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Articles 1 - 30 of 269
Full-Text Articles in Genomics
Model-Based Deep Autoencoders For Clustering Single-Cell Rna Sequencing Data With Side Information, Xiang Lin
Model-Based Deep Autoencoders For Clustering Single-Cell Rna Sequencing Data With Side Information, Xiang Lin
Dissertations
Clustering analysis has been conducted extensively in single-cell RNA sequencing (scRNA-seq) studies. scRNA-seq can profile tens of thousands of genes' activities within a single cell. Thousands or tens of thousands of cells can be captured simultaneously in a typical scRNA-seq experiment. Biologists would like to cluster these cells for exploring and elucidating cell types or subtypes. Numerous methods have been designed for clustering scRNA-seq data. Yet, single-cell technologies develop so fast in the past few years that those existing methods do not catch up with these rapid changes and fail to fully fulfil their potential. For instance, besides profiling transcription …
Dna Methylation-Based Epigenetic Biomarkers In Cell-Type Deconvolution And Tumor Tissue Of Origin Identification, Ze Zhang
Dartmouth College Ph.D Dissertations
DNA methylation is an epigenetic modification that regulates gene expression and is essential to establishing and preserving cellular identity. Genome-wide DNA methylation arrays provide a standardized and cost-effective approach to measuring DNA methylation. When combined with a cell-type reference library, DNA methylation measures allow the assessment of underlying cell-type proportions in heterogeneous mixtures. This approach, known as DNA methylation deconvolution or methylation cytometry, offers a standardized and cost-effective method for evaluating cell-type proportions. While this approach has succeeded in discerning cell types in various human tissues like blood, brain, tumors, skin, breast, and buccal swabs, the existing methods have major …
Investigating The Impact Of Transcription On Mutation Rates, Sarah Patterson
Investigating The Impact Of Transcription On Mutation Rates, Sarah Patterson
Theses and Dissertations
tRNA genes are highly transcribed and perform one of the most fundamental cellular functions. Although a universal pattern observed across all three domains of life is that highly transcribed genes tend to evolve slowly, tRNA genes have been shown previously to evolve rapidly. This rapid sequence evolution could result from relaxed selection, increased mutation rate, or a combination of both. Here, we use mutation-accumulation line sequencing data to show that tRNA genes accumulate more mutations than other gene types. Our results indicate that this elevated mutation rate is a consequence of both elevated transcription-associated mutagenesis and a lack of transcription-coupled …
The Discovery Of A Novel Bacteria From A Large Co-Assembly Of Metagenomes, Matthew Finkelberg
The Discovery Of A Novel Bacteria From A Large Co-Assembly Of Metagenomes, Matthew Finkelberg
Masters Theses
In the summer of 2022, a co-assembly of metagenome was created using the microbes found at Barres Woods in Harvard Forest. 14 samples were taken, and sample was split into the organic and mineral layer, which totals 28 Bulk MAGs. Within this Co-assembly, 4 different genomes were found which were designated with the phylum of FCPU426. Three of which were considered medium quality and one being assigned high quality. The novel phyla first appeared in NCBI and GTDB databases in June 2018. The name FCPU426 dates to 2010 and was named based on the 16s amplicon sequencing.
