# PhD Program in Computational Biology <img src="/slides/phd-program-in-comp-bio-uva/cobi/comp-bio.webp" height="360"/> <div class="bullet"><img src="/slides/phd-program-in-comp-bio-uva/University_of_Virginia_Rotunda_logo.svg" height="60"><img src="/slides/phd-program-in-comp-bio-uva/University_of_Virginia_logo_white.svg" height="60"> </div> --- # In this presentation 1. Computational biology (COBI) program overview - coursework, requirements, faculty 2. Resources at UVA for Computational Biologists 3. UVA's flavor of computational biology --- # 1. Program Overview <img src="/slides/phd-program-in-comp-bio-uva/uva/sunset.jpg" height="300"> --- ## Program Overview - COBI is UVA's newest PhD program, approved in summer 2024. - A component of the Biomedical Sciences (BIMS) umbrella - You are our first recruiting class - You can help shape this program! --- ## Timeline (Similar to other BIMS programs) - **Year 1:** Foundational coursework and lab rotations. - **Year 2:** Finish advanced/elective coursework, mostly research. - **Year 3+** Full-time research and dissertation. - **Duration:** 4-6 years. --- ## Coursework See [compbio.med.virginia.edu/courses/](https://compbio.med.virginia.edu/courses/) - Total: 27 credits of didactic courses (roughly 1 year) - 21 required credits, 3 emphasis credits, 3 elective credits --- ## Required coursework Complete 21 credits of required coursework: - BIMS 7100 → Research Ethics (1 credits) - BIMS 6000 → Core Course in Integrative Biosciences (10 credits) - COBI 8201 → Topics in Computational Biology I (2 credits) - COBI 8202 → Topics in Computational Biology II (2 credits) - COBI 8203 → Advanced Topics in Computational Biology (2 credits) - COBI 8501 → Computational Biology I (2 credits) - COBI 8502 → Computational Biology II (2 credits) --- ## Emphasis requirement Choose one emphasis course: - BME 8315 → Systems Bioengineering and Multi-Scale Models (3 credits) - COBI 8601 → Advanced Computational Genomics (3 credits) - COBI 8602 → Statistical Genetics (3 credits) --- ## Elective coursework Choose 3 additional computational elective credits. Examples: - BIMS 8075 → Recent Advances in Public Health Genomics (3 credits) - BIMS 8380 → Practical Biomedical Statistics I (2 credits) - BME 7370 → Quantitative Biological Reasoning (3 credits) - CS 6316 → Machine Learning (3 credits) --- ## Other program requirements - [x] Coursework - [ ] Qualifying exam - Written and oral defense of a grant proposal - Typically done in year 2-3 - [ ] Dissertation - Written and oral defense of a substantial contribution to the field --- ## Faculty and Collaborations - World-class faculty across UVA schools and departments. - Current faculty list here: https://compbio.med.virginia.edu/faculty/ - The program is just getting started; students will drive faculty joining the program <hr/> | Faculty Member | Department/School | Research Focus | |---------------------|---------------------------------|---------------------------------------------| | Chongzhi Zang | Genome Sciences | Computational epigenomics | | Aakrosh Ratan | Genome Sciences | Cancer genomics | | Ani Manichaikul | Genome Sciences | Statistical genetics | | Jason Papin | Biomedical Engineering | Microbial metabolic network | | Jeff Saucerman | Biomedical Engineering | Cardiovascular systems modeling | | Gustavo Rohde | Biomedical Engineering | Machine learning in image analysis | | Aidong Zhang | Data Science | Biomedical natural language processing | | Tom Hartvigsen | Data Science | Machine learning for health | | Stefan Bekiranov | Biochem. and Mol. Genetics | Computational biology | --- ## Publications Look at recent publications to evaluate quantity, quality, and subject of research going on. [Department of Genome Sciences Publications](https://pubmed.ncbi.nlm.nih.gov/?term=(%22Center%20for%20Public%20Health%20Genomics%22%20OR%20%22Genome%20Sciences%22)%20and%20%22University%20of%20Virginia%22&filter=datesearch.y_1&page=1) [Department of Biochemistry and Molecular Genetics](https://bmg.med.virginia.edu/first-author-publications/first-author-publications) --- # 2. Resources <img src="/slides/phd-program-in-comp-bio-uva/uva/sunset.jpg" height="300"> --- ## Resources and connections for COBI students at UVA Departments that span schools (seminars, retreats, collaborators): - [Department of Genome Sciences](https://med.virginia.edu/genome-sciences/) - Newly formed Department in the School of Medicine - Departmental home of the COBI PhD program. - 15+ faculty, including 9+ computational labs, and hybrid labs - [Department of Biochemistry and Molecular Genetics](https://med.virginia.edu/bmg/) (School of Medicine) - Many faculty using computation to ask biological questions - Tightly aligned with the Department of Genome Sciences - [Department of Biomedical Engineering](https://engineering.virginia.edu/departments/biomedical-engineering) - Spans the schools of Medicine and Engineering - Physically located at the School of Medicine - Computational Bioengineering is a core strength --- ## Resources and connections for COBI students at UVA Departments that span schools (seminars, retreats, collaborators): - [Department of Computer Science](https://engineering.virginia.edu/departments/computer-science) - Located near the health system - [School of Data Science](https://datascience.virginia.edu/) - Officially launched as the 12th school at UVA in 2019 - One of the first standalone schools of data science in the nation. - Growing rapidly - Hosts an annual DataPalooza conference - ... and many others --- ## Resources and connections for COBI students at UVA Other valuable connections: - [Systems and Biomolecular Data Science Training Program](https://engineering.virginia.edu/sbds) - NIH training grant - [Other NIH training programs](https://med.virginia.edu/bims/programs/nih-sponsored-training-programs/) - UVA holds 10 (!) NIH training awards - [Cville BioHub](https://www.cvillebiohub.org/) - Network of 50+ local biotech companies. - [Research Computing](https://www.rc.virginia.edu/) - [Rivanna](https://www.rc.virginia.edu/userinfo/rivanna/) and [Ivy](https://www.rc.virginia.edu/userinfo/ivy/) supercomputers (>50k compute cores) - Interdisciplinary research centers - [UVA Health and School of Medicine](https://uvahealth.com/) - Co-located with Arts/Engineering/Data Science. - [UVA Cancer Center](https://cancer.uvahealth.com/) - National Cancer Institute-designated Comprehensive Cancer Center - [Carter Immunology Center](https://www.immunology.virginia.edu/) --- ## Co-located health system  --- ## NCI-designated Comprehensive Cancer Center  --- ## Carter immunology center  --- # 3. UVA's flavor of computational biology <img src="/slides/phd-program-in-comp-bio-uva/uva/sunset.jpg" height="300"> --- ## UVA's flavor of Computational Biology Strengths: - Computational genomics/epigenomics - Statistical genetics - Systems biology - Data science (Biomedical data science) - Machine learning --- ## Program vision: What makes UVA COBI unique? 1. Research-focused: - Relatively light coursework gets you doing research ASAP - Full-time rotations give you 100% research immersion 2. Tailored to the individual student: - Rotations let you identify your best fit - After base courses, advanced coursework is flexible - BIMS modules give you focused additional courses (if needed) - Broad faculty groups across departments and schools 3. Focus on open science: - GitHub-centered program where students are reviewing each others' code --- ## Finally At UVA it is possible do world-class science while enjoying open spaces, the outdoors, fun events, nearby attractions, all with a reasonable cost of living. 