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Time-frequency representations (TFRs) of signals, such as the windowed Fourier transform (WFT), wavelet transform (WT) and their synchrosqueezed variants (SWFT, SWT), provide powerful analysis tools. However, there are many important issues…
We introduce a novel gene regulatory network (GRN) inference method that integrates optimal transport (OT) with a deep-learning structural inference model. Advances in next-generation sequencing enable detailed yet destructive gene…
Single-molecule transistors provide a unique experimental tool to investigate the coupling between charge transport and the molecular degrees of freedom in individual molecules. One interesting class of molecules for such experiments are…
As programs to support efficient and sustainable energy sources are expanding, research into the potential applications of the hydrogen vector is accelerating. Proton exchange membrane fuel cells are electrochemical converters that…
We investigate theoretically the stochastic dynamics of Resonance Electronic Energy Transfer (RET), in a bi-dimensional overexcited ensemble of donor and acceptor molecules. We find that, after initial optical excitation of all the donors,…
Single-cell RNA sequencing (scRNA-seq), especially temporally resolved datasets, enables genome-wide profiling of gene expression dynamics at single-cell resolution across discrete time points. However, current technologies provide only…
For the vast majority of genes in sequenced genomes, there is limited understanding of how they are regulated. Without such knowledge, it is not possible to perform a quantitative theory-experiment dialogue on how such genes give rise to…
Functional groups and moieties are chemical descriptors of biomolecules that can be used to interpret their properties and functions, leading to the understanding of chemical or biological mechanisms. These chemical building blocks, or…
Neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that is important for signaling in the brain and the gut. Its agonist ligand neurotensin (NTS), a 13-amino-acid peptide, binds with nanomolar affinity from the extracellular…
Spatial transcriptomics enables gene expression profiling with spatial context, offering unprecedented insights into the tissue microenvironment. However, most computational models treat genes as isolated numerical features, ignoring the…
In relation to recent experimental data [1], we develop a theory framework for demonstrating the feasibility of detecting sharp Nuclear Magnetic Resonance (NMR) oscillations in a real time ESR data. The procedure is to follow real time…
MicroRNAs (miRNAs) critically modulate stem cell properties like pluripotency, but the fundamental mechanism remains largely unknown. This study systematically analyzes multiple-omics data and builds a systems physical network including…
The study of structure-spectrum relationships is essential for spectral interpretation, impacting structural elucidation and material design. Predicting spectra from molecular structures is challenging due to their complex relationships.…
We present a sequential transfer learning framework for transformers on functional Magnetic Resonance Imaging (fMRI) data and demonstrate its significant benefits for decoding musical timbre. In the first of two phases, we pre-train our…
Phenotypic drug discovery has attracted widespread attention because of its potential to identify bioactive molecules. Transcriptomic profiling provides a comprehensive reflection of phenotypic changes in cellular responses to external…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
Single-molecule narrowfield microscopy is a versatile tool to investigate a diverse range of protein dynamics in live cells and has been extensively used in bacteria. Here, we describe how these methods can be extended to larger eukaryotic,…
Path sampling approaches have become invaluable tools to explore the mechanisms and dynamics of so-called rare events that are characterized by transitions between metastable states separated by sizeable free energy barriers. Their…
The TGF-beta pathway plays a central role in tissue homeostasis and morphogenesis. It transduces a variety of extracellular signals into intracellular transcriptional responses that control a plethora of cellular processes, including cell…
We apply a Transformer architecture, specifically BERT, to learn flexible and high quality molecular representations for drug discovery problems. We study the impact of using different combinations of self-supervised tasks for pre-training,…