Prioritization of cell types responsive to biological perturbations in single-cell data with Augur

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Spatial proteomics technologies have transformed our understanding of complex tissue architectures by enabling simultaneous analysis of multiple molecular markers and their spatial organization. The high dimensionality of these data, varying marker combina ...

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

Traditional cell cultures have long been fundamental to biological research, offering an alternative to animal models burdened by ethical constraints and procedural intricacies, often lacking relevance to human physiology and disease. Moreover, their inabi ...

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

The last two decades have seen the development of organoid models for many different tissues and organs. Organoids are three-dimensional organ-mimetics derived from stem or progenitor cells comprising various specialized cell types, resembling the architec ...

The adaptation of organisms to their environment depends on the innovative potential inherent to genetic variation. In complex organisms such as mammals, processes like development and immunity require tight gene regulation. Complex forms emerge more often ...

Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the epigenetic mechanisms underlying human cell diversity has been di ...

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

Objectives The endosymbiosis with Symbiodiniaceae is key to the ecological success of reef-building corals. However, climate change is threatening to destabilize this symbiosis on a global scale. Most studies looking into the response of corals to heat str ...

Peroxisomes are eukaryotic organelles that are essential for multiple metabolic pathways, including fatty acid oxidation, degradation of amino acids, and biosynthesis of ether lipids. Consequently, peroxisome dysfunction leads to pediatric-onset neurodegen ...

Breast cancer (BC) is the most diagnosed cancer and a leading cause of cancer-related mortality for women worldwide (Bray Bsc et al. 2024). It is a heterogeneous disease with 19 special histopathological subtypes and 5 molecular subtypes (Tavassoli and Dev ...

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Communication between the intestine and other organs such as the lungs, brain or bones is mediated by several metabolites, like short-chain fatty acids or bile acids, that relay information about nutritional and microbiota status. Bile acids are endogenous ...

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Magnetorheological (MR) valves attracted the interest of researchers across diverse fields, owing to the controllable nature of MR fluid. The use of MR fluid in valves enables fast response, energy efficiency, and robustness, while several studies designed ...

Cyclic GMP-AMP synthase (cGAS) senses aberrant DNA during infection, cancer and inflammatory disease, and initiates potent innate immune responses through the synthesis of 2 ' 3 '-cyclic GMP-AMP (cGAMP)1-7. The indiscriminate activity of cGAS towards DNA d ...

In the last decade, organoid technology has become a cornerstone in cancer research. Organoids are long-term primary cell cultures, usually of epithelial origin, grown in a three-dimensional (3D) protein matrix and a fully defined medium. Organoids can be ...

Redox homeostasis is a key factor in maintaining cellular function and health. The main determinant of the intracellular redox potential is ubiquitous glutathione (GSH) together with its oxidized dimer (GSSG). Importantly, both redox equilibrium and GSH ho ...

Prioritization of cell types responsive to biological perturbations in single-cell data with Augur

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Abstract B037: AI-powered virtual tissues from spatial proteomics for clinical diagnostics and biomedical discovery

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Accessible and highly observable gastrointestinal organoid model systems for studying host-pathogen interactions

Multimodal transcriptomic atlases of mouse spinal cord injury

Bioengineering functional organoid models across scales

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Gene expression of Pocillopora damicornis coral larvae in response to acidification and ocean warming

Fluorescent fatty acid conjugates for live cell imaging of peroxisomes

ER+ breast cancer in 3D scaffold ex vivo for transcriptomics-based functional drug screening and personalized medicine

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Characterization of the gut-bone marrow axis through bile acid signaling

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Modeling and experimental study of a miniaturized magnetorheological valve with high performance

The CRL5-SPSB3 ubiquitin ligase targets nuclear cGAS for degradation

Next-Generation Modeling of Cancer Using Organoids

HaloTag-Based Tools for Live-Cell Imaging and Elucidation of Organellar Redox Biology