Computational Biology

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.

Featured Research

Effect of thermodynamic perturbations on human γD-crystallin

Arlind Kacirani ‘26

Chemical and Environmental Engineering (Haji-Akbari Lab)

Left: Arlind working at his computer in the lab; Right: structure of Structural representation of HγD-crystallin

Modeling the Mesoscale Geometry and Mechanics of Cell Division and Motility

Emmanuel Mintah ‘26

Biomedical Engineering (O’Hern Lab)

Left: Emmanuel; Right: Fluorescent image and corresponding model of MDCK cells

Assessing the quality of computational models of protein-protein interactions

Jake Sumner ‘27

he/him

Computational Biology and Bioinformatics (O’Herm Lab)

Left: Jake looking at a pair of protein structure on his computer; Right: Structures of two proteins interacting in multiple conformations with the question "which structure is the actual structure"

Faculty

  • Stuart Campbell

    Associate Professor; Biomedical Engineering & Cellular and Molecular Physiology
    • Bioengineering
    • Computational Biology
    Research 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 Biology
    • Biological Circuits
    • Computational Biology
    • Systems Biology
    Research 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 Biology
    • Bioinformatics
    • Computational Biology
    • Systems Biology
    Research 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 Engineering
    • Bioinformatics
    • Biological Circuits
    • Computational Biology
    • +1 more
    Research 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 Physics
    • Biological Circuits
    • Computational Biology
    • Neuroscience
    • +1 more
    Research 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 Science
    • Bioinformatics
    • Computational Biology
    Research 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 Engineering
    • Computational Biology
    Research 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 Biology
    • Bioinformatics
    • Biological Circuits
    • Computational Biology
    • +3 more
    Research Interests: The systems biology, biomechanics and molecular biophysics of early spinal column development
  • Joe Howard

    Professor; Molecular Biophysics & Biochemistry and Physics
    • Computational Biology
    • Imaging Biological Systems
    • Neuroscience
    • +2 more
    Research Interests: Microtubules and molecular motors. Branching morphogenesis of neurons. Motility of cilia and flagella. Nerve nets.
  • Jay Humphrey

    Professor; Biomedical Engineering
    • Bioengineering
    • Computational Biology
    • Properties, Structure, Composition of Biological Systems
    Research Interests: ascular mechanics; mechanobiology; design of tissue engineering constructs; computational modeling of vascular development, homeostasis, and disease
  • Farren Isaacs

    Professor; Molecular, Cellular & Developmental Biology
    • Bioengineering
    • Bioinformatics
    • Biological Circuits
    • +2 more
    Research Interests: Synthetic Biology, Genome Engineering, Systems Biology, Bioengineering, Engineered biomaterials & RNAs
  • Aaron Kuan

    Assistant Professor; Neuroscience and Biomedical Engineering
    • Bioinformatics
    • Biological Circuits
    • Computational Biology
    • +2 more
    Research 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 Science
    • Bioinformatics
    • Computational Biology
    • Imaging Biological Systems
    Research Interests: Cryo-EM; numerical analysis and signal processing; geometry of data; computational biology algorithms; mathematics of data science
  • Andre Levchenko

    Professor; Biomedical Engineering
    • Biological Circuits
    • Computational Biology
    Research 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; Physics
    • Biological Circuits
    • Computational Biology
    • Neuroscience
    • +1 more
    Research Interests: Understanding how structure and function emerge in complex living systems, particularly the brain.
  • Michael Mak

    Assistant Professor; Biomedical Engineering
    • Computational Biology
    • Properties, Structure, Composition of Biological Systems
    • Systems Biology
    Research 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 Physics
    • Bioinformatics
    • Biological Circuits
    • Computational Biology
    • +2 more
    Research 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 & Bioinformatics
    • Computational Biology
    • Properties, Structure, Composition of Biological Systems
    • Systems Biology
    • +1 more
    Research 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 Science
    • Biological Circuits
    • Computational Biology
    Research Interests: Bacterial chemotaxis and biofilm formation in complex environments using both experiments and modeling.
  • Anna Marie Pyle

    Professor; Molecular, Cellular & Developmental Biology and Chemistry
    • Computational Biology
    • Properties, Structure, Composition of Biological Systems
    Research Interests: RNA remodeling enzymes; RNA tertiary structure; molecular virology; computational studies of RNA structure
  • Shreya Saxena

    Assistant Professor; Biomedical Engineering
    • Computational Biology
    • Neuroscience
    Research Interests: Investigating topics at the interface of statistical inference, recurrent neural networks, control theory, and neuroscience
  • Edward Stites

    Associate Professor; Laboratory Medicine & Pathology
    • Bioengineering
    • Bioinformatics
    • Biological Circuits
    • +2 more
    Research Interests: mathematical modeling, informed machine learning, cancer biology/disease biology, systems biology, synthetic biology
  • John Tsang

    Professor; Immunobiology and Biomedical Engineering
    • Bioengineering
    • Bioinformatics
    • Biological Circuits
    • +2 more
    Research 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 Biology
    • Bioinformatics
    • Computational Biology
    • PEB Leadership
    Research 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 Science
    • Bioinformatics
    • Computational Biology
    Research 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 Science
    • Bioengineering
    • Computational Biology
    • Properties, Structure, Composition of Biological Systems
    Research Interests: biomechanics and control of animal movement; muscle rheology and biophysics; inverse problems in elasticity and morphoelasticity.
  • Min Wu

    Associate Professor; Cell Biology
    • Biological Circuits
    • Computational Biology
    • Properties, Structure, Composition of Biological Systems
    • +1 more
    Research Interests: Single cell oscillations and travelling waves, membrane curvature, mitosis, cell size
  • Jing Yan

    Assistant Professor, Molecular, Cellular & Developmental Biology
    • Bioengineering
    • Biological Circuits
    • Computational Biology
    • +3 more
    Research 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 Engineering
    • Bioinformatics
    • Computational Biology
    • Neuroscience
    Research Interests: Computational vision, machine learning of neuroscience data, manifold inference and neural circuits.