Related papers: Shaping Epigenetic Memory via Genomic Bookmarking
In statistical genetics an important task involves building predictive models for the genotype-phenotype relationships and thus attribute a proportion of the total phenotypic variance to the variation in genotypes. Numerous models have been…
Cancer radiomics is an emerging discipline promising to elucidate lesion phenotypes and tumor heterogeneity through patterns of enhancement, texture, morphology, and shape. The prevailing technique for image texture analysis relies on the…
The chromatin fiber is a complex of DNA and specific proteins called histones forming the first structural level of organization of eukaryotic chromosomes. In tightly organized chromatin fibers, the short segments of naked DNA linking the…
Soft composite solids, comprising discrete inclusions embedded within a compliant matrix, are emerging candidates for engineering synthetic tissues and soft robotic materials. Current strategies for controlling their nonlinear mechanics,…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…
Genetic algorithms are a well-known example of bio-inspired heuristic methods. They mimic natural selection by modeling several operators such as mutation, crossover, and selection. Recent discoveries about Epigenetics regulation processes…
The identification of reproducible biological patterns from high-dimensional data is a bottleneck for understanding the biology of complex illnesses such as schizophrenia. To address this, we developed a biologically informed, multi-stage…
DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying…
The metazoan genome is replicated in precise cell lineage specific temporal order. However, the mechanism controlling this orchestrated process is poorly understood as no molecular mechanisms have been identified that actively regulate the…
Transcription is a fundamental cellular process, and the first step of gene expression. In human cells, it depends on the binding to chromatin of various proteins, including RNA polymerases and numerous transcription factors (TFs).…
A problem of substantial interest is to systematically map variation in chromatin structure to gene expression regulation across conditions, environments, or differentiated cell types. We developed and applied a quantitative framework for…
Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. CryoEM provides direct visualization of individual macromolecules sampling different conformational and compositional states.…
Combining genome-wide structural models with phenomenological data is at the forefront of efforts to understand the organizational principles regulating the human genome. Here, we use chromosome-chromosome contact data as knowledge-based…
Meiotic recombination is a fundamental feature of sexually reproducing species. It is often required for proper chromosome segregation and plays important role in adaptation and the maintenance of genetic diversity. The molecular mechanisms…
Timely up- or down-regulation of gene expression is crucial for cellular differentiation and function. While gene upregulation via transcriptional activators has been extensively investigated, gene silencing remains understudied, especially…
Stochastic neural networks such as Restricted Boltzmann Machines (RBMs) have been successfully used in applications ranging from speech recognition to image classification. Inference and learning in these algorithms use a Markov Chain Monte…
We note that most existing approaches for molecular graph generation fail to guarantee the intrinsic property of permutation invariance, resulting in unexpected bias in generative models. In this work, we propose GraphEBM to generate…
The three-dimensional organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state - accessibility and the amount of gene expression - of the chromatin. Recent advances in chromosome…
Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of…