Open Access. Powered by Scholars. Published by Universities.®

Bioinformatics Commons

Open Access. Powered by Scholars. Published by Universities.®

2,943 Full-Text Articles 4,382 Authors 352,676 Downloads 116 Institutions

All Articles in Bioinformatics

Faceted Search

2,943 full-text articles. Page 1 of 109.

Phr: Patient Health Record, Quinn Nelson 2018 University of Nebraska at Omaha

Phr: Patient Health Record, Quinn Nelson

Theses/Capstones/Creative Projects

The rapid development of information technology systems has expanded into multiple disciplines and results in systems that are limited by initial design and implementation: the Healthcare Information Technology (HIT) space is no different. The introduction of the Electronic Health Record (EHR) system has changed the way healthcare operates. Initial designs of these systems were focused on serving the needs of insurance companies and healthcare billing departments. Research shows that the design of EHR systems negatively impact provider-patient interactions and the care they receive. This capstone project capitalizes on the collaboration efforts between UNO and UNMC – by joining a research group ...


Mapping Molecular Datasets Back To The Brain Regions They Are Extracted From: Remembering The Native Countries Of Hypothalamic Expatriates And Refugees, Arshad M. Khan, Alice H. Grant, Anais Martinez, Gully APC Burns, Brendan S. Thatcher, Vishwanath T. Anekonda, Benjamin W. Thompson, Zachary S. Roberts, Daniel H. Moralejo, James E. Blevins 2018 University of Texas at El Paso

Mapping Molecular Datasets Back To The Brain Regions They Are Extracted From: Remembering The Native Countries Of Hypothalamic Expatriates And Refugees, Arshad M. Khan, Alice H. Grant, Anais Martinez, Gully Apc Burns, Brendan S. Thatcher, Vishwanath T. Anekonda, Benjamin W. Thompson, Zachary S. Roberts, Daniel H. Moralejo, James E. Blevins

Arshad M. Khan, Ph.D.

This article, which includes novel unpublished data along with commentary and analysis,
focuses on approaches to link transcriptomic, proteomic, and peptidomic datasets mined from
brain tissue to the original locations within the brain that they are derived from using digital atlas
mapping techniques. We use, as an example, the transcriptomic, proteomic and peptidomic
analyses conducted in the mammalian hypothalamus. Following a brief historical overview, we
highlight studies that have mined biochemical and molecular information from the hypothalamus
and then lay out a strategy for how these data can be linked spatially to the mapped locations in a
canonical brain atlas ...


Polygenic Scores For Metabolic Traits And Related Drug Prescriptions In The Michigan Genomics Initiative, Samuel K. Handelman, Xiaomeng Du, Yanhua H. Chen, Elizabeth K. Speliotes 2018 University of Michigan-Ann Arbor

Polygenic Scores For Metabolic Traits And Related Drug Prescriptions In The Michigan Genomics Initiative, Samuel K. Handelman, Xiaomeng Du, Yanhua H. Chen, Elizabeth K. Speliotes

Biology and Medicine Through Mathematics Conference

No abstract provided.


Investigation Into The Amino Acid Characteristic Of Intrinsically Disordered Proteins, Samantha Patterson 2018 University of Wyoming

Investigation Into The Amino Acid Characteristic Of Intrinsically Disordered Proteins, Samantha Patterson

Honors Theses AY 17/18

Caulobacter crescentus, which belongs to the class of Alphaproteobacteria, has a highly organized cytoplasm that includes complex macromolecular structures at the cell poles. These polar complexes are assembled through the activity of a scaffolding protein, known as the Polar Organizing Protein Z (PopZ). PopZ interacts with other proteins via an N-terminal domain that is mostly intrinsically disordered, and contains, an abundance of proline, glutamte, and aspartate (P,E, and D) residues. Surprisingly, scrambling the order of amino acids in the PED region does not affect PopZ function, suggesting that binding affinity and specificity are not dependent on interactions with individual ...


Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Mourin Azar, Dr. Lori Scott 2018 Augustana College, Rock Island Illinois

Functional Studies Of The E. Coli Proc And A Putative Ortholog Mrub_1345, Mourin Azar, Dr. Lori Scott

Meiothermus ruber Genome Analysis Project

This project is part of the Meiothermus ruber genome analysis project, which uses the bioinformatics tools associated with the Guiding Education through Novel Investigation –Annotation Collaboration Toolkit (GENI-ACT) to predict gene function. We investigated the biological function of Escherichia coli and Meiothermus ruber proC genes using the complementation assay. In this research project, mutants of varying severity to the functional state of the protein were developed. The results showed that two or more amino acid deletions reduced or eliminated ProC function. Amino acid substitutions, on the other hand, were not severe enough to impact ProC function. Double and triple mutants ...


