Modeling and analysis of parts and devices of genetic regulation

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Genetically engineered mouse models (GEMMs) are instrumental for modelling local and systemic features of complex diseases, such as cancer. Non-invasive, longitudinal cell detection and monitoring in tumors, metastases and/or the micro-environment is param ...

Physics-informed neural networks (PINNs) have emerged as a powerful tool for solving differential equations by integrating physical laws into the learning process. This work leverages PINNs to simulate gravitational collapse, a critical phenomenon in astro ...

Social insects offer powerful models to investigate mechanisms of elaborate individual behaviors comprising a cooperative community. Workers of the leafcutter ant genus Atta are extreme examples of behavioral segregation among phenotypically distinct worke ...

Scientific Machine Learning (SciML) is a recently emerged research field which combines physics-based and data-driven models for the numerical approximation of differential problems. Physics-based models rely on the physical understanding of the problem at ...

Regulation of melanin-based pigmentation is complex, involving multiple genes. Because different genes can contribute to the same pigmentation phenotype, the genes identified in model organisms may not necessarily apply to wild species. In the barn owl (Ty ...

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 ...

Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

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 ...

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 ...

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 ...

The ability of cancer cells to change and adapt poses a critical challenge to identifying curative solutions. Tumor evolution has been extensively studied from a genetic perspective, to guide clinicians in selecting the most appropriate therapeutic option ...

Recently, Pham et al. used an array of model systems to uncover a role for the enzyme methionine adenosyltransferase (MAT) -1A, which is mainly expressed in liver, in both sensing formaldehyde and regulating transcriptional responses that protect against i ...

Genes implicated in translation control have been associated with autism spectrum disorders (ASDs). However, some important genetic causes of autism, including the 16p11.2 microdeletion, bear no obvious connection to translation. Here, we use proteomics, g ...

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 ...

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 ...

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

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 ...

DNA damage signaling following DNA double-strand breaks (DSBs) involves numerous regulating proteins, which dynamically recognize ('read') and alter ('write' or 'erase') histone post-translational modifications (PTMs). Among these PTMs, the ubiquitin syste ...

vanishing viscosity, networks. This work has received funding from the Alexander von Humboldt-Professorship program, the Transregio 154 Project "Mathematical Modelling, Simulation and Optimization Using the Example of Gas Networks" of the DFG, the grant PI ...

Modeling and analysis of parts and devices of genetic regulation

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A new effLuc/Kate dual reporter allele for tumor imaging in mice

SPINN: Advancing Cosmological Simulations of Fuzzy Dark Matter with Physics Informed Neural Networks

Neuropeptides specify and reprogram division of labor in the leafcutter ant Atta cephalotes

Combining physics-based and data-driven models: advancing the frontiers of research with scientific machine learning

Melanin and Neurotransmitter Signalling Genes Are Differentially Co-Expressed in Growing Feathers of White and Rufous Barn Owls

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Resolving bacterial cell biology: from replisome dynamics to cell wall synthesis

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

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

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

Nongenetic evolution of the tumor: from challenges to new therapeutic opportunities

Formaldehyde regulates one-carbon metabolism and epigenetics

The autism susceptibility kinase, TAOK2, phosphorylates eEF2 and modulates translation

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

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

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

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

A chemical biology approach to decipher chromatin ubiquitylation by RNF168

CONTROL OF HYPERBOLIC AND PARABOLIC EQUATIONS ON NETWORKS AND SINGULAR LIMITS