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Full-Text Articles in Life Sciences

Formulation Of Hybrid Knowledge-Based/Molecular Mechanics Potentials For Protein Structure Refinement And A Novel Graph Theoretical Protein Structure Comparison And Analysis Technique, Aaron Maus Aug 2019

Formulation Of Hybrid Knowledge-Based/Molecular Mechanics Potentials For Protein Structure Refinement And A Novel Graph Theoretical Protein Structure Comparison And Analysis Technique, Aaron Maus

University of New Orleans Theses and Dissertations

Proteins are the fundamental machinery that enables the functions of life. It is critical to understand them not just for basic biology, but also to enable medical advances. The field of protein structure prediction is concerned with developing computational techniques to predict protein structure and function from a protein’s amino acid sequence, encoded for directly in DNA, alone. Despite much progress since the first computational models in the late 1960’s, techniques for the prediction of protein structure still cannot reliably produce structures of high enough accuracy to enable desired applications such as rational drug design. Protein structure refinement ...


Wavelet Analysis Of Short Globular Homologous Proteins In Mesophile And Thermophile Prokaryotes, John B. Linehan Jun 2019

Wavelet Analysis Of Short Globular Homologous Proteins In Mesophile And Thermophile Prokaryotes, John B. Linehan

College of Science and Health Theses and Dissertations

This study looked to identify features related to thermal stability and function in the amino acid chains of short globular proteins from mesophile and thermophile species, within the constraint that the protein fold to perform a speci_c function. To do so 540 homologous pairs of proteins were studied. The amino acid chains were con-verted to hydrophobicity signals by assigning a hydropathy score to each residue in the polypeptide. The hydrophobicity signals were passed through a wavelet packet transform and the resulting spectra analyzed. Bootstrapping was used to gener-ate a control data set to determine if the true ordering of amino ...


Computational Genomic Models For Spatio-Temporal Investigation Of Early Lung Cancer Pathology, Smruthy Sivakumar May 2019

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

UT GSBS 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 ...


Evaluating Predixcan’S Ability To Predict Differential Expression Between Alcoholics And Non-Alcoholics, John E. Drake Jr Jan 2019

Evaluating Predixcan’S Ability To Predict Differential Expression Between Alcoholics And Non-Alcoholics, John E. Drake Jr

Theses and Dissertations

PrediXcan is a recent software for the imputation of gene expression from genotype data alone. Using an overlapping set of transcriptome datasets from postmortem brain tissues of donors with alcohol use disorder and neurotypical controls, which were generated by two different platforms (e.g., Arraystar and Affymetrix), and an additional unrelated transcriptome dataset from lung tissue, we sought to evaluate PrediXcan’s ability to impute gene expression and identify differentially expressed genes. From the Arraystar platform, 1.3% of matched genes between the measured and imputed expression had a Pearson correlation ≥ 0.5. Our attempt to replicate this finding using ...


Exploring Strategies To Integrate Disparate Bioinformatics Datasets, Charbel Bader Fakhry Jan 2019

Exploring Strategies To Integrate Disparate Bioinformatics Datasets, Charbel Bader Fakhry

Walden Dissertations and Doctoral Studies

Distinct bioinformatics datasets make it challenging for bioinformatics specialists to locate the required datasets and unify their format for result extraction. The purpose of this single case study was to explore strategies to integrate distinct bioinformatics datasets. The technology acceptance model was used as the conceptual framework to understand the perceived usefulness and ease of use of integrating bioinformatics datasets. The population of this study included bioinformatics specialists of a research institution in Lebanon that has strategies to integrate distinct bioinformatics datasets. The data collection process included interviews with 6 bioinformatics specialists and reviewing 27 organizational documents relating to integrating ...


Algorithms For Synteny-Based Phylostratigraphy And Gene Origin Classification, Zebulun Arendsee Jan 2019

Algorithms For Synteny-Based Phylostratigraphy And Gene Origin Classification, Zebulun Arendsee

Graduate Theses and Dissertations

With every newly sequenced species we discover hundreds of novel protein coding genes. Many of these "orphan" genes have been experimentally proven to have dramatic functions in development, sexual dimorphism, pathogen resistance, and social traits like symbiosis. Whereas in the past, researchers viewed genes as the product of continuous variation acting on ancient material, we now know that novel genes may arise de novo from non-genic sequence. Thus evolutionary experimentation is not limited to tweaking existing genes or their regulatory patterns. Any orphan genes that arose in the distant past, should appear today as lineage-specific genes (or gene families). The ...