Computational Biology Commons^™

Comparative Analyses Of De Novo Transcriptome Assembly Pipelines For Diploid Wheat, Natasha Pavlovikj

Computer Science and Engineering: Theses, Dissertations, and Student Research

Gene expression and transcriptome analysis are currently one of the main focuses of research for a great number of scientists. However, the assembly of raw sequence data to obtain a draft transcriptome of an organism is a complex multi-stage process usually composed of pre-processing, assembling, and post-processing. Each of these stages includes multiple steps such as data cleaning, error correction and assembly validation. Different combinations of steps, as well as different computational methods for the same step, generate transcriptome assemblies with different accuracy. Thus, using a combination that generates more accurate assemblies is crucial for any novel biological discoveries. Implementing ...

Scalable Software Infrastructure For The Lab And A Specific Investigation Of The Yeast Transcription Factor Eds1, Chase Mateusiak

McKelvey School of Engineering Theses & Dissertations

Individual biology labs handle increasingly large data sets. Ensuring accurate data entry, consistent sample metadata, and ease of access to the data once it is stored, are critical for both the integrity of analysis as well as productivity of the lab. Chapter 1 one of this thesis describes three implementations of software meant to facilitate handling data and metadata in the lab as the size of the data and complexity of analysis scale. The first piece of software is a database and entry interface for storing a large and varied amount of data on biological samples. The second is a ...

Genomic Analysis Of Metabolic Differences Found In Clostridium Perfringens That Cause Necrotic Enteritis In Poultry, Connor Aylor

Dissertations & Theses in Veterinary and Biomedical Science

Clostridium perfringens is a common member of gut microbiota in healthy animals, but can also be an important pathogen in human and veterinary medicine. It produces several protein toxins that contribute to both histotoxic and enteric diseases in animals. Necrotic enteritis in poultry has been associated with the NetB toxin of C. perfringens; however, this toxin alone is insufficient to cause disease in infected chickens. While considerable research has focused on the presence of toxins and virulence factors, little has been done to assess the function of metabolic factors on the ability of the bacteria to cause disease. In this ...

Using Machine Learning To Recognize Chronic Rhinosinusitis, Irene Liu '23

Student Publications & Research

Chronic Rhinosinusitis (CRS) is a nasal disease characterized by the inflammation of the mucosa and paranasal sinuses with a duration of at least 12 consecutive weeks. So, to diagnose CRS, one needs to keep a record of their symptoms for ~12 weeks before they are recommended to get a tomography which will allow physicians to classify them as a patient with CRS or without. This is a timely and costly process; thus, machine learning should be used to speed the process up. Since patients with CRS have more obstructed noses, the sound produced should be different than an individual without ...

Identification Of Dna Methylation Episignatures For Classification And Phenotype/Genotype Correlation In Mendelian Neurodevelopmental Disorders, John Reilly

Electronic Thesis and Dissertation Repository

ABSTRACT: Diagnosis for neurodevelopmental disorders poses numerous challenges, related to the lack of specific findings and limited understanding of clinical impact of the majority of genetic variation. Epigenomics mechanisms involve chemical modifications in DNA that involve a range of cellular mechanisms. DNA methylation is an epigenetic mechanism involving addition and removal of methyl groups to cytosine residues. These methylation signals form episignatures; patterns of methylation that can be used as biomarkers capable of differentiating neurodevelopmental disorders. EpiSigns have enabled molecular diagnosis of a number of genetic conditions, classification of variants of unknown significance, and provided insights into the pathophysiology of ...

Identifying Molecular Markers For Early Detection Of Toxic Cyanobacteria And Dinoflagellate, Shafqat F. Ehsan

St. Mary's University Honors Theses and Projects

Harmful algal Blooms (HABs) develop when algal colonies grow out of control, causing toxicity or injury to humans, fish, shellfish, marine mammals, and birds. Most HABs of public health concern in saltwater generally are caused by eukaryotic dinoflagellates and diatoms. Prokaryotic cyanobacteria are usually responsible for freshwater blooms although they can contribute to saltwater and brackish blooms too. A common monitoring target of both groups is the saxitoxin-encoding genes. Saxitoxin(STX) is responsible for Paralytic shellfish poisoning, a foodborne illness developed from consumption of STX contaminated shellfish. Each cyanobacterial SXT gene cluster contains a set of core genes, common to ...

Comparative Modeling And Evolutionary Comparison Of Serine Protease, A Timber Rattlesnake Venom Protein, Qawer Ayaz

Theses

The aim of this study is to create a homology model of VG35 serine protease and evaluate the evolutionary comparison of secondary structure on basis of protein model using YASARA. This method was furthermore used to predict the potential epitopes which can help in the investigation of future studies.

The VG35 was used to run a BLAST search which gave most resembled serine protease of different species which was then translated and modeled in YASARA. The modeled protein data was then used to determine the secondary structure. This was then used for evolutionary comparison of all proteins to VG35. Then ...

