Statistical Biology
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Biological pattern formation and morphogenesis
Description of current projects: Pairing transcriptomic with morphometric data to explore the regulation of morphogenesis. Studying phenotypic variation, due to genetic and environmental origins, during the dynamics of embryonic development from a whole gene expression and morphological point of view.
Collaborators: Patrick Lemaire, Ed Munro, Alexander, Aulehla
Current teammates: Siqi Liu, Joel Dokemegang, An Truong Pham
Papers
- Characterizing the structural dynamics of nucleolus during cell cycle
- Emergence of a geometric pattern of cell fates from tissue-scale mechanics in the Drosophila eye https://www.youtube.com/watch?v=hD-5YfGzSSA&t=1s
- A mathematical theory for the mechanics of three-dimensional cellular aggregates reveals the mechanical atlas for Ascidian embryogenesis
- Global constraints within the developmental program of the Drosophila wing https://www.youtube.com/watch?v=7cXlfmK5FAE&t=2532s
- Towards a global view of phenotype space
- A jump-distance-based parameter inference scheme for particulate trajectories
- Distinct contributions of tensile and shear stress on E-cadherin levels during morphogenesis
- A scheme for 3-dimensional morphological reconstruction and force inference in the early C. elegans embryo
- Active tension network model suggests an exotic mechanical state realized in epithelial tissues
- Principles of E-cadherin supramolecular organization in vivo
- Collective polarization model for gradient sensing via Dachsous-Fat intercellular signaling
Whole genome expression dynamics
Description of current projects:
Collaborators: Sidharth Goyal, Alexander Aulehla
Current teammates: Spencer O'Farrell, Addison Howe, Dominic Skinner, Eric Johnson
Papers
- Inferring single-cell dynamics with structured dynamical representations of RNA velocity
- Ordered patterning of the sensory system is susceptible to stochastic features of gene expression https://www.youtube.com/watch?v=aRu-AGVyGWc
Ecosystem dynamics
Description of current projects:
Collaborators: Seppe Kuehn, Arjun Raman
Current teammates: Karna Gowda, Siqi Liu, Kyle Crocker, Kiseok Lee, Rathi Kannan
Papers
- Genomic structure predicts metabolite dynamics in microbial communities
- Evolution of generalists by phenotypic plasticity
Cellular and Tissue adaptation
Description of current projects:
Collaborators: David Pincus, Arjun Raman
Current teammates: Ankita Roychoudhury, Annisa Dea, Eric Johnson
Papers
- Towards a global view of phenotype space
The Physics of Machine Learning
Description of current projects:
Collaborators: Arjun Raman, Paul Francois
Current teammates: Bipul Pandey
Papers
High-dimensional dynamical systems
Description of current projects:
Collaborators: All by myself
Current teammates: All by myself
Papers