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Identification Of Relationships Between Patients Through Elements In A Data Warehouse Using The Familial, Associational, And Incidental Relationship (Fair) Initiative: A Pilot Study, Thomas M. English, Rebecca L. Kinney, Michael A. Davis, Ariana Kamberi, Wayne Chan, Rajani S. Sadasivam, Thomas K. Houston 2019 University of Massachusetts Medical School

Identification Of Relationships Between Patients Through Elements In A Data Warehouse Using The Familial, Associational, And Incidental Relationship (Fair) Initiative: A Pilot Study, Thomas M. English, Rebecca L. Kinney, Michael A. Davis, Ariana Kamberi, Wayne Chan, Rajani S. Sadasivam, Thomas K. Houston

Rajani S. Sadasivam

BACKGROUND: Over the last several years there has been widespread development of medical data warehouses. Current data warehouses focus on individual cases, but lack the ability to identify family members that could be used for dyadic or familial research. Currently, the patient's family history in the medical record is the only documentation we have to understand the health status and social habits of their family members. Identifying familial linkages in a phenotypic data warehouse can be valuable in cohort identification and in beginning to understand the interactions of diseases among families.

OBJECTIVE: The goal of the Familial, Associational, and ...


Fusarium Euwallacea: A Serious Threat To The Native And Ornamental Trees And Shrubs In Southern California, Greg Tyler, Yixing Zheng, Michael Kulinich, Hagop Atamian 2019 Chapman University

Fusarium Euwallacea: A Serious Threat To The Native And Ornamental Trees And Shrubs In Southern California, Greg Tyler, Yixing Zheng, Michael Kulinich, Hagop Atamian

Student Scholar Symposium Abstracts and Posters

Fusarium Euwallacea is a fungus that has established symbiotic relationship with the beetle Euwallacea aff. fornicata. The beetle bores through the tree bark and into the sapwood making long tunnels inside the trees. The beetle carries the F. Euwallacea in a specialized structure on its body called mandibular mycangia and cultivates the fungus in the tunnels on which the beetle feeds to grow and reproduce. The growth of the fungus obstructs water and mineral transport in the plant xylem tissue, resulting in dieback, wilt and mortality of the host tree. Fungi are known to secrete proteins called effectors in the ...


Analysis Of Motif Distributions In Regions Of Endocytic Proteins, Chante Bethell, Zuzana Kadlecova, PhD, Stephanie J. Spielman, PhD 2019 Bioinformatics, Rowan University

Analysis Of Motif Distributions In Regions Of Endocytic Proteins, Chante Bethell, Zuzana Kadlecova, Phd, Stephanie J. Spielman, Phd

Student Research Symposium Posters

A short linear motif (SLiM) is a recurring pattern of approximately three to ten amino acids found in proteins. SLiMs are important for cellular signaling and the regulating of proteins, often times by acting as binding sites for protein-binding domains. While SLiMs exist both in ordered regions of proteins where there is a tertiary structure and in disordered regions where there is no structure, they are primarily functional in disordered regions. An important example of SLiM-mediated processes and the focus of this study is endocytosis. Endocytosis is the process by which cells engulf molecules from the extracellular environment. There are ...


Genome-Wide Association Studies In Maize And Sorghum, Preston Hurst 2019 University of Nebraska - Lincoln

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

Theses, Dissertations, and Student Research in Agronomy and Horticulture

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 modification. A series ...


The Full Genome Sequence Of An Antarctic Microbe Constructed Using A Rapid, Portable Sequencer And A Hybrid Assembly, Bruce Wyatt Boles 2019 University of Tennessee, Knoxville

The Full Genome Sequence Of An Antarctic Microbe Constructed Using A Rapid, Portable Sequencer And A Hybrid Assembly, Bruce Wyatt Boles

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

Microbial genomes contain combinations of nucleotides that code for genes which subsequently determines the function of the cell. This information provides significant insight into the unique niche of microbes from extreme environments. Here we use two sequencing technologies, the Oxford Nanopore MinION with accompanying software and Illumina HiSeq, to generate a hybrid genome for a Shewanella strain isolated from an Antarctic glacier. Bioinformatic programs, Albacore and SPAdes, allowed us to decrease the time of genome assembly while also obtaining a large quantity of information related to the Shewanella sp. Our combined approach yielded a high quality genome assembly 5.3 ...


Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney 2019 University of Lynchburg

Co-Occurrence Of Manganese Oxidase Genes Indicates Lateral Transfer Between Classes Of Proteobacteria, Jacob Olichney

Student Scholar Showcase

Pseudomonas putida GB-1 is a model organism for the study of manganese oxidation in bacteria, however, the frequency of co-localization of multiple known and suspected manganese oxidizing proteins, as well as their occurrence between species, is unknown. Eight different genes isolated from known manganese oxidizing bacteria (MnxG, MopA, McoA, PputGB1_2552, PputGB1_2553, MoxA, MofA, and Bacillus MnxG) were tested individually using BioPython and BLAST (Basic Local Alignment Search Tool) on multiple genomic databases. BLAST searches had an expect value cutoff of 1e-50, limiting gene homologs to those with high sequence similarity. The abundance of homologous genes across classes of proteobacteria point ...


Response To Persistent Er Stress In Plants: A Multiphasic Process That Transitions Cells From Prosurvival Activities To Cell Death, Renu Srivastava, Zhaoxia Li, Giulia Russo, Jie Tang, Ran Bi, Usha Muppirala, Sivanandan Chudalayandi, Andrew J. Severin, Mingze He, Samuel I. Vaitkevicius, Carolyn J. Lawrence-Dill, Peng Liu, Ann E. Stapleton, Diane C. Bassham, Federica Brandizzi, Stephen H. Howell 2019 Iowa State University

Response To Persistent Er Stress In Plants: A Multiphasic Process That Transitions Cells From Prosurvival Activities To Cell Death, Renu Srivastava, Zhaoxia Li, Giulia Russo, Jie Tang, Ran Bi, Usha Muppirala, Sivanandan Chudalayandi, Andrew J. Severin, Mingze He, Samuel I. Vaitkevicius, Carolyn J. Lawrence-Dill, Peng Liu, Ann E. Stapleton, Diane C. Bassham, Federica Brandizzi, Stephen H. Howell

Diane Bassham

The unfolded protein response (UPR) is a highly conserved response that protects plants from adverse environmental conditions. The UPR is elicited by endoplasmic reticulum (ER) stress, in which unfolded and misfolded proteins accumulate within the ER. Here, we induced the UPR in maize (Zea mays) seedlings to characterize the molecular events that occur over time during persistent ER stress. We found that a multiphasic program of gene expression was interwoven among other cellular events, including the induction of autophagy. One of the earliest phases involved the degradation by regulated IRE1-dependent RNA degradation (RIDD) of RNA transcripts derived from a family ...


Gogo: An Improved Algorithm To Measure The Semantic Similarity Between Gene Ontology Terms, Chenguang Zhao 2019 The University of Southern Mississippi

Gogo: An Improved Algorithm To Measure The Semantic Similarity Between Gene Ontology Terms, Chenguang Zhao

Master's Theses

Measuring the semantic similarity between Gene Ontology (GO) terms is an essential step in functional bioinformatics research. We implemented a software named GOGO for calculating the semantic similarity between GO terms. GOGO has the advantages of both information-content-based and hybrid methods, such as Resnik’s and Wang’s methods. Moreover, GOGO is relatively fast and does not need to calculate information content (IC) from a large gene annotation corpus but still has the advantage of using IC. This is achieved by considering the number of children nodes in the GO directed acyclic graphs when calculating the semantic contribution of an ...


Scl: A Lattice-Based Approach To Infer Three-Dimensional Chromosome Structures From Single-Cell Hi-C Data, Hao Zhu 2019 The University of Southern Mississippi

Scl: A Lattice-Based Approach To Infer Three-Dimensional Chromosome Structures From Single-Cell Hi-C Data, Hao Zhu

Master's Theses

In contrast to population-based Hi-C data, single-cell Hi-C data are zero-inflated and do not indicate the frequency of proximate DNA segments. There are a limited number of computational tools that can model the three-dimensional structures of chromosomes based on single-cell Hi-C data.

