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Cryo-electron microscopy (cryo-EM) is an indispensable technique for determining the 3D structures of dynamic biomolecular complexes. While typically applied to image a single molecular species, cryo-EM has the potential for structure…
Object detection is a main task in computer vision. Template matching is the reference method for detecting objects with arbitrary templates. However, template matching computational complexity depends on the rotation accuracy, being a…
Modeling the 3D structures of cells and tissues is crucial in biology. Sequential cross-sectional images from electron microscopy provide high-resolution intracellular structure information. The segmentation of complex cell structures…
The interaction of a protein with its environment can be understood and controlled via its 3D structure. Experimental methods for protein structure determination, such as X-ray crystallography or cryogenic electron microscopy, shed light on…
Visual recognition and vision based retrieval of objects from large databases are tasks with a wide spectrum of potential applications. In this paper we propose a novel recognition method from video sequences suitable for retrieval from…
Machine learning models can assist with metamaterials design by approximating computationally expensive simulators or solving inverse design problems. However, past work has usually relied on black box deep neural networks, whose reasoning…
Electron cryotomography (CryoET) is currently the only method capable of visualizing cells in 3D at nanometer resolutions. While modern instruments produce massive amounts of tomography data containing extremely rich structural information,…
Since Perutz, Kendrew and colleagues unveiled the structure of hemoglobin and myoglobin based on X-ray diffraction analysis in the 1950s, X-ray crystallography has become the primary methodology used to determine the 3D structure of…
The recent improvements in cryo-electron microscopy (cryo-EM) in the past few years are now allowing to observe molecular complexes at atomic resolution. As a consequence, numerous structures derived from cryo-EM are now available in the…
Cryo-electron microscopy (cryo-EM) studies using single particle reconstruction are extensively used to reveal structural information on macromolecular complexes. Aiming at the highest achievable resolution, state of the art electron…
Cryogenic electron microscopy (cryo-EM) provides a unique opportunity to study the structural heterogeneity of biomolecules. Being able to explain this heterogeneity with atomic models would help our understanding of their functional…
The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction,…
The mode of action of proteins is to a large extent given by their ability to adopt different conformations. This is why imaging single biomolecules at atomic resolution is one of the ultimate goals of biophysics and structural biology. The…
We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both…
Three-dimensional electron diffraction (3D ED) has emerged as a powerful method for solving the structures of sub-micron-sized particles down to nanoparticles. However, it faces technical challenges when applied to beam-sensitive samples or…
By their very nature microscopy images of cells and tissues consist of a limited number of object types or components. In contrast to most natural scenes, the composition is known a priori. Decomposing biological images into semantically…
Knowledge of a protein's atomic conformational ensemble is critical to determining its function, yet state-of-the-art ensemble prediction models are limited by lack of high-quality conformational data from simulation or experiment. Recent…
In this work, we describe a method for large-scale 3D cell-tracking through a segmentation selection approach. The proposed method is effective at tracking cells across large microscopy datasets on two fronts: (i) It can solve problems…
Many important problems involving molecular property prediction from 3D structures have limited data, posing a generalization challenge for neural networks. In this paper, we describe a pre-training technique based on denoising that…
Single particle cryogenic electron microscopy (cryo-EM) is an imaging technique capable of recovering the high-resolution 3-D structure of biological macromolecules from many noisy and randomly oriented projection images. One notable…