Related papers: Correcting a SHAPE-directed RNA structure by a mut…
Biologically inspired pressure actuated cellular structures can alter their shape through pressure variations. Previous work introduced a computational framework for pressure actuated cellular structures which was limited to two cell rows…
RNA, whose functionality is largely determined by its structure, plays an important role in many biological activities. The prediction of pairwise structural proximity between each nucleotide of an RNA sequence can characterize the…
Deep neural networks are increasingly employed in high-stakes medical applications, despite their tendency for shortcut learning in the presence of spurious correlations, which can have potentially fatal consequences in practice. Whereas a…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe…
Clinical diagnosis is a highly specialized discipline requiring both domain expertise and strict adherence to rigorous guidelines. While current AI-driven medical research predominantly focuses on knowledge graphs or natural text…
Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…
Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe…
Two-sample multiple testing problems of sparse spatial data are frequently arising in a variety of scientific applications. In this article, we develop a novel neighborhood-assisted and posterior-adjusted (NAPA) approach to incorporate both…
We develop a stochastic model for the programmed frameshift of ribosomes synthesizing a protein while moving along a mRNA template. Normally the reading frame of a ribosome decodes successive triplets of nucleotides on the mRNA in a…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
Medical image retrieval is a valuable field for supporting clinical decision-making, yet current methods primarily support 2D images and require fully annotated queries, limiting clinical flexibility. To address this, we propose…
Proteins can exhibit dynamic structural flexibility as they carry out their functions, especially in binding regions that interact with other molecules. For the key SARS-CoV-2 spike protein that facilitates COVID-19 infection, studies have…
We introduce a novel neural representation for maps between 3D shapes based on flow-matching models, which is computationally efficient and supports cross-representation shape matching without large-scale training or data-driven procedures.…
Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…
A full understanding of RNA-mediated biology would require the knowledge of three-dimensional (3D) structures, structural flexibility and stability of RNAs. To predict RNA 3D structures and stability, we have previously proposed a…
Unstructured data is pervasive, but analytical queries demand structured representations, creating a significant extraction challenge. Existing methods like RAG lack schema awareness and struggle with cross-document alignment, leading to…
This paper introduces a new shape-based image reconstruction technique applicable to a large class of imaging problems formulated in a variational sense. Given a collection of shape priors (a shape dictionary), we define our problem as…
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…
Circular RNAs (circRNAs) are important components of the non-coding RNA regulatory network. Previous circRNA identification primarily relies on high-throughput RNA sequencing (RNA-seq) data combined with alignment-based algorithms that…
Morphogenesis, the establishment and repair of emergent complex anatomy by groups of cells, is a fascinating and biomedically-relevant problem. One of its most fascinating aspects is that a developing embryo can reliably recover from…