Related papers: MARADONER: Motif Activity Response Analysis Done R…

The continuous integration of experimental data into coherent models of the brain is an increasing challenge of modern neuroscience. Such models provide a bridge between structure and activity, and identify the mechanisms giving rise to…

Mediation analysis seeks to identify and quantify the paths by which an exposure affects an outcome. Intermediate variables which are effected by the exposure and which effect the outcome are known as mediators. There exists extensive work…

Designing RNA molecules has garnered recent interest in medicine, synthetic biology, biotechnology and bioinformatics since many functional RNA molecules were shown to be involved in regulatory processes for transcription, epigenetics and…

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…

Detecting differences in gene expression is an important part of single-cell RNA sequencing experiments, and many statistical methods have been developed for this aim. Most differential expression analyses focus on comparing expression…

To identify a stationary action profile for a population of competitive agents, each executing private strategies, we introduce a novel active-learning scheme where a centralized external observer (or entity) can probe the agents' reactions…

Identifying variables responsible for changes to a biological system enables applications in drug target discovery and cell engineering. Given a pair of observational and interventional datasets, the goal is to isolate the subset of…

Although deep learning techniques show promising results for many neuroimaging tasks in research settings, they have not yet found widespread use in clinical scenarios. One of the reasons for this problem is that many machine learning…

This paper discusses the latest generation of the MONARC (MOdels of Networked Analysis at Regional Centers) simulation framework, as a design and modelling tool for large scale distributed systems applied to HEP experiments. A…

PROTACs are a promising therapeutic modality that harnesses the cell's built-in degradation machinery to degrade specific proteins. Despite their potential, developing new PROTACs is challenging and requires significant domain expertise,…

Static resource analysis determines the resource consumption (e.g., time complexity) of a program without executing it. Among the numerous existing approaches for resource analysis, affine type systems have been one dominant approach.…

The diversity of expressed genes plays a critical role in cellular specialization, adaptation to environmental changes, and overall cell functionality. This diversity varies dramatically across cell types and is orchestrated by intricate,…

Partial observability and uncertainty are common problems in sequential decision-making that particularly impede the use of formal models such as Markov decision processes (MDPs). However, in practice, agents may be able to employ costly…

Recent breakthroughs in cancer research have come via the up-and-coming field of pathway analysis. By applying statistical methods to prior known gene and protein regulatory information, pathway analysis provides a meaningful way to…

Developing models with high interpretability and even deriving formulas to quantify relationships between biological data is an emerging need. We propose here a framework for ab initio derivation of sequence motifs and linear formula using…

Gene regulation is a dynamic process that underlies all aspects of human development, disease response, and other key biological processes. The reconstruction of temporal gene regulatory networks has conventionally relied on regression…

Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…

In systems biology, attractor landscape analysis of gene regulatory networks is recognized as a powerful computational tool for studying various cellular states from proliferation and differentiation to senescence and apoptosis. Therefore,…

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in…

Natural animal behavior displays rich lexical and temporal dynamics, even in a stable environment. This implies that behavioral variability arises from sources within the brain, but the origin and mechanics of these processes remain largely…