Carly Ziegler

Carly Ziegler

Former MD-PhD Student

Degrees & Affiliations

BS, Biology and Mathematics - University of Pennsylvania Medical Student - Harvard Medical School (HST) PhD Candidate, Biophysics - Harvard University

Background & Interests

Cell Atlas Cell Atlas
Computational Methods Computational Methods
Getting Swole Getting Swole
I Want a Hot Body, but I also Want Tacos I Want a Hot Body, but I also Want Tacos
Immunology Immunology
Infectious Disease Infectious Disease
Medicine Medicine
Outdoor Adventures Outdoor Adventures
R&D R&D
Travel Travel

Biography

Carly G. K. Ziegler (Second First Name Gail) was born in Palo Alto, California, and grew up in Decatur, Georgia. Here, she gained a profound appreciation for southern food, hiking the Appalachian trail, and played supporting roles in Atlanta-based MTV reality shows. She majored in Mathematics and Biology at the University of Pennsylvania, and worked with Dr. John Wherry and Dr. David Artis using network modeling to explore the T cell response to infection. Next, she moved to New York City and worked with Dr. Gregoire Altan-Bonnet at Memorial Sloan-Kettering Cancer Center, studying BCR structure and signaling dynamics in B cell neoplasms.

She joined the Harvard/MIT MSTP program in 2014, completed the first 1/2 of medical school within the Harvard-MIT Health Sciences and Technology MD program. She is completing her PhD within the Harvard Biophysics program, and joined the Shalek lab in 2014. Her primary research interests lie in the interaction between host and pathogen, and how single cell RNA-Sequencing can uncover emergent mechanisms of infection and immunity. She is also interested in the development of new technology and new computational tools to weave in metadata (e.g. space, time, interactions) into single cell RNA-Seq datasets.

Carly spends her free time touring Seattle breweries, hiking with her puppies, making feminist cross-stitchings, rock climbing, and being outdoors whenever possible.

Publications

  • Pita-Juarez et al.,
  • Genome Biology,
  • 2025
Computational Methods Computational Methods
Genomics Genomics
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Carly Ziegler Carly Ziegler
  • Walsh et al.,
  • Nature Immunology,
  • 2025
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Medicine Medicine
Andrew Navia Andrew Navia
Carly Ziegler Carly Ziegler
Josh Bromley Josh Bromley
José Ordovas-Montañes José Ordovas-Montañes
Kyle Kimler Kyle Kimler
Micayla George Micayla George
Riley Drake Riley Drake
Samira Ibrahim Samira Ibrahim
Tasneem Jivanjee Tasneem Jivanjee
Vincent Miao Vincent Miao
  • Long et al.,
  • biorxiv,
  • 2024
Infectious Disease Infectious Disease
Medicine Medicine
Andrew Navia Andrew Navia
Carly Ziegler Carly Ziegler
Josh Bromley Josh Bromley
José Ordovas-Montañes José Ordovas-Montañes
Kyle Kimler Kyle Kimler
Micayla George Micayla George
Riley Drake Riley Drake
Samira Ibrahim Samira Ibrahim
Tasneem Jivanjee Tasneem Jivanjee
Vincent Miao Vincent Miao
  • Ziegler et al.,
  • American Society for Microbiology,
  • 2024
Computational Methods Computational Methods
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Carly Ziegler Carly Ziegler
Josh Bromley Josh Bromley
José Ordovas-Montañes José Ordovas-Montañes
Micayla George Micayla George
Riley Drake Riley Drake
Sam Kazer Sam Kazer
Vincent Miao Vincent Miao
  • Rodel et al.,
  • Frontiers in Microbiology,
  • 2021
Biology Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Microbiology Microbiology
Alex K. Shalek Alex K. Shalek
Carly Ziegler Carly Ziegler
  • Bein et al.,
  • Frontiers in Pharmacology,
  • 2021
Biology Biology
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Medicine Medicine
R&D R&D
Technology Technology
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Carly Ziegler Carly Ziegler
José Ordovas-Montañes José Ordovas-Montañes
Vincent Miao Vincent Miao
  • Genshaft et al.,
  • Nature Communications,
  • 2021
Genomics Genomics
R&D R&D
Technology Technology
Alex Genshaft Alex Genshaft
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Ben Mead Ben Mead
Carly Ziegler Carly Ziegler
Constantine Tzouanas Constantine Tzouanas
  • Ziegler et al.,
  • Cell,
  • 2021
Biology Biology
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Alex K. Shalek Alex K. Shalek
Andrew Navia Andrew Navia
Carly Ziegler Carly Ziegler
Josh Bromley Josh Bromley
José Ordovas-Montañes José Ordovas-Montañes
Micayla George Micayla George
Riley Drake Riley Drake
Vincent Miao Vincent Miao
  • Delorey et al.,
  • Nature,
  • 2021
Biology Biology
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Statistics Statistics
Alex K. Shalek Alex K. Shalek
Carly Ziegler Carly Ziegler
  • Muus et al.,
  • Nature Medicine,
  • 2021
Cell Atlas Cell Atlas
Computational Methods Computational Methods
Genomics Genomics
Immunology Immunology
Infectious Disease Infectious Disease
Statistics Statistics
Alex K. Shalek Alex K. Shalek
Carly Ziegler Carly Ziegler
Marc Wadsworth II Marc Wadsworth II
Sam Allon Sam Allon
Sarah Nyquist Sarah Nyquist