Graduate Training Program in Bioinformatics

生物信息学研究生培训计划

• 批准号: 10612423
• 负责人: Vineet Bafna
• 金额: $ 42.44万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN DIEGO
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10612423
• 关键词: Bioinformatics; Training Programs

Graduate Training Program in Bioinformatics Program Abstract Biology is increasingly becoming an information-driven science. To harness the opportunities of the post- genomic era in furthering health sciences research and improving health care, there is an enormous demand for biologists who are trained in mathematics and computer science and can think quantitatively. However, current disciplinary graduate training programs are not designed to accommodate these rapid changes in the biological research perspective. This need serves as the motivation for the development of specialized graduate training programs that will train students at the interface between biology, engineering and computer science. To address this need, UCSD established an interdisciplinary Graduate Program in Bioinformatics in 2001 under the directorship of Dr. Shankar Subramaniam. In 2008, it was renamed Graduate Program in Bioinformatics and Systems Biology and reorganized. The current program directors Drs. Trey Ideker, Euegene Yeo, and Theresa Gaasterland work closely with the Training Grant co-PIs Dr. Subramaniam, Vineet Bafna, and Theresa Gaasterland, and with an active steering committee containing representative faculty from all five participating UCSD schools and academic divisions. The primary objectives of this (renewal) application of the Training Grant by the three co-PIs are to continue and expand this premier Graduate Program, and support the highest quality students in their truly interdisciplinary training which blends biomedicine, computer science and engineering. The Program will continue to evolve the curriculum (including online offerings) and develop and offer electives that will prepare students for the challenges of big data and computational biomedical research. The program will continue its mode of training that begins with a set of research rotations in laboratories of faculty members, and continues through doctoral research work under the supervision of a PhD advisor and co-advisor who provide complementary interdisciplinary expertise. The Program will also continue a recently established weekly Colloquium, the student Journal Club, and annual retreat. In the course of their training, program students have contributed important discoveries and impactful advances in health sciences research. Alumni of the program are placed in leading positions in Academia and industry. Given the extraordinary number and quality of applicants, the capacity and eagerness of the Program faculty to train the Program’s students, and the institutional support for the Program, this application seeks to increase the number of trainee slots to 12. Following Training Grant support of Graduate students during their course work education and initial research training, all graduate students will be supported by their thesis advisors for the duration of their PhD studies. The Proposal outlines our past success in training students and discusses significant novel strategies for enhancing the training program. The new inception of the UCSD Halicioglu Data Sciences Institute provides great synergy for our Graduate Program and offers the trainees an opportunity to become leaders in the emerging areas of biomedicine that are heavily becoming data science disciplines.

生物信息学研究生培训计划 程序摘要 生物学正日益成为一门信息驱动的科学。为了利用后- 基因组时代在促进健康科学研究和改善医疗保健方面，存在巨大的需求 受过数学和计算机科学训练并能定量思考的生物学家。但目前的 学科研究生培训计划的设计并不能适应生物学领域的这些快速变化， 研究视角这一需要成为发展专业研究生培养的动力 这些课程将培养学生掌握生物学、工程学和计算机科学之间的联系。解决 为了满足这一需求，UCSD在2001年建立了一个跨学科的生物信息学研究生课程， Shankar Subramaniam博士的董事职位2008年，它更名为生物信息学研究生课程， 系统生物学和重组。现任项目主任Trey Ideker博士、Euegene Yeo博士和Theresa博士 Gaasterland与培训补助金共同PI Subramaniam博士，Vineet Bafna和Theresa密切合作 Gaasterland，并有一个积极的指导委员会，其中包括来自所有五个参与的代表性教师 UCSD学校和学术部门。培训补助金的这一（延期）申请的主要目的是 由三个共同PI是继续和扩大这一总理研究生计划，并支持最高质量的 学生在他们真正的跨学科培训，融合生物医学，计算机科学和工程。的 该计划将继续发展课程（包括在线课程），并开发和提供选修课， 将为学生准备大数据和计算生物医学研究的挑战。该计划将 继续其培训模式，开始与一套研究轮换实验室的教师，和 继续通过博士研究工作的博士生导师和共同顾问的监督下，谁提供 互补的跨学科专业知识。该计划还将继续最近建立的每周 座谈会，学生杂志俱乐部，和年度务虚会。在他们的培训过程中，项目学生有 在健康科学研究方面做出了重要发现和有影响力的进展。项目校友 在学术界和工业界都处于领先地位。考虑到数量和质量都非常惊人的 申请人，该计划教师培训该计划学生的能力和热情，以及 为了加强对该计划的机构支持，该申请旨在将受训人员名额增加到12个。 在研究生的课程工作教育和初步研究期间提供培训补助金 培训，所有的研究生将由他们的论文导师为他们的博士研究期间的支持。的 提案概述了我们过去在培训学生方面的成功，并讨论了提高学生能力的重要新战略。 培训计划。UCSD Halicioglu数据科学研究所的新成立提供了巨大的协同作用 为我们的研究生课程，并提供学员有机会成为新兴领域的领导者， 生物医学正在成为数据科学学科。

