Related papers: Probabilistic analysis of the human transcriptome …
This study analyzes rates and ways of data sharing regarding mitochondrial, Y chromosomal and autosomal polymorphisms in a total of 162 papers on human ancient DNA published between 1988 and 2013. For the most part, data are available in…
A fundamental aspect of biological information processing is the ubiquity of sequence-function relationships -- functions that map the sequence of DNA, RNA, or protein to a biochemically relevant activity. Most sequence-function…
In recent years, substantial advancements have been achieved in understanding the diversity of the human virome and its intricate roles in human health and diseases. Despite this progress, the field of human virome research remains nascent,…
A gene expression compendium is a heterogeneous collection of gene expression experiments assembled from data collected for diverse purposes. The widely varied experimental conditions and genetic backgrounds across samples creates a…
Populations of heterogeneous cells play an important role in many biological systems. In this paper we consider systems where each cell can be modelled by an ordinary differential equation. To account for heterogeneity, parameter values are…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
Proteomics will celebrate its 20th year in 2014. In this relatively short period of time, it has invaded most areas of biology and its use will probably continue to spread in the future. These two decades have seen a considerable increase…
The information contained in the genome is insufficient for the control of organism development. Thus, the whereabouts of actual operational directives and workings of the genome remain obscure. In this work, it is suggested that the genome…
Stochastic Process Model has many applications in analysis of longitudinal biodemographic data. Such data contain various physiological variables (sometimes known as covariates). It also can potentially contain genetic information available…
We utilized abundant transcriptomic data for the primary classes of brain cancers to study the feasibility of separating all of these diseases simultaneously based on molecular data alone. These signatures were based on a new method…
Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Just as physicists strive to develop a TOE (theory of everything), which explains and unifies the physical laws of the universe, the life-scientist wishes to uncover the TOE as it relates to cellular systems. This can only be achieved with…
Introduction: Even in effectively conducted randomised trials, the probability of a successful study remains relatively low. With recent advances in the next-generation sequencing technologies, there is a rapidly growing number of…
Natural Language Processing (NLP) has transformed various fields beyond linguistics by applying techniques originally developed for human language to the analysis of biological sequences. This review explores the application of NLP methods…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown.…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
A central challenge in the study of protein evolution is the identification of historic amino acid sequence changes responsible for creating novel functions observed in present-day proteins. To address this problem, we developed a new…
This talk will review a little over a decade's research on applying certain stochastic models to biological sequence analysis. The models themselves have a longer history, going back over 30 years, although many novel variants have arisen…
Proteins are sequences of amino acids that serve as the basic building blocks of living organisms. Despite rapidly growing databases documenting structural and functional information for various protein sequences, our understanding of…