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3,518 full-text articles. Page 7 of 135.

Simplicity Diffexpress: A Bespoke Cloud-Based Interface For Rna-Seq Differential Expression Modeling And Analysis, Cintia C. Palu, Marcelo Ribeiro-Alves, Yanxin Wu, Brendan Lawlor, Pavel V. Baranov, Brian Kelly, Paul Walsh 2019 NSilico Life Science Ltd. and School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland

Simplicity Diffexpress: A Bespoke Cloud-Based Interface For Rna-Seq Differential Expression Modeling And Analysis, Cintia C. Palu, Marcelo Ribeiro-Alves, Yanxin Wu, Brendan Lawlor, Pavel V. Baranov, Brian Kelly, Paul Walsh

Department of Computer Science Articles

One of the key challenges for transcriptomics-based research is not only the processing of large data but also modeling the complexity of features that are sources of variation across samples, which is required for an accurate statistical analysis. Therefore, our goal is to foster access for wet lab researchers to bioinformatics tools, in order to enhance their ability to explore biological aspects and validate hypotheses with robust analysis. In this context, user-friendly interfaces can enable researchers to apply computational biology methods without requiring bioinformatics expertise. Such bespoke platforms can improve the quality of the findings by allowing the researcher to ...


Bacteriophages Of The Lower Urinary Tract, Andrea Garretto, Taylor Miller-Ensminger, Alan J. Wolfe, Catherine Putonti 2019 Loyola University Chicago

Bacteriophages Of The Lower Urinary Tract, Andrea Garretto, Taylor Miller-Ensminger, Alan J. Wolfe, Catherine Putonti

Bioinformatics Faculty Publications

Phages are vital members of the microbiota, having critical roles in shaping bacterial metabolism and community structure. Although phages have been discovered in the urinary tract, such as phages that infect Escherichia coli, sampling them is challenging owing to low biomass, possible contamination when using non-invasive methods and the invasiveness of methods that reduce the potential for contamination. Phages could influence bladder health, but an understanding of the association between phage communities, bacterial populations and bladder health is in its infancy. However, evidence suggests that phages can defend the host against pathogenic bacteria and, therefore, modulation of the microbiome using ...


Rising Rural Body-Mass Index Is The Main Driver Of The Global Obesity Epidemic In Adults, Con Burns, Tara Coppinger, Janette Walton, Et Al 2019 Department of Sport, Leisure & Childhood Studies, Cork Institute of Technology, Cork, Ireland

Rising Rural Body-Mass Index Is The Main Driver Of The Global Obesity Epidemic In Adults, Con Burns, Tara Coppinger, Janette Walton, Et Al

Dept. of Sports, Leisure & Early Childhood Studies Publications

Body-mass index (BMI) has increased steadily in most countries in parallel with a rise in the proportion of the population who live in cities1,2. This has led to a widely reported view that urbanization is one of the most important drivers of the global rise in obesity3,4,5,6. Here we use 2,009 population-based studies, with measurements of height and weight in more than 112 million adults, to report national, regional and global trends in mean BMI segregated by place of residence (a rural or urban area) from 1985 to 2017. We show that, contrary ...


Tissue-Specific Genome Editing In Vivo By Microrna-Repressible Anti-Crispr Proteins, Jooyoung Lee, Haiwei Mou, Raed Ibraheim, Shun-Qing Liang, Wen Xue, Erik J. Sontheimer 2019 University of Massachusetts Medical School

Tissue-Specific Genome Editing In Vivo By Microrna-Repressible Anti-Crispr Proteins, Jooyoung Lee, Haiwei Mou, Raed Ibraheim, Shun-Qing Liang, Wen Xue, Erik J. Sontheimer

University of Massachusetts Medical School Faculty Publications

CRISPR-Cas systems are bacterial adaptive immune pathways that have revolutionized biotechnology and biomedical applications. Despite the potential for human therapeutic development, there are many hurdles that must be overcome before its use in clinical settings. Some clinical safety concerns arise from persistent activity of Cas9 after the desired editing is complete, or from editing activity in unintended cell types or tissues upon in vivo delivery [e.g. by adeno-associated viruses (AAV)]. Although tissue-specific promoters and serotypes with tissue tropisms can be used, suitably compact promoters are not always available for desired cell types, and AAV tissue tropisms are not absolute ...


In Silico Identification Of Genetic Mutations Conferring Resistance To Acetohydroxyacid Synthase Inhibitors: A Case Study Of Kochia Scoparia, Yan Li, Michael D. Netherland, Chaoyang Zhang, Huixiao Hong, Ping Gong 2019 Bennett Aerospace, Inc.

