Morgan C. Giddings

Agent-based modeling of competence phenotype switching in Bacillus subtilis

Suzy Stiegelmeyer, Morgan C. Giddings

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 phenomenon are believed to be due to the …

Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA

Suzy M. Vasa, Katherine E. Deigan, Kevin M. Weeks, Morgan C. Giddings et autres

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 conformationally unconstrained or flexible nucleotides. Each nucleotide in an RNA has the potential to form …

An Agent-Based Model of Signal Transduction in Bacterial Chemotaxis

Jameson Miller, Morgan C. Giddings, Robert B. Bourret, Miles Parker

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 stimuli. Agent-based modeling is a stochastic and bottom-up approach, where …

High-Throughput SHAPE Analysis Reveals Structures in HIV-1 Genomic RNA Strongly Conserved across Distinct Biological States

Kevin M. Weeks, Robert J. Gorelick, David H. Mathews, Kevin A. Wilkinson et autres

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′-hydroxyl acylation analyzed by primer extension) technology, which uses …

Comparative Genome Analysis of Ciprofloxacin-Resistant Pseudomonas aeruginosa Reveals Genes Within Newly Identified High Variability Regions Associated With Drug Resistance Development

Hsun-Cheng Su, Dona Kanavy, Jainab Khatun, Morgan C. Giddings

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 bacterium acquires high-level resistance is still not well …

A Peptide-Spectrum Scoring System Based on Ion Alignment, Intensity, and Pair Probabilities

Morgan C. Giddings, Brian A. Risk, Nathan J. Edwards

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 probabilities: the probability that a fragment ion will randomly …

us (code pays fourni par la source)

GFSWeb: A Web Tool for Genome-Based Identification of Proteins from Mass Spectrometric Samples

Mark Robert Holmes, Morgan C. Giddings, Michael S. Wisz, Melissa Kimball Suarez

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 pace of annotation efforts fails to keep pace …

Peppy: Proteogenomic Search Software

Wendy J. Spitzer, Morgan C. Giddings, Brian A. Risk

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 use of several unintegrated tools. Furthermore, many proteogenomic …

us (code pays fourni par la source)

Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification

Jainab Khatun, Eric D. Hamlett, Morgan C. Giddings

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 remains limited. To improve the accuracy of …

us (code pays fourni par la source)

Baking a mass-spectrometry data PIE with McMC and simulated annealing: predicting protein post-translational modifications from integrated top-down and bottom-up data

Stuart R. Jefferys, Morgan C. Giddings

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 investigating modified proteins, but the data they provide …

us (code pays fourni par la source)

Fragmentation Characteristics of Collision-Induced Dissociation in MALDI TOF/TOF Mass Spectrometry

Kevin Ramkissoon, Jainab Khatun, Morgan C. Giddings

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 analyzed fragmentation in MALDI TOF/TOF mass spectrometry, collecting …

Stochastic model of BKPy Virus replication and assembly

Suzy Stiegelmeyer, Liesl K. Jeffers-Francis, Morgan C. Giddings, Jennifer Webster‐Cyriaque

Abstract 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 kidney transplants. As …

us (code pays fourni par la source)