Morgan C. Giddings
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View article: Agent-based modeling of competence phenotype switching in Bacillus subtilis
Agent-based modeling of competence phenotype switching in Bacillus subtilis Open
BackgroundIt is a fascinating phenomenon that in genetically identical bacteria populations of Bacillus subtilis, a distinct DNA uptake phenotype called the competence phenotype may emerge in 10–20% of the population. Many aspects of the p…
View article: Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA
Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA Open
Hydroxyl-selective electrophiles, including N-methylisatoic anhydride (NMIA) and 1-methyl-7-nitroisatoic anhydride (1M7), are broadly useful for RNA structure analysis because they react preferentially with the ribose 2′-OH group at confor…
View article: An Agent-Based Model of Signal Transduction in Bacterial Chemotaxis
An Agent-Based Model of Signal Transduction in Bacterial Chemotaxis Open
We report the application of agent-based modeling to examine the signal transduction network and receptor arrays for chemotaxis in Escherichia coli, which are responsible for regulating swimming behavior in response to environmental stimul…
View article: High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States
High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States Open
Replication and pathogenesis of the human immunodeficiency virus (HIV) is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2′-hyd…
View article: Peppy: Proteogenomic Search Software
Peppy: Proteogenomic Search Software Open
Proteogenomic searching is a useful method for identifying novel proteins, annotating genes and detecting peptides unique to an individual genome. The approach, however, can be laborious, as it often requires search segmentation and the us…
View article: GFSWeb: A Web Tool for Genome-Based Identification of Proteins from Mass Spectrometric Samples
GFSWeb: A Web Tool for Genome-Based Identification of Proteins from Mass Spectrometric Samples Open
The interpretation of mass spectrometry data for protein identification has become a vital component of proteomics research. However, since most existing software tools rely on protein databases, their success is limited, especially as the…
View article: A Peptide-Spectrum Scoring System Based on Ion Alignment, Intensity, and Pair Probabilities
A Peptide-Spectrum Scoring System Based on Ion Alignment, Intensity, and Pair Probabilities Open
Peppy, the proteogenomic/proteomic search software, employs a novel method for assessing the match quality between an MS/MS spectrum and a theorized peptide sequence. The scoring system uses three score factors calculated with binomial pro…
View article: Comparative Genome Analysis of Ciprofloxacin-Resistant Pseudomonas aeruginosa Reveals Genes Within Newly Identified High Variability Regions Associated With Drug Resistance Development
Comparative Genome Analysis of Ciprofloxacin-Resistant Pseudomonas aeruginosa Reveals Genes Within Newly Identified High Variability Regions Associated With Drug Resistance Development Open
The alarming rise of ciprofloxacin-resistant Pseudomonas aeruginosa has been reported in several clinical studies. Though the mutation of resistance genes and their role in drug resistance has been researched, the process by which the bact…
View article: Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data
Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data Open
Motivation: Post-translational modifications are vital to the function of proteins, but are hard to study, especially since several modified isoforms of a protein may be present simultaneously. Mass spectrometers are a great tool for inves…
View article: Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification
Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification Open
The identification of peptides by tandem mass spectrometry (MS/MS) is a central method of proteomics research, but due to the complexity of MS/MS data and the large databases searched, the accuracy of peptide identification algorithms rema…
View article: Fragmentation Characteristics of Collision-Induced Dissociation in MALDI TOF/TOF Mass Spectrometry
Fragmentation Characteristics of Collision-Induced Dissociation in MALDI TOF/TOF Mass Spectrometry Open
The identification of proteins by tandem mass spectrometry relies on knowledge of the products produced by collision-induced dissociation of peptide ions. Most previous work has focused on fragmentation statistics for ion trap systems. We …
View article: Stochastic model of BKPy Virus replication and assembly
Stochastic model of BKPy Virus replication and assembly Open
BK Polyomavirus (BKPyV), belongs to the same family as SV40 and JC Virus and has recently been associated with both Sjögrens Syndrome and HIV associated Salivary Gland Disease. BKPyV was previously only known for causing the rejection of k…
View article: Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions
Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions Open
Background Proteogenomic mapping is an approach that uses mass spectrometry data from proteins to directly map protein-coding genes and could aid in locating translational regions in the human genome. In concert with the ENcyclopedia of DN…
View article: Ultra-Structure database design methodology for managing systems biology data and analyses
Ultra-Structure database design methodology for managing systems biology data and analyses Open
Background Modern, high-throughput biological experiments generate copious, heterogeneous, interconnected data sets. Research is dynamic, with frequently changing protocols, techniques, instruments, and file formats. Because of these facto…
View article: Mapping phosphoproteins in Mycoplasma genitalium and Mycoplasma pneumoniae
Mapping phosphoproteins in Mycoplasma genitalium and Mycoplasma pneumoniae Open
Background Little is known regarding the extent or targets of phosphorylation in mycoplasmas, yet in many other bacterial species phosphorylation is known to play an important role in signaling and regulation of cellular processes. To dete…
View article: Tracking the evolution of alternatively spliced exons within the Dscamfamily
Tracking the evolution of alternatively spliced exons within the Dscamfamily Open
Background The Dscam gene in the fruit fly, Drosophila melanogaster, contains twenty-four exons, four of which are composed of tandem arrays that each undergo mutually exclusive alternative splicing (4, 6, 9 and 17), potentially generating…