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- Microgravity (5)
- Bisphenol A (BPA) (3)
- Differential gene expression (3)
- Gene enrichment analysis (2)
- Neurodevelopmental disorders (NDDs) (2)
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- Nextflow (2)
- RNA-Seq (2)
- RNA-Sequencing (RNA-Seq) (2)
- 16S rRNA gene amplicons (1)
- 18S rRNA eukaryotic sequences (1)
- Alzheimer's disease (1)
- Alzheimer's treatments. (1)
- Antibiotic Resistance (1)
- Bacterial community composition (1)
- Biofilm (1)
- Bisphenol F (BPF) (1)
- Bisphenol S (BPS) (1)
- Bone loss (1)
- Candida Coculture (1)
- Circadian Rhythm (1)
- Differential Expression (DE) (1)
- Differential Expression Analysis (1)
- Differential expression (1)
- Drosophila melanogaster (1)
- Dynamic programming microRNA (1)
- Embryogenesis. (1)
- Endocrine-disrupting chemical (EDC) (1)
- Endocrine-disrupting compound (EDC) (1)
- Endothelial cells (1)
- Environmental data (1)
Articles 1 - 24 of 24
Full-Text Articles in Bioinformatics
Mrna-Sequencing Pipeline And Pathway Analysis To Determine The Effects Of Bisphenol A On Fragile X Syndrome In Drosophila Melanogaster, Rashi Raghulan
Mrna-Sequencing Pipeline And Pathway Analysis To Determine The Effects Of Bisphenol A On Fragile X Syndrome In Drosophila Melanogaster, Rashi Raghulan
Master's Projects
Neurological disorders (NDDs), like Fragile X Syndrome (FXS), are becoming more prevalent. One outstanding question in the field is how genetic risk factors for NDDs, like Fmr1, converge with environmental risk factors like bisphenol A (BPA). Our research compares and contrasts the different molecular impacts of BPA exposure in wild-type and FXS flies using mRNA-sequencing analysis. This analysis identifies the mutation in the Fmr1 gene is shown to have a stronger effect on the Drosophila than the presence of BPA, resulting in significant differential gene expression that perturbed several neurological pathways. Moreover, numerous genes responsible for genetic human diseases have …
Differential Gene Expression Analysis Of Zebrafish Embryos Exposed To Simulated Microgravity And Insights Into Cellular Effects, Nicholas Lien
Differential Gene Expression Analysis Of Zebrafish Embryos Exposed To Simulated Microgravity And Insights Into Cellular Effects, Nicholas Lien
Master's Projects
Spaceflight consists of many dangers which adversely affects the health of astronauts through hazards such as microgravity and cosmic radiation. One area that is still poorly understood is how spaceflight impacts human reproductive health. This study aims to shed insight into how microgravity may impact the development of embryos. Differential gene expression analysis was performed via Jupyter Notebook and SLURM scripts and run on SJSU’s HPC server as a method of implementing NASA GeneLab’s RNA-Seq Consensus Pipeline. Data for this project utilized RNA-Seq files for early-stage embryonic zebrafish (Danio rerio), stored under GLDS-373. Gene Set Enrichment Analysis was performed to …
Understanding How The Relative Abundance Of Candida Species Impacts Transcriptional Regulation In Coculture Biofilms, Diksha Kool
Understanding How The Relative Abundance Of Candida Species Impacts Transcriptional Regulation In Coculture Biofilms, Diksha Kool
Master's Projects
ABSTRACT Candida albicans and Candida glabrata are common fungal species that can change from commensal to pathogen due to their ability to form robust biofilms. Candida species are the leading cause of life-threatening conditions like Candidemia, and the existing treatments for biofilm-related infections are suboptimal. Research shows that the relative abundance of the two Candida species promotes biofilm formation, enhances pathogenicity, and increases antibiotic resistance. Thus, focusing on the importance of coculture, this paper utilizes RNA sequencing to investigate the gene expression leading to biofilm development in coculture through a time-series study.
