基因组学
In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops…
Previous investigation of coding sequence lengths (CDS) in the bacterial circular chromosome revealed short range correlation in the series of these data. We have further analyzed the averaged periodograms of these series and we found that…
Dendritic cells are known to be activated by a wide range of microbial products, leading to cytokine production and increased levels of membrane markers such as major histocompatibility complex class II molecules. Such activated dendritic…
Despite decades of extensive research, the large-scale analysis of membrane proteins remains a difficult task. This is due to the fact that membrane proteins require a carefully balanced hydrophilic and lipophilic environment, which optimum…
Silver staining detects proteins after electrophoretic separation on polyacrylamide gels. Its main positive features are its excellent sensitivity (in the low nanogram range) and the use of very simple and cheap equipment and chemicals. The…
Protein solubilization for two-dimensional electrophoresis (2DE) has to break molecular interactions to separate the biological contents of the material of interest into isolated and intact polypeptides. This must be carried out in…
In this paper, we describe the context sensitivity problem encountered in partitioning a heterogeneous biological sequence into statistically homogeneous segments. After showing signatures of the problem in the bacterial genomes of…
In this paper, we extend a previously developed recursive entropic segmentation scheme for applications to biological sequences. Instead of Bernoulli chains, we model the statistically stationary segments in a biological sequence as Markov…
In the last ten years, the field of proteomics has expanded at a rapid rate. A range of exciting new technology has been developed and enthusiastically applied to an enormous variety of biological questions. However, the degree of…
the MIAPE Gel Electrophoresis (MIAPE-GE) guidelines specify the minimum information that should be provided when reporting the use of n-dimensional gel electrophoresis in a proteomics experiment. Developed through a joint effort between the…
Because of the outstanding ability of two-dimensional electrophoresis to separate complex mixtures of intact proteins, it would be advantageous to apply it to all types of proteins, including hydrophobic and membrane proteins.…
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…
Developmental transcriptional networks in plants and animals operate in both space and time. To understand these transcriptional networks it is essential to obtain whole-genome expression data at high spatiotemporal resolution. Substantial…
ChIP-seq, which combines chromatin immunoprecipitation with massively parallel short-read sequencing, can profile in vivo genome-wide transcription factor-DNA association with higher sensitivity, specificity and spatial resolution than…
Background: Hybridogenesis is a very interesting example of reproduction which seems to integrate the sexual and clonal processes in one system. In a case of frogs, described in the paper, two parental species - Rana lessonae and Rana…
Social networks exhibit strikingly systematic patterns across a wide range of human contexts. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric…
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly…
We describe the simulation method of modelling the population evolution using Monte Carlo based on the Penna model. Individuals in the populations are represented by their diploid genomes. Genes expressed after the minimum reproduction age…
Intragenomic recombination (crossover) is a very important evolutionary mechanism. The crossover events are not evenly distributed along the natural chromosomes. Monte Carlo simulations revealed that frequency of recombinations decides…
The quality and ease of proteomics analysis depends on the performance of the analytical tools used, and thus of the performances of the protein separation tools used to deconvolute complex protein samples. Among protein samples, membrane…