Biological systems are thought to be exceedingly 'complex'--comprised of many parts and sets of unintuitive interactions between parts conferring system function. My lab is interested in elucidating principles of structure, function, and adaptability relationships with the ultimate goals of (i) characterizing 'personalized' variation in biological systems with high-fidelity, (ii) creating tools to genetically engineer variation in a rational way, and (iii) engineering natural-like, adaptive systems de novo. We use a blend of theory, computation, and experiment applied to a range of model systems spanning neural networks to electronic health record data to complex ecosystems inhabiting humans in addressing these concepts.
Washington University in St. Louis
St. Louis
- Clinical Pathology
2020
University of Texas at Southwestern
Dallas
M.D. - Medicine
2017
University of Texas at Southwestern
Dallas
Ph.D. - Molecular Biophysics
2017
University of Chicago
Chicago
B.A. - Physics
2008
University of Chicago
Chicago
B.S. - Chemistry (Honors)
2008
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom.
Subspecies phylogeny in the human gut revealed by co-evolutionary constraints across the bacterial kingdom. Cell Syst. 2025 Feb 19; 16(2):101167.
PMID: 39826551
ROSIE: AI generation of multiplex immunofluorescence staining from histopathology images.
ROSIE: AI generation of multiplex immunofluorescence staining from histopathology images. bioRxiv. 2024 Nov 18.
PMID: 39605711
Combatting superbugs using the evolutionary record of microbial warfare.
Combatting superbugs using the evolutionary record of microbial warfare. Cell Host Microbe. 2024 Jul 10; 32(7):1037-1039.
PMID: 38991497
An evolution-based framework for describing human gut bacteria.
An evolution-based framework for describing human gut bacteria. bioRxiv. 2023 Dec 05.
PMID: 38105970
Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes.
Defining hierarchical protein interaction networks from spectral analysis of bacterial proteomes. Elife. 2022 08 17; 11.
PMID: 35976223
Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans.
Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans. Nature. 2021 07; 595(7865):91-95.
PMID: 34163075
A Microbiota-Directed Food Intervention for Undernourished Children.
A Microbiota-Directed Food Intervention for Undernourished Children. N Engl J Med. 2021 04 22; 384(16):1517-1528.
PMID: 33826814
Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum.
Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium salinarum. mSystems. 2020 Jul 28; 5(4).
PMID: 32723790
Understanding the mother-breastmilk-infant "triad".
Understanding the mother-breastmilk-infant "triad". Science. 2020 03 06; 367(6482):1070-1072.
PMID: 32139527
Identifying determinants of bacterial fitness in a model of human gut microbial succession.
Identifying determinants of bacterial fitness in a model of human gut microbial succession. Proc Natl Acad Sci U S A. 2020 02 04; 117(5):2622-2633.
PMID: 31969452