Publications

We present a new computational tool for the simulation of aligned assemblies of thin, bendable, but inextensible fibers immersed in a linear Stokes fluid. Such systems are of great importance in cellular mechanics because they arise in many intracellular (e.g., cytoskeleton-cytoplasm interactions) and extracellular (e.g., ciliary locomotion) microscale biological processes. The fiber bed is represented as an anisotropic poroelastic medium that obeys the Euler-Bernoulli beam theory and is hydrodynamically coupled to the viscous fluid through local-slender body theory. We develop two methodologies to solve the resulting fluid-structure interaction problem: (1) a classical approach where the solid is solved in the Lagrangian frame, and the fluid is solved using an Arbitrary-Lagrangian-Eulerian (ALE) method, and (2) a novel approach where the solid equations are expressed in the Eulerian frame and the fiber-fluid system is solved together using an ALE method. In both cases, the resulting set of equations is approximated using a Petrov-Galerkin stabilized finite element method specifically designed for the fiber-fluid interaction problem. Equal-order continuous finite elements are used for the spatial discretization of the deforming physical domain, and finite differences are used for temporal discretization. Both approaches are shown to be numerically stable and convergent at the expected order; and additionally, the pure ALE method can resolve extreme fiber deformations without the need for mesh reconstruction. Finally, our methods are validated by direct comparisons to discrete fiber simulations in two benchmark tests: (a) the shearing of an anchored fiber bed and (b) the emergence and evolution of cell-spanning vortices in cellular geometries.

Solid-phase peptide synthesis enables the study of countless peptides, but aggregation during synthesis hinders production of many sequences of interest. Now, machine learning models enable prior identification of aggregation-prone sequences, and highlight amino acid composition, rather than specific sequence, as the major determinant of aggregation.

Protein denaturation-based assays, such as thermal proximity coaggregation (TPCA) and ion-based proteome-integrated solubility alteration (I-PISA), are powerful tools for characterizing global protein–protein interaction (PPI) networks. These workflows utilize different denaturation methods to probe PPIs, i.e., thermal- or ion-based. How denaturation differences influence PPI network mapping remained to be better understood. Here, we provide an experimental and computational characterization of the effect of the denaturation-based PPI assay on the observed PPI networks. We establish the value of both soluble and insoluble fractions in PPI prediction, determine the ability to minimize sample amount requirement, and assess different relative quantification methods during virus infection. Generating paired TPCA and I-PISA datasets, we define both overlapping sets of proteins and distinct PPI networks specifically captured by these methods. Assessing protein physical properties and subcellar localizations, we show that size, structural complexity, hydrophobicity, and localization influence PPI detection in a workflow-specific manner. We show that the insoluble fractions expand the detectable PPI landscape, underscoring their value in these workflows. Focusing on selected PPI networks (cytoskeletal and DNA repair), we observe the detection of distinct functional populations. Using influenza A infection as a model for cellular perturbation, we demonstrate that the integration of PPI predictions from soluble and insoluble workflows enhances the ability to build biologically informative and interconnected networks. Examining the effects of reducing starting material for TPCA assays, we find that PPI prediction quality remains robust when using a single well of a 96-well plate, a ∼500× reduction in sample input from usual workflows. Introducing simple workflow modifications, we show that label-free data-independent acquisition (DIA) TPCA yields performance comparable to the traditional tandem mass tag (TMT) data-dependent acquisition (DDA) TPCA workflow. This work provides insights into denaturation-based assays, highlights the value of insoluble fractions, and offers practical improvements for enhancing global PPI network mapping.

How developmental timings are regulated is a fundamental open question. Two widely considered mechanisms are the clock, in which an internal timer determines when each stage occurs, and the domino, in which the completion of each stage triggers the next. It is often unclear how to establish either mechanism. Here, we construct a quantitative framework that uses the correlation structure of developmental timings to test the clock and domino mechanisms. We apply this framework to human pre-implantation development by using ~1 million images of 2946 embryos acquired during IVF treatment, establishing mathematical models of developmental rate. We find that a domino mechanism governs the cleavage timings, while a pronuclei fade-triggered clock mechanism governs the morula and blastocyst timings. These results are consistent with the cell cycle oscillator governing the cleavage timings and the accumulation of embryonic gene products or the degradation of maternally deposited factors governing the morula and blastocyst timings. We next investigate the physiological regulators of developmental timing by analyzing how the timings are statistically associated with the clinical pregnancy outcome. While embryos that result in a clinical pregnancy tend to exhibit shorter cleavage timings, this association is primarily driven by patient-specific properties. In contrast, embryo-specific properties independently influence the pregnancy outcome and the cleavage timings, so that factors directly determining implantation potential, such as aneuploidy, can only weakly impact the cleavage timings. Taken together, this work provides a robust framework for decoding developmental timing mechanisms, with significant implications for fundamental biology and clinical practice.

Flagellar motors enable bacteria to navigate their environments by switching rotation direction in response to external cues with high sensitivity. Previous work indicated that the ultrasensitivity of the flagellar motor originates from conformational spread, in which subunits of the switching complex are strongly coupled to their neighbours as in an equilibrium Ising model. However, dynamic single-motor measurements indicated that rotation switching is driven out of equilibrium, and the mechanism for this dissipative driving remains unknown. Here we propose that local mechanical torques on motor subunits can affect their conformation dynamics, based on recent structures observed with cryo-electron microscopy. This gives rise to a tug of war between stator-associated subunits that produces cooperative, non-equilibrium switching responses without requiring nearest-neighbour interactions. Our model predicts that the motor response cooperativity grows with the number of stators driving rotation, which is consistent with published experimental results. Finally, we show that operating out of equilibrium enables motors to achieve high cooperativity with faster responses compared with equilibrium motors. Our results indicate a general role for mechanics in sensitive chemical regulation.

