Cellular Engineering Lab     


Cellular Engineering Lab - People


Sara Capponi (PI, Research Staff Member): Sara is a Computational Biophysicist, with expertise in molecular and dynamical modeling and machine learning. Her research focuses on understanding how natural and artificial biological systems function combining structural biology with physics, mathematics, and computer science.  


Tom Zimmerman (Research Staff Member): Tom is a researcher and master inventor at IBM Almaden. He is interested in signal processing, machine learning, human/data interaction and visualization. Tom's patent cover a wealth of technologies, from position tracking to user input, wireless communication, biometrics and encryption. In the Cellular Engineering project, Tom is responsible for new hardware and software for visualization of large swimming microscopic organisms, as well as IBM education and outreach coordinator.  


Jie Shi (Postdoctoral Researcher): Jie is a Biological Engineer, with expertise in computational biophysics and statistics. In the Cellular Engineering group, Jie works on  engineering immune cells using a combination neural networks and stuctural biology and on designing de novo proteins.


Julie Pope (Program Manager): Julie is a senior program manager at IBM. She is responsible for everything finance and reporting.



Affiliated Members

Barbara Jones, Theoretical Physicist, Science and Solution

Nimrod Megiddo, Theoretical Computer Scientist, CS Theory group


Past Members

Kevin J. Cheng, a biophysics graduate student in the lab of Taras Pogorelov at UIUC. In the Cellular Engineering group, Kevin uses molecular dynamics simulations and machine learning methods to study how bromoform molecules interact with seaweed peroxisome to mitigate climate change and to examine the interactions between WNT and WLS proteins. 

Shangying Wang, a Physicist, with expertise in hybrid learning systems. In the Cellular Engineering group, Shangying worked on engineering immune cells using a combination of dynamical systems and deep neural networks. 

Erik J. Navarro, a biophysics graduate student in the lab of Wallace Marshall at UCSF. In the Cellular Engineering group, Erik uses molecular dynamics simulations and machine learning algorithms to examine the interactions between ACE2 and the receptor binding domain of the spike protein to understand and design general principles of binding processes. 

Simone Bianco, former PI, is an expert in dynamical systems theory and its application to problems of biological relevance. He is interested in understanding how evolution shapes the principles of self-assembly of any living system, from viruses to bacteria, to single cell and multicellular organisms.

Myra Dada, an undergraduate bioengineering student at the University of Chicago. In the Cellular Engineering group, she is using machine learning and dynamical systems to classify and model cellular morphology as a function of tropomyosin expression.

Allyson Park, an undergraduate student from UCB. Allyson works on optimization of the holographic microscope for accurate detection and reconstruction of plankton in the lab and in the wild.

Anamika Agrawal, a physics graduate student in the lab of Elena Koslover at UCSD. In the Cellular Engineering group, Anamika uses dynamical systems to establish design principles of yeast peroxosome for precise cellular engineering.

Vito Paolo Pastore, a former post doc and a bioengineer, with a background in analysis of networks of neurons. Vito uses a combination of machine vision and feature engineering to infer the presence of anomalies in mixed datasets. Now at the Italian Institute of Technology in Genova.

Sujoy Biswas, former postdoc, expert in computer vision and machine learning with a specific research interest in solving large scale visual recognition problems. Currently leading a private research center in India.

Ryan Winstead, an undergraduate student from SFSU. In the lab, Ryan worked on Drosophila spindle dynamic using deep learning.

Peter Ferguson, an undergraduate student from Santa Clara University, who worked on engineering a system to detect chemicals in water using plankton.

Elsa Rousseau, mathematical and computational biology. Elsa has a PhD in Computational Biology, and has worked on disease dynamics and competition of viral species. Currently postdoc at the Corbeil lab at Universite Laval.

Silvia Peschiera, IBM Italy researcher and startup relationship representative. Silvia is interested in cloud and collaboration platforms, as well a bioengineering.

Paolo Malavolta, IBM Italy system and software engineer, specialized in cloud infrastructure and research as a service. Now at Accenture. 

Amanda Paulson, former graduate student in Zev Gartner's lab at UCSF. Amanda is interested in how cellular heterogeneity impacts tissue function.

Jacob Kimmel, former graduate student in Wallace Marshall's lab at UCSF. At IBM Jacob has developed end-to-end deep learning algorithms to track cells under environmental stress. Currently at Calico.

Chang Chang, physics, Peking University (now postdoc @Philip Cluzel lab, Harvard University)

Garrett Nieddu, mathematics of infectious disease, former graduate student with Lora Billings and Eric Forgoston at Montclair State University. Now at Los Alamos in the lab of Ruian Ke.

Lucrezia Maini, Nanotechnologies master student, from the International Master Degree program (Politecnico di Torino, Grenoble INP-Phelma, EPFL Losanne).

Aritra Chowdury , Computer Science graduate student from Bulent Yener's lab at RPI. Aritra is currently research scientist at GE Research.

Cecelia Brown, SFSU graduate student from Blake Riggs' lab, currently enrolled in the Stanford PhD program.

Adrienna Bingham, mathematics, former graudate student in Leah Shaw's lab, working on infectious disease competition models in multipatch systems. Currently at the CDC.

James Gerh, a graduate student in Diana Chu's lab at SFSU. He is modeling the spindle dynamic in c. Elegans.

Mayara Bonani, an undergraduate student from the University of Sao Paolo, Brazil, with an engineering background.

Sita Chandrasekaran, former undergraduate student in Ray Equerra's lab at SFSU, and part of the PINC program. Now at the UCSF-UCB joint Bioengineering program.

Tommaso Martin, research associate at the University of Genova, with a background in systems engineering.



Real last update: 07/11/2021