Bioinformatics Topics

1. Group 1: DNA analysis
   Sequence Analysis
   Computational Genomics
   Protein Structure and Function
   Phylogenetics
   Microarray Analysis
   
2. Group 2: Computing
   Programming
   Algorithms
   Databases
3. Group 3: Other
   General Biology
   Biomedical Informatics
   Statistics
4. Topics in Sequence Analysis
   Departments: Biomedical Engineering, Bioinformatic and Computational Biology, Bioinformatic, Plant Biology, Biochemistry, Computer Science, Bioengineering, Medical Informatics, Biology, Biomolecular Engineering
   Background -General principles of DNA/RNA structure and stability
   The Basics of Sequence Alignment
   -Pair-wise sequence comparison
   -multiple sequence alignment
   -fragment assembly
   -Sequence profiles and profile alignment methods
   -Scoring matrices, BLOSUM
   -Sequence weighting
   Software
   -BLAST, FASTA, CLUSTAL, GRAIL, INSIGHT II, RASMOL, HMMER
   Algorithms and Models
   -Hidden Markov Models
   -Maximum-likelihood estimate
   -Markov Chains
   -Gibbs Sampling
   -Dirichlet Mixtures
   Phylogenetic inference (see topics in Phylogenetics)
   -reconstructing evolutionary relationships
   Structure prediction (see topics in protein structure and modeling)
   -RNA secondary structure prediction
   -protein structure prediction and comparison
   Public Access Databases
   -sequence and structure search tools
   Whole Genome Sequencing (see topics in computational genomics)
   -shotgun approaches
   -EST assembly
   -genome annotation
5. Topics in Computational Genomics
   
   Departments: Bioinformatic, Plant Biology, Computer Science, Biochemistry, Bioinformatic and Computational Biology,
   Biomolecular Engineering, Biochemistry, Biology, Biomedical Informatics
   Whole Genome Reconstruction
   -genome mapping
   -genome assembly
   
   Comparative Genomics
   -General probabilistic graphical models
   -Bayesian Networks
   -Exact inference
   -Learning BNs from data
   -EM and structural EM
   Functional Genomics
   -QTLs & eQTLs
   -Non-coding RNA genes
   -RNA recognition
   -reverse genetics
   -The ENCODE project
   Gene Expression Analysis
   -sequencing methods (including microarrays)
   -clustering
   -EST libraries
   -motif discovery
   -DNA methylation & epigenetic gene regulation
   Genome Annotation
   -gene finding
   -gene indices
   Genetic Regulation
   -gene regulatory regions
   -translational regulation: siRNA and microRNA
   -identifying miRNAs and their targets
   Genomic Technologies
   -PCR technology
   -Genechips
   Genome Diversity
   Genome Structure
   The Human Genome Project
   Genome Databases
   Data Mining Models
   -Hidden Markov Models
   -Probabilistic formulation
   -Mixture models
   -Gaussian Mixtures
   -Biclustering
   -Loss functions
   -Conditional maximum likelihood.
   
   -SVMs
   Proteomics and Metabolomics
   Medical Applications
   -Diseases and phenotypes
   -Pharmaceutical discovery
   -Genomic medicine
   -Copy number variation
   Phylogenetic Inference
   -Parsimony
   -Stationary markov processes
   -Rate matrices
   -Maximum Likelihood -Maximum a posteriori
   -Felsensteins Post-order traversal
   -PhyloHMMs
6. 
   Topics in Protein Structure and Modeling
   
   Departments: Bioinformatic, Computer Science, Biochemistry, Bioinformatic and Computational Biology, Bioengineering,
   Biomolecular Engineering, Biology
   Physico-chemical properties of proteins
   -Protein folding dynamics
   Determining Protein Structure
   Experimental Techniques
   -X-ray Crystallography
   -NMR
   -cryo-EM
   -mass spectrometry
   Computational Techniques
   -SAM-Txx prediction protocol
   -Lattice-based prediction
   -Undertaker protein-folding algorithm
   Classification of Protein Structure
   -Protein families
   -Protein domains and prediction of domain boundaries
   -Homology modeling
   -Comparative modeling of protein structure and threading
   -Significance of structure-structure similarity
   -Expression data analysis (clustering and classification)
   -Structure-structure alignment algorithms
   Protein Function
   -Protein structure-function relationships
   -Prediction of functionally important sites
   Public protein structure databases
   -Structure database search tools
   Protein interactions
   -Protein-protein interaction networks
   -Voronoi diagram, Delaunay triangulation
   RNA secondary structure prediction
   Medical Applications
   -Protein microarrays and detection of autoimmune disease
   -High throughput proteomic disease markers
   -Computational methods for protein microarrays
   -Remote homology detection
   -Proteomic diagnosis of trauma


