Search results | J. Murrey Atkins Library

Title: A VISUAL ANALYTICS APPROACH TO FEATURE DISCOVERY AND SUBSPACE EXPLORATION IN PROTEIN FLEXIBILITY MATRICES
Author: Barlowe, Scott
Date Created: 2011
Subjects--Topical: Computer science, Bioinformatics
Description: The vast amount of information generated by domain scientists makes the transitionfrom data to knowledge difficult and often impedes important discoveries. Forexample, the knowledge gained from protein flexibility data sets can speed advancesin ge...

Title: A new strategy to infer circularity applied to four new complete frog mitogenomes
Author: Machado, Denis Jacob, Janies, Daniel, Brouwer, Cory, Grant, Taran
Date Created: 2018
Subjects--Topical: Genomics, Amphibians, Bioinformatics
Description: We applied a novel strategy to infer sequence circularity and complete assembly of four mitochondrial genomes (mitogenomes) of the frog families Bufonidae (Melanophryniscus moreirae), Dendrobatidae (Hyloxalus subpunctatus and Phyllobates terribili...

Title: A virtual pebble game to emsemble average graph rigidity
Author: Gonzalez, Luis
Date Created: 2011
Subjects--Topical: Computer science, Bioinformatics
Description: Previous works have demonstrated that protein rigidity is related to thermodynamic stability, especially under conditions that favor formation of native structure. Mechanical network rigidity properties of a single conformation are efficiently cal...

Title: ALGORITHMS FOR STRUCTURE BASED-PREDICTION OF TRANSCRIPTION FACTOR BINDING SITES
Author: Farrel, Alvin
Date Created: 2016
Subjects--Topical: Computer science, Biology, Bioinformatics
Description: Transcription factors (TFs) regulate gene expression through binding to specific target DNA sites. Accurate annotation of transcription factor binding sites (TFBSs) at genome scale represents an essential step toward our understanding of gene regu...

Title: ANCESTRAL COMPLEXITY AND LINEAGE SPECIFIC EXPANSIONS OF THE ANIMAL BZIP INTERACTOME
Author: Kane, Eric
Date Created: 2017
Subjects--Topical: Bioinformatics, Evolutionary developmental biology
Description: Protein-protein interactions are central to the regulation and function of transcription factors in time- and cell-specific regulation of the genome. Increases in interactome complexity may serve as a mechanistic driver for evolutionary novelty. T...

Title: Analysis of pollen-specific alternative splicing in Arabidopsis thaliana via semi-quantitative PCR
Author: Loraine, Ann, Estrada, April, Freese, Nowlan H., Blakley, Ivory
Date Created: 2015
Subjects--Topical: Bioinformatics, Pollen, Nucleic acids
Description: Alternative splicing enables a single gene to produce multiple mRNA isoforms by varying splice site selection. In animals, alternative splicing of mRNA isoforms between cell types is widespread and supports cellular differentiation. In plants, at ...

Title: Arabidopsis bioinformatics resources : the current state, challenges, and priorities for the future
Author: Loraine, Ann, Doherty, Colleen, Friesner, Joanna, Gregory, Brian
Date Created: 2019
Subjects--Topical: Bioinformatics, Arabidopsis thaliana
Description: Effective research, education, and outreach efforts by the Arabidopsis thaliana community, as well as other scientific communities that depend on Arabidopsis resources, depend vitally on easily available and publicly-shared resources. These resour...

Title: Arboviruses: The hidden path of an imminent threat
Author: de Bernardi Schneider, Adriano
Date Created: 2018
Subjects--Topical: Virology, Bioinformatics, Epidemiology
Description: Arboviruses are a grade of viruses carried by arthropods, which have been in the headlines due to recent epidemics. Members of this grade are the families Flaviviridae which includes Zika (ZIKV), Dengue (DENV), Yellow Fever (YFV), among other viru...

Title: Assessment of Methods and Environmental Influence on the Nematostella Vectensis Microbiome
Author: Krueger, Quinton
Date Created: 2022
Subjects--Topical: Microbiology, Bioinformatics
Description: Cnidarians are a diverse clade of marine invertebrates that inhabit a variety of environments. The conditions of these habitats are becoming more extreme with the progression of time. These organisms associate with bacteria, which are composed of ...

Title: Assessments of Indel Annotation Programs and Comparative Somatic Indel Analysis in Cancer Genomes
Author: Chen, Jing
Date Created: 2020
Subjects--Topical: Bioinformatics
Description: Insertions and deletions (indels) represent the second largest variation type in human genomes and have been implicated in the development of cancer. Accurate indel annotation is of paramount importance in variants analysis in both healthy and dis...