Bayesian Network Modeling And Inference Of Gwas Catalog, Qiuping Pan 2018 University of Arkansas, Fayetteville

Bayesian Network Modeling And Inference Of Gwas Catalog, Qiuping Pan

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 ...


Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, Bridget E. Hegarty, Jordan Peccia, Ratanachat Racharaks 2018 Yale University

Transcriptomics To Develop Biochemical Network Models In Cyanobacteria, Bridget E. Hegarty, Jordan Peccia, Ratanachat Racharaks

Yale Day of Data

Through targeted genetic manipulations guided by network modeling, we will create a flexible, cyanobacteria-based platform for the production of biofuel-precursors and valuable chemical products. To build gene-metabolite predictive models, we have characterized Synecococcus elongatus sp. UTEX 2973’s (henceforth, UTEX 2973) gene expression and metabolite production under a number of environmental conditions.


The Influence Of Conservation Tillage And Conventional Tillage On Soil Bacterial Diversity In Southern Illinois, Nasser Syed 2018 The University of Southern Mississippi

The Influence Of Conservation Tillage And Conventional Tillage On Soil Bacterial Diversity In Southern Illinois, Nasser Syed

Dissertations

Agriculture in the Midwest United States (Illinois, Indiana, Iowa, Michigan, Minnesota, Ohio, and Wisconsin) is a critically important component of the United States economy and also for world exports of food grain. This is well reflected in the 2012 Census of Agriculture which showed that these states had a market value of crop and livestock products sold in excess of $80,000,000,000 (USDA, 2012). Within the U.S. the three Midwest states, Illinois, Iowa, and Minnesota are ranked 2nd, 3rd, and 4th for the economic value of crops sold. This economic value of agriculture in the Midwest encompasses ...


Similarity Based Classification Of Adhd Using Singular Value Decomposition, Taban Eslami, Fahad Saeed 2018 Western Michigan University

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 ...


Developing A Bioinformatics Program And Supporting Infrastructure In A Biomedical Library, Nathan Hosburgh 2018 National Institutes of Health

Developing A Bioinformatics Program And Supporting Infrastructure In A Biomedical Library, Nathan Hosburgh

Journal of eScience Librarianship

Background: Over the last couple decades, the field of bioinformatics has helped spur medical discoveries that offer a better understanding of the genetic basis of disease, which in turn improve public health and save lives. Concomitantly, support requirements for molecular biology researchers have grown in scope and complexity, incorporating specialized resources, technologies, and techniques.

Case Presentation: To address this specific need among National Institutes of Health (NIH) intramural researchers, the NIH Library hired an expert bioinformatics trainer and consultant with a PhD in biochemistry to implement a bioinformatics support program. This study traces the program from its inception in 2009 ...


Killi-Data News (Winter), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

Valued readers, it is with a heavy heart that I inform you that this is the last issue of Killi-Data News. The good news is that we will be back as Killifish Research Review. The dissolution of Killi-Data International created a prob- lem: how can the newsletter of a defunct organization live on without that organization? But other additional problems were building in the background. The first issue numbered 15 pages. The previous issue was 28 pages. The number of killifish related papers is increasing while time on our end (the editorial team) is running out. It takes a lot ...


Killi-Data News (Fall), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Fall), Tyrone Genade

Killifish Research Review

Many interesting papers have been published over the last three months. The large volume of papers coupled with the start of the new college semester (and the workload it brings) delayed this issue of Killi-Data News. But better late than never—or so I hope! In this issue Richard van der Laan provides an insightful review of the recent Aphanius papers as to their taxonomic implications and questions. The systematic issues he raises show the importance of the Molecular project: we need to get more samples of the various cyprinodontiforme families to resolve unsettled systematic and taxonomic issues. In the ...


Killi-Data News (Summer), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Summer), Tyrone Genade

Killifish Research Review

Over the last three months several interesting and exciting pa- pers have been published. By now most of you have heard the Nothobranchius fish poo news emanating from the Valenzano lab. That paper is reviewed and certainly has repercussions for the health of our captive fish. Polaçik et al have published interesting data with ramifications as to how we breed and incubate annual killifish. The big news in this issue is the paper from the Reznick lab which Jean Huber reviews. The contents of that paper goes to the heart of the question of just what a killifish is. The ...


Killi-Data News (Spring), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don ...


