Computational Biology Commons^™

Cazyme Gene Cluster Diversity In Human Gut Microbiome, Yi Xing

Department of Food Science and Technology: Dissertations, Theses, and Student Research

In gut microbiome research, carbohydrate-active enzyme gene clusters (CGCs) have emerged as key functional units for understanding microbial glycan degradation. Unlike taxonomic or broad pathway annotations, CGCs offer gene-cluster-level resolution and capture substrate-specific microbial functions. However, their diversity and distribution in relation to host metabolic phenotypes, such as obesity, remain poorly characterized. This study tests the hypothesis that the composition and abundance of fiber-targeting CGCs vary between obese and healthy human gut microbiomes, reflecting distinct microbial carbohydrate utilization strategies. To examine this, we constructed a high-quality reference CGC dataset comprising 94,019 clusters from the Unified Human Gastrointestinal Genome and profiled …

Convolutional Neural Network-Based Gene Prediction Using Buffalograss As A Model System, Michael Morikone

Complex Biosystems Program: Dissertations and Student Research

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) …

Exploring The Interactions Between Sars-Cov-2 And Host Proteins, Sojan Shrestha

School of Biological Sciences: Dissertations, Theses, and Student Research

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the current pandemic, Coronavirus Disease 2019 (COVID-19). SARS-CoV-2 is considered to be of zoonotic origin; it originated in non-human animals and was transmitted to humans. Since the early stage of the pandemic, however, the evidence of transmissions from humans to animals (reverse zoonoses) has been found in multiple animal species including mink, white-tailed deer, and pet and zoo animals. Furthermore, secondary zoonotic events of SARS-CoV-2, transmissions from animals to humans, have been also reported. It is suggested that non-human hosts can act as SARS-CoV-2 reservoirs where accumulated …

Deciphering The Genetic Architecture Of Key Female Floral Traits For Hybrid Wheat Seed Production, Juan David 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 …

Sequence-Based Bioinformatics Approaches To Predict Virus–Host Relationships In Archaea And Eukaryotes, Yingshan Li

School of Computing: Dissertations, Theses, and Student Research

Viral metagenomics is independent of lab culturing and capable of investigating viromes of virtually any given environmental niches. While numerous sequences of viral genomes have been assembled from metagenomic studies over the past years, the natural hosts for the majority of these viral contigs have not been determined. Different computational approaches have been developed to predict hosts of bacteria phages. Nevertheless, little progress has been made in the virus-host prediction, especially for viruses that infect eukaryotes and archaea. In this study, by analyzing all documented viruses with known eukaryotic and archaeal hosts, we assessed the predictive power of four computational …

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

School of Computing: Dissertations, Theses, 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 …

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

School of Veterinary and Biomedical Sciences: Dissertations, Theses, and Student Research

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. …

The Differences Of Prokaryotic Pan-Genome Analysis On Complete Genomes And Simulated Metagenome-Assembled Genomes, Tang Li

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Metagenomic assembly is often used in microbiome research. In metagenomic assembly, contigs are binned based on the shared nucleotide composition. These contig bins are called metagenome-assembled genomes (MAGs), each representing a unique bacterial genome recovered from metagenome sequencing. Hundreds of thousands of high-quality MAGs of various ecological environments have been published since 2017, and increasingly more MAGs are being used in pan-genome analyses where unculturable species or species without reference genomes are studied in microbiome research. However, compared to the traditional pan-genome analysis that uses isolate genomes (from a pure strain isolated from a mixed bacterial population), it is not …

Dynamic Observers For Unknown Populations, Chris Guiver, Nathan Poppelreiter, Richard Rebarber, Brigitte Tenhumberg, Stuart Townley

Brigitte Tenhumberg Papers

Dynamic observers are considered in the context of structuredpopulation modeling and management. Roughly, observers combine a known measured variable of some process with a model of that process to asymptotically reconstruct the unknown state variable of the model. We investigate the potential use of observers for reconstructing population distributions described by density-independent (linear) models and a class of density-dependent (nonlinear) models. In both the density-dependent and -independent cases, we show, in several ecologically reasonable circumstances, that there is a natural, optimal construction of these observers. Further, we describe the robustness these observers exhibit with respect to disturbances and uncertainty in …

