Jeremy Muhlich is a Research Associate in the Department of Systems Biology at Harvard Medical School. He serves as the Director of Software Engineering in the Laboratory of Systems Pharmacology. His research focuses on two related topics: building models of cellular signaling networks, and management of complex experimental data.

Featured research

Overview of Ashlar operationAshlar: Fast, high-quality image stitching and co-registration for cyclic microscopy methods such as CyCIF and CODEX. Ashlar can read image data directly from BioFormats-supported microscope vendor file formats as well as a directory of plain TIFF files. Output is saved as pyramidal, tiled OME-TIFF. Jeremy L Muhlich, Yu-An Chen, Clarence Yapp, Douglas Russell, Sandro Santagata, Peter K Sorger, Stitching and registering highly multiplexed whole-slide images of tissues and tumors using ASHLAR, Bioinformatics, Volume 38, Issue 19, 1 October 2022, Pages 4613–4621, doi:10.1093/bioinformatics/btac544.


Hierarchy of model components using PySBPySB: A framework for building mathematical models of biochemical systems as Python programs. PySB abstracts the complex process of creating equations describing interactions among multiple proteins or other biomolecules into a simple and intuitive domain specific programming language. PySB makes it straightforward to divide models into modules and to call libraries of reusable elements (macros) that encode standard biochemical actions. These features promote model transparency, reuse and accuracy. Read more at or see the paper - Lopez, C. F., Muhlich, J. L., Bachman, J. A. & Sorger, P. K. Programming biological models in Python using PySB. Mol Syst Biol 9, (2013). doi:10.1038/msb.2013.1.