Education
- Undergraduate: AB, Molecular and Cellular Biology, Harvard University, 2012
- Graduate: 2020, Yale University
Research Summary
In animals, host defense has two modes: antimicrobial programs, which kill pathogens directly; and sickness, a state of altered physiology and behavior that is actively generated by brain-immune system interactions. The lab is interested in (1) how and (2) why infections make us sick – the neuroimmune interactions that lead to sickness, and their impact on host fitness. Our goal is to understand the mechanistic basis of sickness as a host defense strategy.
Awards & Honors
Education
- Graduate: University of California, San Francisco, 2022
- Undergraduate: Computer Science; University of California, Berkeley, 2017
Research Summary
From the moment that a tumor is born, it is evolving across several levels, including at the genetic, epigenetic, metabolic, and microenvironmental levels. The central goal of the Jones Lab is to develop innovative computational and technological approaches to uncover the mechanisms of tumor evolution, with the ultimate aim of identifying new therapeutic targets and creating predictive models to monitor tumor initiation and progression.
Currently, the lab’s research focuses on three interrelated goals: (1) investigating the molecular mechanisms underlying the spatiotemporal dynamics of copy-number alterations (particularly extrachromosomal DNA) in cancer populations; (2) developing new computational methods to trace cellular lineages; and (3) elucidating the principles by which tumors are organized over time. To pursue these aims, the lab integrates advances in computation and AI with cutting-edge multi-omic approaches (including single-cell, spatial, and long-read technologies), lineage tracing, and high-resolution imaging. Broadly, they expect that their studies will reveal generalizable rules governing tumor progression and treatment resistance, enable the predictive modeling of tumors, and inspire new approaches to intercept tumor progression.
Awards
- Keynote Speaker at Cancer Genetics and Epigenetics Gordon Research Seminar, 2025
- Cancer Grand Challenges Future Leaders Conference Best Talk Awardee, 2024
- NCI K99/R00 Early-Career Pathway to Independence Award, 2024
- UCSF Discovery Fellow, 2019
Education
- PhD, 2024, Evolutionary and Organismic Biology, Harvard University
- MS, 2018, Earth Systems, Stanford University
- B.Sc, 2018, Computer Science, Stanford University
Research Summary
Microbial genomes encode the largest molecular, biochemical, and functional diversity on Earth. We focus on developing machine learning models and experimental approaches to discover and design novel biological functions. We integrate computation with expertise in evolution, ecology, and biochemistry to characterize and harness the functional potential of microbes.
Education
- Graduate: PhD, 2017, University of Washington
- Undergraduate: BS, 2010, Micro/Molecular Biology, Portland State University
Research Summary
Sergey Ovchinnikov uses phylogenetic inference, protein structure prediction/determination, protein design, deep learning, energy-based models, and differentiable programming to tackle evolutionary questions at environmental, organismal, genomic, structural, and molecular scales, with the aim of developing a unified model of protein evolution.
Education
- Graduate: PhD, 2016, Harvard University
- Undergraduate: BS, 2010, Biology, Grambling State University
Research Summary
Ferroptosis is an iron-dependent form of cell death with profound implications in human health and disease. In the context of cancer, the use of ferroptosis inducers to target subpopulations of highly metastatic and therapy-resistant cancer cells has garnered much excitement over the last few years. However, to gain a comprehensive understanding of the full therapeutic potential of ferroptosis, our research focuses on (i) uncovering the molecular factors affecting ferroptosis susceptibility, (ii) studying its impact on the tumor microenvironment, and (iii) developing innovative ways to modulate ferroptosis resistance in vivo. We employ a multidisciplinary approach, combining functional genomics, metabolomics, bioengineering, and a range of in vitro and in vivo models to advance our understanding in this domain and to translate our findings into effective therapies.
