A5066873210- Protein Structure and Dynamics
- Enzyme Structure and Function
- Microtubule and mitosis dynamics
- Wnt/β-catenin signaling in development and cancer
- Cellular Mechanics and Interactions
- RNA and protein synthesis mechanisms
- Advanced Fluorescence Microscopy Techniques
- CRISPR and Genetic Engineering
- Bioinformatics and Genomic Networks
- Microbial Metabolic Engineering and Bioproduction
- Developmental Biology and Gene Regulation
- Genomics and Rare Diseases
- Single-cell and spatial transcriptomics
- Genomics and Phylogenetic Studies
- Biomedical and Engineering Education
- Click Chemistry and Applications
- Advanced Electron Microscopy Techniques and Applications
- Planarian Biology and Electrostimulation
- Mass Spectrometry Techniques and Applications
- Bacterial Genetics and Biotechnology
- Congenital heart defects research
- Axon Guidance and Neuronal Signaling
- Genetics, Bioinformatics, and Biomedical Research
- Modular Robots and Swarm Intelligence
- Tissue Engineering and Regenerative Medicine
The University of Texas at Dallas
2021-2023
Karlsruhe Institute of Technology
2013-2020
Paracrine Wnt/β-catenin signalling is important during developmental processes, tissue regeneration and stem cell regulation. Wnt proteins are morphogens, which form concentration gradients across responsive tissues. Little known about the transport mechanism for these lipid-modified in vertebrates. Here we show that Wnt8a transported on actin-based filopodia to contact responding cells activate neural plate formation zebrafish. Cdc42/N-Wasp regulates of Wnt-positive filopodia. Enhanced...
Abstract Variational autoencoders are unsupervised learning models with generative capabilities, when applied to protein data, they classify sequences by phylogeny and generate de novo which preserve statistical properties of composition. While previous studies focus on clustering features, here, we evaluate the underlying latent manifold in sequence information is embedded. To investigate manifold, utilize direct coupling analysis a Potts Hamiltonian model construct landscape. We showcase...
Fully understanding biomolecular function requires detailed insight into the systems’ structural dynamics. Powerful experimental techniques such as single molecule Förster Resonance Energy Transfer (FRET) provide access to dynamic information yet have be carefully interpreted. Molecular simulations can complement these experiments but typically face limits in accessing slow time scales and large or unstructured systems. Here, we introduce a coarse-grained simulation technique that tackles...
During embryogenesis, morphogens form a concentration gradient in responsive tissue, which is then translated into spatial cellular pattern. The mechanisms by spread through tissue to establish such morphogenetic field remain elusive. Here, we investigate mutually complementary simulations and vivo experiments how Wnt morphogen transport cytonemes differs from typically assumed diffusion-based for patterning of highly dynamic as the neural plate zebrafish. Stochasticity strongly influences...
Abstract Motivation: Molecular dynamics simulations provide detailed insights into the structure and function of biomolecular systems. Thus, they complement experimental measurements by giving access to experimentally inaccessible regimes. Among different molecular techniques, native structure-based models (SBMs) are based on energy landscape theory principle minimal frustration. Typically used in protein RNA folding simulations, coarse-grain system and/or simplify Hamiltonian resulting...
Abstract The 2013 Nobel Prize in Chemistry highlights how crucial computer simulations have become for many scientific and engineering fields. Nowadays, progress is not only driven by the interplay of new experimental measurements increasingly sophisticated theoretical frameworks, but also an incredible toolbox complex computational models meeting ubiquitously available computing power data storage facilities. Quantum mechanical (QM) calculations can be condensed into molecular mechanics...
Abstract The notochord defines the axial structure of all vertebrates during development. Notogenesis is a result major cell reorganization in mesoderm, convergence and extension cells. However, it currently not fully understood how these processes act together coordinated way formation. prechordal plate an actively migrating population central mesoderm anterior to trailing notochordal We show that cells express Protocadherin 18a (Pcdh18a), member cadherin superfamily. find Pcdh18a-mediated...
Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding ever-increasing power of high performance computers current MD face several challenges: fastest movements require time steps a few femtoseconds which are small compared to relevant timescales milliseconds or even seconds for large conformational motions. At same time, scalability number cores is limited mostly due long-range interactions. An appealing alternative...
The full characterization of protein folding is a remarkable long-standing challenge both for experiment and simulation. Working towards complete understanding this process, one needs to cover the diversity existing folds identify general principles driving process. Here, we want understand quantify in routes large representative set topologies covering range from all alpha helical beta barrels guided by key question: Does majority observed contribute process or only particular route? We...
Two-component systems (TCS) are signaling machinery that consist of a histidine kinases (HK) and response regulator (RR). When an environmental change is detected, the HK phosphorylates its cognate While interactions were considered orthogonal, experimental evidence shows prevalence crosstalk between non-cognate HK–RR pairs. Currently, have been demonstrated for TCS proteins in limited number organisms. By providing specificity predictions across entire networks large variety organisms,...
<ns3:p>In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics Structural Variation, Pan-genomes, and SARS-CoV-2 research. </ns3:p><ns3:p> The overarching focus was to assess current status field identify remaining challenges. Furthermore, how combine strengths interests drive research method development forward. Over four days, eight groups each designed developed new...
Native structure based models are a broadly used technique in bio molecular simulation allowing understanding of complex processes the living cell involving macromolecules. Based on energy landscape theory and principle minimal frustration, these find wide application simulating biological as diverse protein or RNA folding assembly, conformational transitions associated with allostery, to prediction. To allow rapid adoption by scientists, especially experimentalists, having no background...
Abstract The notochord defines the axial structure of all vertebrates during development. Notogenesis is a result major cell reorganization in mesoderm, convergence and extension cells. However, it currently not known how these processes act together coordinated way formation. Analysing tissue flow, we determined displacement mesoderm identified, relative to ectoderm, an actively-migrating tip population group trailing notochordal plate Molecularly, cells express Protocadherin18a, member...
<ns3:p>In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics Structural Variation, Pan-genomes, and SARS-CoV-2 research. </ns3:p><ns3:p> The overarching focus was to assess current status field identify remaining challenges. Furthermore, how combine strengths interests drive research method development forward. Over four days, eight groups each designed developed new...
Computer simulations are advancing to become the third pillar of science besides theory and experiment. In this work, I want showcase two interdisciplinary projects in which computer greatly enhanced understanding novel experimental results. Both these works cover events during early developmental stages zebrafish Danio rerio, (Hamilton, 1822) elucidate brain development. The first work clarifies whether or not a short-range transport method via specialized filopodia is able form necessary...