Statistical Biology

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

- The role of intracellular interactions in the collective polarization of tissues and its interplay with cellular geometry https://www.youtube.com/watch?v=Gfoh_u8nFJo

- A jump-distance-based parameter inference scheme for particulate trajectories

- QuBiT: a quantitative tool for analyzing epithelial tubes reveals unexpected patterns of organization in the Drosophila trachea

- 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

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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

- EMBEDR: distinguishing signal from noise in single-cell omics data https://www.youtube.com/watch?v=kPbflUZd7Q0

- Inferring single-cell dynamics with structured dynamical representations of RNA velocity

- Revealing cell-fate bifurcations from transcriptomic trajectories of hematopoiesis https://www.youtube.com/watch?v=WEG7TeeZ0zI

- The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts

- Ordered patterning of the sensory system is susceptible to stochastic features of gene expression https://www.youtube.com/watch?v=aRu-AGVyGWc

- Matrix production and sporulation in Bacillus subtilis biofilms localize to propagating wave fronts

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Ecosystem dynamics

Description of current projects: 

Collaborators: Seppe Kuehn, Arjun Raman

Current teammates: Karna Gowda, Siqi Liu, Kyle Crocker, Kiseok Lee, Rathi Kannan

Papers

- Global patterns in gene content soil microbiomes emerge from ecological interactions https://www.youtube.com/watch?v=M0CBv26Zabs&t=969s

- Genomic structure predicts metabolite dynamics in microbial communities

- Evolution of generalists by phenotypic plasticity

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Cellular and Tissue adaptation​

Description of current projects: 

Collaborators: David Pincus, Arjun Raman

Current teammates: Ankita Roychoudhury, Annisa Dea, Eric Johnson

Papers

- 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

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The Physics of Machine Learning​

Description of current projects: 
Collaborators: Arjun Raman, Paul Francois

Current teammates: Bipul Pandey

Papers

- EMBEDR: distinguishing signal from noise in single-cell omics data https://www.youtube.com/watch?v=kPbflUZd7Q0

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High-dimensional dynamical systems​

Description of current projects:

Collaborators: All by myself

Current teammates: All by myself

Papers