Related papers: Quantitative transcriptional analysis of aging C. …
Recent studies on the phenomenology of ageing in certain many-particle systems which are at a critical point of their non-equilibrium steady-states, are reviewed. Examples include the contact process, the parity-conserving…
Global expression analyses using microarray technologies are becoming more common in genomic research, therefore, new statistical challenges associated with combining information from multiple studies must be addressed. In this paper we…
The electrical resistance decay of a metallic granular packing has been measured as a function of time. This measurement gives information about the size of the conducting cluster formed by the well connected grains. Several regimes have…
Ancestral inference for branching processes in random environments involves determining the ancestor distribution parameters using the population sizes of descendant generations. In this paper, we introduce a new methodology for ancestral…
We investigate aging in glassy systems based on a simple model, where a point in configuration space performs thermally activated jumps between the minima of a random energy landscape. The model allows us to show explicitly a subaging…
Regulation of mRNA decay is a critical component of global cellular adaptation to changing environments. The corresponding changes in mRNA lifetimes can be coordinated with changes in mRNA transcription rates to fine-tune gene expression.…
This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…
Because biological processes can make different loci have different evolutionary histories, species tree estimation requires multiple loci from across the genome. While many processes can result in discord between gene trees and species…
Our work is motivated by and illustrated with application of association networks in computational biology, specifically in the context of gene/protein regulatory networks. Association networks represent systems of interacting elements,…
Ignoring the differences between countries, human reproductive and dispersal behaviors can be described by some standardized models, so whether there is a universal law of population growth hidden in the abundant and unstructured data from…
In this paper we present the application of a novel methodology to scientific citation and collaboration networks. This methodology is designed for understanding the governing dynamics of evolving networks and relies on an attachment…
A theory of aging based on the principles of the kinetics of chemical reactions and the rules of natural selection of organisms is proposed. The theory is based on a hypothesis that the biochemical processes in the organism can be described…
With the increasing amount of experimental data on gene expression and regulation, there is a growing need for quantitative models to describe the data and relate them to the different contexts. The thermodynamic models reviewed in the…
Inference of gene regulatory networks has been an active area of research for around 20 years, leading to the development of sophisticated inference algorithms based on a variety of assumptions and approaches. With the always increasing…
Cellular phenotypes are determined by the dynamical activity of networks of co-regulated genes. Elucidating such networks is crucial for the understanding of normal cell physiology as well as for the dissection of complex pathologic…
Motivation: ``Molecular signatures'' or ``gene-expression signatures'' are used to predict patients' characteristics using data from coexpressed genes. Signatures can enhance understanding about biological mechanisms and have diagnostic…
Epigenetic clocks based on DNA methylation have emerged as powerful tools for estimating biological age, with broad applications in aging research, age-related disease studies, and longevity science. Despite advances across machine learning…
The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…
The aggregation of microarray datasets originating from different studies is still a difficult open problem. Currently, best results are generally obtained by the so-called meta-analysis approach, which aggregates results from individual…
Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions -- lists of the most important players and the pairwise interactions between them.…