Christopher Eichelberger

Simulating protein computing: character recognition via probabilistic transition trees

This paper describes a novel, universal comput- ing technique inspired by molecular biology. This technique - founded in a simulation of protein interactions using a modular, artificial chemistry - provides massively parallel, distributed, probabilistic computing capability that can address complex problems. The authors report on the effectivenes of using the probabilistic heart of simulated proteomic computing to recognize character images, and describe the next steps of the implemen- tation plans that are already in progress.

Systems biology and bioinformatics : a computational approach

Cell Biology An Introduction to Cell Structure Proteins as Tools of the Cell Genes: Directors of the Cell Cell Cycle Bioassays Southern Blotting Fluorescent In Situ Hybridization Sanger (Dideoxy) Method Polymerase Chain Reaction Analyzing Protein Structure and Function Studying Gene Expression and Function-DNA Microarrays Review of Some Computational Methods Introduction to Probability and Stochastic Processes Theories Bayesian Theory Test of Hypothesis Expectation Maximization Method Maximum Likelihood Theory System Identification Theory Computational Structural Biology: Protein Structure Prediction Protein Structure Prediction Methods Data Resources Computational Structural Biology: Protein Sequence Analysis Pairwise Sequence Matching Multiple Sequence Alignment Genomics and Proteomics Genomics Proteomics Methods for Identification of Differentially Expressed Genes or Proteins Why t Test Is Not Enough? Mixture Model Method Genes Involved in Leukemia: A Case Study Binary and Bayesian Networks as Static Models of Regulatory Pathways Binary Regulator Pathways Bayesian Networks: Algorithm Applications and Practical Considerations Metabolic Control Theory for Static Modeling of Metabolic Pathways Basic Ideas Main Concepts in Metabolic Control Theory Mason Method Metabolic Control Model for Galactose Regulation Pathway: A Case Study System Identification and Control Theory for Dynamic Modeling of Biological Pathways Methodology Modeling of Cell Cycle: A Case Study Gene Silencing for Systems Biology A Brief Review of RNA Interference, Small Interfering RNA, and Gene Silencing Mechanisms Pathway Perturbation Using Gene Silencing Simulation and Systems Biology What Is Simulation? Challenges to Effective Simulation Case Studies Software, Databases, and Other Resources for Systems Biology Databases Scoring Matrix Analysis Software Bioinformatics in MATLAB Future Directions Single-Cell Microarray and Systems Biology High-Throughput Protein Assays and Systems Biology Integration of Molecular Data with Higher-Level Datasets Identifying Genes Controlling Macrolevel Changes Molecular-Level Image Systems and Systems Biology Index