Related papers: eQTL Studies: from Bulk Tissues to Single Cells
Variational quantum algorithms (VQAs) are leading strategies for using near-term quantum devices, with a well-studied bottleneck being their trainability. Standard expectation-value objectives with expressive circuits frequently encounter…
The emergence of a predominant phenotype within a cell population is often triggered by a rare accumulation of DNA mutations in a single cell. For example, tumors may be initiated by a single cell in which multiple mutations cooperate to…
Agent-based modeling (ABM) is a powerful tool for understanding self-organizing biological systems, but it is computationally intensive and often not analytically tractable. Equation learning (EQL) methods can derive continuum models from…
Controlling electrically-stimulated quantum light sources (QLS) is key for developing integrated and low-scale quantum devices. The mechanisms leading to quantum emission are complex, as a large number of electronic states of the system…
A fundamental problem in quantum thermodynamics is to properly quantify the work extractable from out-of-equilibrium systems. While for closed systems, maximum quantum work extraction is defined in terms of the ergotropy functional, this…
Extrachromosomal DNA (ecDNA) can drive oncogene amplification, gene expression and intratumor heterogeneity, representing a major force in cancer initiation and progression. The phenomenon becomes even more intricate as distinct types of…
Multimodal single-cell technologies enable the simultaneous collection of diverse data types from individual cells, enhancing our understanding of cellular states. However, the integration of these datatypes and modeling the…
Cell competition is a quality control mechanism in tissues that results in the elimination of less fit cells. Over the past decade, the phenomenon of cell competition has been identified in many physiological and pathological contexts,…
Genetically identical cells in the same population can take on phenotypically variable states, leading to differentiated responses to external signals, such as nutrients and drug-induced stress. Many models and experiments have focused on a…
We study sample covariance matrices arising from multi-level components of variance. Thus, let $ B_n=\frac{1}{N}\sum_{j=1}^NT_{j}^{1/2}x_jx_j^TT_{j}^{1/2}$, where $x_j\in R^n$ are i.i.d. standard Gaussian, and…
Quality diversity~(QD) is a branch of evolutionary computation that gained increasing interest in recent years. The Map-Elites QD approach defines a feature space, i.e., a partition of the search space, and stores the best solution for each…
Classification of entanglement is an important problem in Quantum Resource Theory. In this paper we discuss an embedding of this problem in the context of Topological Quantum Field Theories (TQFT). This approach allows classifying…
Taylor's Law (TL) relates the variance to the mean of a random variable via power law. In ecology it applies to populationsand it is a common empirical pattern shared among different ecosystems. Measurements give power law exponent to be…
Contextuality - the obstruction to describing quantum mechanics in a classical statistical way - has been proposed as a resource that powers quantum computing. The measurement-based model provides a concrete manifestation of contextuality…
Although random cell complexes occur throughout the physical sciences, there does not appear to be a standard way to quantify their statistical similarities and differences. The various proposals in the literature are usually motivated by…
Gene regulatory networks (GRNs) represent the causal relationships between transcription factors (TFs) and target genes in single-cell RNA sequencing (scRNA-seq) data. Understanding these networks is crucial for uncovering disease…
Quantum machine learning (QML) aims to use quantum computers to enhance machine learning, but it is often limited by the required number of samples due to quantum noise and statistical limits on expectation value estimates. While efforts…
Evolutionary dynamics and patterns of molecular evolution are strongly influenced by selection on linked regions of the genome, but our quantitative understanding of these effects remains incomplete. Recent work has focused on predicting…
We present a mathematical model that describes how tumour heterogeneity evolves in a tissue slice that is oxygenated by a single blood vessel. Phenotype is identified with the stemness level of a cell, $s$, that determines its proliferative…
A quantum phase transition is usually achieved by tuning physical parameters in a Hamiltonian at zero temperature. Here, we demonstrate that the ground state of a topological phase itself encodes critical properties of its transition to a…