A comprehensive benchmark of single-cell Hi-C embedding tools
Plummer, D., Lang, X., Zhang, S. et al. A comprehensive benchmark of single-cell Hi-C embedding tools. Nat Commun 16, 9119 (2025). https://doi.org/10.1038/s41467-025-64186-4
CV
Education
- B.S./M.S. in Computer Science, Case Western Reserve University, 2020
- Ph.D in Computer Science, Case Western Reserve University, 2020-2024
Publications
Loop2Loop: Representation Learning of the 3D Genome for Multimodal Single-Cell Integration and In-Silico Chromatin Rewiring
Plummer, D. Loop2Loop: Representation Learning of the 3D Genome for Multimodal Single-Cell Integration and In-Silico Chromatin Rewiring. Doctoral dissertation, Case Western Reserve University. (2024)
Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A
Weng, C., Gu, A., Zhang, S. et al. Single cell multiomic analysis reveals diabetes-associated β-cell heterogeneity driven by HNF1A. Nat Commun 14, 5400 (2023). https://doi.org/10.1038/s41467-023-41228-3
DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution
Zhang, S., Plummer, D., Lu, L. et al. DeepLoop robustly maps chromatin interactions from sparse allele-resolved or single-cell Hi-C data at kilobase resolution. Nat Genet 54, 1013–1025 (2022). https://doi.org/10.1038/s41588-022-01116-w
Portfolio
Honors
- 2019-2020 Robert J. Herbold Endowment Fund Scholar
- 2020 CWRU Computer and Data Sciences Research Award
- 2020 Callahan Fellowship Recipient
- 2021-2022 Biometric Genetic Analysis of Cardiopulmonary Disease NIH T32 Training Fellowship
- 2022-2023 CWRU Computer and Data Sciences Outstanding Researcher Award
- 2023 CVPR Outstanding Demo Award
Teaching
Service and leadership
- CWRUBotix Software Lead (2017-2020)
- Led the software team for CWRU’s entry in NASA’s Robotic Mining Competition with the goal of creating a fully autonomous robot capable of mining in a simulated lunar/martian environment.
- Recruit and teach new team members about how the software system of our robot works
- Hold workshops and lectures on various components of the software system
- Train new undergraduate students to take over the role of software lead
- Developed a real-time computer vision algorithm that utilizes an RGB-D sensor to sense obstacles in front of the robot and map their locations and sizes
- Built a robot localization system that uses an extended Kalman filter to fuse sensor measurements from ultra-wideband radio signals, an inertial mass unit, and wheel odometry measurements.
- Led the software team for CWRU’s entry in NASA’s Robotic Mining Competition with the goal of creating a fully autonomous robot capable of mining in a simulated lunar/martian environment.
- Jump Rope Instructor (2011-Present)
- Started a jump rope club at Case for students to have fun learning new skills, meet new friends, and get active
- Led the largest jump rope workshop in the world (JWTS in Ohio) along with other workshops and camps in the United States, Canada, Germany, the Czech Republic, Bermuda, Portugal, Japan, South Africa, and more
- Coached and mentored athletes of all ages and skill levels, including world champions, national champions, and beginners just learning how to jump rope for the first time
- Jump Rope Competition Organizer and Staff (2018-Present)
- Worked with the American Jump Rope Federation (AMJRF) and International Jump Rope Union (IJRU) to organize and run jump rope competitions around the world, including the US National Championships (2022-Present) and World Championships (2023-Present) and smaller local competitions in the United States and abroad
- Developed and implemented a computer vision-based jump rope judging system for use in competitions, which is currently being explored for integration into official judging systems by the International Jump Rope Union