Awards
- The Margaret and Herman Sokol Postdoctoral Award, 2022
- Ludwig Center at MIT Postdoctoral Fellowship, 2022
- Jane Coffin Childs Memorial Fund Postdoctoral Fellowship, 2017
- HHMI International Predoctoral Research Fellowship, 2013
Education
- Graduate: PhD, 2016, Stanford University
- Undergraduate: BA, 2009, Human Evolutionary Biology, Harvard University
Research Summary
We use the tiny, transparent jellyfish, Clytia hemisphaerica, to ask questions at the interface of nervous system evolution, development, regeneration, and function. Our foundation is in systems neuroscience, where we use genetic and optical techniques to examine how behavior arises from the activity of networks of neurons. Building from this work, we investigate how the Clytia nervous system is so robust, both to the constant integration of newborn neurons and following large-scale injury. Lastly, we use Clytia’s evolutionary position to study principles of nervous system evolution and make inferences about the ultimate origins of nervous systems.
Awards
- Searle Scholar Award, 2024
- Klingenstein-Simons Fellowship Award in Neuroscience, 2023
- Pathway to Independence Award (K99/R00), National Institute of Neurological Disorders and Stroke, 2020
- Life Sciences Research Foundation Fellow, 2017
Education
- PhD, 2016, Stanford University School of Medicine
- BA, 2008, Molecular Biology, Princeton University
Research Summary
Our bodies are tuned to detect and respond to cues from the outside world and from within through exquisite collaborations between cells. For example, the cells lining our airways communicate with sensory neurons in response to chemical and mechanical signals, and evoke key reflexes such as coughing. This cellular collaboration protects our airways from damage and stabilizes breathing, but can become dysregulated in disease. Despite their vital importance to human health, fundamental questions about how sensory transduction is accomplished at these sites remain unsolved. We use the mammalian airways as a model system to investigate how physiological insults are detected, encoded, and addressed at essential barrier tissues — with the ultimate goal of providing new ways to treat autonomic dysfunction.
Awards
- Warren Alpert Distinguished Scholars Award, 2021
- Life Sciences Research Foundation Fellowship, 2018
Education
- PhD, 2015, Johns Hopkins University School of Medicine
- BA, 2009, Molecular Biology & Biochemistry/Physics, Wesleyan University
Research Summary
We investigate crosstalk between CD8+ T cells and their environment at a molecular level, by dissecting the biological and metabolic programs engaged under conditions of stress. Using an array of approaches to model and perturb the local microenvironment, our research aims to reveal both the adaptive molecular changes as well as intrinsic vulnerabilities in T cells that arise within the tumor niche. Our goal is to understand how disease states remodel the fundamental mechanisms that regulate immune cell function and contribute to pathogenesis.
Awards
Education
- PhD, 2016, University of Toronto
- BSc, 2010, Biochemistry, McMaster University
Research Summary
The immune system mounts destructive responses to protect the host from threats, including pathogens and tumors. However, a trade-off emerges: if immune responses cause too much damage, they can compromise host tissue function. Conversely, if they fail to generate sufficient damage, the host may succumb to a given threat. How is the optimal balance achieved? The Wong lab investigates how cells communicate with one another and their surrounding tissue environment to accurately control the magnitude of immune responses, both in time and space. To this end, we combine the tools of immunology with interdisciplinary methods—including high-resolution fluorescence microscopy, computational approaches, and gene manipulations—to resolve, model, and perturb the control of immune responses in intact tissues. Ultimately, we aim to understand how subtle shifts in control can lead to widely divergent host outcomes, including the successful elimination of threats, tolerance, autoimmunity, chronic infection, and cancer.
Education
- PhD, 2016, MIT
- BS, 2008, Chemistry, University of Puerto Rico-Mayagüez
Research Summary
We study chromatin — the complex of DNA and proteins that make up our chromosomes. We aim to understand how post-translational modifications to these building-blocks, as well as the factors that regulate these events, play essential roles in maintaining the integrity of cells, tissues, and ultimately entire organisms. We implement a combination of functional genomics, biochemical, genetic, and epigenomic approaches to study how chromatin and epigenetic factors decode the chemical language of chromatin, and how these are dysregulated in diseases such as cancer.
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