- Group 1: DNA analysis
Sequence Analysis
Computational Genomics
Protein Structure and Function
Phylogenetics
Microarray Analysis
- Group 2: Computing
Programming
Algorithms
Databases
- Group 3: Other
General Biology
Biomedical Informatics
Statistics
- 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
- 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
-
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
- 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
- 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
- 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
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
-
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
- 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
- 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
- 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
Sequence Analysis
Computational Genomics
Protein Structure and Function
Phylogenetics
Microarray Analysis
Programming
Algorithms
Databases
General Biology
Biomedical Informatics
Statistics
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
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
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
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
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
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
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
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
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
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
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
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