Comparison Of An Oxford Nanopore Technologies Sequencing Platform To Existing Sequencing Methods For Differential Expression Studies, Nikola Klier
Master's Projects
As the genomics revolution continues, there is constant pressure to make sequencing technology more accessible and practical for a growing series of applications. Existing sequencing technologies are often prohibitively expensive, limiting their use for novel diagnostic and research applications. Additionally, existing technologies are often limited by short read lengths, which may present problems to certain quantitative sequencing applications. One such application is Differential Expression Analysis, in which RNA-Seq is performed in paired samples under different experimental conditions to identify differences in gene expression. In this study, an Oxford Nanopore Technologies sequencing platform was used to conduct a differential expression study …
Mirna-Seq Analysis Pipeline And R Shiny App, Alexis Torres
Mirna-Seq Analysis Pipeline And R Shiny App, Alexis Torres
Master's Projects
ABSTRACT Thrombosis in the internal jugular vein (IJV) has been identified as a risk factor for astronauts undergoing spaceflight, following a 2019 study in which one astronaut developed a thrombus, and several others experienced stagnant or retrograde blood flow. To better understand this phenomenon, a model that simulates the effects of microgravity on blood flow in the IJV is being developed. mRNA and microRNA NGS sequencing will be used to study the transcriptome of human umbilical vein endothelial cells (HUVEC) in simulated microgravity conditions. A microRNA sequencing (miRNA-seq) pipeline has been developed to quantify the miRNA sequencing results. A graphical …
An Investigation Of Segmental Duplications Across Topologically Associating Domains, Sara Bell
An Investigation Of Segmental Duplications Across Topologically Associating Domains, Sara Bell
Master's Projects
High-throughput chromosome conformation capture (Hi-C) reveals organization within genomes. Topologically associating domains (TADs) make up one level of organization and are identified by applying algorithms to Hi-C data. TADs have boundaries disrupted by structural variants (SVs), hypothesized to form due to recombination that occurs between segmental duplications (SDs). Little research is available about the effects of SDs at TAD boundaries. This project aimed to understand the distribution of SDs near TADs and determine any overlap between the two features. We analyzed public data and found SDs to have low breakpoint frequency and coverage at TAD boundaries. We then processed a …
A Lims-Less System For Genotyping Data In Marker-Assisted Selection, Alex Rios
A Lims-Less System For Genotyping Data In Marker-Assisted Selection, Alex Rios
Master's Projects
Climate change and feeding the growing human population are two tightly intertwined problems we face now. Innovations across several agricultural sectors are needed to meet these challenges as we proceed into the future. Seed companies and plant breeders are at the forefront of producing new plant varieties that must survive under the unique stresses of extreme weather patterns caused by changing climates. This project aims to provide breeders with faster marker results by streamlining the data process of marker-assisted selection (MAS). Manually managing genotyping data in MAS can take several hours or days to compile results for breeders. Although some …
Metagenomic Analysis Of Microbial 18s Eukaryotes Communities And Environmental Factors In The Western Antarctic Peninsula Waters During Austral Summers, Idan Siman-Tov
Master's Projects
Little is known about the environmental factors that impact eukaryotic microbial populations in the Western Antarctic Peninsula. Metagenomic and environmental data have been collected over the course of three consecutive austral summers in the Western Antarctic Peninsula off Palmer Station. More than 13 million 18S rRNA eukaryotic sequences have been taxonomically identified and categorized from the Antarctic water samples collected. Here we will investigate the environmental factors that affect eukaryotic organism populations, as well as possible indicator species that could provide insight as to the status of other eukaryotic species. Due to climate change, understanding these factors and identifying status …
Conservation And Prevalence Of Sequence Paired Sites In Humans, Punit Sundar
Conservation And Prevalence Of Sequence Paired Sites In Humans, Punit Sundar
Master's Projects
