Related papers: FRETtranslator: translating FRET traces into RNA s…
The observation that, through a titration mechanism, microRNAs (miRNAs) can act as mediators of effective interactions among their common targets (competing endogenous RNAs or ceRNAs) has brought forward the idea ('ceRNA hypothesis') that…
Vision Transformer (ViT) architectures represent images as collections of high-dimensional vectorized tokens, each corresponding to a rectangular non-overlapping patch. This representation trades spatial granularity for embedding…
Down regulation of mRNA translation is an important problem in various bio-medical domains ranging from developing effective medicines for tumors and for viral diseases to developing attenuated virus strains that can be used for…
Messenger RNA (mRNA) sequences as therapeutics require optimized design to ensure efficient translation, structural stability, and minimal immunogenicity. This study presents a two-stage in-silico framework that integrates deep learning and…
Long non-coding RNAs (lncRNAs) serve as crucial regulators in numerous biological processes. Although they share sequence similarities with messenger RNAs (mRNAs), lncRNAs perform entirely different roles, providing new avenues for…
Event stream data often exhibit hierarchical structure in which multiple events co-occur, resulting in a sequence of multisets (i.e., bags of events). In electronic health records (EHRs), for example, medical events are grouped into a…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
Induced pluripotent stem cells (iPSCs) provide a great model to study the process of reprogramming and differentiation of stem cells. Single-cell RNA sequencing (scRNA-seq) enables us to investigate the reprogramming process at single-cell…
Transport through semiconductor nanostructures is a quantum-coherent process. This paper focuses on systems in which the electron's dynamics is ballistic and the transport is dominated by the scattering from structure boundaries. Opposite…
The ribosome flow model on a ring (RFMR) is a deterministic model for translation of a circularized mRNA. We derive a new spectral representation for the optimal steady-state production rate and the corresponding optimal steady-state…
The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {\it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the…
To accelerate Magnetic Resonance (MR) imaging procedures, Multi-Contrast MR Reconstruction (MCMR) has become a prevalent trend that utilizes an easily obtainable modality as an auxiliary to support high-quality reconstruction of the target…
Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in…
The nonlinear Fourier transform (NFT), a powerful tool in soliton theory and exactly solvable models, is a method for solving integrable partial differential equations governing wave propagation in certain nonlinear media. The NFT…
The versatility of self-attention mechanism earned transformers great success in almost all data modalities, with limitations on the quadratic complexity and difficulty of training. To apply transformers across different data modalities,…
Large scale self-supervised pre-training of Transformer language models has advanced the field of Natural Language Processing and shown promise in cross-application to the biological `languages' of proteins and DNA. Learning effective…
Spatiotemporal learning is challenging due to the intricate interplay between spatial and temporal dependencies, the high dimensionality of the data, and scalability constraints. These challenges are further amplified in scientific domains,…
Proteins are the active working horses in our body. These biomolecules perform all vital cellular functions from DNA replication and general biosynthesis to metabolic signaling and environmental sensing. While static 3D structures are now…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
Recent real-time semantic segmentation methods usually adopt an additional semantic branch to pursue rich long-range context. However, the additional branch incurs undesirable computational overhead and slows inference speed. To eliminate…