Related papers: Probing 3D Chromatin Structure Awareness in Evo2 D…
How genes affect tissue scale organization remains a longstanding biological puzzle. As experimental efforts aim to quantify gene expression, chromatin organization, cellular structure, and tissue structure, computational modeling lags…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
Vision-Language-Action models have emerged as a promising paradigm for robotic manipulation by unifying perception, language grounding, and action generation. However, they often struggle in scenarios requiring precise spatial…
Recent white-box OOD detection methods for LLMs -- including CED, RAUQ, and WildGuard confidence scores -- appear effective, but we show they are structurally confounded by sequence length (|r| >= 0.61) and collapse to near-chance under…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
Visual object recognition in unseen and cluttered indoor environments is a challenging problem for mobile robots. This study presents a 3D shape and color-based descriptor, TOPS2, for point clouds generated from RGB-D images and an…
Complex 3D scene understanding has gained increasing attention, with scene encoding strategies playing a crucial role in this success. However, the optimal scene encoding strategies for various scenarios remain unclear, particularly…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
Molecular and genetic definitions of human-specific changes to genomic regulatory networks (GRNs) contributing to development of unique to human phenotypes remain a highly significant challenge. Genome-wide proximity placement analysis of…
Structure-based drug discovery faces the dual challenge of accurately capturing 3D protein-ligand interactions while navigating ultra-large chemical spaces to identify synthetically accessible candidates. In this work, we present a unified…
Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of…
Language Models (LMs) have greatly influenced diverse domains. However, their inherent limitation in comprehending 3D molecular structures has considerably constrained their potential in the biomolecular domain. To bridge this gap, we focus…
3D object detection plays a crucial role in autonomous systems, yet existing methods are limited by closed-set assumptions and struggle to recognize novel objects and their attributes in real-world scenarios. We propose OVODA, a novel…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
A deep Transformer model with good evaluation score does not mean each subnetwork (a.k.a transformer block) learns reasonable representation. Diagnosing abnormal representation and avoiding it can contribute to achieving a better evaluation…
This paper aims to retrieve proteins with similar structures and semantics from large-scale protein dataset, facilitating the functional interpretation of protein structures derived by structural determination methods like cryo-Electron…
Understanding degradation in battery cathodes and other functional materials requires simultaneous knowledge of structural, chemical, and electronic changes in three dimensions (3D). Here, we present a simultaneous ADF-EDS-EELS tomography…
Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly understood. In this work, we investigate the role of…
We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes and the vertical distance $d$…
We present ChromoSkein, a web-based tool for visualizing three-dimensional chromatin models. The spatial organization of chromatin is essential to its function. Experimental methods, namely Hi-C, reveal the spatial conformation but output a…