The novel phylum …
The Detection Of Putative Recessive Lethal Haplotypes In Irish Sheep Populations, Rory Mcauley
The Detection Of Putative Recessive Lethal Haplotypes In Irish Sheep Populations, Rory Mcauley
ORBioM (Open Research BioSciences Meeting)
In livestock populations, recessive lethal alleles are a known contributor to poor reproductive performance due to embryonic death in homozygous individuals. Despite their lethal effect in the recessive form, these alleles may be maintained at high frequencies among carrier animals because of their positive pleiotropic effects on economically important traits. Although several such recessive alleles have been identified in cattle and pig populations, limited studies have been completed in sheep, and none within Irish sheep populations. Genotype data for 69,034 animals from five major Irish sheep breeds genotyped on a variety of panels was available for this study. Only animals …
Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone
Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone
Complex Biosystems PhD Program: Dissertations
The task of gene prediction has been largely stagnant in algorithmic improvements compared to when algorithms were first developed for predicting genes thirty years ago. Rather than iteratively improving the underlying algorithms in gene prediction tools by utilizing better performing models, most current approaches update existing tools through incorporating increasing amounts of extrinsic data to improve gene prediction performance. The traditional method of predicting genes is done using Hidden Markov Models (HMMs). These HMMs are constrained by having strict assumptions made about the independence of genes that do not always hold true. To address this, a Convolutional Neural Network (CNN) …
Tracing Evolution Of Gene Transfer Agents Using Comparative Genomics, Roman Kogay
Tracing Evolution Of Gene Transfer Agents Using Comparative Genomics, Roman Kogay
Dartmouth College Ph.D Dissertations
The accumulating evidence suggest that viruses and their components can be domesticated by their hosts, equipping them with convenient molecular toolkits for various functions. One of such domesticated system is Gene Transfer Agents (GTAs) that are produced by some bacteria and archaea. GTAs morphologically resemble small phage-like particles and contain random fragments of their host genome. They are produced only by a small fraction of the microbial population and are released through a lysis of the host cell. Bioinformatic analyses suggest that GTAs are especially abundant in the taxonomic class of Alphaproteobacteria, where they are vertically inherited and evolve …
Genome-Scale Methylation Analysis In Blood And Tumor Identifies Immune Profile, Age Acceleration, And Dna Methylation Alterations Associated With Bladder Cancer Outcomes, Ji-Qing Chen
Dartmouth College Ph.D Dissertations
Bladder cancer patients receive frequent screening due to the high tumor recurrence rate (more than 60%). Nowadays, the conventional monitoring method relies on cystoscopy which is highly invasive and increases patient morbidity and burden to the health care system with frequent follow-up. As a result, it is urgent to explore novel markers related to the outcomes of bladder cancer. Immune profiles have been associated with cancer outcomes and may have the potential to be biomarkers for outcomes management. However, little work has been conducted to investigate the associations of immune cell profiles with bladder cancer outcomes. Here, I utilized the …
Integrating Omim And Intact Data For The Analysis Of Gene-Phenotype Interactions In Complex Diseases: A Linux-Based Computational Tool For Network Analysis, Devin Keane
All Theses
The field of genetics is constantly evolving. New advances in bioinformatics and computational approaches are leading to exciting new developments in our ability to treat and prevent diseases. Computational genetics provides valuable insights into the complex mechanisms and layers of biological communication that shape an organism's phenotype. Understanding these mechanisms is critical to advancing human health.
The study of diseases in genetics requires a comprehensive understanding of the interactions between various biological processes, including gene expression, protein synthesis, RNA, metabolism, and cell-cell communication. To effectively address the root causes of such diseases, multi-disciplinary approaches that integrate information from different levels …
Reconstructing Mutational Lineages In Breast Cancer By Multi-Patient-Targeted Single Cell Dna Sequencing, Jake Leighton
Reconstructing Mutational Lineages In Breast Cancer By Multi-Patient-Targeted Single Cell Dna Sequencing, Jake Leighton
Dissertations & Theses (Open Access)
Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer with high rates of metastasis and recurrence, where TNBC patients have a poor 5-year survival and ~50% are non-responsive to chemotherapy. Aneuploidy is a cancer hallmark that is pervasive in over 90% of breast cancer patients and is indicative of complex genomic rearrangements that are acquired during tumor initiation. Although copy number aberrations have been extensively studied in relation to aneuploidy and TNBC initiation, little is currently known regarding the timing and impact of single nucleotide variants (SNVs) contributing to these early transformative genomic events. Paramount to novel …
Clustering And Analysis Of G Quadruplex Sequences., Aryan Neupane
Clustering And Analysis Of G Quadruplex Sequences., Aryan Neupane
Electronic Theses and Dissertations
G quadruplex structures are secondary structures located throughout the genome of various organisms with involvement in regulatory functions in different transcription, translation, genome stability, epigenetic regulation as well as cell division. Even with the diverse acknowledgement of G4 structure in vivo, there are no current search tools for G quadruplexes based on already identified G quadruplexes and identified families across different genomes based on sequence diversity. Construction of families of G4 sequences and identifying their polymorphisms within disease and disorders will lead to a better understanding of their functional roles and will further research into the biophysical modeling of interactions …
Effects Of Cyanobacteria Harmful Algal Blooms On The Microbial Community Within Lake Okeechobee, Fl, Usa, Paisley S. Samuel
Effects Of Cyanobacteria Harmful Algal Blooms On The Microbial Community Within Lake Okeechobee, Fl, Usa, Paisley S. Samuel
All HCAS Student Capstones, Theses, and Dissertations
The Lake Okeechobee (Lake O) watershed is a Floridian freshwater ecosystem that has been affected by the increased frequency and intensity of harmful cyanobacterial bloom (cyanoHAB) events occurring over recent decades. Lake O has several ecological and economic purposes such as providing habitats for various organisms and providing drinking water to urban communities surrounding the lake. Toxic cyanoHAB events are posing a threat to the ecosystem and economy of the lake due to the degradation of water quality. This study investigates how the microbial community structure within Lake O is affected by annual cyanobacterial harmful algal blooms over several years …
Soil Microbial Community Composition Of White Oak Mountain, Tennessee, Matthew Gano, Timothy D. Trott
Soil Microbial Community Composition Of White Oak Mountain, Tennessee, Matthew Gano, Timothy D. Trott
Research in Biology
Abstract - Soil microbial communities are responsible for nutrient cycling in terrestrial ecosystems and have symbiotic and parasitic relationships with the plant community. However, little is known about the factors that determine the soil microbial community composition. In this study we examined how spring wildflower diversity and geographical factors influence the soil microbial community composition of the second growth oak hickory forests of White Oak Mountain in Southeast Tennessee. The characterization of the soil microbial community was completed with 16S/18S/ITS rDNA amplicon sequencing of total DNA extracted from soil samples that were normalized for each sample plot. Here we characterize …
The Genomics Of Autism-Related Genes Il1rapl1 And Il1rapl2: Insights Into Their Cortical Distribution, Cell-Type Specificity, And Developmental Trajectories, Jacob Weaver
MUSC Theses and Dissertations
Neuropsychiatric disorders have a significant impact on modern society. These disorders affect a large percentage of the population: schizophrenia has a world-wide prevalence of 1% and autism spectrum disorders (ASD) affects 1 in 59 school-aged children in the US. There is substantial evidence that most neuropsychiatric disorders have a genetic component. Thus, with the advent of high throughput sequencing much effort has gone into identifying genetic variants associated with these disorders. The emerging picture from these studies is a complex one where hundreds of genes with small effects interact with a varied landscape of common variants to result in disease. …
A Standardized Pipeline For Isolation And Assembly Of Genomes From Symbiotic Bacteria In Whole Louse Genomic Sequence Data., Mohammad Mikail I. Bala
A Standardized Pipeline For Isolation And Assembly Of Genomes From Symbiotic Bacteria In Whole Louse Genomic Sequence Data., Mohammad Mikail I. Bala
Theses and Dissertations