7. Topics in Phylogenetics
   Departments: Computer Science, Biochemistry, Bioinformatic and Computational Biology, Bioengineering, Biology, Biomedical Informatics, Computer Science
   Molecular basis of evolution
   History of Phylogenetic Inference
   Characters: Homology, Morphology, Molecular
   Phylogenetic Tree Construction
   -Alignment Strategies
   -Optimality Criteria – Parsimony, ML, ME
   -Algorithmic Approaches
   -Searching Tree Space
   -Character Weighting in Parsimony
   -Clustering methods
   -Hypothesis Testing: Paired Sites, Parametric Bootstraps -Multiple Data Sets/Partitioned Models
   -Molecular Clocks
   -Ancestral Character State Reconstruction
   Models of Sequence Evolution
   -Model Selection
   -Method Performance
   Support for Constructed Trees
   -Consensus Trees
   -G1, PTP, Decay, Bootstrap
   -Jacknife & Bayesian Nodal Probabilities
   Non-tree Based Methods
   Software tools for phylogenetic analysis
   Genome comparisons
   Protein structure evolution
   


8. Topics in Microarray Analysis
   
   Departments: Biomedical Informatics, Biology, Biostatistics
   Review of the basic biology of gene expression
   Overview of microarray technology
   Microarray Data Analysis – Statistical Techniques
   -regression
   -discriminant analysis
   -clustering
   -classification
   -simple graphical models
   Methods for computational and biological validation
   
9. Topics in Programming
   
   Departments: Bioinformatic, Computer Science, Biomedical Engineering, Biology, Plant Biology, Bioinformatic and Computational Biology
   General Programming Concepts (in alphabetical order)
   -algorithm design
   -arrays
   -complex data structures
   -control structures
   -data types
   -debugging
   -designing modules
   -dynamic programming
   -file input/output
   -functions
   -graphics programming
   -hashes
   -introduction to machine learning
   -multiprocessing & multithreaded programming
   -network programming with sockets
   -object oriented programming
   -pointers
   -recursion
   -regular expressions
   -sorting
   -subroutines
   -web programming (HTML, CGI)
   Languages Taught and Language-Specific Topics
   HTML
   SQL
   Perl
   BioPerl
   -Genomic resources
   -Accessing Remote databases
   C
   -Flow Control
   -C Structures
   -Interface to UNIX
   -Using a C Application Programming Interface (API)
   Java
   -Using Java Classes
   -GUI Layout
   -Java Events
   -Java Exception Handling
   UNIX
   -Using UNIX for basic data processing
   -UNIX command-line tools
   -UNIX shell programming
   -Using UNIX development tools
   Intro to relational databases
   
   Bioinformatic Applications
   -DNA sequence analysis
   -parsing FASTA and GenBank files
   -processing BLAST output files
   
10. 
    Topics in Algorithms
    
    Departments: Bioinformatic, Computer Science, Biomedical Engineering, Bioengineering, Medical Informatics
    Concepts of Optimization
    -Continuous vs Discrete Optimization
    -Constrained and Unconstrained Optimization
    -Global and Local Optimization
    -Stochastic and Deterministic Optimization
    Optimization Algorithms
    -Linear and Nonlinear programming
    -Combinatorial optimization
    -Heuristic search methods
    
    Exact string matching problems
    -Suffix trees
    -Suffix tree algorithms
    Applications
    -Prediction of genetic regulatory network
    -Protein structure prediction
    -Design of microarray experiment, analysis of microarray data
    -Biological signal finding
    -Neural Networks
    Greedy algorithms
    
