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We investigate the trends of information backflow associated with the dynamics of a sub-part of a disordered spin-1/2 transverse field Heisenberg chain for different regimes of the Hamiltonian. Towards this aim, the decay profile of…
Understanding the oscillating behaviors that govern organisms' internal biological processes requires interdisciplinary efforts combining both biological and computer experiments, as the latter can complement the former by simulating…
DNA is a leading candidate as the next archival storage media due to its density, durability and sustainability. To read (and write) data DNA storage exploits technology that has been developed over decades to sequence naturally occurring…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
We introduce the Poisson Log-Normal Graphical Model for count data, and present a normality transformation for data arising from this distribution. The model and transformation are feasible for high-throughput microRNA (miRNA) sequencing…
In shotgun sequencing, the input string (typically, a long DNA sequence composed of nucleotide bases) is sequenced as multiple overlapping fragments of much shorter lengths (called \textit{reads}). Modelling the shotgun sequencing pipeline…
Multiple biological processes are driven by oscillatory gene expression at different time scales. Pulsatile dynamics are thought to be widespread, and single-cell live imaging of gene expression has lead to a surge of dynamic, possibly…
We introduce a new statistical test based on the observed spacings of ordered data. The statistic is sensitive to detect non-uniformity in random samples, or short-lived features in event time series. Under some conditions, this new test…
Large language models (LLMs) increasingly solve difficult problems by producing "reasoning traces" before emitting a final response. However, it remains unclear how accuracy and decision commitment evolve along a reasoning trajectory, and…
Background: Spatial transcriptomics have emerged as a powerful tool in biomedical research because of its ability to capture both the spatial contexts and abundance of the complete RNA transcript profile in organs of interest. However,…
Spiking neural networks (SNNs) can be used for implementing cost-efficient artificial intelligence computing or mechanistic modelling of experimentally observed neural data. In the latter, fitting neural data with recurrent SNNs (RSNNs)…
The dynamics of gene transcription is tightly regulated in eukaryotes. Recent experiments have revealed various kinds of transcriptional dynamics, such as RNA polymerase II pausing, that involves regulation at the transcription initiation…
In this work, we provide a specifc trigonometric stochastic numerical method for linear oscillators with high constant frequencies, driven by a nonlinear time-varying force and a random force. We present some theoretical considerations and…
The seismocardiographic signal is a promising alternative to the traditional ECG in the analysis of the cardiac activity. In particular, the systolic complex is known to be the most informative part of the seismocardiogram, thus requiring…
Oscillatory dynamics are ubiquitous in biological networks. Possible sources of oscillations are well understood in low-dimensional systems, but have not been fully explored in high-dimensional networks. Here we study large networks…
We revisit a simple model class for machine learning on graphs, where a random walk on a graph produces a machine-readable record, and this record is processed by a deep neural network to directly make vertex-level or graph-level…
Biochemical oscillations are ubiquitous in nature and allow organisms to properly time their biological functions. In this paper, we consider minimal Markov state models of nonequilibrium biochemical networks that support oscillations. We…
In human microbiome studies, sequencing reads data are often summarized as counts of bacterial taxa at various taxonomic levels specified by a taxonomic tree. This paper considers the problem of analyzing two repeated measurements of…
Currently running and forthcoming precision neutrino oscillation experiments aim to unambiguously determine the neutrino mass ordering, the charge-parity violating phase in the lepton sector and the possible existence of physics Beyond the…
Modern cell-perturbation experiments expose cells to panels of hundreds of stimuli, such as cytokines or CRISPR guides that perform gene knockouts. These experiments are designed to investigate whether a particular gene is upregulated or…