We developed SCL (Single-Cell Lattice), a computational method to reconstruct three-dimensional (3D) structures of chromosomes based on single-cell Hi-C data. We designed a loss function and a 2D Gaussian function specifically for the characteristics of single-cell Hi-C data. A chromosome is represented as beads-on-a-string and stored in a 3D cubic lattice. Metropolis-Hastings simulation and simulated annealing are used ...


Agbiodata Consortium Recommendations For Sustainable Genomics And Genetics Databases For Agriculture, Lisa Harper, Jacqueline Campbell, Ethalinda K. S. Cannon, Monica Poelchau, Carson Andorf, Clayton Birkett, Steve Cannon, David Grant, Zhi-Liang Hu, Gerard Lazo, Rex Nelson, Carissa Park, James Reecy, Taner Z. Sen, Doreen Ware, Margaret Woodhouse 2019 United States Department of Agriculture

Agbiodata Consortium Recommendations For Sustainable Genomics And Genetics Databases For Agriculture, Lisa Harper, Jacqueline Campbell, Ethalinda K. S. Cannon, Monica Poelchau, Carson Andorf, Clayton Birkett, Steve Cannon, David Grant, Zhi-Liang Hu, Gerard Lazo, Rex Nelson, Carissa Park, James Reecy, Taner Z. Sen, Doreen Ware, Margaret Woodhouse

James M Reecy

The future of agricultural research depends on data. The sheer volume of agricultural biological data being produced today makes excellent data management essential. Governmental agencies, publishers and science funders require data management plans for publicly funded research. Furthermore, the value of data increases exponentially when they are properly stored, described, integrated and shared, so that they can be easily utilized in future analyses. AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development, curation and management, with the goal of creating database ...


Large-Scale Gene Co-Expression Network As A Source Of Functional Annotation For Cattle Genes, Hamid Beiki, Ardeshir Nejati-Javaremi, Abbas Pakdel, Ali Masoudi-Nejad, Zhi-Liang Hu, James M. Reecy 2019 Iowa State University

Large-Scale Gene Co-Expression Network As A Source Of Functional Annotation For Cattle Genes, Hamid Beiki, Ardeshir Nejati-Javaremi, Abbas Pakdel, Ali Masoudi-Nejad, Zhi-Liang Hu, James M. Reecy

James M Reecy

Background: Genome sequencing and subsequent gene annotation of genomes has led to the elucidation of many genes, but in vertebrates the actual number of protein coding genes are very consistent across species (~20,000). Seven years after sequencing the cattle genome, there are still genes that have limited annotation and the function of many genes are still not understood, or partly understood at best. Based on the assumption that genes with similar patterns of expression across a vast array of tissues and experimental conditions are likely to encode proteins with related functions or participate within a given pathway, we constructed ...


Go‐Faang Meeting: A Gathering On Functional Annotation Of Animal Genomes, Christopher K. Tuggle, Elisabetta Giuffra, Stephen N. White, Laura Clarke, Huaijun Zhou, Pablo J. Ross, Herve Acloque, James M. Reecy, Alan Archibald, Rebecca R. Bellone, Michele Boichard, Amanda Chamberlain, Hans Cheng, Richard P. M. A. Crooijmans, Mary E. Delany, Carrie J. Finno, Martien A. M. Groenen, Ben Hayes, Joan K. Lunney, Jessica L. Petersen, Graham S. Plastow, Carl J. Schmidt, Jiuzhou Song, Mick Watson 2019 Iowa State University