The completion of the Human Genome Project in 2003 made it possible to leverage the power of computers to quicken biological discoveries. The human genome contains rich information relevant to the proper functions of cells that is computationally arduous and costly to investigate in a laboratory setting. Specifically, gene expression levels in cells can be impacted when functionally relevant motifs in the DNA are mutated preventing proper transcription factor binding. To study the consequences of such mutations, it is necessary to first identify such functionally relevant regions of the genome using computational approaches. A signaling pathway that is of particular …
The Impact Of Bisphenol A And Its Analogues On Neurodevelopmental Transcriptomes In Drosophila Melanogaster, An Nguyen
Master's Projects
Bisphenol A (BPA) is an endocrine-disrupting compound (EDC) that can act as an agonist or antagonist to interfere with multiple signaling pathways, including neurological pathways. The impact of BPA related to neurodevelopmental disorders (NDDs) is one of the biggest concerns in BPA exposure in humans. Therefore, BPA analogues are used to replace BPA in manufacturing and BPA-free products. However, most BPA analogues, including Bisphenol F (BPF) and Bisphenol S (BPS), act the same way as BPA on estrogen and androgen receptors. RNASequencing (RNA-seq) analysis was used to investigate the impact of BPA, BPF, and BPS on neurodevelopmental transcriptomes in Drosophila …
Spaceflight And Differential Gene Expression Analysis Of Mice Quadriceps Exposed To Microgravity, Tommy Nguyen
Spaceflight And Differential Gene Expression Analysis Of Mice Quadriceps Exposed To Microgravity, Tommy Nguyen
Master's Projects
he trip to Mars and back is planned for the next 20 years. Improvement in technology and research has allowed data analysis, at a larger scale, on spaceflight specimen. However, research involving spaceflight is decentralized, as research is spread across laboratories with different methodologies. NASA’S GeneLab is a public repository for spaceflight-related omics data and promotes centralizing spaceflight RNA-Seq studies using NASA’s RNA-Seq pipeline. Jonathan Oribello, a SJSU’s Bioinformatics graduate and now an employee at GeneLab, has implemented Nextflow to NASA’s RNA-Seq pipeline. The Nextflow RNA-Seq pipeline was ran on San Jose State University’s College of Science High Performance Computing …
Mrna-Sequencing Pipeline For Differential Gene Expression Analysis, Crystal Han
Mrna-Sequencing Pipeline For Differential Gene Expression Analysis, Crystal Han
Master's Projects
Endothelial cells (ECs) line the insides of blood vessels and play a key role in the coagulation and vascular repair system. Under normal circumstances, ECs are constantly expressing anticoagulants to prevent clots and maintain healthy blood flow. But when there is an injury to the vessel, endothelial cells become centrally involved in orchestrating the complex series of events that would lead to the clotting of the wound. Thus, ECs are dynamic and respond accordingly based on changes in their local environment. Unfortunately, endothelial cells can sometimes misinterpret cues from the environment and initiate coagulation when there is no vessel damage …
Effective Cancer Detection Using Higher-Order Genome Architecture And Chromatin Interactions, My Chung
Effective Cancer Detection Using Higher-Order Genome Architecture And Chromatin Interactions, My Chung
Master's Projects
Cancer is a complex disease which requires interactions between cell-intrinsic alterations and tumor microenvironment. The connection between epigenetics and genomic structure plays a key role in chromatin interaction which promotes enhancer-promoter interactions for transcriptional activities. Alterations of chromatin states in oncogenic signaling pathway potentially cause cancer cell-intrinsic changes and inappropriate instructions to normal cell cycles, leading to abnormal cell growth. Resulting phenotypic changes are correlated to underlying changes in higher-order chromatin structure such as topologically associating domains (TADs) and compartments. In cancer cells, TAD structure is usually altered to facilitate the communication between enhancers and promoters in addition to higher …
An Examination Of Bone Loss During Space Travel With Differential Gene Expression Analysis, Claudia Vo
An Examination Of Bone Loss During Space Travel With Differential Gene Expression Analysis, Claudia Vo
Master's Projects
