The Problem:
Evolution produces systems that display remarkable structural and functional properties that can rival or exceed the performance of man-made systems. For example, protein molecules fold spontaneously into precise, well-ordered structures and can carry out specific binding, catalysis of difficult chemical reactions, and allosteric regulation. At a larger spatial scale, networks of proteins assemble to form metabolic and signaling systems that show efficient and selective processing of material and information. These performance characteristics can coexist with robustness to random perturbation and the capacity to adapt to new functional states as conditions of selection vary in the environment. The goal of our laboratory is to understand the design principles that underlie structure, function, and adaptation in biological systems. For maximal experimental and theoretical power, we focus at the atomic to cellular scale.
The Strategy:
Our approach is to break the problem down into three essential tasks: (1) to define the pattern of constraints that specify biological systems, (2) to determine the underlying physics, and (3) to understand the generative process that produces these (and not other) architectures. In other words, we wish to understand what nature has built, how it works, and why it is built the way it is. Answers to these core questions lie at the essence of understanding and engineering biological systems, and more fundamentally, to explain how they are even possible through the random, algorithmic process that we call evolution. Read more about the three core directions and about current problems being addressed in our laboratory... .
Benchmarking female breast cancer survival in africa, Central and South america, and asia (SURVCAN-3).
Benchmarking female breast cancer survival in africa, Central and South america, and asia (SURVCAN-3). J Natl Cancer Inst. 2026 Aug 22.
PMID: 42633567
BCAR: a fast and indel-tolerant barcode-sequence mapper.
BCAR: a fast and indel-tolerant barcode-sequence mapper. Bioinformatics. 2026 08 03; 42(8).
PMID: 42500985
The Phenotypic Landscape of a Circadian Clock.
The Phenotypic Landscape of a Circadian Clock. bioRxiv. 2026 Apr 27.
PMID: 42094528
Simple biological controllers drive the evolution of soft modes.
Simple biological controllers drive the evolution of soft modes. Proc Natl Acad Sci U S A. 2026 Apr 28; 123(17):e2523032123.
PMID: 42012951
BCAR: A fast and general barcode-sequence mapper for correcting sequencing errors.
BCAR: A fast and general barcode-sequence mapper for correcting sequencing errors. bioRxiv. 2026 Mar 31.
PMID: 41959368
ProT-VAE: Protein Transformer Variational AutoEncoder for functional protein design.
ProT-VAE: Protein Transformer Variational AutoEncoder for functional protein design. Proc Natl Acad Sci U S A. 2025 Oct 14; 122(41):e2408737122.
PMID: 41052325
Simple biological controllers drive the evolution of soft modes.
Simple biological controllers drive the evolution of soft modes. ArXiv. 2025 Jul 16.
PMID: 40709308
Direct visualization of electric-field-stimulated ion conduction in a potassium channel.
Direct visualization of electric-field-stimulated ion conduction in a potassium channel. Cell. 2025 Jan 09; 188(1):77-88.e15.
PMID: 39793560
Natural Language Prompts Guide the Design of Novel Functional Protein Sequences.
Natural Language Prompts Guide the Design of Novel Functional Protein Sequences. bioRxiv. 2024 Nov 11.
PMID: 39605414
Deep-learning-based design of synthetic orthologs of SH3 signaling domains.
Deep-learning-based design of synthetic orthologs of SH3 signaling domains. Cell Syst. 2024 08 21; 15(8):725-737.e7.
PMID: 39106868