Nathan Sheffield headshot

Nathan Sheffield

Assistant Professor
Unit: School of Medicine
Department: PBHS Public Health Sciences Admin
Office location and address
21 Hospital Dr
Charlottesville, Virginia 22903
HFSP Postdoc, Computational Epigenomics, Center for Molecular Medicine, Vienna, 2013-2015
HFSP Postdoc, Computational Epigenomics, Center for Personal Dynamic Regulomes, Stanford University, 2016 (return phase)
Ph.D. Computational Biology & Bioinformatics, Duke University, 2013
B.S. Bioinformatics, Brigham Young University, 2008

I use computation to ask and answer biological questions. My biological interest is to understand gene regulation: How does DNA encode regulatory networks that enable cellular differentiation? Gene regulatory systems are finely tuned, and when they break down, it can lead to diseases like cancer. To better understand normal and diseased gene regulation, I collect high-throughput genome-scale data in single cells and cell populations, and then harness the power of supercomputing, machine learning, and software engineering to answer questions about biological systems.

I completed my PhD at Duke in 2013, working on computational analysis of gene regulation in primates and among human cell-types with Terry Furey (now at UNC), Greg Crawford (Duke), and Boris Lenhard (Imperial College London). After my PhD, I was an HFSP Postdoctoral Fellow in Christoph Bock’s Lab at the Center for Molecular Medicine, Vienna, Austria, with the return phase of my fellowship in Howard Chang’s Lab at Stanford.

University of Virginia Cancer Center Support Grant Yr31-35
Source: U.S. NIH Cancer Institute
February 01, 2022 – January 31, 2027
A modular data analysis ecosystem using portable encapsulated projects
Source: U.S. NIH Institute of General Medical Science
August 01, 2018 – July 31, 2023
Kidney development: Cell fate and precursors of disease in the young and adult YRS 6-10
Source: U.S. NIH Institute of Diabetes & Digestive & Kidne
September 15, 2017 – August 31, 2022
MD-CANC Cancer Center Support Grant
Source: U.S. NIH Cancer Institute
February 01, 2017 – January 31, 2022
American Cancer Society- Institutional Research Grant
Source: American Cancer Society
January 01, 2017 – June 19, 2021
PHS 5960: Supervised Independent Research
Credits: 1–6
Supervised Independent Research
CS 6501: Special Topics in Computer Science
Credits: 3
Course content varies by section and is selected to fill timely and special interests and needs of students. See CS 7501 for example topics. May be repeated for credit when topic varies. Prerequisite: Instructor permission.
BIMS 8601: Computational Genomics
Credits: 3
Students will learn foundational computational methods for analysis of data from genome, epigenome, and transcriptome sequencing experiments. The course will cover various biological data types, algorithms, statistical and computational methods, and application areas in genomics and systems biology. Prior coursework/experience in linear algebra, UNIX, and R and Python programming required.
BIMS 8993: Non-topical Research: Visiting Research Graduate Traineeship Program
Credits: 1–12
This course is for visiting research students participating in the BIMS Visiting Research Graduate Trianeeship Program (VRGTP). Students in this course are dual enrolled in their home institution and will participate in research for a minimum of 4 semesters. The research will assist them in completing their degree at their home institution. Non-degree students.
BME 8999: Master's Research
Credits: 1–12
Master's Research
BIOC 9995: Topical Research: Biochemistry and Molecular Genetics
Credits: 3–12
Topical Research
BIOC 9998: Non-Topical Research: Preparation for Doctoral Research
Credits: 1–12
Non-Topical Research: Preparation for Doctoral Research
CELL 9999: Non-Topical Research
Credits: 1–12
For doctoral dissertation, taken under the supervision of a dissertation director.
BME 9999: Dissertation
Credits: 1–12
Formal record of student commitment to doctoral research under the guidance of a faculty advisor. May be repeated as necessary.
BIOC 9999: Non-Topical Research
Credits: 1–12
For doctoral dissertation, taken under the supervision of a dissertation director.