Go‐Faang Meeting: A Gathering On Functional Annotation Of Animal Genomes, Christopher K. Tuggle, Elisabetta Giuffra, Stephen N. White, Laura Clarke, Huaijun Zhou, Pablo J. Ross, Herve Acloque, James M. Reecy, Alan Archibald, Rebecca R. Bellone, Michele Boichard, Amanda Chamberlain, Hans Cheng, Richard P. M. A. Crooijmans, Mary E. Delany, Carrie J. Finno, Martien A. M. Groenen, Ben Hayes, Joan K. Lunney, Jessica L. Petersen, Graham S. Plastow, Carl J. Schmidt, Jiuzhou Song, Mick Watson

James M Reecy

The Functional Annotation of Animal Genomes (FAANG) Consortium recently held a Gathering On FAANG (GO‐FAANG) Workshop in Washington, DC on October 7–8, 2015. This consortium is a grass‐roots organization formed to advance the annotation of newly assembled genomes of domesticated and non‐model organisms (www.faang.org). The workshop gathered together from around the world a group of 100+ genome scientists, administrators, representatives of funding agencies and commodity groups to discuss the latest advancements of the consortium, new perspectives, next steps and implementation plans. The workshop was streamed live and recorded, and all talks, along with speaker ...


Bioinformatic Analyses In Early Host Response To Porcine Reproductive And Respiratory Syndrome Virus (Prrsv) Reveals Pathway Differences Between Pigs With Alternate Genotypes For A Major Host Response Qtl, Martine Schroyen, Christopher Eisley, James E. Koltes, Eric Fritz-Waters, Igseo Choi, Graham S. Plastow, Leluo Guan, Paul Stothard, Hua Bao, Arun Kommadath, James M. Reecy, Joan K. Lunney, Robert R. R. Rowland, Jack C. M. Dekkers, Christopher K. Tuggle 2019 Iowa State University

Bioinformatic Analyses In Early Host Response To Porcine Reproductive And Respiratory Syndrome Virus (Prrsv) Reveals Pathway Differences Between Pigs With Alternate Genotypes For A Major Host Response Qtl, Martine Schroyen, Christopher Eisley, James E. Koltes, Eric Fritz-Waters, Igseo Choi, Graham S. Plastow, Leluo Guan, Paul Stothard, Hua Bao, Arun Kommadath, James M. Reecy, Joan K. Lunney, Robert R. R. Rowland, Jack C. M. Dekkers, Christopher K. Tuggle

James M Reecy

Background: A region on Sus scrofa chromosome 4 (SSC4) surrounding single nucleotide polymorphism (SNP) marker WUR10000125 (WUR) has been reported to be strongly associated with both weight gain and serum viremia in pigs after infection with PRRS virus (PRRSV). A proposed causal mutation in the guanylate binding protein 5 gene (GBP5) is predicted to truncate the encoded protein. To investigate transcriptional differences between WUR genotypes in early host response to PRRSV infection, an RNA-seq experiment was performed on globin depleted whole blood RNA collected on 0, 4, 7, 10 and 14 days post-infection (dpi) from eight littermate pairs with one ...


Similarities And Differences Between Variants Called With Human Reference Genome Hg19 Or Hg38, Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuantin Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong 2019 U.S. Food and Drug Administration

Similarities And Differences Between Variants Called With Human Reference Genome Hg19 Or Hg38, Bohu Pan, Rebecca Kusko, Wenming Xiao, Yuantin Zheng, Zhichao Liu, Chunlin Xiao, Sugunadevi Sakkiah, Wenjing Guo, Ping Gong, Chaoyang Zhang, Weigong Ge, Leming Shi, Weida Tong, Huixiao Hong

Faculty Publications

Background

Reference genome selection is a prerequisite for successful analysis of next generation sequencing (NGS) data. Current practice employs one of the two most recent human reference genome versions: HG19 or HG38. To date, the impact of genome version on SNV identification has not been rigorously assessed.

Methods

We conducted analysis comparing the SNVs identified based on HG19 vs HG38, leveraging whole genome sequencing (WGS) data from the genome-in-a-bottle (GIAB) project. First, SNVs were called using 26 different bioinformatics pipelines with either HG19 or HG38. Next, two tools were used to convert the called SNVs between HG19 and HG38. Lastly ...


