Publications

Key challenges for human genetics, precision medicine and evolutionary biology include deciphering the regulatory code of gene expression and understanding the transcriptional effects of genome variation. However, this is extremely difficult because of the enormous scale of the noncoding mutation space. We developed a deep learning–based framework, ExPecto, that can accurately predict, ab initio from a DNA sequence, the tissue-specific transcriptional effects of mutations, including those that are rare or that have not been observed. We prioritized causal variants within disease- or trait-associated loci from all publicly available genome-wide association studies and experimentally validated predictions for four immune-related diseases. By exploiting the scalability of ExPecto, we characterized the regulatory mutation space for human RNA polymerase II–transcribed genes by in silico saturation mutagenesis and profiled > 140 million promoter-proximal mutations. This enables probing of evolutionary constraints on gene expression and ab initio prediction of mutation disease effects, making ExPecto an end-to-end computational framework for the in silico prediction of expression and disease risk.

GIANT2 (Genome-wide Integrated Analysis of gene Networks in Tissues) is an interactive web server that enables biomedical researchers to analyze their proteins and pathways of interest and generate hypotheses in the context of genome-scale functional maps of human tissues. The precise actions of genes are frequently dependent on their tissue context, yet direct assay of tissue-specific protein function and interactions remains infeasible in many normal human tissues and cell-types. With GIANT2, researchers can explore predicted tissue-specific functional roles of genes and reveal changes in those roles across tissues, all through interactive multi-network visualizations and analyses. Additionally, the NetWAS approach available through the server uses tissue-specific/cell-type networks predicted by GIANT2 to re-prioritize statistical associations from GWAS studies and identify disease-associated genes. GIANT2 predicts tissue-specific interactions by integrating diverse functional genomics data from now over 61 400 experiments for 283 diverse tissues and cell-types. GIANT2 does not require any registration or installation and is freely available for use at http://giant-v2.princeton.edu.

Abstract Spindles are self-organized microtubule-based structures that segregate chromosomes during cell division. The mass of the spindle is controlled by the balance between microtubule turnover and nucleation. The mechanisms that control the spatial regulation of microtubule nucleation remain poorly understood. While previous work found that microtubule nucleators bind to microtubules in the spindle, it is still unclear whether this binding regulates the activity of those nucleators. Here we use a combination of experiments and mathematical modeling to investigate this issue. We measured the concentration of microtubules and soluble tubulin in and around the spindle. We found a very sharp decay in the concentration of microtubules at the spindle interface. This is inconsistent with a model in which the activity of nucleators is independent of their association with microtubules but consistent with a model in which microtubule nucleators are only active when bound to preexisting microtubules. This argues that the activity of microtubule nucleators is greatly enhanced when bound to microtubules. Thus, microtubule nucleators are both localized and activated by the microtubules they generate.

We investigate the dynamics of hydrodynamically interacting motile and non-motile stress-generating swimmers or particles as they invade a surrounding viscous fluid. Colonies of aligned pusher particles are shown to elongate in the direction of particle orientation and undergo a cascade of transverse concentration instabilities. Colonies of aligned puller particles instead are found to elongate in the direction opposite the particle orientation and exhibit dramatic splay as the group moves into the bulk. A linear stability analysis of concentrated line distributions of particles is performed and growth rates are found, using an active slender-body approximation, to match the results of numerical simulations. Thin concentrated bands of aligned pusher particles are always unstable, while bands of aligned puller particles can either be stable (immotile particles) or unstable (motile particles) with a growth rate which is non-monotonic in the force dipole strength. We also prove a surprising "no-flow theorem": a distribution initially isotropic in orientation loses isotropy immediately but in such a way that results in no fluid flow anywhere at any time.

It is well-known that by placing judiciously chosen image point forces and doublets to the Stokeslet above a flat wall, the no-slip boundary condition can be conveniently imposed on the wall [Blake, J. R. Math. Proc. Camb. Philos. Soc. 70(2), 1971: 303.]. However, to further impose periodic boundary conditions on directions parallel to the wall usually involves tedious derivations because single or double periodicity in Stokes flow may require the periodic unit to have no net force, which is not satisfied by the well-known image system. In this work we present a force-neutral image system. This neutrality allows us to represent the Stokes image system in a universal formulation for non-periodic, singly periodic and doubly periodic geometries. This formulation enables the black-box style usage of fast kernel summation methods. We demonstrate the efficiency and accuracy of this new image method with the periodic kernel independent fast multipole method in both non-periodic and doubly periodic geometries. We then extend this new image system to other widely used Stokes fundamental solutions, including the Laplacian of the Stokeslet and the Rotne-Prager-Yamakawa tensor.