Meta-Analysis Of Two Rnaseq Datasets To Determine Diagnostic Biomarkers And Drug Target Candidates For Periodontitis, Carlos Moreno

Annual Research Symposium

No abstract provided.

The Low Abundance Of Cpg In The Sars-Cov-2 Genome Is Not An Evolutionarily Signature Of Zap, Ali Afrasiabi, Hamid Alinejad-Rokny, Azad Khosh, Mostafa Rahnama, Nigel Lovell, Zhenming Xu, Diako Ebrahimi

Plant Pathology Faculty Publications

The zinc finger antiviral protein (ZAP) is known to restrict viral replication by binding to the CpG rich regions of viral RNA, and subsequently inducing viral RNA degradation. This enzyme has recently been shown to be capable of restricting SARS-CoV-2. These data have led to the hypothesis that the low abundance of CpG in the SARS-CoV-2 genome is due to an evolutionary pressure exerted by the host ZAP. To investigate this hypothesis, we performed a detailed analysis of many coronavirus sequences and ZAP RNA binding preference data. Our analyses showed neither evidence for an evolutionary pressure acting specifically on CpG ...

The Case For Altruism In Institutional Diagnostic Testing, Ivan Specht, Kian Sani, Yolanda Botti-Lodovico, Michael Hughes, Kristin Heumann, Amy Bronson, John Marshall, Emily Baron, Eric Parrie, Olivia Glennon, Ben Fry, Andres Colubri, Pardis C. Sabeti

COVID-19 Publications by UMass Chan Authors

Amid COVID-19, many institutions deployed vast resources to test their members regularly for safe reopening. This self-focused approach, however, not only overlooks surrounding communities but also remains blind to community transmission that could breach the institution. To test the relative merits of a more altruistic strategy, we built an epidemiological model that assesses the differential impact on case counts when institutions instead allocate a proportion of their tests to members' close contacts in the larger community. We found that testing outside the institution benefits the institution in all plausible circumstances, with the optimal proportion of tests to use externally landing ...

Comparative Transcriptomic Analysis Of Cancer Testis Genes In Ovarian Cancer, Zayne Knuth

Dissertations, Master's Theses and Master's Reports

Cancer testis genes are common targets for the development of immunotherapy for cancer treatment. Ovarian cancer is one of the leading causes of death in women cancer patients. Cancer testis genes play a role in tumorigenesis, but it is not clear how these genes are activated. This study utilized differential expression analysis between The Cancer Genome Atlas (TCGA) ovarian cancer data, Genotype-Tissue Expression (GTEx) non-cancerous ovary and testis data, and cell line data to identify a list of cancer testis genes that have a novel expression profile. To identify ovarian cancer testis genes, we obtained normal ovary tissue data and ...

Characterizing Long Covid: Deep Phenotype Of A Complex Condition, Rachel R. Deer, Feifan Liu, Melissa A. Haendel, Peter N. Robinson

COVID-19 Publications by UMass Chan Authors

BACKGROUND: Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 (PASC or "long COVID"), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations. Patient-led studies are of particular importance for understanding the natural history of COVID-19, but integration is hampered because they often use different terms to describe the same symptom or condition. This significant disparity in patient versus clinical characterization motivated the proposed ontological approach to specifying manifestations, which will improve capture and integration of future long COVID studies.

METHODS: The Human Phenotype Ontology ...

Wormcat 2.0 Defines Characteristics And Conservation Of Poorly Annotated Genes In Caenorhabditis Elegans [Preprint], Daniel P. Higgins, Caroline M. Weisman, Dominique Lui, Frank A. D’Agostino, Amy K. Walker

UMass Chan Medical School Faculty Publications

Genome-wide measurement of mRNA or protein levels provides broad data sets for biological discovery. However, subsequent computational methods are essential for uncovering the functional implications of the data as well as intuitively visualizing the findings. Current computational tools are biased toward well-described pathways, limiting their utility for novel discovery. Recently, we developed an annotation and category enrichment tool for Caenorhabditis elegans genomic data, WormCat, that provides an intuitive visualization output. Unlike GO, which excludes genes with no annotation information, WormCat 2.0 retains these genes as a special UNASSIGNED category. Here, we show that the UNASSIGNED gene category enrichment exhibits ...

Improved Radiation Expression Profiling In Blood By Sequential Application Of Sensitive And Specific Gene Signatures, Eliseos J. Mucaki, Ben C. Shirley, Peter K. Rogan

Biochemistry Publications

Purpose. Combinations of expressed genes can discriminate radiation-exposed from normal control blood samples by machine learning based signatures (with 8 to 20% misclassification rates). These signatures can quantify therapeutically-relevant as well as accidental radiation exposures. The prodromal symptoms of Acute Radiation Syndrome (ARS) overlap those present in Influenza and Dengue Fever infections. Surprisingly, these human radiation signatures misclassified gene expression profiles of virally infected samples as false positive exposures. The present study investigates these and other confounders, and then mitigates their impact on signature accuracy.

