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The Wheat Transcriptome and Discovery of Functional Gene Networks
Gene expression patterns have been a widely applied source of information to start understanding gene function in multiple plant species. In wheat,...
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Large-scale foundation model on single-cell transcriptomics
Large pretrained models have become foundation models leading to breakthroughs in natural language processing and related fields. Develo**...
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Open-source curation of a pancreatic ductal adenocarcinoma gene expression analysis platform (pdacR) supports a two-subtype model
Pancreatic ductal adenocarcinoma (PDAC) is an aggressive disease for which potent therapies have limited efficacy. Several studies have described the...
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Celloscope: a probabilistic model for marker-gene-driven cell type deconvolution in spatial transcriptomics data
Spatial transcriptomics maps gene expression across tissues, posing the challenge of determining the spatial arrangement of different cell types....
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Context-aware transcript quantification from long-read RNA-seq data with Bambu
Most approaches to transcript quantification rely on fixed reference annotations; however, the transcriptome is dynamic and depending on the context,...
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The Theory of Gene Family Histories
Most genes are part of larger families of evolutionary-related genes. The history of gene families typically involves duplications and losses of...
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Tree ecophysiology in the context of climate change
Forest structure and function strongly depend on and concurrently influence environmental conditions. Tree performance is generally governed by its...
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PEATmoss: A Gene Expression Atlas for Bryophytes
PEATmoss is an interactive gene expression atlas for bryophytes, which originally unified Physcomitrium patens RNA-seq and microarray expression data...
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Biological Algorithm of Involution: Ontology of Gene Expressions
In the previous chapter, a topological model of genomic architecture using the formalism of the involuted manifold was discussed. It was suggested...
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Reduced selection for antibiotic resistance in community context is maintained despite pressure by additional antibiotics
Selection for antibiotic resistance at very low antibiotic concentrations has been demonstrated for individual antibiotics in single species...
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Map** the epigenomic landscape of human monocytes following innate immune activation reveals context-specific mechanisms driving endotoxin tolerance
BackgroundMonocytes are key mediators of innate immunity to infection, undergoing profound and dynamic changes in epigenetic state and immune...
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Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure
BackgroundNumerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including...
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Harissa: Stochastic Simulation and Inference of Gene Regulatory Networks Based on Transcriptional Bursting
Gene regulatory networks, as a powerful abstraction for describing complex biological interactions between genes through their expression products...
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The Gene as a Natural Kind
What is a gene? Does it represent a natural kind, or is it just a tool for genomics? A clear answer to these questions has been challenged by...
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Gene Expression Regulation in Plant Abiotic Stress Response
This chapter extensively explores the molecular mechanisms governing gene expression in plants facing abiotic stresses, with a specific focus on...
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Dictys: dynamic gene regulatory network dissects developmental continuum with single-cell multiomics
Gene regulatory networks (GRNs) are key determinants of cell function and identity and are dynamically rewired during development and disease....
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Model-Based Design of Synthetic Antisense RNA for Predictable Gene Repression
Our enhanced understanding of RNA folding and function has increased the use of small RNA regulators. Among these RNA regulators, synthetic antisense...
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Ocean to Tree: Leveraging Single-Molecule RNA-Seq to Repair Genome Gene Models and Improve Phylogenomic Analysis of Gene and Species Evolution
Understanding gene evolution across genomes and organisms, including ctenophores, can provide unexpected biological insights. It enables powerful...
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The art of modeling gene regulatory circuits
The amazing complexity of gene regulatory circuits, and biological systems in general, makes mathematical modeling an essential tool to frame and...
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Investigating Pseudomonas aeruginosa Gene Function During Pathogenesis Using Mobile-CRISPRi
CRISPR interference (CRISPRi) is a robust gene silencing technique that is ideal for targeting essential and conditionally essential (CE) genes....