Shankar Mukherji

Shankar Mukherji

Assistant Professor of Physics
PhD, Massachusetts Institute of Technology/Harvard Medical School
research interests:
  • Biophysics
  • Quantitative Biology

contact info:

mailing address:

  • Washington University
    MSC 1105-110-02
    One Brookings Drive
    St. Louis, MO 63130-4899

Shankar Mukherji uses a combination of theory and experimental techniques from a systems and synthetic biology perspective to uncover the design principles that govern cellular function. 

Arguably the grandest goal in cellular biophysics is the uncovering of design principles that govern all aspects of cellular function. Efforts in systems and synthetic cell biology have focused mainly on the design principles of gene expression and signaling systems. A quantitative understanding of eukaryotic cellular organization in space, however, would afford biophysicists and bioengineers with a powerful opportunity to predict how the physical architecture of the cell constrains and regulates fundamental life processes. To unleash this potential, it is imperative to understand one of the defining features of the eukaryotic cell: its organization into spatial compartments known as organelles.

Coordinating organelle abundance and activity with developmental and environmental cues is one of the chief ways the cell can match its biochemical capabilities with its physiological demands. How does the cell orchestrate flows of matter and energy to produce exquisitely defined organelles at the nanometer and femtoliter scales of a cell? Can we engineer the decision-making processes in the cell to control organelle copy number, size, and composition in vivo and can this allow us to rationally alter cellular metabolism and signaling toward desired goals?

Mukherji's group uses a combination of theory and experiment to uncover the design principles that control:

  1. how the cell regulates organelle biogenesis
  2. how, in turn, organelles communicate with the rest of the cell to regulate cellular physiology

Shankar completed his undergraduate degrees in mathematics and physics from MIT. He then obtained his doctorate in biomedical engineering from the Harvard-MIT Division of Health Science and Technology in the laboratory of Alexander van Oudenaarden. Prior to his arrival at Washington University, Shankar was a postdoctoral fellow with Erin O'Shea at the FAS Center for Systems Biology at Harvard.

recent courses

Physics of Living Systems (Physics 354/454)

One of the grand challenges in contemporary biophysics is placing our understanding of cellular systems on a firm quantitative footing. How does the collective activity of molecules enable the cell to sense its environment, make decisions, grow and develop? This course, aimed at physical and life science students, will serve as an introduction to the physical principles and mathematical techniques underlying the analysis of systems and synthetic biology. Topics will include modeling gene and signaling networks, the regulation of intracellular structures, and pattern formation in development. Students in this course can expect to learn both analytical and computer simulation approaches to fundamental problems in biology, biophysics, and biotechnology. Graduate students will explore the subject in more depth.

    Biophysics Laboratory (Physics 360)

    This laboratory course consists of "table-top" experiments in biological physics that are designed to introduce the student to concepts, methods, and biological model systems in biophysics. Most experiments combine experimentation with computer simulations. The list of available experiments includes electrophysiology, human bioelectricity, optical tweezers, ultrasonic imaging, mass spectrometer, and viscosity measurements.

      Physics I (Physics 191)

      Calculus-based introduction to the concepts, laws, and structure of physics. Topics include kinematics, Newton's laws, energy, linear momentum, angular momentum, the conservation laws, gravitational force, harmonic motion, wave motion and interference, sound, and special relativity

        Selected Publications

        Amiri KP, Kalish A, Mukherji S (2022). Robustness and universality in organelle size control. Physical Review Letters (accepted).

        Grosswendt S, Kretzmer H, Smith ZD, Kumar AS, Hetzel S, Wittler L, Klages S, Timmermann B, Mukherji S, Meissner A (2020). Epigenetic regulator function through mouse gastrulation. Nature 584, 102–108.

        Mukherji S, O’Shea EK (2014). Mechanisms of organelle biogenesis govern stochastic fluctuations in organelle abundance. eLife 3, e02678.

        Teng SW, Mukherji S, Moffitt JR, de Buyl S, O’Shea EK (2013). Robust circadian oscillations in growing cyanobacteria require transcriptional feedback. Science 340, 737-740.

        Mukherji S, Ebert MS, Zheng G, Tsang JS, Sharp PA, van Oudenaarden A (2011). MicroRNAs can generate thresholds in target gene expression. Nature Genetics 43(9), 854-859.