Related papers: Genome organization: experiments and modelling
Introduction to the Special Issue: Genome-Wide Association Studies
This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene…
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the…
We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of…
This unit describes strategies for studying the proteomes of organelles, which is one example of targeted proteomics. It relies heavily on previously published units dealing with organelle preparation, protein solubilization, and proteomics…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
This paper presents our computational methodology using Genetic Algorithms (GA) for exploring the nature of RNA editing. These models are constructed using several genetic editing characteristics that are gleaned from the RNA editing system…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
As computer scientists working in bioinformatics/computational biology, we often face the challenge of coming up with an algorithm to answer a biological question. This occurs in many areas, such as variant calling, alignment, and assembly.…
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is…
This is a position paper written as an introduction to the special volume on quantum algorithms I edited for the journal Mathematical Structures in Computer Science (Volume 20 - Special Issue 06 (Quantum Algorithms), 2010).
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…
Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range…
Since the completion of the human genome sequencing project in 2001, significant progress has been made in areas such as gene regulation editing and protein structure prediction. However, given the vast amount of genomic data, the segments…
There are many experimental data indicating the correlations of the changes in high level of organization of chromatin in human cells and changes in the state of the whole organism related to disease, state of tiredness or aging. In our…
The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study and of two algorithms for determining the presence of a particular (known) genome in this medium.…
In [N. A. Baas, Emergence, Hierarchies, and Hyper-structures, in C.G. Langton ed., Artificial Life III, Addison Wesley, 1994.] a general framework for the study of Emergence and hyper-structure was presented. This approach is mostly…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
Gene regulatory networks are powerful abstractions of biological systems. Since the advent of high-throughput measurement technologies in biology in the late 90s, reconstructing the structure of such networks has been a central…