Spaceflight poses many risks to human health due to the harsh conditions of microgravity, cosmic radiation, and confinement. One of the impacts that spaceflight entails is bone loss, which is a risk to astronauts as future space missions will require long travel durations. To elucidate the role of genetics in spaceflight bone loss, in this study differential gene expression analysis was performed using Nextflow-RCP, an adaptation of NASA Genelab’s RNA-Seq Consensus pipeline. The dataset for this project was GLDS-241, which contained samples from mice femoral skin. To gain a comprehensive understanding of the genes involved in bone loss, the results …
Detection Of Antibiotic Resistance Genes In The Wastewater Microbial Metagenome, Alan Caparaz Le
Detection Of Antibiotic Resistance Genes In The Wastewater Microbial Metagenome, Alan Caparaz Le
Master's Projects
The existential threat of emerging antibiotic resistance in microbial communities poses significant risks to public health. In particular, wastewater can serve as a point of confluence for pharmaceuticals and antibiotic-resistant bacteria from urban and agricultural settings. While this is a prime environment for genetic drift and horizontal transfer of antibiotic resistance genes (ARGs) and mobile genetic elements, it also presents an opportunity for resistome monitoring via shotgun metagenomic sequencing and downstream analysis. This project reports the application of a hybrid assembly approach for the detection of ARGs within DNA derived from a wastewater sample collected from the San José-Santa Clara …
Transcriptional Profiling Of Neurological Development Of Drosophila Following Bisphenol A Exposure, Eden Johnson
Transcriptional Profiling Of Neurological Development Of Drosophila Following Bisphenol A Exposure, Eden Johnson
Master's Projects
The ubiquitous environmental chemical bisphenol A (BPA) is an emerging risk factor for neurodevelopmental disorders (NDDs). BPA is an endocrine-disrupting chemical (EDC) that is thought to interfere with neuron development by changing neuronal gene expression. Impacting neurodevelopment in this manner can cause lasting changes in behavior and potentially lead to the development of NDDs. Delineating the molecular processes that incur changes in gene expression following BPA exposure will advance our understanding of how BPA impacts neurodevelopmental pathways and affects the pathophysiology of NDDs. An RNA-Sequencing (RNA-Seq) analysis pipeline was created for transcriptional profiling of neurological development in wild-type Drosophila melanogaster …
Summer Marine Bacterial Community Composition Of The Western Antarctic Peninsula, Codey Phoun
Summer Marine Bacterial Community Composition Of The Western Antarctic Peninsula, Codey Phoun
Master's Projects
The Western Antarctic Peninsula has experienced dramatic warming due to climate change over the last 50 years and the consequences to the marine microbial community are not fully clear. The marine bacterial community are fundamental contributors to biogeochemical cycling of nutrients and minerals in the ocean. Molecular data of bacteria from the surface waters of the Western Antarctic Peninsula are lacking and most existing studies do not capture the annual variation of bacterial community dynamics. In this study, 15 different 16S rRNA gene amplicon samples covering 3 austral summers were processed and analyzed to investigate the marine bacterial community composition …
Differential Gene Expression Analysis Of Mice Thymi After Spaceflight, Roshani Codipilly
Differential Gene Expression Analysis Of Mice Thymi After Spaceflight, Roshani Codipilly
Master's Projects
With increases in space travel and a desire to inhabit the moon and Mars comes a pressing need to understand the impact of spaceflight on the body. Some effects are already known, such as reduced cardiac function and bone loss, but one area that needs to be further explored is the immune system. Differential gene expression analysis of mice thymi was performed to determine the impact of spaceflight on the immune system. The dataset that was analyzed, GLDS-289, was obtained from GeneLab, a space-omics database developed by NASA. Differential gene expression analysis was accomplished using a Nextflow implementation of GeneLab’s …
Meta-Analysis Of Natural Vs Pharmaceutical Interventions For Alzheimer's Disease, Tamara Vrublevskaya
Meta-Analysis Of Natural Vs Pharmaceutical Interventions For Alzheimer's Disease, Tamara Vrublevskaya
Master's Projects
