Related papers: FRETtranslator: translating FRET traces into RNA s…
mRNA translation is a crucial process that leads to protein synthesis in living cells. Therefore, it is a process that needs to work optimally for a cell to stay healthy and alive. With advancements in microscopy and novel experimental…
We show that the quantum decoherence of Forster resonant energy transfer between two optically active molecules can be described by a spin-boson model. This allows us to give quantitative criteria, in terms of experimentally measurable…
Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins. Modeling these sequences is key to understand disease mechanisms and is an active research area in computational…
Single-cell RNA sequencing (scRNA-seq) technologies have enabled the profiling of gene expression for a collection of cells across time during a dynamic biological process. Given that each time point provides only a static snapshot,…
Rapid single shot spin readout is a key ingredient for fault tolerant quantum computing with spin qubits. An RF-SET (radio-frequency single electron transistor) is predominantly used as its the readout timescale is far shorter than the spin…
Translation is an important process for prokaryotic and eukaryotic cells to produce necessary proteins for cell growth. Numerious experiments have been performed to explore the translational properties. Diverse models have also been…
Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…
High-resolution time-frequency (TF) analysis plays crucial role in characterizing multicomponent signal (MCSs) and estimating oscillatory properties. Linear time-frequency representations (TFRs) such as classical short-time Fourier…
RNA function is tied to secondary structure, operating through dynamic and heterogeneous structural ensembles. While current analysis tools typically output single static structures or averaged contact maps, chemical probing methods like…
Single-cell RNA sequencing (scRNA-seq) data exhibit strong and reproducible statistical structure. This has motivated the development of large-scale foundation models, such as TranscriptFormer, that use transformer-based architectures to…
Single-molecule FRET is widely used to study helicases by detecting distance changes between a fluorescent donor and an acceptor anchored to overhangs of a forked DNA duplex. However, it has lacked single-base pair (1-bp) resolution…
The near-field spectroscopic information is critically important to determine the Forster resonant energy transfer(FRET) rate and the distance dependence in the vicinity of metal surfaces. The high density of evanescent near-field modes in…
Single-cell RNA sequencing (scRNA-seq) and spatially-resolved imaging/sequencing technologies have revolutionized biomedical research. On one hand, scRNA-seq provides information about a large portion of the transcriptome for individual…
Searching for novel molecular compounds with desired properties is an important problem in drug discovery. Many existing frameworks generate molecules one atom at a time. We instead propose a flexible editing paradigm that generates…
Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene…
The ongoing miniaturization in nanoscience and -technology challenges the sensitivity and selectivity of experimental analysis methods to the ultimate level of single atoms and molecules. A promising new approach, addressed here, focuses on…
The ribosome flow model (RFM) is a phenomenological model for the unidirectional flow of particles along a 1D chain of $n$ sites. The RFM has been extensively used to study the dynamics of ribosome flow along a single mRNA molecule during…
The Fractional Fourier Transform (FRT) corresponds to an arbitrary-angle rotation in the phase space, e.g. the time-frequency (TF) space, and generalizes the fundamentally important Fourier Transform. FRT applications range from classical…
Single-cell trajectory analysis aims to reconstruct the biological developmental processes of cells as they evolve over time, leveraging temporal correlations in gene expression. During cellular development, gene expression patterns…
A rising interest in the modality extension of foundation language models warrants discussion on the most effective, and efficient, multimodal training approach. This work focuses on neural machine translation (NMT) and proposes a joint…