Many insects are known to harbour intracellular and heritable bacteria (endosymbionts), which provide their hosts with adaptive traits. Whole insect gDNA shotgun sequencing projects often sequence the genome of endosymbiont, in addition to the insect’s genome. There are approximately 600 whole genome shotgun libraries from insects available on the public repository (NCBI), which can be mined to obtain endosymbiont genomes. The assembly and annotation of endosymbiont genomes can contribute towards the exploration of their role as obligate symbiotic partners. However, de novo assembly of an endosymbiont genome, continues to be challenging, when the host and/or enteric bacterial gDNA is present …
Cell Signaling And Stress Response In The Yeast Saccharomyces Cerevisiae: A Study Of Snf1, Scott E. Arbet Ii
Cell Signaling And Stress Response In The Yeast Saccharomyces Cerevisiae: A Study Of Snf1, Scott E. Arbet Ii
Graduate Theses, Dissertations, and Problem Reports
Saccharomyces cerevisiae are yeast that are unicellular eukaryotic organisms that are well studied as a model organism for understanding fundamental cellular processes. The ability of yeast to sense nutrient availability is crucial for their survival, growth, and reproduction. Yeast cells use various mechanisms to sense and respond to nutrient availability, including transporter-mediated uptake, receptor-mediated signaling, and sensing of metabolites. The subcellular localization of nutrient-sensing components is crucial for yeast function in nutrient sensing and signaling. Protein complexes, such as the AMP-activated protein kinase (AMPK) pathway, in nutrient sensing and response, as well as the downstream effects of these pathways …
Selection Pressure On Surface Exposed Virus Proteins, Sareh Bagherichimeh
Selection Pressure On Surface Exposed Virus Proteins, Sareh Bagherichimeh
Electronic Thesis and Dissertation Repository
Viral infection requires the interaction between virus surface-exposed (SE) proteins and host cell receptors. This can result in an “arms race” that is assumed to drive accelerated rates of evolution, and some well known examples of diversifying selection involve surface pro- teins (HIV-1 env, influenza hemagglutinin). We conducted a systematic analysis to determine whether this is truly a distinctive feature of SE virus proteins, in comparison to non-SE proteins encoded by the same genomes.
We obtained reference and all neighbour genomes of 52 human viruses from the NCBI Viral Genomes database. The coding sequences (CDS) of each genome extracted by …
Deciphering The Genetic Architecture Of Key Female Floral Traits For Hybrid Wheat Seed Production, Juan Jimenez
Deciphering The Genetic Architecture Of Key Female Floral Traits For Hybrid Wheat Seed Production, Juan Jimenez
Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research
Wheat (Triticum aestivum L.) is a staple cereal that provides 20% of the calories and proteins in human intake (Ray et al., 2013). Global population is projected to increase to 9.7 billion by 2050. Food production must increase by 70% to feed this future population. Wheat production is in crisis due to political and environmental challenges and is projected to decline by 0.8% in 2022 (FAO, 2022). To ensure food security yield genetic gain must increase by around 1.4% annually. Taking advantage of heterosis, hybrid wheat has the potential to boost grain yield. However, hybrid wheat seed production systems …
Large Genomes Assembly Using Mapreduce Framework, Yuehua Zhang
Large Genomes Assembly Using Mapreduce Framework, Yuehua Zhang
All Dissertations
Knowing the genome sequence of an organism is the essential step toward understanding its genomic and genetic characteristics. Currently, whole genome shotgun (WGS) sequencing is the most widely used genome sequencing technique to determine the entire DNA sequence of an organism. Recent advances in next-generation sequencing (NGS) techniques have enabled biologists to generate large DNA sequences in a high-throughput and low-cost way. However, the assembly of NGS reads faces significant challenges due to short reads and an enormously high volume of data. Despite recent progress in genome assembly, current NGS assemblers cannot generate high-quality results or efficiently handle large genomes …
Spatiotemporal Transcriptome Diversity And Responses To Salinity Tolerance In The Extremophyte Schrenkiella Parvula, Chathura Wijesinghege
Spatiotemporal Transcriptome Diversity And Responses To Salinity Tolerance In The Extremophyte Schrenkiella Parvula, Chathura Wijesinghege
LSU Doctoral Dissertations
Schrenkiella parvula is an extremophyte model related to the most widely studied plant model, Arabidopsis thaliana and Brassica crops in the mustard family (Brassicaceae). It can thrive in highly saline environments where the soil is enriched in Na+, K+, Li+, borates, and chlorides. Understanding how this extremophyte can survive high salinity with genomic adaptations can provide insight into developing stress resilient crops in the future. Gene expression of S. parvula in response to salt has been investigated using shoot and root tissue from mature vegetative-phase plants. However, prior studies have not examined the transcript …
