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Many cellular responses to surrounding cues require temporally concerted transcriptional regulation of multiple genes. In prokaryotic cells, a single-input-module motif with one transcription factor regulating multiple target genes can…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses…
It often is emphasized that gene expression is noisy. A seemingly contradictory view is that control mechanisms have been optimized to squeeze as much information as possible out of a limited number of molecules. Here we revisit these…
Stem cell regeneration is a vital biological process in self-renewing tissues, governing development and tissue homeostasis. Gene regulatory network dynamics are pivotal in controlling stem cell regeneration and cell type transitions.…
At the heart of neural network force fields (NNFFs) is the architecture of neural networks, where the capacity to model complex interactions is typically enhanced through widening or deepening multilayer perceptrons (MLPs) or by increasing…
In this paper, we set up the theoretical foundations for a high-dimensional functional factor model approach in the analysis of large cross-sections (panels) of functional time series (FTS). We first establish a representation result…
Functional magnetic resonance imaging (fMRI) has become one of the most common imaging modalities for brain function analysis. Recently, graph neural networks (GNN) have been adopted for fMRI analysis with superior performance.…
In recent years, Multi-modal Foundation Models (MFMs) and Embodied Artificial Intelligence (EAI) have been advancing side by side at an unprecedented pace. The integration of the two has garnered significant attention from the AI research…
Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…
A blood cell lineage consists of several consecutive developmental stages from the pluri- or multipotent stem cell to a state of terminal differentiation. Despite their importance for human biology, the regulatory pathways and gene networks…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
Motivation: Identifying drug-target interactions (DTIs) is a key step in drug repositioning. In recent years, the accumulation of a large number of genomics and pharmacology data has formed mass drug and target related heterogeneous…
Neural collaborative filtering (NCF) and recurrent recommender systems (RRN) have been successful in modeling user-item relational data. However, they are also limited in their assumption of static or sequential modeling of relational data…
The recent development of single-cell transcriptomics has enabled gene expression to be measured in individual cells instead of being population-averaged. Despite this considerable precision improvement, inferring regulatory networks…
Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude larger than the number of training examples, making it difficult to avoid overfitting, even when…
It is well known that the general transcription factors (GTF) specifically recognize correct TATA boxes, distinguishing them from many others. Employing the principles of determinacy analysis (mathematical theory of rules) we analyzed a…
This article explores a general factor structure for high-dimensional nonstationary functional time series, encompassing a wide range of factor models studied in the existing literature. We investigate the asymptotic spectral behaviors of…
Elucidating gene function is one of the ultimate goals of plant science. Despite this, only ~15% of all genes in the model plant Arabidopsis thaliana have comprehensively experimentally verified functions. While bioinformatical gene…
Transcription factor binding to the surface of DNA regulatory regions is one of the primary causes of regulating gene expression levels. A probabilistic approach to model protein-DNA interactions at the sequence level is through Position…