    Algorithm complexity
    Sorting
    Recursion
    Dynamic programming and space management
    Parallel and grid computing
    Simulation
    Introduction to Machine Learning
    Feature Spaces
    Hidden Markov Models
    SVMs


11. Topics in Databases
    
    Departments: Computer Science, Biomedical Engineering, Plant Biology, Information and Library Science
    Relational data models and database management systems
    -Relational database design
    -Foreign Keys
    -Relational Integrity
    -Entity-Relationship modeling
    -Normalization
    -Transactions
    SQL
    -simple queries
    -calculated fields
    -sorting and grouping results
    -aggregate functions
    -multi-table queries (inner join, outer join)
    -subqueries
    -combining result tables
    -create and alter tables
    ORACLE
    
    Biological Databases
    Object-Oriented Databases
    Web based programming tools to make databases accessible
    Data integration and security
12. Topics in General Biology
    Departments: Bioinformatic, Bioinformatic and Computational Biology, Biology, Medical Informatics, Biomedical Engineering
    Molecular Biology
    -Synthesis, structure, and function of DNA, RNA, and proteins
    -Regulation and control of the synthesis of RNA and proteins
    -Introduction to molecular biology of eukaryotes.
    -molecular biological techniques (genetics, recombinant DNA techniques)
    -cell structure and cell cycle
    Genetics
    -relationships among genes
    -regulation of gene expression
    -use of genetic systems to probe genetic problems
    -Mendelian genetics
    -genomics
    -rules of inheritance in eukaryotic organisms
    -DNA replication
    -molecular approaches to analyze DNA.
    -DNA structure
    -location of DNA within the cell
    -movement of genes within a chromosome
    -genetic maps
    -chromosome abnormalities
    -mutations
    -prokaryotic genetics
    -genetic recombination
    -DNA movement in the genome
    -protein synthesis
13. Topics in Biomedical Informatics
    
    Departments: Information and Library Science, Biomedical Informatics, Medical Informatics
    Basics of Biomedical Informatics
    -Overview of Discipline and Its History
    -Biomedical Computing
    -Electronic Medical Records (EMR)
    -Decision Support and Health Care Quality
    -Standards, Privacy and Security, Costs and Implementation
    -Evidence-Based Medicine and Medical Decision-Making
    -Imaging Informatics and Telemedicine
    -Bibliographic Retrieval
    -Networking
    -Web-based Interactions
    Information Retrieval
    -Text Based
    -Image Based
    -Genomics
    -Terms, Models, and Resources
    -Health and Biomedical Information
    -Evaluation of Systems
    -Content
    -Indexing
    -Retrieval
    -Evaluation
    -Lexical-Statistical Systems
    -Augmenting Systems for the User
    Health sciences informatics
    -Health sciences information centers
    -Health information professionals and roles
    -Information resources
    -Information organization and access
14. Topics in Statistics
    
    Departments: Bioinformatic, Medical Informatics, Biostatistics, Biomolecular Engineering
    Statistical Foundations
    -random variables
    -probability
    -statistical inference
    -confidence intervals
    -hypothesis testing
    -correlation and regression Advanced Statistical Concepts
    -sample size and power considerations
    -analysis of variance and multiple comparisons
    -multiple regression and statistical control of confounding
    -logistic regression
    -survival analysis
    -multiple testing issues and step-down procedures
    -length model versus stop character for finite strings
    -use of log-probability for computations
    -constructing a model from data
    -training, cross-training, and testing
    -Z-scores (Gaussian dist.) and fat tails of extreme-value (Gumbel dist.)
    -machine learning
    -supervised learning
    -dimensionality reduction
    -clustering
    -decision trees
    -maximum entropy
    -Bayes’ Rule and its applications
    Algorithms, Models, and Processes
    
    -Stochastic Processes (Poisson, Markov, Random Walks)
    -Maximum Likelihood, Likelihood Ratios, and Sequential Analysis
    -Gibbs Sampler
    -Bootstrap Estimation
    Biological Applications
    -pairwise and multiple sequence alignment
    -gene and protein classification
    -phylogenetic tree construction.
    -high dimension functional genomics data
    -gene and motif finding
    Programming in R, Perl