Changes In Gene Expression From Long-Term Warming Revealed Using Metatranscriptome Mapping To Fac-Sorted Bacteria, Christopher A. Colvin
Changes In Gene Expression From Long-Term Warming Revealed Using Metatranscriptome Mapping To Fac-Sorted Bacteria, Christopher A. Colvin
Masters Theses
Soil microbiomes play pivotal roles to the health of the environment by maintaining metabolic cycles. One question is how will climate change affect soil bacteria over time and what could the repercussions be. To answer these questions, the Harvard Forest Long-Term Warming Experiment was established to mimic predicted climate change by warming plots of land 5℃ above ambient conditions. In 2017, 14 soil core samples were collected from Barre Woods warming experiment to mark 15 years since the establishment of the soil warming in that location. These samples underwent traditional metatranscriptomics to generate an mRNA library as well as a …
Towards More Complete Metagenomic Analyses Through Circularized Genomes And Conjugative Elements, Benjamin R. Joris
Towards More Complete Metagenomic Analyses Through Circularized Genomes And Conjugative Elements, Benjamin R. Joris
Electronic Thesis and Dissertation Repository
Advancements in sequencing technologies have revolutionized biological sciences and led to the emergence of a number of fields of research. One such field of research is metagenomics, which is the study of the genomic content of complex communities of bacteria. The goal of this thesis was to contribute computational methodology that can maximize the data generated in these studies and to apply these protocols human and environmental metagenomic samples.
Standard metagenomic analyses include a step for binning of assembled contigs, which has previously been shown to exclude mobile genetic elements, and I demonstrated that this phenomenon extends to all conjugative …
Identification And Characterization Of Genetic Elements That Regulate A C-Di-Gmp Mediated Multicellular Trait In Pseudomonas Fluorescens, Collin Kessler
Identification And Characterization Of Genetic Elements That Regulate A C-Di-Gmp Mediated Multicellular Trait In Pseudomonas Fluorescens, Collin Kessler
Electronic Theses and Dissertations
Microbial communities contain densely packed cells where competition for space and resources are fierce. These communities are generally referred to as biofilms and provide advantages to individual cells against immunological and antimicrobial intervention, dehydration, and predation. High intracellular pools of cyclic diguanylate monophosphate (c-di-GMP) cause cells to aggregate during biofilm formation through the production of diverse extracellular polymers. Genes that encode c-di-GMP catalytic enzymes are commonly mutated during chronic infections where opportunists display enhanced resistance to phagocytosis and antibiotics. Our lab uses an emergent multicellular trait in the model organism Pseudomonas fluorescens Pf0-1 to study the emergence of c-di-GMP mutations …
Methods And Tools To Improve Performance Of Plant Genome Analysis, Drew Ferrell
Methods And Tools To Improve Performance Of Plant Genome Analysis, Drew Ferrell
Theses and Dissertations
Multi -omics data analysis and integration facilitates hypothesis building toward an understanding of genes and pathway responses driven by environments. Methods designed to estimate and analyze gene expression, with regard to treatments or conditions, can be leveraged to understand gene-level responses in the cell. However, genes often interact and signal within larger structures such as pathways and networks. Complex studies guided toward describing dynamic genetic pathways and networks require algorithms or methods designed for inference based on gene interactions and related topologies. Classes of algorithms and methods may be integrated into generalized workflows for comparative genomics studies, as multi -omics …
A Genomic Investigation Of Divergence Between Tuna Species, Pavel V. Dimens
A Genomic Investigation Of Divergence Between Tuna Species, Pavel V. Dimens
Dissertations
Effective management and conservation of marine pelagic fishes is heavily dependent on a robust understanding of their population structure, their evolutionary history, and the delineation of appropriate management units. The Yellowfin tuna (Thunnus albacares) and the Blackfin tuna (Thunnus atlanticus) are two exploited epipelagic marine species with overlapping ranges in the tropical and sub-tropical Atlantic Ocean. This work analyzed genome-wide genetic variation of both species in the Atlantic basin to investigate the occurrence of population subdivision and adaptive variation. A de novo assembly of the Blackfin tuna genome was generated using Illumina paired-end sequencing data and …