项目成果

Application of a Machine Learning Algorithm in Prediction of Abusive Head Trauma in Children.

机器学习算法在预测儿童虐待性头部创伤中的应用。

• DOI: 10.1016/j.jpedsurg.2023.09.027
• 发表时间: 2024
• 期刊: Journal of pediatric surgery
• 影响因子: 2.4
• 作者: Jadhav,Priyanka;Sears,Timothy;Floan,Gretchen;Joskowitz,Katie;Nienow,Shalon;Cruz,Sheena;David,Maya;deCos,Víctor;Choi,Pam;Ignacio,RomeoC
• 通讯作者: Ignacio,RomeoC

Germline genetic biomarkers to stratify patients for personalized radiation treatment.

• DOI: 10.1186/s12967-022-03561-x
• 发表时间: 2022-08-12
• 期刊: JOURNAL OF TRANSLATIONAL MEDICINE
• 影响因子: 7.4
• 作者: Deichaite, Ida;Hopper, Austin;Krockenberger, Lena;Sears, Timothy J.;Sutton, Leisa;Ray, Xenia;Sharabi, Andrew;Navon, Ami;Sanghvi, Parag;Carter, Hannah;Moiseenko, Vitali
• 通讯作者: Moiseenko, Vitali

Variability of temperature measurements recorded by a wearable device by biological sex.

• DOI: 10.1186/s13293-023-00558-z
• 发表时间: 2023-11-01
• 期刊: BIOLOGY OF SEX DIFFERENCES
• 影响因子: 7.9
• 作者: Bruce, Lauryn Keeler;Kasl, Patrick;Soltani, Severine;Viswanath, Varun K.;Hartogensis, Wendy;Dilchert, Stephan;Hecht, Frederick M.;Chowdhary, Anoushka;Anglo, Claudine;Pandya, Leena;Dasgupta, Subhasis;Altintas, Ilkay;Gupta, Amarnath;Mason, Ashley E.;Smarr, Benjamin L.
• 通讯作者: Smarr, Benjamin L.

Artificial intelligence-guided discovery of gastric cancer continuum.

• DOI: 10.1007/s10120-022-01360-3
• 发表时间: 2023-03
• 期刊: GASTRIC CANCER
• 影响因子: 7.4
• 作者: Vo, Daniella;Ghosh, Pradipta;Sahoo, Debashis
• 通讯作者: Sahoo, Debashis

Host biology, ecology and the environment influence microbial biomass and diversity in 101 marine fish species.

• DOI: 10.1038/s41467-022-34557-2
• 发表时间: 2022-11-17
• 期刊: NATURE COMMUNICATIONS
• 影响因子: 16.6
• 作者: Minich, Jeremiah J.;Harer, Andreas;Vechinski, Joseph;Frable, Benjamin W.;Skelton, Zachary R.;Kunselman, Emily;Shane, Michael A.;Perry, Daniela S.;Gonzalez, Antonio;McDonald, Daniel;Knight, Rob;Michael, Todd P.;Allen, Eric E.
• 通讯作者: Allen, Eric E.