Methods. This study investigated recall by previous and novel radiation signatures independently derived from multiple ...

Metabolic Modeling Of Cystic Fibrosis Airway Microbiota From Patient Samples, Arsh Vyas

Masters Theses

Cystic Fibrosis (CF) is a genetic disorder, found with higher prevalence in the Caucasian population, affecting > 30,000 individuals in the United States and > 70,000 worldwide. Due to the astoundingly high rate of mortality among CF patients being attributed to respiratory failure brought on by chronic bacterial infections and subsequent airway inflammation, there has been a lot of focus on systematically analyzing CF lung airway communities. While it is observed traditionally that Pseudomonas aeruginosa is the most threatening and persistent CF colonizer due to high antibiotic resistance, recent studies have elicited the roles of other pathogens and it has ...

Factorbook: An Updated Catalog Of Transcription Factor Motifs And Candidate Regulatory Motif Sites [Preprint], Henry E. Pratt, Gregory Andrews, Nishigandha Phalke, Michael J. Purcaro, Arjan Van Der Velde, Jill E. Moore, Zhiping Weng

UMass Chan Medical School Faculty Publications

The human genome contains roughly 1,600 transcription factors (TFs) (1), DNA-binding proteins recognizing characteristic sequence motifs to exert regulatory effects on gene expression. The binding specificities of these factors have been profiled both in vitro, using techniques such as HT-SELEX (2), and in vivo, using techniques including ChIP-seq (3, 4). We previously developed Factorbook, a TF-centric database of annotations, motifs, and integrative analyses based on ChIP-seq data from Phase II of the ENCODE Project. Here we present an update to Factorbook which significantly expands the breadth of cell type and TF coverage. The update includes an expanded motif catalog ...

Human 5’-Tailed Mirtrons Are Processed By Rnasep, Mohammad Farid Zia

Dissertations

Approximately a thousand microRNAs (miRNAs) are documented from human cells. A third appear to transit non-canonical pathways that typically bypass processing by Drosha, the dedicated nuclear miRNA producing enzyme. The largest class of non-canonical miRNAs are mirtrons which eschew Drosha to mature through spliceosome activity. While mirtrons are found in several configurations, the vast majority of human mirtron species are 5’-tailed. For these mirtrons, a 3’ splice site defines the 3’ end of their hairpin precursor while a “tail” of variable length separates the 5’ base of the hairpin from the nearest splice site. How this tail is removed ...

Swarmtcr: A Computational Approach To Predict The Specificity Of T Cell Receptors, Ryan Ehrlich, Larisa Kamga, Anna Gil, Katherine Luzuriaga, Liisa K. Selin, Dario Ghersi

Open Access Publications by UMass Chan Authors

BACKGROUND: With more T cell receptor sequence data becoming available, the need for bioinformatics approaches to predict T cell receptor specificity is even more pressing. Here we present SwarmTCR, a method that uses labeled sequence data to predict the specificity of T cell receptors using a nearest-neighbor approach. SwarmTCR works by optimizing the weights of the individual CDR regions to maximize classification performance.

RESULTS: We compared the performance of SwarmTCR against another nearest-neighbor method and showed that SwarmTCR performs well both with bulk sequencing data and with single cell data. In addition, we show that the weights returned by SwarmTCR ...

In Silico Identification Of A Streptococcus Phage From An Unpasteurized Dairy Product

Symposium of Student Scholars

This study aimed to identify novel phages from a West African dairy product, nunu, to better understand the uncharacterized virosphere of a food microbiome. Nunu is a yogurt-like product from spontaneous fermentation of unpasteurized cow milk without a standardized starter culture. Phages and their bacterial hosts make up a microbiome, where their collective metagenome can be studied in silico, or computationally, after next generation sequencing (NGS). The targeted dataset for our study can be found in the Sequence Read Archives under the accession number of ERX2041567. This study utilized several bioinformatics software tools with customized settings: Kraken2, MetaVelvet, Edena, NCBI-BLAST ...

In Silico Isolation Of A Novel Phage For Food Safety Applications Against Pathogenic E. Coli, Daisy Mcgrath

Symposium of Student Scholars

With the advent of next-generation sequencing (NGS) on metagenomes, the elucidation of all genetic material from microbiomes has prompted a renewed interest towards uncultivated members of the virosphere. We describe the discovery of a novel phage from a metagenomic dataset on the West African fermented dairy product, nunu, with a custom bioinformatics workflow to potentially serve as a biocontrol agent against pathogenic E. coli. Initial dataset of ERR2014814 from NCBI was first subjected to Kraken2 to extract novel sequencing reads for further de novo assembly into contigs by MetaVelvet. Resultant contigs served as potential partial phage genomes, then searched against ...