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DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
We propose a two-step domain shift-invariant mitosis cell detection method based on Faster RCNN and a convolutional neural network (CNN). We generate various domain-shifted versions of existing histopathology images using a stain…
RNA secondary structure is an important computational model to understand how genetic variation maps into phenotypic (structural) variation. Evolutionary innovation in RNA structures is facilitated by neutral networks, large connected sets…
Non-coding RNAs (ncRNAs) play pivotal roles in gene expression regulation and the pathogenesis of various diseases. Accurate classification of ncRNAs is essential for functional annotation and disease diagnosis. To address existing…
This paper proposes a new two-step procedure for sparse-view tomographic image reconstruction. It is called RISING, since it combines an early-stopped Rapid Iterative Solver with a subsequent Iteration Network-based Gaining step. So far,…
All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy…
Radio map, or pathloss map prediction, is a crucial method for wireless network modeling and management. By leveraging deep learning to construct pathloss patterns from geographical maps, an accurate digital replica of the transmission…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
Many non-coding RNAs are known to play a role in the cell directly linked to their structure. Structure prediction based on the sole sequence is however a challenging task. On the other hand, thanks to the low cost of sequencing…
Statistical shape modeling (SSM) is an essential tool for analyzing variations in anatomical morphology. In a typical SSM pipeline, 3D anatomical images, gone through segmentation and rigid registration, are represented using…
RNA structure and functional dynamics play fundamental roles in controlling biological systems. Molecular dynamics simulation, which can characterize interactions at an atomistic level, can advance the understanding on new drug discovery,…
Mapping conformational heterogeneity of macromolecules presents a formidable challenge to X-ray crystallography and cryo-electron microscopy, which often presume its absence. This has severely limited our knowledge of the conformations…
We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA…
We have established an RNA Mapping Database (RMDB) to enable a new generation of structural, thermodynamic, and kinetic studies from quantitative single-nucleotide-resolution RNA structure mapping (freely available at…
Medical image restoration is essential for improving the usability of noisy, incomplete, and artifact-corrupted clinical scans, yet existing methods often rely on task-specific retraining and offer limited control over the trade-off between…
One of the main goals of DNA nanotechnology is to provide a viable solution to the limitations of top-down approaches in microfabrication schemes. Although a completely practical bottom-up approach is yet to be realized, there has been…
The task of RNA design given a target structure aims to find a sequence that can fold into that structure. It is a computationally hard problem where some version(s) have been proven to be NP-hard. As a result, heuristic methods such as…
3D fragment reassembly aims to recover the rigid poses of unordered fragment point clouds or meshes in a common object coordinate system to reconstruct the complete shape. The problem becomes particularly challenging as the number of…
Statistical shape analysis is a powerful tool to assess organ morphologies and find shape changes associated to a particular disease. However, imbalance in confounding factors, such as demographics might invalidate the analysis if not taken…