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SURGE: uncovering context-specific genetic-regulation of gene expression from single-cell RNA sequencing using latent-factor models
Genetic regulation of gene expression is a complex process, with genetic effects known to vary across cellular contexts such as cell types and...
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Niche-DE: niche-differential gene expression analysis in spatial transcriptomics data identifies context-dependent cell-cell interactions
Existing methods for analysis of spatial transcriptomic data focus on delineating the global gene expression variations of cell types across the...
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New Context Significantly Changes Expression of Irs2 Gene in Hippocampal Areas
AbstractMemory formation is a complex process involving changes in the synaptic activity and gene expression encoding the insulin-like growth...
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Gene birth in a model of non-genic adaptation
BackgroundOver evolutionary timescales, genomic loci can switch between functional and non-functional states through processes such as...
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A multimodal deep learning model to infer cell-type-specific functional gene networks
BackgroundFunctional gene networks (FGNs) capture functional relationships among genes that vary across tissues and cell types. Construction of...
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SCORPiOs, a Novel Method to Reconstruct Gene Phylogenies in the Context of a Known WGD Event
Phylogenetic gene trees recapitulate the evolutionary history of genes across species, forming an essential framework for comparative genomic...
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Position Effect Variegation: Role of the Local Chromatin Context in Gene Expression Regulation
AbstractPosition effect variegation (PEV) is a phenomenon wherein the expression level of a gene strongly depends on its genomic position. PEV can be...
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De novo assembly of transcriptomes and differential gene expression analysis using short-read data from emerging model organisms – a brief guide
Many questions in biology benefit greatly from the use of a variety of model systems. High-throughput sequencing methods have been a triumph in the...
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Extracting functionally accurate context-specific models of Atlantic salmon metabolism
Constraint-based models (CBMs) are used to study metabolic network structure and function in organisms ranging from microbes to multicellular...
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An adenine base editor variant expands context compatibility
Adenine base editors (ABEs) are precise gene-editing agents that convert A:T pairs into G:C through a deoxyinosine intermediate. Existing ABEs...
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Structure-primed embedding on the transcription factor manifold enables transparent model architectures for gene regulatory network and latent activity inference
BackgroundModeling of gene regulatory networks (GRNs) is limited due to a lack of direct measurements of genome-wide transcription factor activity...
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Plakophilin 2 gene therapy prevents and rescues arrhythmogenic right ventricular cardiomyopathy in a mouse model harboring patient genetics
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a fatal genetic heart disease characterized by cardiac arrhythmias, in which fibrofatty...
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Determinants of p53 DNA binding, gene regulation, and cell fate decisions
The extent to which transcription factors read and respond to specific information content within short DNA sequences remains an important question...
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Endoplasmic reticulum stress-related gene model predicts prognosis and guides therapies in lung adenocarcinoma
BackgroundThe prognosis and survival of lung adenocarcinoma (LUAD) patients are still not promising despite recent breakthroughs in treatment....
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xenoGI 3: using the DTLOR model to reconstruct the evolution of gene families in clades of microbes
To understand genome evolution in a group of microbes, we need to know the timing of events such as duplications, deletions and horizontal transfers....
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A mixed-effects stochastic model reveals clonal dominance in gene therapy safety studies
BackgroundMathematical models of haematopoiesis can provide insights on abnormal cell expansions (clonal dominance), and in turn can guide safety...
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Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model
BackgroundMicrobiomes are generally characterized by high diversity of coexisting microbial species and strains, and microbiome composition typically...
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Gene Networks Inference by Reinforcement Learning
Gene Regulatory Networks inference from gene expression data is an important problem in systems biology field, involving the estimation of gene-gene...
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ALAN is a computational approach that interprets genomic findings in the context of tumor ecosystems
Gene behavior is governed by activity of other genes in an ecosystem as well as context-specific cues including cell type, microenvironment, and...
