Computer software; Development; Genes; Genome; Genomic DNA; Guanine + Cytosine Composition; Heterogeneity; Libraries; Mammals; Modeling; National Institute of General Medical Sciences; Open Reading Frames; Parents; Performance; Poaceae; Population; Positioning Attribute; Process; Protein Isoforms; Proteins; Research; Students; Supervision; Testing; Training; Transcript; Viral; Work; base; design; evidence base; genome annotation; improved; interest; metagenome; multiple omics; parent grant; reconstruction; summer research; tool; transcriptome; undergraduate student

Administrative Supplement to Parent Grant R01 GM128145 Addressing Open Challenges of Computational Genome Annotation PI Mark Borodovsky Abstract Improving gene finding in eukaryotic genomes is a large and important part of the parent proposal. With Andrey Zaznaev, the Georgia Tech Deans’s list junior student, who is very interested in making contribution in computational biology, we will work on additional aim of the proposal – developing an improved algorithm for gene prediction in eukaryotic genomes that are distinguished by their complexity - long- and short-range inhomogeneity of genome GC composition. The undergraduate student will create tools for generating a library of GC- dependent models of protein-coding regions in each genome. He also will develop an extension of the gene finding algorithm that will be able to use the new models.

家长补助金行政补充 R01 GM128145 解决计算基因组注释的开放挑战 PI 马克·博罗多夫斯基 抽象的 改善真核基因组中的基因发现是亲本的一个重要组成部分 提议。佐治亚理工学院院长名单上的大三学生安德烈·扎兹纳耶夫 (Andrey Zaznaev) 非常出色。 有兴趣在计算生物学领域做出贡献，我们将致力于实现以下目标 该提案——开发一种改进的真核基因组基因预测算法 以其复杂性而著称 - 基因组 GC 的长程和短程不均匀性 作品。本科生将创建用于生成 GC 库的工具- 每个基因组中蛋白质编码区的依赖模型。他还将开发一个扩展 能够使用新模型的基因查找算法。

项目成果

StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes.

• DOI: 10.3389/fbinf.2021.704157
• 发表时间: 2021
• 期刊: FRONTIERS IN BIOINFORMATICS
• 作者: Gemayel, Karl;Lomsadze, Alexandre;Borodovsky, Mark
• 通讯作者: Borodovsky, Mark

TSEBRA: transcript selector for BRAKER.

• DOI: 10.1186/s12859-021-04482-0
• 发表时间: 2021-11-25
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Gabriel L;Hoff KJ;Brůna T;Borodovsky M;Stanke M
• 通讯作者: Stanke M

A reference genome for ecological restoration of the sunflower sea star, Pycnopodia helianthoides

• DOI: 10.1093/jhered/esad054
• 发表时间: 2023-10-27
• 期刊: JOURNAL OF HEREDITY
• 影响因子: 3.1
• 作者: Schiebelhut，Lauren M.;DeBiasse，Melissa B.;Dawson，Michael N.
• 通讯作者: Dawson，Michael N.

BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database.

• DOI: 10.1093/nargab/lqaa108
• 发表时间: 2021-03
• 期刊: NAR genomics and bioinformatics
• 影响因子: 4.6
• 作者: Brůna T;Hoff KJ;Lomsadze A;Stanke M;Borodovsky M
• 通讯作者: Borodovsky M

VARUS: sampling complementary RNA reads from the sequence read archive.

VARUS：从序列读取存档中采样互补 RNA 读取。

• DOI: 10.1186/s12859-019-3182-x
• 发表时间: 2019
• 期刊: BMC bioinformatics
• 影响因子: 3
• 作者: Stanke,Mario;Bruhn,Willy;Becker,Felix;Hoff,KatharinaJ
• 通讯作者: Hoff,KatharinaJ