Bioimaging and Functional Genomics

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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 ...

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 ...

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 ...

Clustering in education, particularly in large-scale online environments like MOOCs, is essential for understanding and adapting to diverse student needs. However, the effectiveness of clustering depends on its interpretability, which becomes challenging w ...

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 ...

Microscopy is one of the essential tools to quantify and advance our understanding of living systems. Modern digital microscopes enable measurements at unprecedented spatiotemporal scale, so automated processing methods are required to complete tasks such ...

The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preservi ...

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 ...

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Cartilage homeostasis, crucial for musculoskeletal function, is orchestrated by interconnected biophysical cues. In healthy cartilage, repetitive compressive loading not only elicits a range of mechanical stimuli but also induces a gradual transient temper ...

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 ...

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 ...

Deep learning has revolutionized the field of computer vision, a success largely attributable to the growing size of models, datasets, and computational power. Simultaneously, a critical pain point arises as several computer vision applications are deploye ...

Background & Aims: Current therapies for the treatment of alcohol-related liver disease (ALD) have proven largely ineffective. Patients relapse and the disease progresses even after liver transplantation. Altered epigenetic mechanisms are characteristic of ...

Long-term consumption of lipid-rich foods can contribute to common metabolic diseases and systemic low-grade inflammation. However, dietary responses and the development of non-communicable diseases are shaped by genetic factors and gene-by-environment int ...

Urban proximity planning is foreseen as a solution to foster a “sustainable” city, including economic viability, environmental soundness and social inclusivity. This paper focuses on the inclusivity aspects by questioning the adoption of urban proximities: ...

Regulation of gene expression is a complex but highly guided process. While genomic technologies and computational approaches have allowed high-throughput mapping of cis-regulatory elements (CREs) and their interactions in 3D, their precise role in regulat ...

Cell segmentation is a critical step for quantitative single-cell analysis in microscopy images. Existing cell segmentation methods are often tailored to specific modalities or require manual interventions to specify hyper-parameters in different experimen ...

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

Bioimaging and Functional Genomics

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The dynamic genetic determinants of increased transcriptional divergence in spermatids

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

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

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

Interpret3C: Interpretable Student Clustering Through Individualized Feature Selection

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

Label-Efficient Deep Learning Methods for Event Detection, Object Segmentation and Cell Tracking in Biological Microscopy Images

Live-cell imaging powered by computation

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

Orchestrating chromosome conformation capture analysis with Bioconductor

Synergetic Support of Cartilage Homeostasis via Coupled Thermal-Hydrostatic Pressure Stimuli

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

Multimodal transcriptomic atlases of mouse spinal cord injury

Fast and Future: Towards Efficient Forecasting in Video Semantic Segmentation

Anti-miR-873-5p improves alcohol-related liver disease by enhancing hepatic deacetylation via SIRT1

Identifying genetic and dietary modulators of metabolic disorders using systems genetics

Planning urban proximities: An empirical analysis of how residential preferences conflict with the urban morphologies and residential practices

Chromatin modules and their implication in genomic organization and gene regulation

The multimodality cell segmentation challenge: toward universal solutions

Statistical learning quantifies transposable element-mediated cis-regulation