Bioinformatics Topics

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1 Οκτ 2013 (πριν από 3 χρόνια και 8 μήνες)

165 εμφανίσεις

Commonly Taught
Bioinformatics Topics

Derived from Syllabi of
19

Universities


Group 1*: DNA analysis


Sequence Analysis**


Computational Genomics


Protein Structure and
Function


Phylogenetics


Microarray Analysis


Group 2: Computing


Programming


Algorit
hms


Databases


Group 3: Other


General Biology


Biomedical Informatics


Statistics


Law and Ethics


*Group 1 is the most common, followed by 2 and then 3.

**Within each group, the most common topics are listed first


Topics in Sequence Analysis


Departme
nts:
Biomedical Engineering, Bioinformatics and Computational Biology,
Bioinformatics, Plant Biology, Biochemistry, Computer Science, Bioengineering,
Medical Informatics, Biology, Biomolecular Engineering


Background


-
General principles of DNA/RNA stru
cture 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


S
oftware


-
BLAST, FASTA, CLUSTAL, GRAIL, INSIGHT II, RASMOL,
HMMER


Algorithms

and Models


-
Hidden Markov Models


-
Maximum
-
likelihood estimate


-
Markov Chains


-
Gibbs Sampling



-
Dirichlet Mixtures


P
hylogenetic inference

(see topics in Ph
ylogenetics)


-
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 s
earch tools


Whole Genome Sequencing

(see topics in computational genomics)


-
shotgun approaches



-
EST assembly


-
genome annotation


Topics in Computational Genomics


Departments:
Bioinformatics, Plant Biology, Computer Science,
Biochemistry,
Bioinformatics and Computational Biology, Biomolecular Engineering, Biochemistry,
Biology, Biomedical Informatics


Whole
G
enome
R
econstruction


-
genome mapping



-
g
enome assembly



C
omparative
G
enomics



-
General probabilistic graphi
cal models


-
Bayesian Networks


-
Exact inference


-
Learning BNs from data


-
EM and structural EM


F
unctional
G
enomics



-
QTLs & eQTLs



-
Non
-
coding RNA genes



-
RNA recognition


-
r
everse
g
enetics



-
The ENCODE project



Gene
E
xpr
ession
A
nalysis



-
sequencing methods

(including

microarrays)


-
c
lustering


-
EST
l
ibraries



-
m
otif discovery


-
DNA methylation & epigenetic gene regulation


Genome
A
nnotation



-
g
ene finding



-
g
ene
i
ndices



Genetic
R
egulation




-
gene regulatory regions


-
t
ranslational regulation: siRNA and microRNA



-
i
dentifying miRNAs and their targets


Genomic Technologies


-
PCR technology


-
Genechips


G
enome
D
iversity


G
enome
S
tructure


The Human Genome Project


Genome
D
atabas
es


Data Mining
Models


-
H
idden
M
arkov
M
odel
s


-
Probabilistic formulation


-
Mixture models


-
Gaussian Mixtures


-
Biclustering


-
Loss functions


-
Conditional maximum likelihood.


-
Linear regression, GLMs, perceptrons, Neural nets



-
SVMs


Proteomics and
M
etabolomics



Medical Applications


-
Diseases and phenotypes


-
Pharmaceutical discovery


-
Genomic medicine


-
Copy number variation


Phylogenetic Inference


-
Parsimony


-
Stationary markov processes


-
Rate matri
ces


-
Maximum Likelihood


-
Maximum a posteriori


-
Felsensteins Post
-
order traversal


-
PhyloHMMs



Topics in Protein Structure and Modeling


Departments:
Bioinformatics, Computer Science, Biochemistry, Bioinformatics and
Computational Biology,
Bioengineering, Biomolecular Engineering, Biology


Physico
-
c
hemical properties of proteins


-
Protein folding dynamics


Determining Protein Structure


Experimental Techniques


-
X
-
ray Crystallography


-
NMR


-
cryo
-
EM


-
mass s
pectrometry


Computational Techniques


-
SAM
-
Txx prediction protocol


-
Lattice
-
based prediction


-
Undertaker protein
-
folding algorithm


Classification of Protein Structure


-
Pr
otein families


-
Protein domains and p
rediction of
domain boundaries


-
Homology modeling


-
Comparative modeling of protein structure and threading


-
Significance of structure
-
structur
e similarity


-
Expression data analysis (clustering and classification)


-
Structure
-
structure alignment algor
ithms


Protein Function


-
Protein structure
-
fun
ction relationships


-
Prediction o
f functionally important sites


Publ
ic protein structure databases


-
S
tructure 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 micr
oarrays


-
Remote homology detection



-
Proteomic diagnosis of trauma


Topics in Phylogenetics


Departments:
Computer Science, Biochemistry, Bioinformatics 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


