Related papers: The Stanford RNA Mapping Database for sharing and …
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…
Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are…
Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the…
Summary: We introduce RBPBind, a web-based tool for the quantitative prediction of RNA-protein interactions. Given a user-specified RNA and a protein selected from a set of several common RNA-binding proteins, RBPBind computes the binding…
An important challenge in cancer systems biology is to uncover the complex network of interactions between genes (tumor suppressor genes and oncogenes) implicated in cancer. Next generation sequencing provides unparalleled ability to probe…
Structured Adaptive Mesh Refinement (Structured AMR) enables simulations to adapt the domain resolution to save computation and storage, and has become one of the dominant data representations used by scientific simulations; however,…
Rare diseases often manifest with distinctive facial phenotypes in children, offering valuable diagnostic cues for clinicians and AI-assisted screening systems. However, progress in this field is severely limited by the scarcity of curated,…
Proteins perform much of the work in living organisms, and consequently the development of efficient computational methods for protein representation is essential for advancing large-scale biological research. Most current approaches…
We describe the atomic database of the XSTAR spectral modeling code, summarizing the systematic upgrades carried out in the past twenty years to enable the modeling of K lines from chemical elements with atomic number $Z\leq 30$ and recent…
We address the problem of registering synchronized color (RGB) and multi-spectral (MS) images featuring very different resolution by solving stereo matching correspondences. Purposely, we introduce a novel RGB-MS dataset framing 13…
Due to rapid advancements in deep learning techniques, the demand for large-volume high-quality databases grows significantly in chemical research. We developed a quantum-chemistry database that includes 443,106 small organic molecules with…
Much of the world's most valued data is stored in relational databases and data warehouses, where the data is organized into many tables connected by primary-foreign key relations. However, building machine learning models using this data…
RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA…
The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which can tremendously impact their cost and…
Crosslinking Mass Spectrometry (MS) can uncover protein-protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats,…
A key requirement for leveraging supervised deep learning methods is the availability of large, labeled datasets. Unfortunately, in the context of RGB-D scene understanding, very little data is available -- current datasets cover a small…
Defect phase diagrams provide a unified description of crystal defect states for materials design and are central to the scientific objectives of the Collaborative Research Centre (CRC) 1394. Their construction requires the systematic…
DNA has immense potential as an emerging data storage medium. The principle of DNA storage is the conversion and flow of digital information between binary code stream, quaternary base, and actual DNA fragments. This process will inevitably…
Raman spectroscopy provides a vibrational profile of the molecules and thus can be used to uniquely identify different kind of materials. This sort of fingerprinting molecules has thus led to widespread application of Raman spectrum in…
Structured RNA plays many functionally relevant roles in molecular life. Structural information, while required to understand the functional cycles in detail, is challenging to gather. Computational methods promise to complement…