Biomolecular condensates are a class of important biomaterials inside the cell that have unique sequence-defined mechanical properties. This project will examine mitochondrial nucleoid biomolecular condensates, which are formed from mitochondrial DNA (mtDNA) and packaging protein TFAM. Very little is known about how the mechanical properties of the mitochondrial nucleoids are encoded by the TFAM and mtDNA sequences, though this new knowledge could shed light on how mitochondria biophysically regulate (...)
Life Sciences Alliance SURF
Engn - Chemical & Biochemical Engineering
Biochemistry, Biomedical Engineering, Chemical Engineering, (...)
"The organization of the cell's genome in three dimensions is fundamental to different cellular functions. The nucleus is divided into distinct chromosomal territories and each chromsome is segregated into active or repressed regions. While the utility of organizing the chormsome remains under investigation, it is known that multiple mechanisms orchestrate DNA organization. Crucially, Topologically Associating Domains (TADs) serve as key structural units, forming DNA loops that physically segregate (...)
Life Sciences Alliance SURF
SAS - DLS - Cell Biology and Neuroscience
Cell & Molecular Biology, Genomics , Life Sciences
"Here, we aim to develop surrogate deep learning models to replace finite element (FE) modeling and optimization for characterizing the mechanical response of soft tissues such as brain white matter. The forward problem of predicting the evolution of stress for a given tissue geometry—typically performed using FE modeling—is replaced by a recurrent neural network (RNN) that learns the structure–property relationship between tissue microstructure, material properties and stress-strain behavior. The (...)
Life Sciences Alliance SURF
Engn - Mechanical & Aerospace Engineering
Artificial Intelligence, Data Science, Life Sciences
This research project introduces a Unified Computational Framework to integrate cell morphology with single-cell transcriptomics. The proposal employs deep learning to perform morphometrics, extracting fine-grained, structural features (shape, size, morphology) of individual cochlear cells from immunofluorescent images. This structural information is then unified with corresponding single-cell genomics data, to reveal the molecular identity of the same cell types through their gene expression profiles. (...)
Life Sciences Alliance SURF
SAS - DLS - Cell Biology and Neuroscience
Artificial Intelligence, Data Science, Life Sciences
"Evolutionary biology has traditionally been a retrospective discipline, focusing on the history of life on Earth. However, the rapid evolution of many extant organisms, such as microbial pathogens in response to drugs or ecosystems in response to climate change, has motivated the need to make evolution a predictive, quantitative science. Can we predict the future evolution of these organisms?
Before making evolutionary predictions, we first must understand how predictable evolution even is. (...)
Life Sciences Alliance SURF
SAS - DLS - Molecular Biology & Biochemistry
Biochemistry, Cell & Molecular Biology, Artificial (...)
