UCSC Graduate Program in Genome Sciences

UCSC 基因组科学研究生项目

• 批准号: 10657495
• 负责人: Angela Norie Brooks
• 金额: $ 31.61万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA CRUZ
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-07-01 至 2027-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10657495
• 关键词: genome sciences; programs

ABSTRACT The UCSC Graduate Training Program in Genome Science combines cutting-edge computational biology training in a multidisciplinary biomedical science and engineering environment. Among other strengths, UC Santa Cruz is a world leader in computational biology, bioinformatics, genomic technologies and RNA biology. The goals of the program are to prepare trainees for advanced academic and industry careers in biomedical genomics. Our training program develops critical thinking skills, provides rigorous hands-on training in computer science, statistics, and biological sciences, and develops scientific communication skills. The proposed program will provide support for six trainees, each with a two-year appointment. Our trainee applicant pool consists of PhD students who have already joined UCSC’s interdisciplinary genomics and biomedical sciences community and completed three hands-on laboratory rotations during their first year of study, at least one of which must be conducted in the laboratory of a GS Program faculty member. Genome Science trainees participate in several innovative training activities. Each year, our trainees will organize and run a bootcamp for each year’s incoming PhD cohort of students who are accepted by the Dept. of Biomolecular Engineering. This 10-day activity is designed and implemented by the T32 trainees with feedback and guidance from faculty. The centerpiece of the bootcamp is an ambitious hands-on activity for the incoming grad cohort to tackle. Previous activities have included building a functional DropSeq single-cell RNA sequencing machine (2017), as well as genome sequencing and assembly of the banana slug – UCSC’s mascot (2019). Trainees receive training in labs of 26 faculty, including a winner of the MacArthur Award, members of the National Academy of Sciences, and a Nobel Laureate. Formal coursework for trainees includes graduate- level instruction in bioethics, programming, practical genomics, statistics, and scientific writing. These courses cover essential topics in rigor and reproducibility and responsible conduct of research. Working with the Graduate Advising Committee and their faculty mentors, trainees develop Individual Development Plans which may involve further coursework to address specific deficiencies or special interests. In coordination with the NHGRI DAP program, trainees will also serve as mentors to undergraduate students. Program success will be assessed via several quantitative metrics of trainee productivity, such as the timing and number of publications and success in applying for extramural research funds, as well as career outcomes that are tracked following the award of PhDs. These metrics will be assessed by the Genome Sciences Executive Committee. The program is interdisciplinary, including 26 program faculty from 8 departments. Most trainees and approximately half of program faculty are affiliated with the Biomolecular Engineering Department, as nearly all BME faculty have genomics-focused research programs.

抽象的 UCSC 基因组科学研究生培训项目结合了尖端计算生物学 在多学科生物医学科学和工程环境中进行培训。除其他优势外，UC Santa Cruz 是计算生物学、生物信息学、基因组技术和 RNA 生物学领域的世界领先者。 该计划的目标是让学员为生物医学领域的高级学术和行业职业做好准备 基因组学。我们的培训计划培养批判性思维能力，提供严格的计算机实践培训 科学、统计学和生物科学，并培养科学沟通技巧。 拟议的计划将为六名学员提供支持，每名学员的任期为两年。我们的实习生 申请人池由已经加入 UCSC 跨学科基因组学的博士生组成， 生物医学科学界，并在第一年完成了三次实践实验室轮换 研究，其中至少一项必须在 GS 项目教员的实验室中进行。 基因组科学学员参加多项创新培训活动。每年，我们的学员都会 为每年被该部门录取的即将入学的博士生组织和举办训练营。 生物分子工程系。本次为期10天的活动由T32学员设计并实施 教师的反馈和指导。训练营的核心是一项雄心勃勃的实践活动 即将到来的毕业生群体要解决。之前的活动包括构建功能性 DropSeq 单细胞 RNA 测序机（2017），以及香蕉蛞蝓的基因组测序和组装 - UCSC 的吉祥物 （2019）。学员在 26 名教职人员的实验室接受培训，其中包括麦克阿瑟奖获得者、 美国国家科学院院士和诺贝尔奖获得者。实习生的正式课程包括研究生- 生物伦理学、编程、实用基因组学、统计学和科学写作方面的水平指导。这些课程 涵盖严谨性、可重复性以及负责任的研究行为等重要主题。与毕业生一起工作 咨询委员会及其教师导师、学员制定个人发展计划，其中可能涉及 进一步的课程作业以解决具体缺陷或特殊兴趣。与 NHGRI DAP 协调 计划中，学员还将担任本科生的导师。 计划的成功将通过学员生产力的几个定量指标进行评估，例如时间安排 发表的论文数量、申请校外研究基金的成功率以及职业成果 授予博士学位后进行跟踪。这些指标将由基因组科学评估 执行委员会。 该项目是跨学科的，包括来自8个系的26名项目教师。大多数学员和 大约一半的项目教师隶属于生物分子工程系，因为几乎所有 BME 教师拥有以基因组学为重点的研究项目。

项目成果

Robust classification of wound healing stages in both mice and humans for acute and burn wounds based on transcriptomic data.

• DOI: 10.1186/s12859-023-05295-z
• 发表时间: 2023-04-25
• 期刊: BMC bioinformatics
• 影响因子: 3

A computational approach for positive genetic identification and relatedness detection from low-coverage shotgun sequencing data.

• DOI: 10.1093/jhered/esad041
• 发表时间: 2023-08-23
• 期刊: The Journal of heredity

LincRNA-Cox2 Regulates Smoke-induced Inflammation in Murine Macrophages.

LincRNA-Cox2 调节小鼠巨噬细胞中烟雾引起的炎症。

• DOI: 10.1165/rcmb.2022-0413oc
• 发表时间: 2023
• 期刊: American journal of respiratory cell and molecular biology
• 影响因子: 6.4
• 作者: Salih,MaysMohammed;Robinson,ElektraKantzari;Malekos,Eric;Perez,Elizabeth;Capili,Allyson;Kim,Kihwan;Zhang,WilliamZ;Cloonan,SuzanneM;Carpenter,Susan
• 通讯作者: Carpenter,Susan