Part1. The utility of the Exposome Paradigm -- Chapter1. Using Exposomics to assess cumulative risks from multiple environmental stressors -- Chapter2. Sequencing the Public Health Exosome -- Chapter3. The US Military and the Exposome -- Chapter4. Framing Fetal and Early Life Exposome within Epidemiology -- Part2. Measuring the internal exposome -- Chapter5. Epigenetics and the exposome -- Chap…
Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks -- Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks -- Towards an Integrated Protein-Protein Interaction Network -- The Factor Graph Network Model for Biological Systems -- Pairwise Local Alignment of Protein Interaction Networks Guided by Models of Evolution -- Finding Nov…
Predicting Genetic Regulatory Response Using Classification: Yeast Stress Response -- Detecting Functional Modules of Transcription Factor Binding Sites in the Human Genome -- Fishing for Proteins in the Pacific Northwest -- PhyloGibbs: A Gibbs Sampler Incorporating Phylogenetic Information -- Application of Kernel Method to Reveal Subtypes of TF Binding Motifs -- Learning Regulatory Network Mo…
Quantification and Calculation in Nature -- The Cells of the Brain -- Brain: A Distributed Intelligent Processing System -- Neural Computational Mechanisms Supporting Cognitive Processes -- The Brain and Quantum Computation -- Memetics and Cognitive Mathematics -- Modeling of Arithmetic Reasoning -- Brain Maps of Arithmetic Processes in Children and Adults -- Arithmetic Learning Capability in C…
Medical Bioinformatics: Detecting Molecular Diseases with Case-Based Reasoning -- Prototype Based Recognition of Splice Sites -- Contact Based Image Compression in Biomedical High-Throughput Screening Using Artificial Neural Networks -- Discriminative Clustering of Yeast Stress Response -- A Dynamic Model of Gene Regulatory Networks Based on Inertia Principle -- Class Prediction with Microarray…
Markov Models in Molecular Evolution -- to Applications of the Likelihood Function in Molecular Evolution -- to Markov Chain Monte Carlo Methods in Molecular Evolution -- Population Genetics of Molecular Evolution -- Practical Approaches for Data Analysis -- Maximum Likelihood Methods for Detecting Adaptive Protein Evolution -- HyPhy: Hypothesis Testing Using Phylogenies -- Bayesian Analysis of…
Probability Theory (i): One Random Variable -- Probability Theory (ii): Many Random Variables -- Statistics (i): An Introduction to Statistical Inference -- Stochastic Processes (i): Poisson Processes and Markov Chains -- The Analysis of One DNA Sequence -- The Analysis of Multiple DNA or Protein Sequences -- Stochastic Processes (ii): Random Walks -- Statistics (ii): Classical Estimation Theor…
Part I: The Neural Foundations -- From Classical Connectionist Models to Probabilistic / Generalised Regression Neural Networks (PNNs / GRNNs) -- The Kernel Memory Concept – A Paradigm Shift from Conventional Connectionism -- The Self-Organising Kernel Memory (SOKM) -- Part II: Artificial Mind Systems -- The Artificial Mind System (AMS), Modules, and their Interactions -- Sensation and Percep…
Biology in a Nutshell -- Words -- Word Distributions and Occurrences -- Physical Mapping of DNA -- Genome Rearrangements -- Sequence Alignment -- Rapid Alignment Methods: FASTA and BLAST -- DNA Sequence Assembly -- Signals in DNA -- Similarity, Distance, and Clustering -- Measuring Expression of Genome Information -- Inferring the Past: Phylogenetic Trees -- Genetic Variation in Populations -- …
Preprocessing data from genomic experiments -- Preprocessing Overview -- Preprocessing High-density Oligonucleotide Arrays -- Quality Assessment of Affymetrix GeneChip Data -- Preprocessing Two-Color Spotted Arrays -- Cell-Based Assays -- SELDI-TOF Mass Spectrometry Protein Data -- Meta-data: biological annotation and visualization -- Meta-data Resources and Tools in Bioconductor -- Querying On…