Related papers: Morphologically Intelligent Perturbation Predictio…
The process of morphogenesis is an evolution of the shape of an organism together with the differentiation of its parts. This process encompasses numerous biological processes ranging from embryogenesis to regeneration following crisis such…
Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by…
Cell deformability is an essential determinant for tissue-scale mechanical nature, such as fluidity and rigidity, and is thus crucial for understanding tissue homeostasis and stable developmental processes. However, numerical simulations…
Morphological development into evolutionary patterns under structural instability is ubiquitous in living systems and often of vital importance for engineering structures. Here we propose a data-driven approach to understand and predict…
Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot…
Virtual cell modeling predicts molecular state changes under genetic perturbations in silico, which is essential for biological mechanism studies. However, existing approaches suffer from unconstrained reasoning, uninterpretable…
Predicting the effects of chemical and genetic perturbations on quantitative cell states is a central challenge in computational biology, molecular medicine and drug discovery. Recent work has leveraged large-scale single-cell data and…
Simulating in silico cellular responses to interventions is a promising direction to accelerate high-content image-based assays, critical for advancing drug discovery and gene editing. To support this, we introduce MorphGen, a…
Cellular response to a perturbation is the result of a dynamic system of biological variables linked in a complex network. A major challenge in drug and disease studies is identifying the key factors of a biological network that are…
AlphaFold 3 represents a transformative advancement in computational biology, enhancing protein structure prediction through novel multi-scale transformer architectures, biologically informed cross-attention mechanisms, and geometry-aware…
Biological systems can form complex three-dimensional structures through the collective behavior of agents that share a common update rule and operate without central control. How such distributed control gives rise to precise global…
We present a new experimental-computational technology of inferring network models that predict the response of cells to perturbations and that may be useful in the design of combinatorial therapy against cancer. The experiments are…
The living body is composed of innumerable fine and complex structures and although these structures have been studied in the past, a vast amount of information pertaining to them still remains unknown. When attempting to observe these…
Single-cell perturbation modeling is fundamental for understanding and predicting cellular responses to genetic perturbations. However, existing approaches, from causal representation learning to foundation models, often struggle with an…
Morphological profiling is a valuable tool in phenotypic drug discovery. The advent of high-throughput automated imaging has enabled the capturing of a wide range of morphological features of cells or organisms in response to perturbations…
Dynamical systems in the life sciences are often composed of complex mixtures of overlapping behavioral regimes. Cellular subpopulations may shift from cycling to equilibrium dynamics or branch towards different developmental fates. The…
Deep learning has revolutionized medical and biological imaging, particularly in segmentation tasks. However, segmenting biological cells remains challenging due to the high variability and complexity of cell shapes. Addressing this…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
Microelectronic morphogenesis is the creation and maintenance of complex functional structures by microelectronic information within shape-changing materials. Only recently has in-built information technology begun to be used to reshape…
The phase field model can accurately simulate the evolution of microstructures with complex morphologies, and it has been widely used for cell modeling in the last two decades. However, compared to other cellular models such as the…