Predicting Protein Residue-Residue Contacts Using Random Forests And Deep Networks, Joseph Luttrell IV, Tong Liu, Chaoyang Zhang, Zheng Wang 2019 University of Southern Mississippi

Predicting Protein Residue-Residue Contacts Using Random Forests And Deep Networks, Joseph Luttrell Iv, Tong Liu, Chaoyang Zhang, Zheng Wang

Faculty Publications

No abstract provided.


Poster: Image Disguising For Privacy-Preserving Deep Learning, Sagar Sharma, Keke Chen 2019 Wright State University - Main Campus

Poster: Image Disguising For Privacy-Preserving Deep Learning, Sagar Sharma, Keke Chen

Keke Chen

No abstract provided.


Towards Practical Privacy-Preserving Analytics For Iot And Cloud Based Healthcare Systems, Sagar Sharma, Keke Chen, Amit P. Sheth 2019 Wright State University - Main Campus

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

Keke Chen

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 that ...


Poster: Privacy-Preserving Boosting With Random Linear Classifiers, Sagar Sharma, Keke Chen 2019 Wright State University - Main Campus

Poster: Privacy-Preserving Boosting With Random Linear Classifiers, Sagar Sharma, Keke Chen

Keke Chen

We propose SecureBoost, a privacy-preserving predictive modeling framework, that allows service providers (SPs) to build powerful boosting models over encrypted or randomly masked user submit- ted data. SecureBoost uses random linear classifiers (RLCs) as the base classifiers. A Cryptographic Service Provider (CSP) manages keys and assists the SP’s processing to reduce the complexity of the protocol constructions. The SP learns only the base models (i.e., RLCs) and the CSP learns only the weights of the base models and a limited leakage function. This separated parameter holding avoids any party from abusing the final model or conducting model-based attacks ...


Augmented Personalized Health: Using Semantically Integrated Multimodal Data For Patient Empowered Health Management Strategies, Amit P. Sheth, Hong Y. Yip, Utkarshani Jaimini, Dipesh Kadariya, Vaikunth Sridharan, R. Venkataramanan, Tanvi Banerjee, Krishnaprasad Thirunarayan, Maninder Kalra 2019 Wright State University - Main Campus

Augmented Personalized Health: Using Semantically Integrated Multimodal Data For Patient Empowered Health Management Strategies, Amit P. Sheth, Hong Y. Yip, Utkarshani Jaimini, Dipesh Kadariya, Vaikunth Sridharan, R. Venkataramanan, Tanvi Banerjee, Krishnaprasad Thirunarayan, Maninder Kalra

Krishnaprasad Thirunarayan

Healthcare as we know it is in the process of going through a massive change from:

1. Episodic to continuous

2. Disease-focused to wellness and quality of life focused

3. Clinic-centric to anywhere a patient is

4. Clinician controlled to patient empowered

5. Being driven by limited data to 360-degree, multimodal personal-public-population physical-cyber-social big data-driven URL: https://mhealth.md2k.org/2018-tech-showcase-home


Personalized Prediction Of Suicide Risk For Web-Based Intervention, Amanuel Alambo, Manas Gaur, Ugur Kursuncu, Krishnaprasad Thirunarayan, Jeremiah Schumm, Jyotishman Pathak, Amit P. Sheth 2019 Wright State University - Main Campus

Personalized Prediction Of Suicide Risk For Web-Based Intervention, Amanuel Alambo, Manas Gaur, Ugur Kursuncu, Krishnaprasad Thirunarayan, Jeremiah Schumm, Jyotishman Pathak, Amit P. Sheth

Krishnaprasad Thirunarayan

Across the United States, suicide is the second leading cause of death for people aged between 15 and 34, and younger people are more prone to mental health problems, suicidal thoughts, and behaviors. For instance, 80% of patients with Borderline Personality Disorder have suicide-related behaviors, and between 4-9% of them commit suicide. Moreover, the social stigma associated with mental health issues and suicide deter patients from sharing their experiences directly with others. In such a situation, social media that provides a free and open forum for voluntary expression can provide insights into suicide ideation and self-destructive behavior.

Reddit is a ...


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