Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
Results
Showing 1 to 20 of 66 for “"Hi-C"”.
-
Modelling transcription factors diffusion in 3D using Hi-C data
… can upregulate or downregulate the rate at which transcription occurs. Their main mechanism of functioning is described by their ability to interact to DNA, namely, to find their target site and bind to it. In the search mechanism also known as facilitated diffusion, TFs can float freely …
-
Investigating mechanisms of genome folding by single-cell Hi-C
… years researchers have begun to reveal the hierarchy of mammalian DNA folding from the 10 nm fibre to the intact whole genome. One of the key approaches used is the single-cell Hi-C. My lab and I developed a single-cell Hi-C protocol that combines imaging and Hi-C processing on the same …
-
SCL: A Lattice-Based Approach to Infer Three-Dimensional Chromosome Structures from Single-Cell Hi-C Data
<p>In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.</p> …
-
The integration of fine-scale DNA-DNA associations by inclusion of Hi-C DNA cross-linking information into metagenomic community analysis
… lead to significant discoveries. Motivated by this, metagenomics eliminates the culturing dependency by directly sampling DNA from an environment; successfully shedding light on the once unseen majority. The technical limitations of present-day sequencing technologies have meant, however, that …
-
Polymer models of chromosomes
Studies of chromosomes have a long history. Since late XIX century, microscopy studies have revealed that chromosomal organization as seen by light microscopy is different among organisms, cell types, or stages of the cell cycle. However, the internal organization of chromosomes at scales below the …
-
Patterns and processes driving chromosome organization
In this thesis, we focus on different approaches to studying the organization of chromosomes with in the nucleus of cells. We employ both genomic analysis of chromosome interaction maps, and polymer simulations to answer various questions that are relevant to the field. The first two chapters of …
-
3D Chromatin Structure and Gene Regulation: Integrated Genome Structure, Transcriptomics and Epigenetics
… enhancer–promoter communication, but bulk Hi-C data obscure single-cell variability, while sparse single-cell Hi-C limits structural resolution. This dissertation develops computational approaches to reconstruct single-cell chromatin conformations, integrate them with functional genomics, …
-
Toward sequence-to-structure predictions of chromatin: Generative AI sheds light on genome organization
… environment complicate investigations into this system. This thesis alleviates these challenges and holds the potential to accelerate genome organization research by presenting several methodological advances. An efficient Hi-C inversion algorithm appears first. This technique extracts …
-
Single-molecule G-quadruplex visualisation in live cells and 3D chromatin
… enhancers, transcription factor and architectural protein binding sites. However, the roles of G4s in biology remains elusive. Whilst G4s can exist in a folded or unfolded state, methods are required to ensure that endogenous G4 detection does not perturb G4 folding dynamics. In this …
-
Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks
… from three-dimensional genome topology (based on Hi-C) and DNA sequence patterns. We used the experimental data from immortalised myelogenous leukemia (K562) and healthy lymphoblastoid (GM12878) cell lines to train the learning models and assess prediction performance. We have tested various SdA …
-
Modeling Genome Organization in Eukaryotic and Prokaryotic Cells Using Folding Determinant Interactions
… by nuclear landmarks and regulatory factors. In this thesis, I develop polymer-based chain-growth Monte Carlo frameworks to investigate genome folding in both mammalian and bacterial systems. For mammalian cells, I model how lamina-associated domains (LADs) and specific fold interactions (SFIs) …
-
Transcription Factor Binding Dynamics and Spatial Co-localization In Human Genome
… chromosome modifications; however, the relationship between genome spatial organisation and transcription factor binding is not well studied. Using the recently available high resolution Hi-C contact map of human GM12878 lymphoblastoid cells, we investigated computationally the genome-wide …
-
Linker Histone Medicated Regulation of Mitotic Chromosome Compaction and Individualization
… Here, I investigated the role of the linker histone variant H1.8 in regulating mitotic chromosome structure. I showed that H1.8 suppresses binding of condensins and topo II to mitotic chromatin in Xenopus egg extracts. Using an in vitro reconstitution system, I showed that H1.8 inhibits …
-
Integrative analysis of transcriptional activity and genome architecture changes upon viral infections
To study the interplay between spatial nuclear architecture and transcriptional activity during viral infections, I employed a genome-wide chromosome conformation capture approach (Hi-C) on infected murine and human cells and further enriched those libraries for genomic loci of interest and the …
-
ADHD Subtypes and the Convergent Validity of the Brief Three-Factor Approach and D-KEFS Color-Word Interference Test
… between subtypes of ADHD. The first aim of this study is to examine the convergent validity between the D-KEFS CWIT, a performance-based EF task, and the recently revised three-factor BRIEF. The second aim of this study is to examine whether there are differences between ADHD-I and ADHD-HI/C …
-
Investigating 3D genome organisation in Caenorhabditis elegans with Accessible Region Conformation Capture (ARC-C)
… in various organisms to study chromatin architecture. However, these methods have limitations: most of them are limited to restriction-fragment resolution and all of them, with the exception of Hi-C, only survey a pre-defined subset of the genome. I developed a variant of Hi-C, named …
-
Predicting genomic interactions using deep learning
… contribute to the regulation of gene expression. Hi-C and related approaches have enabled profiling of these interactions, though how the instructions for these interactions are encoded in the genome is still largely not understood. We develop a deep learning model, Deep3DGenome, to predict …
-
Identificazione e analisi funzionale di fattori regolatori dei geni globinici
… “Genome Wide Chromosome Conformation Capture” (Hi-C), followed by a novel technique for a selective enrichment at these target regions, to characterize whether they are involved in long range physical interactions able to modulate HBS1L-MYB and BCL11A expression. As a first step we optimized a …
-
Computational Methods for Integrating Microscopy with Chromatin Structures
… the distances between pairs of genomic loci, which gives indirect information about their positions. By applying these techniques to single cells, it has become possible to calculate a structure from the observed distance restraints. Through the prior constraints placed on the model, such as …
-
The interplay of global chromosomal organisation, promoter-enhancer interactions and transcription
All somatic cells within an organism contain the same genetic material, yet they display pronounced differences in function and morphology. Precise control of gene expression is of fundamental importance to allow cells to properly develop, maintain homeostasis, and respond to external stimuli. The …
Page 1 of 4