Related papers: Inferring Compensatory Kinase Networks in Yeast us…
Existing multi-behavior recommendations tend to prioritize performance at the expense of explainability, while current explainable methods suffer from limited generalizability due to their reliance on external information. Neuro-Symbolic…
Deciphering gene regulatory networks is a central problem in computational biology. Here, we explore the use of multi-modal neural networks to learn predictive models of gene expression that include cis and trans regulatory components. We…
Gene regulatory networks constitute the first layer of the cellular computation for cell adaptation and surveillance. In these webs, a set of causal relations is built up from thousands of interactions between transcription factors and…
Kinetic parameters such as the turnover number ($k_{cat}$) and Michaelis constant ($K_{\mathrm{M}}$) are essential for modelling enzymatic activity but experimental data remains limited in scale and diversity. Previous methods for…
In this paper, we study the large-scale protein interaction network of yeast uti lizing a stochastic method based upon percolation of random graphs. In order to find the global features of connectivities in the network, we introduce numeric…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
Eye movements are intricate and dynamic biosignals that contain a wealth of cognitive information about the subject. However, these are ambiguous signals and therefore require meticulous feature engineering to be used by machine learning…
Cell signaling networks are complex and often incompletely characterized, making it difficult to obtain a comprehensive picture of the mechanisms they encode. Mathematical modeling of these networks provides important clues, but the models…
MOTIVATION: A central goal of postgenomic biology is the elucidation of the regulatory relationships among all cellular constituents that together comprise the 'genetic network' of a cell or microorganism. Experimental manipulation of gene…
We consider causal inference in the presence of unobserved confounding. We study the case where a proxy is available for the unobserved confounding in the form of a network connecting the units. For example, the link structure of a social…
Many complex systems can be represented as networks composed by distinct layers, interacting and depending on each others. For example, in biology, a good description of the full protein-protein interactome requires, for some organisms, up…
Project Yanasse presents a method for discovering new proofs of theorems in one area of mathematics by transferring proof strategy patterns (e.g., Lean 4 tactic invocation patterns) from a structurally distant area. The system extracts…
The budding yeast {\it Saccharomyces cerevisiae} is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual…
This paper develops a declarative language, P-log, that combines logical and probabilistic arguments in its reasoning. Answer Set Prolog is used as the logical foundation, while causal Bayes nets serve as a probabilistic foundation. We give…
Statistical inference of genetic regulatory networks is essential for understanding temporal interactions of regulatory elements inside the cells. For inferences of large networks, identification of network structure is typical achieved…
Motivation: Signaling pathways control a large variety of cellular processes. However, currently, even within the same database signaling pathways are often curated at different levels of detail. This makes comparative and cross-talk…
Most network-based protein (or gene) function prediction methods are based on the assumption that the labels of two adjacent proteins in the network are likely to be the same. However, assuming the pairwise relationship between proteins or…
Residue-residue interactions that fold a protein into a unique three-dimensional structure and make it play a specific function impose structural and functional constraints on each residue site. Selective constraints on residue sites are…
Gene expression (GE) data capture valuable condition-specific information ("condition" can mean a biological process, disease stage, age, patient, etc.) However, GE analyses ignore physical interactions between gene products, i.e.,…
We introduce two time-delay models of metabolic oscillations in yeast cells. Our model tests a hypothesis that the oscillations occur as multiple pathways share a limited resource which we equate to the number of available ribosomes. We…