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Ben O'Shaughnessy's group uses mathematical modeling, computational modeling, and machine learning methods to study embryo development, neurotransmission, exocytosis, cell division, and other fundamental processes in health and disease.

Neurotransmission, neurotransmitter release, exocytosis

We study neurotransmission and the machinery that releases neurotransmitters by exocytosis at neuronal synapses in the brain. This remarkable machinery achieves the millisecond temporal resolution required for neural circuits to encode information for cognition, sensation, and coordinated motor activity. Its misregulation is associated with neurodegenerative and neurodevelopmental disorders. Similar mechanisms govern secretion of other essential bioactive compounds, including hormones such as insulin, cytokines in the immune system and enzymes.

Development of the embryo

The programs of development transform the early embryo of a few identical cells into the complex adult organism with extraordinary robustness to stochastic variations. We use machine learning and computational analysis to investigate the mechanisms that sculpt tissue and enforce robustness. We seek mechanisms of developmental disease to motivate prevention strategies.

Mechanics of cell division, mechanosensing

We investigate one of life’s most essential force-generating machines, the actomyosin contractile ring that divides cells at the end of the cell cycle during cytokinesis. Cell division propagates the genome and allows organisms to grow and repair, and its misregulation is the essential feature of cancer. Related interests in mechanobiology are mechanosensing and remodeling in the actomyosin cytoskeleton and regulation of cell wall growth in cell walled organisms.

Entry by the SARS-CoV-2 virus

SARS-CoV-2 causes the global pandemic COVID-19. We use atomistic and coarse-grained molecular dynamics simulations to study how the virus uses its surface spike glycoprotein machinery to invade lung, nasal mucosa or small intestine cells by binding target cell ACE2 receptors and fusing its membrane envelope with target membranes. For comparison, we quantitatively analyze cryo-electron tomograms by our experimental collaborators.

Featured Publication

Rui Su is awarded his Ph.D.

January 5, 2023

Rui's research investigated mechanisms of exocytosis and endocytosis, and cell entry by the SARS-CoV-2 virus.

Congratulations Rui!

Dong An and Hongkang Zhu present Microsymposium talks at the annual ASCB meeting, Washington DC.

December 04, 2022

Dong An and Hongkang Zhu present Microsymposium talks at the annual ASCB meeting, Washington DC.

Congratulations, Dong and Hongkang!

Tianyi Zhu gives a talk at the annual ASCB meeting Washington DC

December 04, 2022

Tianyi presented her work: Contractile Actomyosin Cables and Pulling Forces from Adjacent Tissue Cooperate to Drive Drosophila Germ-band Extension at the Cell Bio 2022 conference held by the American society of Cell Biology (ASCB).

Congratulations, Tianyi!

Ioana-Cristina Butu joins the group

November 02, 2022

Ioana-Cristina Butu has joined our group as a PhD researcher. 
Welcome, Cristina!

Hongkang Zhu presents an invited talk in the ASCB Emerging Researcher Seminar Series

June 16, 2022

Hongkang gave a talk about his work on the physical mechanisms of Drosophila gastrulation in the Emerging Researcher Seminar Series held by the American Society of Cell Biology (ASCB).

Congradulations, Hongkang!

Zeeshan Khan joins the group

June 1, 2022

Zeeshan Khan has joined our group as a REU undergraduate researcher. 
Welcome, Zeeshan!

Stephanie Morales joins the group

June 1, 2022

Stephanie Morales has joined our group as an undergraduate researcher. 
Welcome, Stephanie!

Kunal Gaikwad joins the group

May 31, 2022

Kunal Gaikwad has joined our group as a MS researcher. 
Welcome, Kunal!

Ioana-Cristina Butu joins the group

November 22, 2021

Ioana-Cristina Butu has joined our group as a MS researcher. 
Welcome, Cristina!

Summer undergad CoV2 research project

August 13, 2021

Chelsea Mikal joined the O’Shaughnessy group this summer and worked on computational modeling of SARS-CoV-2 spike protein as her summer project. She made a video to present the project https://vimeo.com/586723204.

COVID-19 HPC Consortium Award - Continued

June 01, 2021

Microsoft Azure will continue supporting the O’Shaughnessy group with high-performance computing resources till May 31st 2022. This is a continuation of the award from the COVID-19 HPC Consortium for investigating the mechanisms of SARS-CoV-2 entry mediated by the spike protein.

Tianyi Zhu joins the group

November 16, 2020

Tianyi Zhu has joined the group for her PhD research. 
Welcome, Tianyi!

Yamini Ananth joins the group

November 3, 2020

Yamini Ananth has joined our group as an undergraduate researcher. 
Welcome, Yamini!

Summer undergad/MS CoV2 research project

September 08, 2020

In the O'Shaughnessy and Simunovic research groups a team of undergrad and Ms students used modeling tools and designed organoid experiments to study the SARS CoV-2 virus.

COVID-19 HPC Consortium Award

August 20, 2020

The O’Shaughnessy group has been awarded Microsoft high-performance computing resources to research SARS-CoV-2. These resources enable our group to investigate the mechanisms by which the SARS-CoV-2 enters cells. 

Zach McDargh presents at ZIPS seminar

August 14, 2020

Postdoc Zach McDargh presented his work on the mechanisms by which Ca2+ triggers neurotransmitter release in the brain at the Zuckerman Mind Brain Behavior Institute as part of the Zuckerman Institute Postdoctoral Seminar series. Congratulations Zach!

Hongkang Zhu joins the group

August 28, 2019

Hongkang Zhu has joined our group to perform his doctoral research.
Welcome, Hongkang!

Jin Zeng joins the group

August 28, 2019

Jin Zeng has joined our group to perform his doctoral research.
Welcome, Jin!

Quantitative Aspects of Membrane Fusion and Fission Meeting

May 6, 2019

We presented our research on neurotransmitter release in the brain at the Quantitative Aspects of Membrane Fusion and Fission Meeting in beautiful Padova, Italy.

Dong An joins the group

October 24, 2018

Dong An has joined our group to perform his doctoral research.
Welcome, Dong!

Roberto Alonso-Matilla joins our group

August 27, 2018

Roberto Alonso-Matilla joins our group as a postdoc. Welcome Roberto! 

Nadiv Dharan joins our group

July 15, 2018

Nadiv Dharan joins our group as a postdoc.
Welcome to Nadiv! 

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© O'Shaughnessy Group 2018