Polerovirus Genomic Variation And Mechanisms Of Silencing Suppression By P0 Protein, Natalie M. Holste

School of Biological Sciences: Dissertations, Theses, and Student Research

The family Luteoviridae consists of three genera: Luteovirus, Enamovirus, and Polerovirus. The genus Polerovirus contains 32 virus species. All are transmitted by aphids and can infect a wide variety of crops from cereals and wheat to cucurbits and peppers. However, little is known about how this wide range of hosts and vectors developed. In poleroviruses, aphid transmission and virion formation is mediated by the coat protein read-through domain (CPRT) while silencing suppression and phloem limitation is mediated by Protein 0 (P0)—a protein unique to poleroviruses. P0 gives poleroviruses a great advantage amongst plant viruses and diversifies polerovirus species, but the …

Evolutionary And Ecological Determinism Of Host Specificity In Arthropod Parasites, Joseph Levey

UCARE: Research Products

Understanding why some diseases infect more species than others is crucial for predicting where and when disease will spread, which can inform the management of wildlife, agriculture, and human health. Currently, large scale patterns of host-parasite dynamics are being studied to understand where to look for and how to manage emerging human diseases (Leroy 2005; Benelli 2018). Previous research has used the Global Mammal Parasite Database (GMPD) to look at host breadth—the number and diversity of species a pathogen can infect—for various groups of parasites, e.g. helminths, arthropods, fungi, etc., from a host-centric perspective (Stephens et al. 2017; Park et …

Genome-Wide Association Studies In Maize And Sorghum, Preston Hurst

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Genome-wide association studies are used to identify genetic variants associated with a particular phenotype. GWAS has been used in a variety of taxa, from humans, to fish to plants . The present analysis is focused on two species important to the human species: maize and sorghum. A GWAS in maize was carried out on the modification of the Ga1-s allele. The Ga1 locus has long been studied as being involved in a unilateral crossing barrier . However, it has long been suspected that the locus is modified by background genetic factors . GWAS was used to observe candidates for this …

Contemporary Sexual Selection Does Not Explain Variation In Male Display Traits Among Populations, J. Colton Watts, Allissa Flynn, Brigitte Tenhumberg, Eileen Hebets

Brigitte Tenhumberg Papers

Sexual selection is widely hypothesized to facilitate the evolution of reproductive isolation through divergence in sexual traits and sexual trait preferences among populations. However, direct evidence of divergent sexual selection causing intraspecific trait divergence remains limited. Using the wolf spider Schizocosa crassipes, we characterized patterns of female mate choice within and among geographic locations and related those patterns to geographic variation in male display traits to test whether divergent sexual selection caused by mate choice explains intraspecific trait variation. We found evidence of phenotypic selection on male behavior arising from female mate choice, but no evidence that selection varied …

Copy Number Variation In The Porcine Genome Detected From Whole-Genome Sequence, Rebecca Anderson

Honors Program: Senior Projects (Public)

Copy number variations (CNVs) are large insertions, deletions, and duplications in the genome that vary between individuals in a species. These variations are known to impact a broad range of phenotypes from molecular-level traits to higher-order clinical phenotypes. CNVs have been linked to complex traits in humans such as autism, attention deficit hyperactivity disorder, nervous system disorders, and early-onset extreme obesity. In this study, whole-genome sequence was obtained from 72 founders of an intensely phenotyped experimental swine herd at the U.S. Meat Animal Research Center (USMARC) in Clay Center, Nebraska. This included 24 boars (12 Duroc and 12 Landrace) and …

A Systematic Approach To Rna-Associated Motif Discovery, Tian Gao, Jiang Shu, Juan Cui

School of Computing: Faculty Publications

Background: Sequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The downstream analysis of RNA binding sites has encouraged the investigation of novel sequence motifs, which resulted in exceptional new challenges for identifying motifs from very short sequences (e.g., small non-coding RNAs or truncated messenger RNAs), where conventional methods tend to be ineffective. To address these challenges, we propose a novel motif-finding method and validate it on a wide range of RNA applications.