What I Talk About When I Talk About Integration Of Single-Cell Data, Yang Xu
What I Talk About When I Talk About Integration Of Single-Cell Data, Yang Xu
Doctoral Dissertations
Over the past decade, single-cell technologies evolved from profiling hundreds of cells to millions of cells, and emerged from a single modality of data to cover multiple views at single-cell resolution, including genome, epigenome, transcriptome, and so on. With advance of these single-cell technologies, the booming of multimodal single-cell data creates a valuable resource for us to understand cellular heterogeneity and molecular mechanism at a comprehensive level. However, the large-scale multimodal single-cell data also presents a huge computational challenge for insightful integrative analysis. Here, I will lay out problems in data integration that single-cell research community is interested in and …
Development Of Graphical Models And Statistical Physics Motivated Approaches To Genomic Investigations, Yashwanth Lagisetty
Development Of Graphical Models And Statistical Physics Motivated Approaches To Genomic Investigations, Yashwanth Lagisetty
Dissertations & Theses (Open Access)
Identifying genes involved in disease pathology has been a goal of genomic research since the early days of the field. However, as technology improves and the body of research grows, we are faced with more questions than answers. Among these is the pressing matter of our incomplete understanding of the genetic underpinnings of complex diseases. Many hypotheses offer explanations as to why direct and independent analyses of variants, as done in genome-wide association studies (GWAS), may not fully elucidate disease genetics. These range from pointing out flaws in statistical testing to invoking the complex dynamics of epigenetic processes. In the …
Decoding Copy Number Substructure And Evolution From Single Cell Genomics, Darlan Conterno Minussi
Decoding Copy Number Substructure And Evolution From Single Cell Genomics, Darlan Conterno Minussi
Dissertations & Theses (Open Access)
Aneuploidy is a prominent feature in Triple-Negative Breast Cancers (TNBC), however, the evolution of genotypes during tumor expansion remains poorly understood. The prevalent model of TNBC evolution is the Punctuated Copy Number Evolution (PCNE), in which tumors undergo a period of elevated genomic instability, acquiring complex genomic rearrangements within a short timeframe followed by clonal stasis. However, these observations rely on limited cell numbers and inherent experimental bias from first-generation single cell technologies. Therefore, the evolutionary trajectory after the punctuated burst remains unknown. To address this question, we sequenced 9,765 cells from 8 primary TNBCs and 6,413 cells from 4 …
Genome Evolution In The Salicaceae: Genetic Novelty, Horizontal Gene Transfer, And Comparative Genomics, Timothy Yates
Genome Evolution In The Salicaceae: Genetic Novelty, Horizontal Gene Transfer, And Comparative Genomics, Timothy Yates
Doctoral Dissertations
Genome evolution is a powerful force which shapes genomes over time through processes like mutation, horizontal transfer, and sexual reproduction. Although questions which aim to explore genome evolution are broad, they are all understood through the discovery and comparison of genetic variation. For example, genetic diversity may explain differences in phenotypes, etiology of disease, and is essential for phylogenomic analysis. Recently, the democratization of next generation and third generation DNA sequencing technologies have allowed for genomics to produce large amounts of sequence data. This has facilitated the capture of genetic variation at species and population scales.
Populus and Salix are …
Haplotype-Informed Allelic Imbalance Detection From Rna In Cancer, Zuhal Ozcan
Haplotype-Informed Allelic Imbalance Detection From Rna In Cancer, Zuhal Ozcan
Dissertations & Theses (Open Access)
Comprehensive genomic and transcriptomic characterization of tumors has uncovered enrichment for distinct aneuploidy and expression patterns, demonstrating the utility of molecular based classification of cancers and their subtypes. Existing cohorts with transcriptomic profiling from next-generation sequencing contain an untapped potential to also relate genomics with rich clinical phenotypes. Yet, derivation of somatic copy number and expression profiles from analyses of RNA has remained elusive. Further, DNA analysis in these cohorts is not always feasible due to limited tissue availability or financial constraints. Here, we present a statistical approach that overcomes these challenges using haplotype information to aid detection of somatic …