Related papers: Identifying topologically associating domains usin…
In computer-aided drug discovery (CADD), virtual screening (VS) is used for identifying the drug candidates that are most likely to bind to a molecular target in a large library of compounds. Most VS methods to date have focused on using…
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…
Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind a variety of specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic…
Dynamic graphs are rife with higher-order interactions, such as co-authorship relationships and protein-protein interactions in biological networks, that naturally arise between more than two nodes at once. In spite of the ubiquitous…
Spatial Transcriptomics (ST) is a technology that measures gene expression profiles within tissue sections while retaining spatial context. It reveals localized gene expression patterns and tissue heterogeneity, both of which are essential…
Graphical models find numerous applications in biology, chemistry, sociology, neuroscience, etc. While substantial progress has been made in graph estimation, it remains largely unexplored how to select significant graph signals with…
Motivation: The three-dimensional (3D) organization of the genome plays a critical role in regulating gene expression and maintaining cellular homeostasis. Disruptions in this spatial organization can result in abnormal chromatin…
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…
Exploring the shape of point configurations has been a key driver in the evolution of TDA (short for topological data analysis) since its infancy. This survey illustrates the recent efforts to broaden these ideas to model spatial…
Reliable and interpretable tumor classification from clinical imaging remains a core challenge. The main difficulties arise from heterogeneous modality quality, limited annotations, and the absence of structured anatomical guidance. We…
Chromatin is a highly compact and dynamic nuclear structure that consists of DNA and associated proteins. The main organizational unit is the nucleosome, which consists of a histone octamer with DNA wrapped around it. Histone proteins are…
Local feature matching remains a fundamental challenge in computer vision. Recent Area to Point Matching (A2PM) methods have improved matching accuracy. However, existing research based on this framework relies on inefficient pixel-level…
The principles that govern the organization of genomes, which are needed for a deeper understanding of how chromosomes are packaged and function in eukaryotic cells, could be deciphered if the three-dimensional (3D) structures are known.…
Event cameras provide microsecond-level temporal resolution, low latency, and high dynamic range, offering potential for perception under fast motion and challenging illumination conditions. However, existing Event-based Object Detection…
Spatial transcriptomics (ST) measures gene expression at a set of spatial locations in a tissue. Communities of nearby cells that express similar genes form \textit{spatial domains}. Specialized ST clustering algorithms have been developed…
We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics…
Understanding how genetic variants influence cellular-level processes is an important step towards understanding how they influence important organismal-level traits, or "phenotypes", including human disease susceptibility. To this end…
The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance…
DNA language models like Evo2 now fit million-token contexts large enough to cover entire TADs, yet whether they learn 3D chromatin structure, a key regulatory layer acting atop primary sequence, remains untested and questionable, given…
Automatic diagnosis (AD), a critical application of AI in healthcare, employs machine learning techniques to assist doctors in gathering patient symptom information for precise disease diagnosis. The Transformer-based method utilizes an…