Related papers: Inferring Gene Regulatory Network Using An Evoluti…

Inferring Gene Regulatory Networks (GRNs) from gene expression data is crucial for understanding biological processes. While supervised models are reported to achieve high performance for this task, they rely on costly ground truth (GT)…

We propose a new method in which a generative network (GN) integrate into a reduced-order model (ROM) framework is used to solve inverse problems for partial differential equations (PDE). The aim is to match available measurements and…

The solution of high-dimensional inference and prediction problems in computational biology is almost always a compromise between mathematical theory and practical constraints such as limited computational resources. As time progresses,…

Most existing swarm pattern formation methods depend on a predefined gene regulatory network (GRN) structure that requires designers' priori knowledge, which is difficult to adapt to complex and changeable environments. To dynamically adapt…

We extend biologically-informed neural networks (BINNs) for genomic prediction (GP) and selection (GS) in crops by integrating thousands of single-nucleotide polymorphisms (SNPs) with multi-omics measurements and prior biological knowledge.…

Determining gene regulatory network (GRN) structure is a central problem in biology, with a variety of inference methods available for different types of data. For a widely prevalent and challenging use case, namely single-cell gene…

Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the always increasing…

One of the most interesting, difficult, and potentially useful topics in computational biology is the inference of gene regulatory networks (GRNs) from expression data. Although researchers have been working on this topic for more than a…

One of the focus areas of modern scientific research is to reveal mysteries related to genes and their interactions. The dynamic interactions between genes can be encoded into a gene regulatory network (GRN), which can be used to gain…

This paper presents a novel method for statistical inference in high-dimensional binary models with unspecified structure, where we leverage a (potentially misspecified) sparsity-constrained working generalized linear model (GLM) to…

The vast majority of biological sequences encode unknown functions and bear little resemblance to experimentally characterized proteins, limiting both our understanding of biology and our ability to harness functional potential for the…

Gene regulatory network inference uses genome-wide transcriptome measurements in response to genetic, environmental or dynamic perturbations to predict causal regulatory influences between genes. We hypothesized that evolution also acts as…

Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…

Knowing gene regulatory networks (GRNs) is important for understanding various biological mechanisms. In this paper, we present a method, QWENDY, that uses single-cell gene expression data measured at four time points to infer GRNs. Based…

Despite theoretical advantages, causal methods for Gene Regulatory Network (GRN) inference from single-cell RNA-seq data consistently fail to match or outperform correlation-based baselines in many realistic benchmarks, a persistent puzzle…

We introduce a novel gene regulatory network (GRN) inference method that integrates optimal transport (OT) with a deep-learning structural inference model. Advances in next-generation sequencing enable detailed yet destructive gene…

Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…

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…

Accurately inferring Gene Regulatory Networks (GRNs) is a critical and challenging task in biology. GRNs model the activatory and inhibitory interactions between genes and are inherently causal in nature. To accurately identify GRNs,…

Inferring gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data is a complex challenge that requires capturing the intricate relationships between genes and their regulatory interactions. In this study, we tackle…