Title: Bioinformatics and biomolecular tools for biomarker discovery in peripheral blood lymphocytes from patients with Sporadic Amyotrophic Lateral Sclerosis
Author: Baciu, Cristina
Date Created: 2012
Subjects--Topical: Bioinformatics
Description: Sporadic Amyotrophic lateral sclerosis (sALS) is a complex, invariably fatal, disease with a poorly understood cause, despite many studies. Diagnostic biomarkers that precede active symptoms would be an immense help to clinicians, for patient mana...

Title: CHARACTERIZING NEXT-GENERATION SEQUENCING (NGS) PLATFORMS FOR MULTIPLEXED BIOSENSING AND APTAMER DISCOVERY: G-QUADRUPLEX APTAMERS AS A CASE STUDY
Author: Patil, Sushant
Date Created: 2016
Subjects--Topical: Molecular biology, Bioinformatics, Biochemistry
Description: Aptamers are single-stranded DNA or RNA molecules forming unique three dimensional structures that can bind to their targets (generally proteins or metabolites or other nucleic acids) with high specificity and affinity. Screening for aptamers requ...

Title: COMPARATIVE ANALYSIS OF REPEAT LANDSCAPES IN AVENA (OAT)
Author: Burkes, Shelvasha
Date Created: 2020
Subjects--Topical: Biology, Bioinformatics, Botany
Description: Avena sativa, or common oat, is a staple crop and member of the Poaceae or Grass family. Following behind wheat, maize and rice, oats account for 10.5 million hectares of the world’s produced crops as of 2017. Phytocompounds such as β-glucan, aven...

Title: Changes in Lysozyme flexibility upon mutation are frequent, large and long-ranged
Author: Jacobs, Donald J., Verma, Deeptak, Livesay, Dennis R.
Date Created: 2012
Subjects--Topical: Bioinformatics, Statistics
Description: We investigate changes in human c-type lysozyme flexibility upon mutation via a Distance Constraint Model, which gives a statistical mechanical treatment of network rigidity. Specifically, two dynamical metrics are tracked. Changes in flexibility ...

Title: DATA ANALYSIS WORKFLOW FOR GAS CHROMATOGRAPHY MASS SPECTROMETRY-BASED METABOLOMICS STUDIES
Author: Ni, Yan
Date Created: 2014
Subjects--Topical: Bioinformatics
Description: Metabolomics has emerged as an integral part of systems biology research that attempts to comprehensively study low molecular weight organic and inorganic metabolites under certain conditions within a biological system. Technological advances in t...

Title: DE NOVO PREDICTION OF CIS-REGULATORY MODULES IN EUKARYOTIC ORGANISMS
Author: Niu, Meng
Date Created: 2014
Subjects--Topical: Bioinformatics
Description: Gene regulation networks (GRNs) are the bases for virtually all biological processes. To gain a global understanding of GRNs encoded in a genome, we first need to identify in all the cis-regulatory elements (CREs) recognized by transcription facto...

Title: DO DYNAMIC ALLOSTERIC EFFECTS OCCUR IN IGG4 ANTIBODIES?
Author: Baker, Lonnie
Date Created: 2020
Subjects--Topical: Bioinformatics, Biophysics
Description: Antibodies are large, multi-chain proteins which play a critical roll in the func-tioning of vertebrate immune systems. Immune effector cells which are responsiblefor the destruction of foreign antigens do not randomly target molecules but rely on...

Title: Data Mining the Serous Ovarian Tumor Transcriptome
Author: Tickle, Timothy
Date Created: 2011
Subjects--Topical: Bioinformatics, Genetics
Description: Ovarian cancer is the most lethal gynecologic cancer in the United States. If caught in early stages, patient survival rate is 94%, late stage survival rates drop to 28%. It is because most cases are caught in late stages that high mortality is se...

Title: ELUCIDATING FUNCTIONAL MECHANISMS IN PROTEINS USING THE DISTANCE CONSTRAINT MODEL
Author: Singer, Christopher
Date Created: 2019
Subjects--Topical: Bioinformatics, Biophysics, Physics
Description: Protein thermodynamics has been shown to be insightful and illuminating to the functional mechanisms behind biological function. By characterizing proteins and protein families according to their enthalpy and entropy we can make inferences to the ...

Title: ELUCIDATING THE EFFECTS OF MUTATION AND EVOLUTIONARY DIVERGENCE UPON PROTEIN STRUCTURE QUANTITATIVE STABILITY/FLEXIBILITY RELATIONSHIPS
Author: Verma, Deeptak
Date Created: 2012
Subjects--Topical: Bioinformatics
Description: The importance of flexibility and stability on protein function has been recognized for over five decades. A protein must be flexible enough to mediate a reaction pathway, yet rigid enough to achieve high fidelity in molecular recognition. To unde...