Showing posts with label Bioinformatic Topics. Show all posts
Showing posts with label Bioinformatic Topics. Show all posts

Thursday, May 28, 2015

Bioinformatics Topics

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

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