We show using theory and experiments that a small particle moving along an elastic membrane through a viscous fluid is repelled from the membrane due to hydro-elastic forces. The viscous stress field produces an elastic disturbance leading to particle-wave coupling. We derive an analytic expression for the particle trajectory in the lubrication limit, bypassing the construction of the detailed velocity and pressure fields. The normal force is quadratic in the parallel speed, and is a function of the tension and bending resistance of the membrane. Experimentally, we measure the normal displacement of spheres sedimenting along an elastic membrane and find quantitative agreement with the theoretical predictions with no fitting parameters. We experimentally demonstrate the effect to be strong enough for particle separation and sorting. We discuss the significance of these results for bio-membranes and propose our model for membrane elasticity measurements.

Cilia and flagella are essential building blocks for biological fluid transport and locomotion at the micrometre scale. They often beat in synchrony and may transition between different synchronization modes in the same cell type. Here, we investigate the behaviour of elastic microfilaments, protruding from a surface and driven at their base by a configuration-dependent torque. We consider full hydrodynamic interactions among and within filaments and no slip at the surface. Isolated filaments exhibit periodic deformations, with increasing waviness and frequency as the magnitude of the driving torque increases. Two nearby but independently driven filaments synchronize their beating in-phase or anti-phase. This synchrony arises autonomously via the interplay between hydrodynamic coupling and filament elasticity. Importantly, in-phase and anti-phase synchronization modes are bistable and coexist for a range of driving torques and separation distances. These findings are consistent with experimental observations of in-phase and anti-phase synchronization in pairs of cilia and flagella and could have important implications on understanding the biophysical mechanisms underlying transitions between multiple synchronization modes.

One-dimensional crystals of passively-driven particles in microfluidic channels exhibit collective vibrational modes reminiscent of acoustic ‘phonons’. These phonons are induced by the long-range hydrodynamic interactions among the particles and are neutrally stable at the linear level. Here, we analyze the effect of particle activity – self-propulsion – on the emergence and stability of these phonons. We show that the direction of wave propagation in active crystals is sensitive to the intensity of the background flow. We also show that activity couples, at the linear level, transverse waves to the particles' rotational motion, inducing a new mode of instability that persists in the limit of large background flow, or, equivalently, vanishingly small activity. We then report a new phenomenon of phonons switching back and forth between two adjacent crystals in both passively-driven and active systems, similar in nature to the wave switching observed in quantum mechanics, optical communication, and density stratified fluids. These findings could have implications for the design of commercial microfluidic systems and the self-assembly of passive and active micro-particles into one-dimensional structures.

An important but missing component in the application of the kernel independent fast multipole method (KIFMM) is the capability for flexibly and efficiently imposing singly, doubly, and triply periodic boundary conditions. In most popular packages such periodicities are imposed with the hierarchical repetition of periodic boxes, which may give an incorrect answer due to the conditional convergence of some kernel sums. Here we present an efficient method to properly impose periodic boundary conditions using a near-far splitting scheme. The near-field contribution is directly calculated with the KIFMM method, while the far-field contribution is calculated with a multipole-to-local (M2L) operator which is independent of the source and target point distribution. The M2L operator is constructed with the far-field portion of the kernel function to generate the far-field contribution with the downward equivalent source points in KIFMM. This method guarantees the sum of the near-field & far-field converge pointwise to results satisfying periodicity and compatibility conditions. The computational cost of the far-field calculation observes the same O(N) complexity as FMM and is designed to be small by reusing the data computed by KIFMM for the near-field. The far-field calculations require no additional control parameters, and observes the same theoretical error bound as KIFMM. We present accuracy and timing test results for the Laplace kernel in singly periodic domains and the Stokes velocity kernel in doubly and triply periodic domains.