The purpose of this research is to present a way to compare interventions by collecting all available drug clinical trials for a disease of interest. The assessment is done using Meta-Analysis, a method for evaluating data from several studies to arrive at a combined estimate of treatment effect. The evaluation is done in R on a given set of studies to answer the question – which Alzheimer's Disease intervention (pharmaceutical vs. natural) show better outcomes and fewer adverse effects. The research covers many types of interventions across diverse patient populations. On a small subset of papers, natural treatments showed better …
Differential Gene Expression Analysis Of Rodents Exposed To Long-Term Space Flight And Insights Into Physiological Effects, Jonathan Oribello
Differential Gene Expression Analysis Of Rodents Exposed To Long-Term Space Flight And Insights Into Physiological Effects, Jonathan Oribello
Master's Projects
Space travel presents inherent risks to human health and a better understanding of space biology is required to mitigate harm in an oncoming age of increased space travel. Omics analysis will play a central role in better understanding human health in space. In this project, differential gene expression analysis was performed on GLDS-104, an open science dataset provided by NASA’s GeneLab. GeneLab’s RNA-Seq Consensus Pipeline was implemented using Nextflow, performed on San Jose State University’s College of Science High Performance Computing Cluster, and optimized for computational resource efficiency. Comparison of the Nextflow implemention developed in this project to GeneLab’s posted …
Bioinformatics Metadata Extraction For Machine Learning Analysis, Zachary Tom
Bioinformatics Metadata Extraction For Machine Learning Analysis, Zachary Tom
Master's Projects
Next generation sequencing (NGS) has revolutionized the biological sciences. Today, entire genomes can be rapidly sequenced, enabling advancements in personalized medicine, genetic diseases, and more. The National Center for Biotechnology Information (NCBI) hosts the Sequence Read Archive (SRA) containing vast amounts of valuable NGS data. Recently, research has shown that sequencing errors in conventional NGS workflows are key confounding factors for detecting mutations. Various steps such as sample handling and library preparation can introduce artifacts that affect the accuracy of calling rare mutations. Thus, there is a need for more insight into the exact relationship between various steps of the …
Ab Initio Protein Structure Prediction Algorithms, Maciej Kicinski
Ab Initio Protein Structure Prediction Algorithms, Maciej Kicinski
Master's Projects
Genes that encode novel proteins are constantly being discovered and added to databases, but the speed with which their structures are being determined is not keeping up with this rate of discovery. Currently, homology and threading methods perform the best for protein structure prediction, but they are not appropriate to use for all proteins. Still, the best way to determine a protein's structure is through biological experimentation. This research looks into possible methods and relations that pertain to ab initio protein structure prediction. The study includes the use of positional and transitional probabilities of amino acids obtained from a non-redundant …
Rna Secondary Structure Prediction Tool, Meenakshee Mali
Rna Secondary Structure Prediction Tool, Meenakshee Mali
Master's Projects
Ribonucleic Acid (RNA) is one of the major macromolecules essential to all forms of life. Apart from the important role played in protein synthesis, it performs several important functions such as gene regulation, catalyst of biochemical reactions and modification of other RNAs. In some viruses, instead of DNA, RNA serves as the carrier of genetic information. RNA is an interesting subject of research in the scientific community. It has lead to important biological discoveries. One of the major problems researchers are trying to solve is the RNA structure prediction problem. It has been found that the structure of RNA is …
A Microrna Target Prediction Algorithm, Rupinder Singh
A Microrna Target Prediction Algorithm, Rupinder Singh
Master's Projects
MicroRNA target prediction using the experimental methods is a challenging task. To accelerate the process of miRNA target validation, many computational methods are used. Computational methods yield many potential candidates for experimental validation. This project is about developing a new computational method using dynamic programming to predict miRNA targets with more accuracy. The project discusses the currently available computational methods and develops a new algorithm using the currently available knowledge about miRNA interactions.