A5000271407- Gene Regulatory Network Analysis
- Bioinformatics and Genomic Networks
- Viral Infectious Diseases and Gene Expression in Insects
- Fungal and yeast genetics research
- Gene expression and cancer classification
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Genetics, Bioinformatics, and Biomedical Research
- Advanced Fluorescence Microscopy Techniques
- Biomedical Text Mining and Ontologies
- Heat shock proteins research
- RNA modifications and cancer
- Bacterial Genetics and Biotechnology
- Experimental Learning in Engineering
- Computational Drug Discovery Methods
- Evolution and Genetic Dynamics
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Bacteriophages and microbial interactions
- Biomedical and Engineering Education
- CRISPR and Genetic Engineering
- Meat and Animal Product Quality
- Plant and Fungal Interactions Research
- Retinal Diseases and Treatments
- Retinal Development and Disorders
Loyola Marymount University
2008-2021
Stanford University
1999-2014
Dankook University
2010
National Institute of Advanced Industrial Science and Technology
2010
Vassar College
2004
Gladstone Institutes
2002-2003
University of California, San Francisco
2002-2003
University of California, Santa Cruz
1995-1996
Abstract Background Microarray technologies have evolved rapidly, enabling biologists to quantify genome-wide levels of gene expression, alternative splicing, and sequence variations for a variety species. Analyzing displaying these data present significant challenge. Pathway-based approaches analyzing microarray proven useful presenting generating testable hypotheses. Results To address the growing needs community we released version 2 Gene Map Annotator Pathway Profiler (GenMAPP), new...
A variety of new procedures have been devised to handle the two-sample comparison (e.g., tumor versus normal tissue) gene expression values as measured with microarrays. Such methods are required in part because some defining characteristics microarray-based studies: (i) very large number genes contributing measures which far exceeds samples (observations) available and (ii) fact that by virtue pathway/network relationships, tend be highly correlated. These concerns exacerbated regression...
Despite widespread calls for the incorporation of mathematical modeling into undergraduate biology curriculum, there is lack a common understanding around definition modeling, which inhibits progress. In this paper, we extend "Rule Four," initially used in calculus reform efforts, to framework models and that inclusive varying disciplinary definitions each. This unifying allows us both build on strengths each discipline its students bring, but also identify gaps activities practiced by...
We investigated the dynamics of a gene regulatory network controlling cold shock response in budding yeast, Saccharomyces cerevisiae. The medium-scale network, derived from published genome-wide location data, consists 21 transcription factors that regulate one another through 31 directed edges. expression levels individual were modeled using mass balance ordinary differential equations with sigmoidal production function. Each equation includes rate, degradation weights denote magnitude and...
Bioinformatics relies more than ever on information technologies. This pressures scientists to keep up with software development best practices. However, traditional computer science curricula do not necessarily expose students collaborative and long-lived development. Using open source principles, practices, tools forms an effective pedagogy for paper reports a bioinformatics teaching framework implemented through courses introducing the field. The led initial product release consisting of...
GenMAPP (Gene MicroArray Pathway Profiler) is a free, stand-alone computer program designed for viewing and analyzing gene expression data on MAPPs representing biological pathways or any other functional grouping of genes. A MAPP special file format produced with the graphics tools in that depicts relationship between genes products. When linked to an dataset, automatically dynamically color-codes according criteria supplied by user. MAPPFinder accessory works annotations from Gene Ontology...
GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A network (GRN) consists genes, transcription factors, the connections between them which govern level expression mRNA protein from genes. The original motivation came our efforts to perform parameter estimation forward simulation dynamics differential equations model small GRN with 21 nodes 31 edges. We wanted quick easy way visualize weight parameters represent direction magnitude influence...
Models and the process of modeling are fundamental to discipline biology, therefore should be incorporated into undergraduate biology courses. In this essay, we draw upon literature our own teaching experiences provide practical suggestions for how introduce models introductory students. We begin by demonstrating ubiquity in including representations science itself. advocate a model that highlights parallel tracks mathematical experimental investigations. With recognition, suggest ways which...
GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A network consists genes, transcription factors, the connections between them which govern level expression mRNA protein from genes. The original motivation came our efforts to perform parameter estimation forward simulation dynamics differential equations model small GRN with 21 nodes 31 edges. We wanted quick easy way visualize weight parameters represent direction magnitude influence...
GRNsight is a web application and service for visualizing models of gene regulatory networks (GRNs). A network consists genes, transcription factors, the connections between them which govern level expression mRNA protein from genes. The original motivation to create came our efforts perform parameter estimation forward simulation dynamics differential equations model small GRN with 21 nodes 31 edges. We wanted quick easy way visualize weight parameters represent direction magnitude...
Models and the process of modeling are fundamental to discipline biology, therefore should be incorporated into undergraduate biology courses. In this essay, we draw upon literature our own teaching experiences provide practical suggestions for how introduce models introductory students. We begin by demonstrating ubiquity in including representations science itself. advocate a model that highlights parallel tracks mathematical experimental investigations. With recognition, suggest ways which...
An important question in undergraduate curricula is that of incorporating computing into STEM courses for majors and non-majors alike. What does it mean to teach “computing” this context? are some the benefits challenges students instructors such courses? This paper contributes dialog by describing three have been developed taught at Harvey Mudd College Loyola Marymount University. Each case study describes course objectives, implementation challenges, assessments.