Related papers: Modeling DNA methylation dynamics with approaches …
We investigate the kinetics of the DNA melting transition using modified versions of the Peyrard-Dauxois-Bishop and Poland-Scheraga models that include long and short range interactions. Using Brownian dynamics and Monte Carlo simulations,…
Markov chains are simple yet powerful mathematical structures to model temporally dependent processes. They generally assume stationary data, i.e., fixed transition probabilities between observations/states. However, live, real-world…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
We propose a deep generative Markov State Model (DeepGenMSM) learning framework for inference of metastable dynamical systems and prediction of trajectories. After unsupervised training on time series data, the model contains (i) a…
We present a phenomenological dynamical model able to describe the stretching features of the curve of DNA length vs applied force. As concerns the chain, the model is based on the discrete wormlike chain model with elastic modifications,…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. The Waddington landscape posits that gene circuits in a cell form a potential landscape of different cell types, wherein cells follow attractors of…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…
An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically…
Bone metastasis analysis is a significant challenge in pathology and plays a critical role in determining patient quality of life and treatment strategies. The microenvironment and specific tissue structures are essential for pathologists…
Array comparative genomic hybridization(CGH) is a high resolution technique to assess DNA copy number variation. Identifying breakpoints where copy number changes will enhance the understanding of the pathogenesis of human diseases, such as…
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
Collective migration of eukaryotic cells is often guided by chemotaxis, and is critical in several biological processes, such as cancer metastasis, wound healing, and embryogenesis. Understanding collective chemotaxis has challenged…
Predictive modeling of the evolutionary dynamics of cancer is a challenge issue in computational cancer biology. In this paper, we propose a general mathematical model framework for the evolutionary dynamics of cancer with plasticity and…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
Cell lineage decisions occur in three-dimensional spatial patterns that are difficult to identify by eye. There is an ongoing effort to replicate such patterns using mathematical modeling. One approach uses long ranging cell-cell…
Inference of evolutionary trees and rates from biological sequences is commonly performed using continuous-time Markov models of character change. The Markov process evolves along an unknown tree while observations arise only from the tips…
Cellular nuclei recognition serves as a fundamental and essential step in the workflow of digital pathology. However, with disparate source organs and staining procedures among histology image clusters, the scanned tiles inherently conform…