Related papers: A Field Approach to 3D Gene Expression Pattern Cha…

Identification and characterization of large protein complexes is a mainstay of biochemical toolboxes. Utilization of cross-linking chemicals can facilitate the capture and identification of transient or weak interactions of a transient…

We present Factor Fields, a novel framework for modeling and representing signals. Factor Fields decomposes a signal into a product of factors, each represented by a classical or neural field representation which operates on transformed…

Guidance of generative models is typically achieved by modifying the probability flow vector field through the addition of a guidance field. In this paper, we instead propose the Source-Guided Flow Matching (SGFM) framework, which modifies…

Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the graph-structured and geometric aspects of the…

Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…

In nature the three-dimensional structure of a protein is encoded in the corresponding gene. In this paper we describe a new method for encoding the three-dimensional structure of a protein into a binary sequence. The feature of the method…

Embryonic development leads to the reproducible and ordered appearance of complexity from egg to adult. The successive differentiation of different cell types, that elaborates this complexity, result from the activity of gene networks and…

In medical genetics, each genetic variant is evaluated as an independent entity regarding its clinical importance. However, in most complex diseases, variant combinations in specific gene networks, rather than the presence of a particular…

We investigate the problem of facial expression recognition using 3D data. Building from one of the most successful frameworks for facial analysis using exclusively 3D geometry, we extend the analysis from a curve-based representation into…

Deep generative models and neural operators have demonstrated significant potential for 3D aerodynamic inference. However, they often face inherent challenges in maintaining physical consistency and preserving high-frequency features,…

To ensure fast gene activation, Transcription Factors (TF) use a mechanism known as facilitated diffusion to find their DNA promoter site. Here we analyze such a process where a TF alternates between 3D and 1D diffusion. In the latter (TF…

Gene expression programming, a genotype/phenotype genetic algorithm (linear and ramified), is presented here for the first time as a new technique for the creation of computer programs. Gene expression programming uses character linear…

Directed evolution is an iterative laboratory process of designing proteins with improved function by iteratively synthesizing new protein variants and evaluating their desired property with expensive and time-consuming biochemical…

MOTIVATION: Left ventricular (LV) hypertrophy is a strong predictor of cardiovascular outcomes, but its genetic regulation remains largely unexplained. Conventional phenotyping relies on manual calculation of LV mass and wall thickness, but…

Many dynamical systems can be described in terms of structured flows combining source/sink behavior, cyclic dynamics, and topology-constrained transport. These features arise across a wide range of domains, including physical, engineered,…

Experimental characterization of blood flow in living organisms is crucial for understanding the development and function of cardiovascular systems, but there have been no techniques reported for snapshot imaging of thick samples in large…

3D Gaussian Splatting (3DGS) has begun incorporating rich information from 2D foundation models. However, most approaches rely on a bottom-up optimization process that treats raw 2D features as ground truth, incurring increased…

There is now a certain consensus that Transcription Factors (TFs) reach their target sites, where they regulate gene transcription, via a mechanism dubbed facilitated diffusion (FD). In FD, the TF cycles between events of 3D-diffusion in…

The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…

Transcription is regulated through binding factors to gene promoters to activate or repress expression, however, the mechanisms by which factors find targets remain unclear. Using single-molecule fluorescence microscopy, we determined in…