Related papers: Evolutionary genomics of transposable elements in …
Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution,…
We propose a class of evolutionary models that involves an arbitrary exchangeable process as the breeding process and different selection schemes. In those models, a new genome is born according to the breeding process, and then a genome is…
In this paper we present the first mathematical analysis of the protein interaction network found in the yeast, S. cerevisiae. We show that, (a) the identified protein network display a characteristic scale-free topology that demonstrate…
An approximation to the ~4 Mbp basic genome shared by 32 strains of E. coli representing six evolutionary groups has been derived and analyzed computationally. A multiple-alignment of the 32 complete genome sequences was filtered to remove…
Promoters and enhancers are cis-regulatory elements (CREs), DNA sequences that bind transcription factor (TF) proteins to up- or down-regulate target genes. Decades-long efforts yielded TF-DNA interaction models that predict how strongly an…
DNA bending on length scales shorter than a persistence length plays an integral role in the translation of genetic information from DNA to cellular function. Quantitative experimental studies of these biological systems have led to a…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
The effort to identify genes with periodic expression during the cell cycle from genome-wide microarray time series data has been ongoing for a decade. However, the lack of rigorous modeling of periodic expression as well as the lack of a…
So far, stellar population studies have mainly focused on the evolution of single and binary stars. Recent observations show that triple and higher order multiple star systems are common, especially among massive stars. Introducing…
BACKGROUND: The uncoupling protein (UCP) genes belong to the superfamily of electron transport carriers of the mitochondrial inner membrane. Members of the uncoupling protein family are involved in thermogenesis and determining the…
Many stars do not live alone, but instead have one or more stellar companions. Observations show that these binaries, triples and higher-order multiples are common. Whereas the evolution of single stars and binaries have been studied…
Gene regulation in Eukaryotes is mainly effected through transcription factors binding to rather short recognition motifs generally located upstream of the coding region. We present a novel computational method to identify regulatory…
We propose a deep generative approach using latent temporal processes for modeling and holistically analyzing complex disease trajectories, with a particular focus on Systemic Sclerosis (SSc). We aim to learn temporal latent representations…
Invasive species are a growing threat to ecosystems, particularly in aquatic environments. The Trojan Y Chromosome (TYC) strategy is a promising biological method for reducing invasive populations by introducing genetically modified males…
Quantitative understanding of the principles regulating nucleosome occupancy on a genome-wide level is a central issue in eukaryotic genomics. Here, we address this question using budding yeast, Saccharomyces cerevisiae, as a model…
The goal of this dissertation is to study the sequence polymorphism in retrotransposable elements of Entamoeba histolytica. The Quasispecies theory, a concept of equilibrium (stationary), has been used to understand the behaviour of these…
Transposons are small, self-replicating DNA sequences found in every branch of life. Often, one transposon will parasitize another, forming a tiny intracellular ecosystem. In some species these ecosystems thrive, while in others they go…
We investigate the dynamical properties of the transcriptional regulation of gene expression in the yeast Saccharomyces Cerevisiae within the framework of a synchronously and deterministically updated Boolean network model. By means of a…
Let $n\geq 3,$ and let $Y$ be a simply connected, simple algebraic group of type $D_{n+1}$ over an algebraically closed field $K.$ Also let $X$ be the subgroup of type $B_n$ of $Y,$ embedded in the usual way. In this paper, we correct an…
We present molecular phylogenetic investigation of Thuidiaceae, especially on Thudium and Pelekium. Three chloroplast sequences (trnL-F, rps4, and atpB-rbcL) and one nuclear sequence (ITS) were analyzed. Data partitions were analyzed…