What rules govern biological processes and systems? Labs working on simulating and modeling of biological processes work to identify these rules to create computational models that can be compared to experimental results. The interplay between experimental and computational systems illuminates aspects of biological processes and systems that would not otherwise be evident.
Computational Biology
Featured Research
Effect of thermodynamic perturbations on human γD-crystallin
Arlind Kacirani ‘26
Chemical and Environmental Engineering (Haji-Akbari Lab)
Modeling the Mesoscale Geometry and Mechanics of Cell Division and Motility
Emmanuel Mintah ‘26
Biomedical Engineering (O’Hern Lab)
Assessing the quality of computational models of protein-protein interactions
Jake Sumner ‘27
he/him
Computational Biology and Bioinformatics (O’Herm Lab)
Faculty
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Stuart Campbell
Associate Professor; Biomedical Engineering & Cellular and Molecular PhysiologyResearch Interests: Understanding mechanisms that underlie genetics forms of heart disease using computational and experimental tools and approaches. -
Hattie Chung
Assistant Professor; Cardiovascular Medicine and Molecular, Cellular, and Developmental BiologyResearch Interests: We study the molecular basis of cellular heterogeneity and tissue organization in health and disease through the lens of systems biology by pioneering novel computational and experimental tools, with applications to cardiovascular disease and ovarian aging. -
Martina Dal Bello
Assistant Professor; Ecology and Evolutionary BiologyResearch Interests: research in the Dal Bello lab focuses on how microbes respond to and modify their environment, and how these feedback processes shape species interactions, assembly processes, and the function of microbial communities. -
Purushottam Dixit
Assistant Professor; Biomedical EngineeringResearch Interests: Build machine learning methds that are rooted in statistical physics to analyze high quality high dimensional “omics” data from biological systems -
Thierry Emonet
Professor; Molecular, Cellular & Developmental Biology and PhysicsResearch Interests: We combine theory and experiments to understand the computations organisms perform to navigate chemical environments. Bacteria: we analyze information processing in individual cells, the molecular basis of individuality, and how biological diversity benefits populations. Fruit flies: we examine how insects perform goal oriented olfactory navigation, and how they adapt decision-making strategies in real time as odor signal statistics and environmental conditions change -
Mark Gerstein
Professor: Biomedical Informatics, Molecular Biophysics & Biochemistry, Computer Science, and Statistics & Data ScienceResearch Interests: Bioinformatics; biological database design, genomics; human genome annotation; gene expression analysis; data mining; macromolecular structure and function -
Amir Haji-Akbari
Assistant Professor; Chemical & Environmental EngineeringResearch Interests: Our group uses techniques rooted in molecular thermodynamics and computational chemistry to study the thermodynamics, kinetics and mechanism of phase transitions. We are interested in phenomena characterized as rare events. We are currently pursuing three active areas of interest: (i) crystal nucleation, (ii) hindered transport of ions and solutes through nanoporous membranes and channels, (iii) protein dynamics, folding and aggregation. -
Scott Holley
Professor; Molecular, Cellular & Developmental BiologyResearch Interests: The systems biology, biomechanics and molecular biophysics of early spinal column development -
Joe Howard
Professor; Molecular Biophysics & Biochemistry and PhysicsResearch Interests: Microtubules and molecular motors. Branching morphogenesis of neurons. Motility of cilia and flagella. Nerve nets. -
Jay Humphrey
Professor; Biomedical EngineeringResearch Interests: ascular mechanics; mechanobiology; design of tissue engineering constructs; computational modeling of vascular development, homeostasis, and disease -
Farren Isaacs
Professor; Molecular, Cellular & Developmental BiologyResearch Interests: Synthetic Biology, Genome Engineering, Systems Biology, Bioengineering, Engineered biomaterials & RNAs -
Aaron Kuan
Assistant Professor; Neuroscience and Biomedical EngineeringResearch Interests: Electron microscopy and X-ray imaging techniques to enable 3D imaging of neuronal circuits combined with behavior and functional imaging to reveal how circuit connectivity underlies brain activity and cognition. -
Roy Lederman
Assistant Professor; Statistics and Data ScienceResearch Interests: Cryo-EM; numerical analysis and signal processing; geometry of data; computational biology algorithms; mathematics of data science -
Andre Levchenko
Professor; Biomedical EngineeringResearch Interests: Systems Biology; Signal Transduction and Cell-Cell Communication; Cell Decision Making; Microfluidics and Micro- and Nano-fabrication; Stem Cell Engineering -
Christopher Lynn
Assistant Professor; PhysicsResearch Interests: Understanding how structure and function emerge in complex living systems, particularly the brain. -
Michael Mak
Assistant Professor; Biomedical EngineeringResearch Interests: Multiscale mechanobiology in cancer and development, from molecular to multicellular levels, integrating microfluidics, wet-lab experiments, and computational approaches. -
Simon Mochrie
Professor; Physics and Applied PhysicsResearch Interests: Quantitative microscopy and image analysis. Chromatin organization and dynamics. Nuclear envelope physics. Phase transitions of soft matter -
Corey O'Hern
Professor; Mechanical Engineering & Materials Science, Physics, Applied Physics and Graduate Program in Computational Biology & BioinformaticsResearch Interests: Statistical mechanics of nonequilibrium systems; glass and jamming transitions in soft matter; computational biology; protein structure, interactions, and design. -
Amir Pahlavan
Assistant Professor; Mechanical Engineering & Materials ScienceResearch Interests: Bacterial chemotaxis and biofilm formation in complex environments using both experiments and modeling. -
Anna Marie Pyle
Professor; Molecular, Cellular & Developmental Biology and ChemistryResearch Interests: RNA remodeling enzymes; RNA tertiary structure; molecular virology; computational studies of RNA structure -
Shreya Saxena
Assistant Professor; Biomedical EngineeringResearch Interests: Investigating topics at the interface of statistical inference, recurrent neural networks, control theory, and neuroscience -
Edward Stites
Associate Professor; Laboratory Medicine & PathologyResearch Interests: mathematical modeling, informed machine learning, cancer biology/disease biology, systems biology, synthetic biology -
John Tsang
Professor; Immunobiology and Biomedical EngineeringResearch Interests: Systems and quantitative immunology; human immunology; single cell biology; predicting and modeling immune responses; synthetic immunology: predictive engineering of immune cell trafficking and sensing; immune homeostasis maintenance and set point establishment mechanisms; integrating dynamical modeling and machine learning to understand emergent immune system behavior across temporal and spatial scales. -
Paul Turner
Professor; Ecology & Evolutionary BiologyResearch Interests: Evolutionary genetics and genomics of microbes, experimental evolution, virus disease emergence and of virus evolvability, combining microbiology, computational biology, genomics, molecular biology and mathematical-modeling approaches -
David van Dijk
Assistant Professor; Medicine (Cardiovascular Medicine) and Computer ScienceResearch Interests: Machine Learning; Computational Biology; Genomics; Single-cell Analysis; Deep Learning; Computational Neuroscience; Machine Learning in biophysics and biochemistry -
Madhusudhan Venkadesan
Associate Professor; Mechanical Engineering & Materials ScienceResearch Interests: biomechanics and control of animal movement; muscle rheology and biophysics; inverse problems in elasticity and morphoelasticity. -
Min Wu
Associate Professor; Cell BiologyResearch Interests: Single cell oscillations and travelling waves, membrane curvature, mitosis, cell size -
Jing Yan
Assistant Professor, Molecular, Cellular & Developmental BiologyResearch Interests: Imaging and modeling the developmental process of bacterial communities, characterizing and understanding the soft matter properties of bacterial biofilms, designing new bioinspired materials and surfaces -
Steven Zucker
Professor; Computer Science and Biomedical EngineeringResearch Interests: Computational vision, machine learning of neuroscience data, manifold inference and neural circuits.