In Silico Identification Of Genetic Mutations Conferring Resistance To Acetohydroxyacid Synthase Inhibitors: A Case Study Of Kochia Scoparia, Yan Li, Michael D. Netherland, Chaoyang Zhang, Huixiao Hong, Ping Gong

Faculty Publications

Mutations that confer herbicide resistance are a primary concern for herbicide-based chemical control of invasive plants and are often under-characterized structurally and functionally. As the outcome of selection pressure, resistance mutations usually result from repeated long-term applications of herbicides with the same mode of action and are discovered through extensive field trials. Here we used acetohydroxyacid synthase (AHAS) of Kochia scoparia (KsAHAS) as an example to demonstrate that, given the sequence of a target protein, the impact of genetic mutations on ligand binding could be evaluated and resistance mutations could be identified using a biophysics-based computational approach. Briefly, the ...


Synthesis And Evaluation Of Novel Silica Hydride-Based Stationary Phases For Bioanalytical Application, Seiichiro Watanabe 2019 San José State University

Synthesis And Evaluation Of Novel Silica Hydride-Based Stationary Phases For Bioanalytical Application, Seiichiro Watanabe

Seiichiro Watanabe

Most HPLC columns are packed with silanol-rich (Si-OH) type-B silica material that often participates in undesired electrostatic interactions with the analyte solutes and produces poor peak shape [1,2]. These silanols are also known to facilitate surface hydration necessary for HILIC retention mode for polar analyte molecules. However, the hydrated surface composition can easily fluctuate, and thus results in a poor reproducibility and requires lengthy equilibration step. In this study, four novel stationary phases have been developed by using the TYPE-CTM Silica Hydride material, which has replaced up to 95% of the surface silanols with silicon-hydride (Si-H) groups. One of ...


Anti-Crispr Vs. Crispr: The Evolutionary Arms Race Between Microorganisms, Rachael M. St. Jacques 2019 James Madison University

Anti-Crispr Vs. Crispr: The Evolutionary Arms Race Between Microorganisms, Rachael M. St. Jacques

Masters Theses, 2010-2019

CRISPR arrays are a defense mechanism employed by bacteria against viral invaders. Cas proteins do the work in detecting, capturing, and integrating the viral DNA into the CRISPR array (Barrangou et al., 2007). Anti-CRISPR proteins are produced by phages, viruses that infect bacteria, to stop the bacterial host’s CRISPR-Cas complex from interrupting the phage life cycle (Bondy-Denomy, et al., 2015).

SEA-PHAGES is a course-based bacteriophage research network composed of 120 colleges and known at James Madison University as Viral Discovery. JMU uses the unsequenced Streptomyces griseus ATCC10137 as a host for bacteriophage discovery and propagation, and in this study ...


Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim 2019 CUNY Queensborough Community College

Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim

Open Educational Resources

This material briefly reintroduces the DNA double Helix structure, explains SNP and INDEL mutations in genes and describes FASTA, FASTQ, BAM and VCF file formats. It also explains the index creation, alignment, sorting, marking duplicates and variant calling steps of a simple preprocessing workflow and how to write a Perl script to automate the execution of these steps on a Virtual Machine Image.


Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim 2019 CUNY Queensborough Community College

Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim

Open Educational Resources

This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided, connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to enter the data folder, which includes gene-sequencing input files and print the first five line of each file remotely. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program of the VMI can be used to do the exercise.


Bamorc: A Software Package For Accurate And Robust 13C Reference Correction Of Protein Nmr Spectra, Xi Chen, Andrey Smelter, Hunter N. B. Moseley 2019 University of Kentucky

Bamorc: A Software Package For Accurate And Robust 13C Reference Correction Of Protein Nmr Spectra, Xi Chen, Andrey Smelter, Hunter N. B. Moseley

Molecular and Cellular Biochemistry Faculty Publications

We describe Bayesian Model Optimized Reference Correction (BaMORC), a software package that performs 13C chemical shifts reference correction for either assigned or unassigned peak lists derived from protein NMR spectra. BaMORC provides an intuitive command line interface that allows non-nuclear magnetic resonance (NMR) experts to detect and correct 13C chemical shift referencing errors of unassigned peak lists at the very beginning of NMR data analysis, further lowering the bar of expertise required for effective protein NMR analysis. Furthermore, BaMORC provides an application programming interface for integration into sophisticated protein NMR data analysis pipelines, both before and after the ...


Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim 2019 CUNY Queensborough Community College

Designing Computational Biology Workflows With Perl - Part 1, Esma Yildirim

Open Educational Resources

This material introduces Linux File System structures and demonstrates how to use commands to communicate with the operating system through a Terminal program. Basic program structures and system() function of Perl are discussed. A brief introduction to gene-sequencing terminology and file formats are given.


Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim 2019 CUNY Queensborough Community College

Designing Computational Biology Workflows With Perl - Part 2, Esma Yildirim

Open Educational Resources

This material introduces the AWS console interface, describes how to create an instance on AWS with the VMI provided and connect to that machine instance using the SSH protocol. Once connected, it requires the students to write a script to automate the tasks to create VCF files from two different sample genomes belonging to E.coli microorganisms by using the FASTA and FASTQ files in the input folder of the virtual machine. The same exercise can be applied if the VMI is installed on a local machine using virtualization software (e.g. Oracle VirtualBox). In this case, the Terminal program ...


Designing Computational Biology Workflows With Perl - Part 1 & 2, Esma Yildirim 2019 CUNY Queensborough Community College

Designing Computational Biology Workflows With Perl - Part 1 & 2, Esma Yildirim

Open Educational Resources

This manual guides the instructor to combine the partial files of the virtual machine image and construct sequencer.ova file. It is accompanied by the partial files of the virtual machine image.


Scl: A Lattice-Based Approach To Infer Three-Dimensional Chromosome Structures From Single-Cell Hi-C Data, Hao Zhu 2019 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 ...


Gogo: An Improved Algorithm To Measure The Semantic Similarity Between Gene Ontology Terms, Chenguang Zhao 2019 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 ...


Computational Genomic Models For Spatio-Temporal Investigation Of Early Lung Cancer Pathology, Smruthy Sivakumar 2019 The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences

Computational Genomic Models For Spatio-Temporal Investigation Of Early Lung Cancer Pathology, Smruthy Sivakumar

The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences Dissertations and Theses (Open Access)

Lung cancer, of which non-small cell lung cancer (NSCLC) is the most common form, is the second most prevalent cancer and the leading cause of cancer-related deaths. NSCLCs primarily comprise adenocarcinomas (LUAD) and squamous cell carcinomas (LUSC). Advances in early detection and prevention have been limited by the lack of early-stage biomarkers and targets. A comprehensive molecular characterization of premalignant lesions and tumor-adjacent normal tissue can aid in better understanding NSCLC pathogenesis. However, these investigations are further challenged by limited tissue availability and low cellular fractions of detectable somatic mutations.

Therefore, there is a dearth of knowledge about the pathogenesis ...


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 ...


Do Metabolic Networks Follow A Power Law? A Psamm Analysis, Ryan Geib, Lubos Thoma, Ying Zhang 2019 University of Rhode Island

Do Metabolic Networks Follow A Power Law? A Psamm Analysis, Ryan Geib, Lubos Thoma, Ying Zhang

Senior Honors Projects

Inspired by the landmark paper “Emergence of Scaling in Random Networks” by Barabási and Albert, the field of network science has focused heavily on the power law distribution in recent years. This distribution has been used to model everything from the popularity of sites on the World Wide Web to the number of citations received on a scientific paper. The feature of this distribution is highlighted by the fact that many nodes (websites or papers) have few connections (internet links or citations) while few “hubs” are connected to many nodes. These properties lead to two very important observed effects: the ...


Surveying Apicomplexan Diversity And Dynamics In Narragansett Bay, Evelyn Spencer 2019 University of Rhode Island

Surveying Apicomplexan Diversity And Dynamics In Narragansett Bay, Evelyn Spencer

Senior Honors Projects

Parasites play an important role in marine ecosystems and their diversity is generally understudied. Apicomplexans, a group of parasitic protists in the phylum Alveolata, infect a wide variety of animal hosts and are abundant in ecosystems spanning from Polar Regions to Neotropical rainforests. Previous data generated from marine sediments in Antarctica, Naples Bay, and off the coast of Oslo, exhibit high diversity and numbers of apicomplexans. Abundance and diversity of these protists are unknown for Narragansett Bay, despite the fact that they infect many commercially important species. The aim of my study was to obtain abundance data and understand genetic ...


Learning To Detect And Understand Drug Discontinuation Events From Clinical Narratives, Feifan Liu, Richeek Pradhan, Emily Druhl, Elaine Freund, Weisong Liu, Brian C. Sauer, Fran Cunningham, Adam J. Gordon, Celena B. Peters, Hong Yu 2019 University of Massachusetts Medical School

Learning To Detect And Understand Drug Discontinuation Events From Clinical Narratives, Feifan Liu, Richeek Pradhan, Emily Druhl, Elaine Freund, Weisong Liu, Brian C. Sauer, Fran Cunningham, Adam J. Gordon, Celena B. Peters, Hong Yu

Population and Quantitative Health Sciences Publications

OBJECTIVE: Identifying drug discontinuation (DDC) events and understanding their reasons are important for medication management and drug safety surveillance. Structured data resources are often incomplete and lack reason information. In this article, we assessed the ability of natural language processing (NLP) systems to unlock DDC information from clinical narratives automatically.

MATERIALS AND METHODS: We collected 1867 de-identified providers' notes from the University of Massachusetts Medical School hospital electronic health record system. Then 2 human experts chart reviewed those clinical notes to annotate DDC events and their reasons. Using the annotated data, we developed and evaluated NLP systems to automatically identify ...


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