Results: We first perform motif analysis on microRNAs and longer RNA fragments from …

Linking Taxonomic Diversity And Trophic Function: A Graph-Based Theoretical Approach, Marcella M. Jurotich, Kaitlyn Dougherty, Barbara Hayford, Sally Clark

Transactions of the Nebraska Academy of Sciences and Affiliated Societies

The purpose of this study is to develop a novel, visual method in analyzing complex functional trait data in freshwater ecology. We focus on macroinvertebrates in stream ecosystems under a gradient of habitat degradation and employ a combination of taxonomic and functional trait diversity analyses. Then we use graph theory to link changes in functional trait diversity to taxonomic richness and habitat degradation. We test the hypotheses that: 1) taxonomic diversity and trophic functional trait diversity both decrease with increased habitat degradation; 2) loss of taxa leads to a decrease in trophic function as visualized using a bipartite graph; and …

Testing The Independence Hypothesis Of Accepted Mutations For Pairs Of Adjacent Amino Acids In Protein Sequences, Jyotsna Ramanan, Peter Revesz

School of Computing: Faculty Publications

Evolutionary studies usually assume that the genetic mutations are independent of each other. However, that does not imply that the observed mutations are independent of each other because it is possible that when a nucleotide is mutated, then it may be biologically beneficial if an adjacent nucleotide mutates too. With a number of decoded genes currently available in various genome libraries and online databases, it is now possible to have a large-scale computer-based study to test whether the independence assumption holds for pairs of adjacent amino acids. Hence the independence question also arises for pairs of adjacent amino acids within …

Incremental Phylogenetics By Repeated Insertions: An Evolutionary Tree Algorithm, Peter Revesz, Zhiqiang Li

School of Computing: Faculty Publications

We introduce the idea of constructing hypothetical evolutionary trees using an incremental algorithm that inserts species one-by-one into the current evolutionary tree. The method of incremental phylogenetics by repeated insertions lead to an algorithm that can be used on DNA, RNA and amino acid sequences. According to experimental results on both synthetic and biological data, the new algorithm generates more accurate evolutionary trees than the UPGMA and the Neighbor Joining algorithms.

Comparative Genomics, Transcriptomics, And Physiology Distinguish Symbiotic From Free-Living Chlorella Strains, Cristian F. Quispe, Olivia Sonderman, Maya Khasin, Wayne R. Riekhof, James L. Van Etten, Kenneth Nickerson

Kenneth Nickerson Papers

Most animal–microbe symbiotic interactions must be advantageous to the host and provide nutritional benefits to the endosymbiont. When the host provides nutrients, it can gain the capacity to control the interaction, promote self-growth, and increase its fitness. Chlorella-like green algae engage in symbiotic relationships with certain protozoans, a partnership that significantly impacts the physiology of both organisms. Consequently, it is often challenging to grow axenic Chlorella cultures after isolation from the host because they are nutrient fastidious and often susceptible to virus infection. We hypothesize that the establishment of a symbiotic relationship resulted in natural selection for nutritional and metabolic …

Genomic Prediction Of Gene Bank Wheat Landraces, José Crossa, Diego Jarquin, Jorge Franco, Paulino Pérez-Rodríguez, Juan Burgueño, Carolina Saint-Pierre, Prashant Vikram, Carolina Sansaloni, Cesar Petroli, Denis Akdemir, Clay Sneller, Matthew Reynolds, Maria Tattaris, Thomas Payne, Carlos Guzman, Roberto J. Peña, Peter Wenzl, Sukhwinder Singh

Department of Agronomy and Horticulture: Faculty Publications

This study examines genomic prediction within 8416 Mexican landrace accessions and 2403 Iranian landrace accessions stored in gene banks. The Mexican and Iranian collections were evaluated in separate field trials, including an optimum environment for several traits, and in two separate environments (drought, D and heat, H) for the highly heritable traits, days to heading (DTH), and days to maturity (DTM). Analyses accounting and not accounting for population structure were performed. Genomic prediction models include genotype × environment interaction (G × E). Two alternative prediction strategies were studied: (1) random cross-validation of the data in 20% training (TRN) and 80% …

A Computational Model Of The Spread Of Ancient Human Populations Based On Mitochondrial Dna Samples, Peter Revesz

School of Computing: Conference and Workshop Papers

The extraction of mitochondrial DNA (mtDNA) from ancient human population samples provides important data for the reconstruction of population influences, spread and evolution from the Neolithic to the present. This paper presents a mtDNA-based similarity measure between pairs of human populations and a computational model for the evolution of human populations. In a computational experiment, the paper studies the mtDNA information from five Neolithic and Bronze Age populations, namely the Andronovo, the Bell Beaker, the Minoan, the Rössen and the Únětice populations. In the past these populations were identified as separate cultural groups based on geographic location, age and the …

Mutations Of Adjacent Amino Acid Pairs Are Not Always Independent, Jyotsna Ramanan, Peter Revesz

School of Computing: Conference and Workshop Papers

Evolutionary studies usually assume that the genetic mutations are independent of each other. This paper tests the independence hypothesis for genetic mutations with regard to protein coding regions. According to the new experimental results the independence assumption generally holds, but there are certain exceptions. In particular, the coding regions that represent two adjacent amino acids seem to change in ways that sometimes deviate significantly from the expected theoretical probability under the independence assumption.

Bioinformatic Game Theory And Its Application To Cluster Multi-Domain Proteins, Brittney Keel

Department of Mathematics: Dissertations, Theses, and Student Research

The exact evolutionary history of any set of biological sequences is unknown, and all phylogenetic reconstructions are approximations. The problem becomes harder when one must consider a mix of vertical and lateral phylogenetic signals. In this dissertation we propose a game-theoretic approach to clustering biological sequences and analyzing their evolutionary histories. In this context we use the term evolution as a broad descriptor for the entire set of mechanisms driving the inherited characteristics of a population. The key assumption in our development is that evolution tries to accommodate the competing forces of selection, of which the conservation force seeks to …

Classification Of Genomic Sequences By Latent Semantic Analysis, Samuel F. Way

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

Evolutionary distance measures provide a means of identifying and organizing related organisms by comparing their genomic sequences. As such, techniques that quantify the level of similarity between DNA sequences are essential in our efforts to decipher the genetic code in which they are written.

Traditional methods for estimating the evolutionary distance separating two genomic sequences often require that the sequences first be aligned before they are compared. Unfortunately, this preliminary step imposes great computational burden, making this class of techniques impractical for applications involving a large number of sequences. Instead, we desire new methods for differentiating genomic sequences that eliminate …

Efficient And Robust Rna-Seq Process For Cultured Bacteria And Complex Community Transcriptomes, Georgia Giannoukos, Dawn M. Ciulla, Katherine Huang, Brian J. Haas, Jacques Izard, Joshua Z. Levin, Jonathan Livny, Ashlee M. Earl, Dirk Gevers, Doyle V. Ward, Chad Nusbaum, Bruce W. Birren, Andreas Gnirke

Department of Food Science and Technology: Faculty Publications

We have developed a process for transcriptome analysis of bacterial communities that accommodates both intact and fragmented starting RNA and combines efficient rRNA removal with strand-specific RNA-seq. We applied this approach to an RNA mixture derived from three diverse cultured bacterial species and to RNA isolated from clinical stool samples. The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA.

A Study Of Correlations Between The Definition And Application Of The Gene Ontology, Yuji Mo

Department of Computer Electronics and Engineering: Dissertations, Theses, and Student Research

When using the Gene Ontology (GO), nucleotide and amino acid sequences are annotated by terms in a structured and controlled vocabulary organized into relational graphs. The usage of the vocabulary (GO terms) in the annotation of these sequences may diverge from the relations defined in the ontology. We measure the consistency of the use of GO terms by comparing GO's defined structure to the terms' application. To do this, we first use synthetic data with different characteristics to understand how these characteristics influence the correlation values determined by various similarity measures. Using these results as a baseline, we found that …