The growing availability of biological data resources has transformed research, yet their effective use remains challenging: selecting appropriate sources requires domain knowledge, data are fragmented across databases, and synthesizing results into reliable conclusions is labor-intensive. Although large language models promise to address these barriers, their impact in biomedicine has been limited by unsupported statements, incorrect claims, and lack of provenance. We introduce Alvessa, an evidence-grounded agentic research assistant designed around verifiability. Alvessa integrates entity recognition, orchestration of pre-validated biological tools, and data-constrained answer generation with statement-level verification against retrieved records, explicitly flagging unsupported claims and guiding revision when reliability criteria are not met. We evaluate Alvessa on dbQA from LAB-Bench and GenomeArena, a benchmark of 720 questions spanning gene and variant annotation, pathways, molecular interactions, miRNA targets, drug-target evidence, protein structure, and gene-phenotype associations. Alvessa substantially improves accuracy relative to general-purpose language models and performs comparably to coding-centric agents while producing fully traceable outputs. Using adversarial perturbations, we show that detection of fabricated statements depends critically on access to retrieved evidence. We further demonstrate application to drug discovery, where evidence-grounded synthesis enables identification of candidate targets missed or misattributed by literature-centered reasoning alone. Alvessa and GenomeArena are released to the community to support reproducible, verifiable AI-assisted biological research.

Cryogenic electron microscopy (cryo-EM) has emerged as a powerful method for resolving the structure of biological macromolecules. Recently, several computational methods have been developed to study the heterogeneity of molecules in single-particle cryo-EM. In this study, we analyze a publicly available dataset of TRPV1 using five such methods: 3DFlex, 3DVA, cryoDRGN, ManifoldEM, and Bayesian ensemble reweighting. We find significant heterogeneity, but each method produces different results, with some detecting only compositional or conformational heterogeneity. To compare these diverse results, we develop AnaVox to quantitatively determine agreement between heterogeneity methods. Furthermore, applying Bayesian ensemble reweighting combined with molecular dynamics simulations supports the presence of these rarer states within the sample. This study shows that although current methods reveal the presence of heterogeneity, their stochasticity and potential bias present challenges for their routine use. However, with future development, these tools will enable the use of cryo-EM data for quantitative biophysical investigations.

Cryogenic electron microscopy (cryo-EM) has emerged as a powerful method for resolving the structure of biological macromolecules. Recently, several computational methods have been developed to study the heterogeneity of molecules in single-particle cryo-EM. In this study, we analyze a publicly available dataset of TRPV1 using five such methods: 3DFlex, 3DVA, cryoDRGN, ManifoldEM, and Bayesian ensemble reweighting. We find significant heterogeneity, but each method produces different results, with some detecting only compositional or conformational heterogeneity. To compare these diverse results, we develop AnaVox to quantitatively determine agreement between heterogeneity methods. Furthermore, applying Bayesian ensemble reweighting combined with molecular dynamics simulations supports the presence of these rarer states within the sample. This study shows that although current methods reveal the presence of heterogeneity, their stochasticity and potential bias present challenges for their routine use. However, with future development, these tools will enable the use of cryo-EM data for quantitative biophysical investigations.

Many tasks in single-particle cryo-electron microscopy (cryo-EM), such as 2D/3D classification and homo/heterogeneous reconstruction, require optimizing model parameters to minimize the discrepancy between observed data and a forward model. The standard Mean Squared Error (MSE) loss function is computationally efficient but suffers from a non-convex rugged loss landscape, particularly for high-resolution heterogeneity inference. In this work, we investigate the practical utility of Sliced Wasserstein (SW) distances. We implement exact W2 estimators (inverse-CDF and greedy matching) of projections alongside a computationally efficient proxy based on the L2 norm of CDFs, a formulation akin to the sliced Cramér–von Mises distance. We establish the latter as a robust, fully differentiable workhorse for the cryo-EM forward model. We evaluate its performance against the MSE in joint inference tasks recovering pose, CTF parameters, and conformational heterogeneity. Our results demonstrate that SW significantly broadens the basin of attraction, enabling robust gradient-based optimization from distant initializations where MSE fails. Using a helical spiral toy model, we highlight how SW losses are sensitive to per-particle contrast, where background noise level miscalibration can induce geometric bias in the inferred structure. We show that this bias is manageable through a joint optimization strategy that treats background contrast as a learnable parameter. Finally, we validate the approach on a synthetic dataset using the Zernike3D framework, showing that the SW loss works and yields an accurate landscape representations, comparable with MSE. These findings establish SW as a powerful tool for navigating the rugged landscapes of cryo-EM forward model parameters

Parkinson’s Disease (PD) is characterized by the loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc), which is associated with changes in microglia function. While age remains the biggest risk factor, the underlying molecular cause of PD onset and its concurrent neuroinflammation are not well understood. Many identified PD risk genes have been directly linked to dopamine neuron impairment, while others are linked to immune cell function. In this study, we found that the PD risk gene FAM49B is critically expressed in microglia of the human SNpc and is downregulated with age and PD. We utilized human and murine microglia cells to demonstrate the role of FAM49B in regulating fundamental microglial functions such as cytoskeletal maintenance, migration, surface adherence, energy homeostasis, autophagy, and, importantly, inflammatory response. Downregulation of microglial FAM49B, as observed in the SNpc of aging individuals, led to significant alterations in these cellular functions, which are associated with increased microglial activation. Thus, our study highlights novel cell-type-specific roles of FAM49B and provides a potential mechanism for susceptibility to neuroinflammation, and reactive gliosis observed in both PD and normal aging.