David Sigfredo Angulo

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A significant consequence of protein phosphorylation is to alter protein-protein interactions, leading to dynamic regulation of the components of protein complexes that direct many core biological processes. Recent proteomic studies have populated databases with extensive compilations of cellular phosphoproteins and phosphorylation sites and a similarly(More)
Proteomic researchers who study mass spectrometry data have expressed a need for an accurate public database of empirically derived curated mass spectrum information. Lack of such a database limits proteomic researchers in their ability to identify and study proteins. Until recently, storage space and computing power has been the limiting factor in(More)
In this paper, we introduced a framework for experiment management that simplifies the users’ interaction with grid environments by managing a large number of tasks to be conducted as part of the experiment by the individual scientist. Our framework is an extension to the Java CoG Kit. We have developed a client-server approach that allows us to utilize the(More)
In this paper, we address the problem of searching huge biological databases on the scale of at least several gigabytes by utilizing parallel processing. Biological databases storing DNA sequences, protein sequences, or mass spectra are growing exponentially. Searches through these databases consume exponentially growing computational resources as well. We(More)
alpha-Synuclein (alpha-syn) is an intrinsically unstructured 140-residue neuronal protein of uncertain function that is implicated in the etiology of Parkinson's disease. Tertiary contact formation rate constants in alpha-syn, determined from diffusion-limited electron-transfer kinetics measurements, are poorly approximated by simple random polymer theory.(More)
Workflow management is an important part of scientific experiments. A common pattern that scientists are using is based on repetitive job execution on a variety of different systems, and managing such job execution is necessary for large-scale scientific workflows. The workflow system should also be client-based and able to handle multiple security contexts(More)
The manipulation of codon selection in synthetic genes greatly influences expression of the gene's products i.e. proteins. Biologists frequently have multiple objectives when constructing a synthetic gene for a given protein sequence and are often limited by the tools and mechanisms used to design genes in vitro. Poor codon choice and mRNA secondary(More)
Dr. Lee Hood founded the Institute of Systems Biology (ISB) in 2000. After graduate school at California Institute of Technology, he stayed with the university as a professor and pioneered the DNA sequencer. This invention serves as the foundation of molecular biology today and has made the Human Genome Project a reality. He has also played a role in(More)
Database searching for protein identification is an efficient approach for MS/MS spectra identification compared to the existing approaches, such as protein identification with antibodies, and chemical degradation. In order for a database search to give reliable results, the database itself, as well as the searching algorithm, must be reliable. However,(More)
Mass spectrometry (MS) is an analytical method biologists and chemists use to sequence and identify unknown proteins. Although sensitivity and sample analysis modalities differ, mass spectrometers basically consist of an ion source, a mass analyzer, and a detector. The final output is a single mass spectrum or a series of mass spectra depending on the(More)