Killi-Data News (Winter), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Winter), Tyrone Genade

Killifish Research Review

This is the fourth edition, and concluding issue of the first volume, of Killi-Data News and I am happy that it has been well received by readers. At 25 pages this issue is a bit thin- ner than the last but this is because we agreed to make the cut-off for submissions the 1 st of December so we could get this edition out by the New Year. This is an exciting edition full of new species descrip- tions and analyses that will keep taxonomists busy for years to come. Costa has given us two molecular phylogenies on Melanorivulus as ...


Killi-Data News (Spring), Tyrone Genade 2018 Northwestern College, Iowa

Killi-Data News (Spring), Tyrone Genade

Killifish Research Review

This is the start of Killi-Data News’ second year. In this first issue of the year we have the usual review of research pub- lications as well as input from Martin Reichard on his lab’s Nothobranchius research. Martin is responding to my reviews of his lab’s work in the previous edition. I am serious about making sure the content in this newsletter is reliable but I erred in the previous edition and Martin has written extensively to correct my mistake in the section “Erratum”. This reply is welcomed and owed to readers. I must confess that I don ...


A Parental Requirement For Dual-Specificity Phosphatase 6 In Zebrafish, Jennifer M. Maurer, Charles G. Sagerstrom 2018 University of Massachusetts Medical School

A Parental Requirement For Dual-Specificity Phosphatase 6 In Zebrafish, Jennifer M. Maurer, Charles G. Sagerstrom

Open Access Articles

BACKGROUND: Signaling cascades, such as the extracellular signal-regulated kinase (ERK) pathway, play vital roles in early vertebrate development. Signals through these pathways are initiated by a growth factor or hormone, are transduced through a kinase cascade, and result in the expression of specific downstream genes that promote cellular proliferation, growth, or differentiation. Tight regulation of these signals is provided by positive or negative modulators at varying levels in the pathway, and is required for proper development and function. Two members of the dual-specificity phosphatase (Dusp) family, dusp6 and dusp2, are believed to be negative regulators of the ERK pathway and ...


Copy Number Variation In The Porcine Genome Detected From Whole-Genome Sequence, Rebecca Anderson 2018 University of Nebraska-Lincoln

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

Honors Theses, University of Nebraska-Lincoln

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 ...


Bpwrapper: Bioperl-Based Sequence And Tree Utilities For Rapid Prototyping Of Bioinformatics Pipelines, Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas, William McCaig, Girish Ramrattan, Saymon Akther, Amanda Larracuente, Lia Di, Filipe G. Vieira, Weigang Qiu 2018 CUNY Hunter College

Bpwrapper: Bioperl-Based Sequence And Tree Utilities For Rapid Prototyping Of Bioinformatics Pipelines, Yözen Hernández, Rocky Bernstein, Pedro Pagan, Levy Vargas, William Mccaig, Girish Ramrattan, Saymon Akther, Amanda Larracuente, Lia Di, Filipe G. Vieira, Weigang Qiu

Publications and Research

Abstract:

Background: Automated bioinformatics workflows are more robust, easier to maintain, and results more reproducible when built with command-line utilities than with custom-coded scripts. Command-line utilities further benefit by relieving bioinformatics developers to learn the use of, or to interact directly with, biological software libraries. There is however a lack of command-line utilities that leverage popular Open Source biological software toolkits such as BioPerl (http://bioperl.org) to make many of the well-designed, robust, and routinely used biological classes available for a wider base of end users.

Results: Designed as standard utilities for UNIX-family operating systems, BpWrapper makes functionality of ...


Atacseqqc: A Bioconductor Package For Post-Alignment Quality Assessment Of Atac-Seq Data, Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu 2018 Duke University

Atacseqqc: A Bioconductor Package For Post-Alignment Quality Assessment Of Atac-Seq Data, Jianhong Ou, Haibo Liu, Jun Yu, Michelle A. Kelliher, Lucio H. Castilla, Nathan D. Lawson, Lihua Julie Zhu

University of Massachusetts Medical School Faculty Publications

BACKGROUND: ATAC-seq (Assays for Transposase-Accessible Chromatin using sequencing) is a recently developed technique for genome-wide analysis of chromatin accessibility. Compared to earlier methods for assaying chromatin accessibility, ATAC-seq is faster and easier to perform, does not require cross-linking, has higher signal to noise ratio, and can be performed on small cell numbers. However, to ensure a successful ATAC-seq experiment, step-by-step quality assurance processes, including both wet lab quality control and in silico quality assessment, are essential. While several tools have been developed or adopted for assessing read quality, identifying nucleosome occupancy and accessible regions from ATAC-seq data, none of the ...


Digital Commons powered by bepress