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

COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
  • Delorey et al.,
  • Nature,
  • 2021
  • Genomics
  • Cell Atlas
  • Computational Methods
  • Biology
  • Immunology
  • Infectious Disease
  • Statistics
  • Carly Ziegler
  • Alex K. Shalek
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
  • Muus et al.,
  • Nature Medicine,
  • 2021
  • Immunology
  • Cell Atlas
  • Computational Methods
  • Genomics
  • Infectious Disease
  • Statistics
  • Sam Allon
  • Sarah Nyquist
  • Marc Wadsworth II
  • Carly Ziegler
  • Alex K. Shalek
A single-cell and spatial atlas of autopsy tissues reveals pathology and cellular targets of SARS-CoV-2
  • Delorey et al.,
  • bioRxiv,
  • 2021
  • Immunology
  • Infectious Disease
  • Biology
  • Genomics
  • Computational Methods
  • Cell Atlas
  • Statistics
  • Carly Ziegler
  • Alex K. Shalek
Impaired local intrinsic immunity to SARS-CoV-2 infection in severe COVID-19
  • Ziegler et al.,
  • bioRxiv,
  • 2021
  • Immunology
  • Genomics
  • Microbiology
  • Infectious Disease
  • Biology
  • Carly Ziegler
  • Vincent Miao
  • Andrew Navia
  • Josh Bromley
  • Micayla George
  • Riley Drake
  • Alex K. Shalek
  • José Ordovas-Montañes
Single cell profiling of COVID-19 patients: an international data resource from multiple tissues
  • Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia et al.,
  • medRxiv,
  • 2020
  • Genomics
  • Infectious Disease
  • Biology
  • Immunology
  • Cell Atlas
  • Carly Ziegler
  • Vincent Miao
  • Andrew Navia
  • Josh Bromley
  • José Ordovas-Montañes
  • Alex K. Shalek
Lymph nodes are innervated by a unique population of sensory neurons with immunomodulatory potential
  • Huang et al.,
  • Cell,
  • Immunology
  • Genomics
  • Biology
  • Carly Ziegler
  • Marko Vukovic
  • José Ordovas-Montañes
  • Alex K. Shalek
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is detected in specific cell subsets across tissues
  • Ziegler et al.,
  • Cell,
  • 2020
  • Genomics
  • Cell Atlas
  • Infectious Disease
  • Biology
  • Statistics
  • Immunology
  • Carly Ziegler
  • Sam Allon
  • Sarah Nyquist
  • Vincent Miao
  • Constantine Tzouanas
  • Marc Wadsworth II
  • Sam Kazer
  • Travis Hughes
  • Benjamin Doran
  • James Gatter
  • Marko Vukovic
  • Ben Mead
  • Shaina Carroll
  • Alex K. Shalek
  • José Ordovas-Montañes
Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells
  • Muus et al.,
  • bioRxiv,
  • Infectious Disease
  • Statistics
  • Genomics
  • Biology
  • Cell Atlas
  • Immunology
  • Computational Methods
  • Sam Allon
  • Sarah Nyquist
  • José Ordovas-Montañes
  • Marc Wadsworth II
  • Carly Ziegler
  • Alex K. Shalek
Integrated single-cell analysis of multicellular immune dynamics during hyperacute HIV-1 infection
  • Kazer et al.,
  • Nature Medicine,
  • 2020
  • Genomics
  • Biology
  • Statistics
  • Computational Methods
  • Infectious Disease
  • Immunology
  • Sam Kazer
  • Toby Aicher
  • Shaina Carroll
  • José Ordovas-Montañes
  • Vincent Miao
  • Carly Ziegler
  • Sarah Nyquist
  • Alex K. Shalek
SARS-CoV-2 receptor ACE2 is an interferon-stimulated gene in human airway epithelial cells and is enriched in specific cell subsets across tissues
  • Ziegler et al.,
  • SSRN,
  • Genomics
  • Immunology
  • Cell Atlas
  • Computational Methods
  • Biology
  • Infectious Disease
  • Medicine
  • Carly Ziegler
  • Sam Allon
  • Sarah Nyquist
  • Vincent Miao
  • Marc Wadsworth II
  • Sam Kazer
  • Travis Hughes
  • Benjamin Doran
  • James Gatter
  • Marko Vukovic
  • Constantine Tzouanas
  • Shaina Carroll
  • Alex K. Shalek
  • José Ordovas-Montañes
Spatially-resolved live cell tagging and isolation using protected photoactivatable cell dyes
  • Genshaft et al.,
  • bioRxiv,
  • 2020
  • Cancer
  • R&D
  • Genomics
  • Chemistry
  • Biology
  • Technology
  • Alex Genshaft
  • Carly Ziegler
  • Constantine Tzouanas
  • Ben Mead
  • Andrew Navia
  • Alex K. Shalek
Sensory neurons innervate peripheral lymph nodes and locally regulate gene expression in postsynaptic endothelium, stromal cells, and innate leukocytes
  • Huang et al.,
  • bioRxiv,
  • 2019
  • Immunology
  • Genomics
  • Computational Methods
  • Biology
  • Cell Atlas
  • Carly Ziegler
  • Marko Vukovic
  • José Ordovas-Montañes
  • Alex K. Shalek
Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection
  • Kazer S.W. et al.,
  • bioRxiv,
  • 2019
  • Infectious Disease
  • Immunology
  • Biology
  • Genomics
  • Sam Kazer
  • Toby Aicher
  • Shaina Carroll
  • José Ordovas-Montañes
  • Carly Ziegler
  • Sarah Nyquist
  • Alex K. Shalek
Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses
  • Douam F. et al.,
  • Nature Communications,
  • 2018
  • Infectious Disease
  • Genomics
  • Biology
  • Immunology
  • Alex K. Shalek
  • Carly Ziegler
Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction
  • Genshaft et al.,
  • Genome Biology,
  • 2016
  • Genomics
  • R&D
  • Chemistry
  • Biology
  • Technology
  • Alex Genshaft
  • Jay Prakadan
  • Carly Ziegler
  • Alex K. Shalek
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
  • Tirosh et al.,
  • Science,
  • 2016
  • Medicine
  • Genomics
  • Biology
  • Cancer
  • Jay Prakadan
  • Marc Wadsworth II
  • Alex Genshaft
  • Travis Hughes
  • Carly Ziegler
  • Sam Kazer
  • Aleth Gaillard
  • Kellie Kolb
  • Alex K. Shalek