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Long non-coding RNAs (lncRNAs) are emerging regulatory molecules implicated in chronic disease pathogenesis, including Type 2 Diabetes Mellitus (T2D). We investigated ten literature reported lncRNAs associated with T2D: MALAT1, MEG3, MIAT,…
Detecting chemical modifications on RNA molecules remains a key challenge in epitranscriptomics. Traditional reverse transcription-based sequencing methods introduce enzyme- and sequence-dependent biases and fragment RNA molecules,…
Two-dimensional (2D) Nuclear Magnetic Resonance (NMR) spectroscopy, particularly Heteronuclear Single Quantum Coherence (HSQC) spectroscopy, plays a critical role in elucidating molecular structures, interactions, and electronic properties.…
Proteins perform critical processes in all living systems: converting solar energy into chemical energy, replicating DNA, as the basis of highly performant materials, sensing and much more. While an incredible range of functionality has…
Bacterial cells are sensitive to a range of external signals used to learn the environment. These incoming external signals are then processed using a Gene Regulatory Network (GRN), exhibiting similarities to modern computing algorithms. An…
Model-driven analysis of biophysical phenomena is gaining increased attention and utility for medical imaging applications. In magnetic resonance imaging (MRI), the availability of well-established models for describing the relations…
The modeling of bio-molecular system across molecular scales remains a central challenge in scientific research. Large language models (LLMs) are increasingly applied to bio-molecular discovery, yet systematic evaluation across multi-scale…
DNA language models are increasingly used to represent genomic sequence, yet their effectiveness depends critically on how raw nucleotides are converted into model inputs. Unlike natural language, DNA offers no canonical boundaries, making…
Ensembl's human non-coding and protein coding genes are used to automatically find DNA pattern motifs. The Backus-Naur form (BNF) grammar for regular expressions (RE) is used by genetic programming to ensure the generated strings are legal.…
DNA minicircles are closed double-stranded DNA (dsDNA) fragments that have been demonstrated to be an important experimental tool to understand supercoiled, or stressed, DNA mechanics, such as nucleosome positioning and DNA-protein…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
A novel group of small non-coding RNA, known as microRNA (miRNA) is predicted to regulate as high as 90% of the coding genes in human. The diversity and abundance of miRNA targets offer an enormous level of combinatorial possibilities and…
Image super-resolution (SR) in resource-constrained scenarios demands lightweight models balancing performance and latency. Convolutional neural networks (CNNs) offer low latency but lack non-local feature capture, while Transformers excel…
The Deep Material Network (DMN) has emerged as a powerful framework for multiscale materials modeling, enabling efficient and accurate prediction of material behavior across different length scales. Unlike conventional data-driven…
Delineating how animal behavior arises from neural activity is a foundational goal of neuroscience. However, as the computations underlying behavior unfold in networks of thousands of individual neurons across the entire brain, this…
Deep neural networks excel in mapping genomic DNA sequences to associated readouts (e.g., protein-DNA binding). Beyond prediction, the goal of these networks is to reveal to scientists the underlying motifs (and their syntax) which drive…
It has been estimated that about 30% of the genes in the human genome are regulated by microRNAs (miRNAs). These are short RNA sequences that can down-regulate the levels of mRNAs or proteins in animals and plants. Genes regulated by miRNAs…
Formal methods have enabled breakthroughs in many fields, such as in hardware verification, machine learning and biological systems. The key object of interest in systems biology, synthetic biology, and molecular programming is chemical…
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…