Computational Biology: Publications
Read the latest papers published by our research teams.
Results
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In-Context Denoising with One-Layer Transformers: Connections between Attention and Associative Memory Retrieval
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Heuristic energy-based cyclic peptide design
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Charge distribution and helicity tune the binding of septin's amphipathic helix domain to membranes
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Charge distribution and helicity tune the binding of septin's amphipathic helix domain to membranes
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Formation of Drosophila germ cells requires spatial patterning of phospholipids
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Simulation-based inference of single-molecule experiments
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InstaMap: instant-NGP for cryo-EM density maps
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Counting particles could give wrong probabilities in Cryo-Electron Microscopy
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Counting particles could give wrong probabilities in Cryo-Electron Microscopy
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Active Hydrodynamic Theory of Euchromatin and Heterochromatin
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Coarse-graining bacterial diffusion in disordered media to surface states
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Recent Advances in Membrane Protein Simulations
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Bacterial motility depends on a critical flagellum length and energy-optimized assembly
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PLUMED Tutorials: a collaborative, community-driven learning ecosystem
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PLUMED Tutorials: a collaborative, community-driven learning ecosystem
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A model for boundary-driven tissue morphogenesis
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A new statistical metric for robust target detection in cryo-EM using 2D template match
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CyclicCAE: A Conformational Autoencoder for Efficient Heterochiral Macrocyclic Backbone Sampling
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Stochastic dynamics of granular hopper flows: A configurational mode controls the stability of clogs
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Nongenetic adaptation by collective migration
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The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation
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The ManifoldEM method for cryo-EM: a step-by-step breakdown accompanied by a modern Python implementation
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In vivo measurements of receptor tyrosine kinase activity reveal feedback regulation of a developmental gradient
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Geometry of Optimal Control in Chemical Reaction Networks in the Adiabatic Limit
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Geometric model for dynamics of motor-driven centrosomal asters
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CryoLike: A python package for cryo-electron microscopy image-to-structure likelihood calculations
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Classical variational phase-field models cannot predict fracture nucleation
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CryoLike: A python package for cryo-electron microscopy image-to-structure likelihood calculations
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The 2024 New York City Integrative Structural Biology Symposium
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Uniqueness, regularity and characteristic flow for a non strictly convex singular variational problem
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Liquid Filled Elastomers: From Linearization to Elastic Enhancement
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Learning locally dominant force balances in active particle systems
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Estimating the tails of the spectrum of the Hessian of the log-likelihood for \textit{ab-initio} single-particle reconstruction in electron cryomicroscopy
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A robust and versatile computational peptide design pipeline to inform wet-lab experiments
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Nuclear instance segmentation and tracking for preimplantation mouse embryos
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Dynamic allostery drives autocrine and paracrine TGF-β signaling
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Automated single-cell omics end-to-end framework with data-driven batch inference
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Heterogeneity in ligand-bound TRPV1: A comparison of methods in cryo-EM and molecular dynamics simulation
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Mechanics and morphology of proliferating cell collectives with self-inhibiting growth
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Active learning of Boltzmann samplers and potential energies with quantum mechanical accuracy
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Spatiotemporal dynamics of nucleocytoplasmic transport
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Minimal motifs for habituating systems
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New Statistical Metric for Robust Target Detection in Cryo-EM Using 2DTM
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Collagen-targeted protein nanomicelles for the imaging of non-alcoholic steatohepatitis
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Active morphodynamics of intracellular organelles in the trafficking pathway
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Innate immune epigenomic landscape following controlled human influenza virus infection
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Supercharged Phosphotriesterase for improved Paraoxon activity
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OpenRAND: A performance portable, reproducible random number generation library for parallel computations