Related papers: Deciphering regulation in eukaryotic cell: from se…
We propose a methodology for the identification of transcription factors involved in the deregulation of genes in tumoral cells. This strategy is based on the inference of a reference gene regulatory network that connects transcription…
Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…
This dissertation explores the application of machine learning in molecular biology, focusing on gene expression regulation and cellular behavior at the single-cell level. Using modern neural networks, the research addresses key challenges…
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…
The main goal of Systems Biology research is to reconstruct biological networks for its topological analysis so that reconstructed networks can be used for the identification of various kinds of disease. The availability of high-throughput…
Gene regulation is a complex process involving the role of several genomic elements which work in concert to drive spatio-temporal expression. The experimental characterization of gene regulatory elements is a very complex and…
Recent breakthroughs in cancer research have come via the up-and-coming field of pathway analysis. By applying statistical methods to prior known gene and protein regulatory information, pathway analysis provides a meaningful way to…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
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…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
One of the outstanding challenges in comparative genomics is to interpret the evolutionary importance of regulatory variation between species. Rigorous molecular evolution-based methods to infer evidence for natural selection from…
Deciphering how DNA sequence encodes gene regulation remains a central challenge in biology. Advances in machine learning and functional genomics have enabled sequence-to-function (seq2func) models that predict molecular regulatory readouts…
Modelling gene regulatory networks not only requires a thorough understanding of the biological system depicted but also the ability to accurately represent this system from a mathematical perspective. Throughout this chapter, we aim to…
Gene regulation involves a hierarchy of events that extend from specific protein-DNA interactions to the combinatorial assembly of nucleoprotein complexes. The effects of DNA sequence on these processes have typically been studied based…
We discuss two new approaches to extract relevant biological information on the Transcription Factors (and in particular to identify their binding sequences) from the statistical distribution of oligonucleotides in the upstream region of…
Models of transcriptional regulation that assume equilibrium binding of transcription factors have been very successful at predicting gene expression from sequence in bacteria. However, analogous equilibrium models do not perform as well in…
The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle…