Computer Sciences Commons^™

Recta: Regulon Identification Based On Comparative Genomics And Transcriptomics Analysis, Xin Chen, Anjun Ma, Adam Mcdermaid, Hanyuan Zhang, Chao Liu, Huansheng Cao, Qin Ma

School of Computing: Faculty Publications

Regulons, which serve as co-regulated gene groups contributing to the transcriptional regulation of microbial genomes, have the potential to aid in understanding of underlying regulatory mechanisms. In this study, we designed a novel computational pipeline, regulon identification based on comparative genomics and transcriptomics analysis (RECTA), for regulon prediction related to the gene regulatory network under certain conditions. To demonstrate the effectiveness of this tool, we implemented RECTA on Lactococcus lactis MG1363 data to elucidate acid-response regulons. A total of 51 regulons were identified, 14 of which have computational-verified significance. Among these 14 regulons, five of them were computationally predicted to …

Ai-Human Collaboration Via Eeg, Adam Noack

All College Thesis Program, 2016-2019

As AI becomes ever more competent and integrated into our lives, the issue of AI-human goal misalignment looms larger. This is partially because there is often a rift between what humans explicitly command and what they actually mean. Most contemporary AI systems cannot bridge this gap. In this study we attempted to reconcile the goals of human and machine by using EEG signals from a human to help a simulated agent complete a task.

Computer Vision Evidence Supporting Craniometric Alignment Of Rat Brain Atlases To Streamline Expert-Guided, First-Order Migration Of Hypothalamic Spatial Datasets Related To Behavioral Control, Arshad Khan, Jose Perez, Claire Wells, Olac Fuentes

Selected Works Temporary Series

The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982) or Swanson (S, first published in 1992) as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. Such data migration would allow …

Computer Vision Evidence Supporting Craniometric Alignment Of Rat Brain Atlases To Streamline Expert-Guided, First-Order Migration Of Hypothalamic Spatial Datasets Related To Behavioral Control, Khan, Jose Perez, Claire Wells, Olac Fuentes

Departmental Papers (Biology)

The rat has arguably the most widely studied brain among all animals, with numerous reference atlases for rat brain having been published since 1946. For example, many neuroscientists have used the atlases of Paxinos and Watson (PW, first published in 1982) or Swanson (S, first published in 1992) as guides to probe or map specific rat brain structures and their connections. Despite nearly three decades of contemporaneous publication, no independent attempt has been made to establish a basic framework that allows data mapped in PW to be placed in register with S, or vice versa. …

Region Based Gene Expression Via Reanalysis Of Publicly Available Microarray Data Sets., Ernur Saka

Electronic Theses and Dissertations

A DNA microarray is a high-throughput technology used to identify relative gene expression. One of the most widely used platforms is the Affymetrix® GeneChip® technology which detects gene expression levels based on probe sets composed of a set of twenty-five nucleotide probes designed to hybridize with specific gene targets. Given a particular Affymetrix® GeneChip® platform, the design of the probes is fixed. However, the method of analysis is dynamic in nature due to the ability to annotate and group probes into uniquely defined groupings. This is particularly important since publicly available repositories of microarray datasets, such as ArrayExpress and NCBI’s …

Self-Organized Structures: Modeling Polistes Dominula Nest Construction With Simple Rules, Matthew Harrison

Electronic Theses and Dissertations

The self-organized nest construction behaviors of European paper wasps (Polistes dominula) show potential for adoption in artificial intelligence and robotic systems where centralized control proves challenging. However, P. dominula nest construction mechanisms are not fully understood. This research investigated how nest structures stimulate P. dominula worker action at different stages of nest construction. A novel stochastic site selection model, weighted by simple rules for cell age, height, and wall count, was implemented in a three-dimensional, step-by-step nest construction simulation. The simulation was built on top of a hexagonal coordinate system to improve precision and performance. Real and idealized …

Bayesian Network Modeling And Inference Of Gwas Catalog, Qiuping Pan

Graduate Theses and Dissertations

Genome-wide association studies (GWASs) have received an increasing attention to understand genotype-phenotype relationships. The Bayesian network has been proposed as a powerful tool for modeling single-nucleotide polymorphism (SNP)-trait associations due to its advantage in addressing the high computational complex and high dimensional problems. Most current works learn the interactions among genotypes and phenotypes from the raw genotype data. However, due to the privacy issue, genotype information is sensitive and should be handled by complying with specific restrictions. In this work, we aim to build Bayesian networks from publicly released GWAS statistics to explicitly reveal the conditional dependency between SNPs and …

Efficient Reduced Bias Genetic Algorithm For Generic Community Detection Objectives, Aditya Karnam Gururaj Rao

Theses

The problem of community structure identification has been an extensively investigated area for biology, physics, social sciences, and computer science in recent years for studying the properties of networks representing complex relationships. Most traditional methods, such as K-means and hierarchical clustering, are based on the assumption that communities have spherical configurations. Lately, Genetic Algorithms (GA) are being utilized for efficient community detection without imposing sphericity. GAs are machine learning methods which mimic natural selection and scale with the complexity of the network. However, traditional GA approaches employ a representation method that dramatically increases the solution space to be searched by …

Similarity Based Classification Of Adhd Using Singular Value Decomposition, Taban Eslami, Fahad Saeed

Parallel Computing and Data Science Lab Technical Reports

Attention deficit hyperactivity disorder (ADHD) is one of the most common brain disorders among children. This disorder is considered as a big threat for public health and causes attention, focus and organizing difficulties for children and even adults. Since the cause of ADHD is not known yet, data mining algorithms are being used to help discover patterns which discriminate healthy from ADHD subjects. Numerous efforts are underway with the goal of developing classification tools for ADHD diagnosis based on functional and structural magnetic resonance imaging data of the brain. In this paper, we used Eros, which is a technique for …

Big Fish, Big Data: Discussing The State Of Salmon And Improving King Salmon Regulation Through A Population Model, Creed Coram 18

Honor Scholar Theses

No abstract provided.

Evaluating Reproducibility In Computational Biology Research, Morgan Oneka

Honors Projects

For my Honors Senior Project, I read five research papers in the field of computational biology and attempted to reproduce the results. However, for the most part, this proved a challenge, as many details vital to utilizing relevant software and data had been excluded. Using Geir Kjetil Sandve's paper "Ten Simple Rules for Reproducible Computational Research" as a guide, I discuss how authors of these five papers did and did not obey these rules of reproducibility and how this affected my ability to reproduce their results.

Volume 10, Taylor Hogg, Tiffany Carter, Brandyn Johnson, Haleigh James, Josh Baker, Tyler Cernak, Kirsten Bauer, Allie Snavely, Mary Zell Galen, Eric Powell, Thomas Wise, Katie Kinsey, Beth Barbolla, Maeleigh Ferlet, Rebecca Morra, Michala Day, Alexandra Evangelista, Max Flores, Harley Hodges, Clardene Jones, Harrison Samaniego, Jamesha Watson, Abby Gargiulo, Heather Green, Haley Klepatzki, Juan Guevara, Dani Bondurant, Michael Joseph Link Jr., Pamela Dahl, Maeve Losen, Charlotte Murphey

Incite: The Journal of Undergraduate Scholarship

Introduction Dr. Roger A. Byrne

An Analysis of Media Framing in Cases of Violence Against Women by Taylor Hogg

Writing in the Discipline of Nursing by Tiffany Carter

Photography by Brandyn Johnson

The Hidden Life of Beef Cattle: A Study of Cattle Welfare on Traditional Ranches and Industrial Farms by Haleigh James

Bloodworth's by Josh Baker and Tyler Cernak

Prosimians: Little Bodies, Big Significance by Kirsten Bauer

Skinformed by Allie Snavely

Coopertition and Gracious Professionalism: The Effects of First Robotics Folklore and Culture on the Stem Community by Mary Zell Galen

Tilt by Eric Powell And Thomas Wise

The Millennial …

Tracing Actin Filament Bundles In Three-Dimensional Electron Tomography Density Maps Of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, Jing He

Computer Science Faculty Publications

Cryo-electron tomography (cryo-ET) is a powerful method of visualizing the three-dimensional organization of supramolecular complexes, such as the cytoskeleton, in their native cell and tissue contexts. Due to its minimal electron dose and reconstruction artifacts arising from the missing wedge during data collection, cryo-ET typically results in noisy density maps that display anisotropic XY versus Z resolution. Molecular crowding further exacerbates the challenge of automatically detecting supramolecular complexes, such as the actin bundle in hair cell stereocilia. Stereocilia are pivotal to the mechanoelectrical transduction process in inner ear sensory epithelial hair cells. Given the complexity and dense arrangement of actin …

Prediction Of Lncrna-Disease Associations Based On Inductive Matrix Completion, Chengqian Lu, Mengyun Yang, Feng Luo, Fang-Xiang Wu, Min Li, Yi Pan, Yaohang Li, Jianxin Wang

Computer Science Faculty Publications

Motivation: Accumulating evidences indicate that long non-coding RNAs (lncRNAs) play pivotal roles in various biological processes. Mutations and dysregulations of lncRNAs are implicated in miscellaneous human diseases. Predicting lncRNA–disease associations is beneficial to disease diagnosis as well as treatment. Although many computational methods have been developed, precisely identifying lncRNA–disease associations, especially for novel lncRNAs, remains challenging.

Results: In this study, we propose a method (named SIMCLDA) for predicting potential lncRNA– disease associations based on inductive matrix completion. We compute Gaussian interaction profile kernel of lncRNAs from known lncRNA–disease interactions and functional similarity of diseases based on disease–gene and gene–gene onotology …

Using Computer Algorithms To Elucidate Zebra Finch Reproductive Behaviour, Tanya T. Shoot, Sophie C. Edwards, Robert J. Martin, Susan D. Healy, David F. Sherry, Mark J. Daley

Western Research Forum

Birds that experience variation in climatic conditions must maintain a stable nest temperature during incubation for successful hatching of offspring. Varying nest structure and incubation behaviour may be the methods birds use to regulate nest temperature. We used a modeling approach to investigate how birds adjust incubation behaviour to ambient temperature.

Hidden Markov Models (HMM) have been used previously to predict the spatial distribution of animals based on the models’ ability to classify movement behaviour. We used a HMM to predict zebra finch (Taeniopygia guttata) incubation behaviour and nest structure from a nest temperature data set. The full …

Seed Dormancy-Life Form Profile For 358 Species From The Xishuangbanna Seasonal Tropical Rainforest, Yunnan Province, China Compared To World Database, Qinying Lan, Shouhua Yin, Huiyin He, Yunhong Tan, Qiang Liu, Yongmei Xia, Bin Wen, Carol C. Baskin, Jerry M. Baskin

Biology Faculty Publications

Seed dormancy profiles are available for the major vegetation regions/types on earth. These were constructed using a composite of data from locations within each region. Furthermore, the proportion of species with nondormant (ND) seeds and the five classes of dormancy is available for each life form in each region. Using these data, we asked: will the results be the same if many species from a specific area as opposed to data compiled from many locations are considered? Germination was tested for fresh seeds of 358 species in 95 families from the Xishuangbanna seasonal tropical rainforest (XSTRF): 177 trees, 66 shrubs, …

Towards Practical Privacy-Preserving Analytics For Iot And Cloud Based Healthcare Systems, Sagar Sharma, Keke Chen, Amit P. Sheth

Kno.e.sis Publications

Modern healthcare systems now rely on advanced computing methods and technologies, such as IoT devices and clouds, to collect and analyze personal health data at unprecedented scale and depth. Patients, doctors, healthcare providers, and researchers depend on analytical models derived from such data sources to remotely monitor patients, early-diagnose diseases, and find personalized treatments and medications. However, without appropriate privacy protection, conducting data analytics becomes a source of privacy nightmare. In this paper, we present the research challenges in developing practical privacy-preserving analytics in healthcare information systems. The study is based on kHealth - a personalized digital healthcare information system …

The Pharmacogene Variation (Pharmvar) Consortium: Incorporation Of The Human Cytochrome P450 (Cyp) Allele Nomenclature Database, Andrea Gaedigk, Magnus Ingelman-Sundberg, Neil A. Miller, J Steven Leeder, Michelle Whirl-Carrillo, Teri E. Klein

Manuscripts, Articles, Book Chapters and Other Papers

The Human Cytochrome P450 (CYP) Allele Nomenclature Database, a critical resource to the pharmacogenetics and genomics communities, will be transitioning to the Pharmacogene Variation (PharmVar) Consortium. In this report we provide a summary of the current database, provide an overview of the PharmVar consortium and highlight the PharmVar database which will serve as the new home for pharmacogene nomenclature.

Automating Data Analysis For Two-Dimensional Gas Chromatography/Time-Of-Flight Mass Spectrometry Non-Targeted Analysis Of Comparative Samples, Ivan A. Titaley, O. Maduka Ogba, Leah Chibwe, Eunha Hoh, Paul H.-Y. Cheong, Staci L. Massey Simonich

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Non-targeted analysis of environmental samples, using comprehensive two‐dimensional gas chromatography coupled with time-of-flight mass spectrometry (GC × GC/ToF-MS), poses significant data analysis challenges due to the large number of possible analytes. Non-targeted data analysis of complex mixtures is prone to human bias and is laborious, particularly for comparative environmental samples such as contaminated soil pre- and post-bioremediation. To address this research bottleneck, we developed OCTpy, a Python™ script that acts as a data reduction filter to automate GC × GC/ToF-MS data analysis from LECO^® ChromaTOF^® software and facilitates selection of analytes of interest based on peak area …

Auditing Snomed Ct Hierarchical Relations Based On Lexical Features Of Concepts In Non-Lattice Subgraphs, Licong Cui, Olivier Bodenreider, Jay Shi, Guo-Qiang Zhang

Computer Science Faculty Publications

Objective—We introduce a structural-lexical approach for auditing SNOMED CT using a combination of non-lattice subgraphs of the underlying hierarchical relations and enriched lexical attributes of fully specified concept names. Our goal is to develop a scalable and effective approach that automatically identifies missing hierarchical IS-A relations.

Methods—Our approach involves 3 stages. In stage 1, all non-lattice subgraphs of SNOMED CT’s IS-A hierarchical relations are extracted. In stage 2, lexical attributes of fully-specified concept names in such non-lattice subgraphs are extracted. For each concept in a non-lattice subgraph, we enrich its set of attributes with attributes from its ancestor …

Growth Performance, Organ-Level Ionic Relations And Organic Osmoregulation Of Elaeagnus Angustifolia In Response To Salt Stress, Zhengxiang Liu, Jiangfeng Zhu, Xiuyan Yang, Haiwen Wu, Qi Wei, Hairong Wei, Huaxin Zhang

Michigan Tech Publications, Part 1

Elaeagnus angustifolia is one of the most extensively afforested tree species in environment-harsh regions of northern China. Despite its exceptional tolerance to saline soil, the intrinsic adaptive physiology has not been revealed. In this study, we investigated the growth, organ-level ionic relations and organic osmoregulation of the seedlings hydroponically treated with 0, 100 and 200 mM NaCl for 30 days. We found that the growth characteristics and the whole-plant dry weight were not obviously stunted, but instead, were even slightly stimulated by the treatment of 100 mM NaCl. In contrast, these traits were significantly inhibited by 200 mM NaCl treatment. …

The Effect Of Poplar Psngs1.2 Overexpression On Growth, Secondary Cell Wall, And Fiber Characteristics In Tobacco, Tingting Lu, Lulu Liu, Minjing Wei, Yingying Liu, Zianshang Qu, Chuanping Yang, Hairong Wei, Zhigang Wei

Michigan Tech Publications, Part 1

The glutamine synthetase (GS1) is a key enzyme that catalyzes the reaction of glutamate and ammonia to produce glutamine in the nitrogen (N) metabolism. Previous studies on GS1s in several plant species suggest that overexpression of GS1s can enhance N utilization, accelerate plant vegetative growth, and change wood formation. In this study, we isolated a GS1 gene, termed PsnGS1.2, from Populus simonii × Populus nigra. This gene was expressed at a higher level in roots, and relatively lower but detectable levels in xylem, leaves and phloem of P. simonii × P. nigra. The protein encoded by PsnGS1.2 is …

Model File Name: 1ehz-Trna(Thick).Stl, Michelle Howell, Karin Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1ehz-tRNA(thick).stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of Phe-tRNA in a thick stick-representation (PDB: 1ehz), designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com under the name “tRNA-Phe small”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following materials: Strong & Flexible Plastic and Elasto Plastic.

Model File Name: 1lmb-Dbd-Tfmono.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-DBD-TFmono.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of the DNA binding domain of a Lambda repressor transcription factor monomer that accompanies the full color DNA helix (PDB: 1lmb). It is in a cartoon ribbon representation with key amino acid residues in stick representation to highlight interactions with the DNA. This model is designed to accompany a teaching module illustrating transcription factor-DNA binding. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Lambda TF DBD”. This model has been printed …

Model File Name: 1ehz-Trna(Thin-Big).X3d, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1ehz-tRNA(thin-big).x3d

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of Phe-tRNA in a large, but thin stick-representation (PDB: 1ehz), designed to go with a teaching module comparing DNA and RNA basic structures and functions. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “Full color Phe-tRNA (1ehz)”. This model has been printed successfully using these parameters on Shapeways’ laser sintering printer in the following material: Strong & Flexible Plastic.

Model File Name: 1lmb-Dnalong_Fordimer-Test6b.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-DNAlong_fordimer-test6b.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of the 19-bp segment of DNA to which Lambda repressor transcription factor interacts (PDB: 1lmb). It is in a stick representation and has been designed with sites to add magnets to illustrate binding interactions with the transcription factor. Sphere magnets with a 1/8” diameter can be purchased separately from K&J Magnets. The model can interact with the dimer form of the transcription factor. This model is designed to accompany a teaching module illustrating transcription factor-DNA binding. The printable model …

Model File Name: 1lmb-Tfdimer-Mags-Joints-Jnd-Sc1-8-Parts-V4b.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: 1lmb-TFdimer-mags-joints-jnd-sc1-8-parts-v4b.stl

Additional files: 1lmb-Lys-Ser-extras-v4b.stl and 1lmb-TFdimer-Leu-v4b.stl

Authors: Michelle E Howell, Karin van Dijk, Rebecca L Roston

This is a teaching model of a ribbon and stick representation of the transcription factor lambda repressor (PDB: 1lmb). Key amino acid residues are in stick representation to illustrate the interactions between the repressor and the DNA to which it binds. Some of these residues have been designed with sites to add magnets to illustrate these interactions. Sphere magnets with a 1/8” diameter can be purchased separately from K&J Magnets. Some of the residues can be interchanged with other …

Model File Name: Dna-294bp-Magnet-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-294bp-magnet-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (294 bp). The DNA model has small sites on the ends where the user can glue magnets to mimic circular DNA, and to aid in manipulating the model. Disc magnets with a diameter of 1/8” or 1/10” and thickness of 1/16” can be purchased online from K&J Magnetics and glued into the magnet sites. The model is designed to go with a teaching module on DNA supercoiling. The model can …

Model File Name: Dna-294bp-Handle-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-294bp-handle-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (294 bp). The DNA model has small handles on the ends to aid in holding and manipulating the model. The model is designed to go with a teaching module on DNA supercoiling. The model can be accompanied by Nucleosome and H1 histone models to demonstrate DNA packaging in the cell. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “294bp DNA (handles)”. …

Model File Name: Dna-420bp-Handle-Supercoil.Stl, Michelle Howell, Karin V. Van Dijk, Kalika Mahato, Rebecca Roston

3-D Printed Model Structural Files

Model file name: DNA-420bp-handle-supercoil.stl

Authors: Michelle E Howell, Karin van Dijk, Kalika Mahato, Rebecca L Roston

This is a teaching model of a long, thin representation of double stranded DNA (420 bp). The DNA model has small handles on the ends to aid in holding and manipulating the model. The model is designed to go with a teaching module on DNA supercoiling. The model can be accompanied by Nucleosome and H1 histone models to demonstrate DNA packaging in the cell. The printable model is already uploaded to Shapeways.com in the MacroMolecules shop under the name “420bp DNA (handles)”. …