-
Searchin
g Tree Space


-
Character Weighting in Parsimony


-
C
lustering methods


-
Hypothesis Testing: Paired Sites, Parametric Bootstraps


-
Multiple Data Sets/Partitioned Models


-
Molecular Clocks


-
Ancestral Character State Reconstruction


Mod
els

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 t
ools for phylogenetic a
nalysis


Genome comparisons


Protein structure evolution



Topics in Microarray Analysis


Departments:
Biomedical Informatics, Biology, Biostatistics


R
eview of the basic biology of gene expression


O
verview of microarray technology


Microarray Data Analy
sis


Statistical Techniques


-
regression


-
discriminant analysis


-
clustering


-
classification


-
simple graphical models


Methods for computational and biological validation



Topics in Programming


Departments:
Bioinformatics, Computer Sc
ience, Biomedical Engineering, Biology,
Plant Biology, Bioinformatics 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 soc
kets


-
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 E
vents


-
Java Exception Handl
i
ng


UNIX


-
Using UNIX for basic data processing


-
UNIX command
-
line tools


-
UNIX shell programming


-
Using UNIX development tools


Intro to relational databases


Bioinformatics Applications


-
DNA sequence

analysis


-
parsing FASTA and GenBank files


-
processing BLAST output files



Topics in Algorithms


Departments:
Bioinformatics, Computer Science, Biomedical Engineering,
Bioengineering, Medical Informatics


Concepts of
O
ptimization


-
Continuous
vs Discrete Optimization


-
Constrained and Unconstrained Optimization


-
Global and Local Optimization


-
Stochastic and Deterministic Optimization


Optimization Algorithms



-
L
inear

and Nonlinear

programming


-
C
ombinatorial optimization





-
H
euristic search methods


Exact string matching problems


-
Suffix trees


-
Suffix tree algorithms


Applications


-
Prediction of genetic regulatory network


-
P
rotein structure prediction


-
D
esign of microarray experiment
, analysis of microa
rray data



-
Bi
ological signal finding


-
Neural Networks


G
reedy algorithms


A
lgorithm complexity


S
orting


Recursion


D
ynamic programming and space management


P
arallel and grid computing


S
imulation


Introduction to Machine Learning


Feature Spac
es


Hidden Markov Models


S
VMs

Topics in Databases


Departments:
Computer Science, Biomedical Engineering, Plant Biology, Information
and Library Science


R
elational data models and database management systems


-
Relational database design


-
Foreign
Keys


-
Relational Integrity


-
Entity
-
Relationship modeling


-
Normalization


-
Transactions


SQL



-
s
imple
q
ueries


-
c
alculated
f
ields


-
s
orting

and grouping

r
esults


-
a
ggregate
f
unctions


-
m
ulti
-
table
q
ueries (
in
ner
j
oin,
o
uter
j
o
in)


-
s
ubqueries



-
c
ombining
r
esult
tables


-
c
reate

and a
lter
t
ables


ORACLE


Biological Data
b
ases


Object
-
Oriented Databases


Web based programming tools to make databases accessible


Data integration and security


Topics in General Biology


D
epartments:
Bioinformatics, Bioinformatics 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

expres
sion


-
use

of genetic systems to probe genetic

problems


-
M
endelian genetics


-
g
enomics


-
rules of inheritance in
eukaryotic

organisms


-
DNA replication


-
molecular approaches to analyze DNA.


-
DNA
structure


-
location of DNA

within

the cell


-
movement of g
enes

within a chromosome


-
genetic maps


-
c
hromosome abnormalities


-
mutations


-
prokaryot
ic genetics


-
genetic recombination


-
DNA move
ment

in

the genome


-
protein synthesis



Topics in Biomedical Informat
ics


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 Suppo
rt 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 Interac
tions


Information Retrieval


-
Text Based


-
Image Based


-
Genomics


-
Terms, Models, and Resources


-
Health and Biomedical Information


-
Evaluation of Systems


-
Content


-
Indexing


-
Retrieval


-
Evaluation


-
Lexical
-
Statist
ical 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 Statis
tics


Departments:
Bioinformatics, Medical Informatics, Biostatistics, Biomolecular
Engineering


Statistical Foundations


-
r
andom
v
ariables


-
p
robability


-
s
tatistical
i
nference


-
confidence intervals


-
hypothesis testing


-
correlation a
nd 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


-
m
ultiple testing issues and step
-
down procedures


-
length model versus stop character for finite strings


-
use of log
-
probability for computations


-
c
onstructing a model from data


-
t
raining, cross
-
training, and testing


-
Z
-
scores (Gaussian
dist.) and fat tails of extreme
-
value (Gumbel dist.)


-
m
achine
l
earning


-
s
upervised
l
earning


-
dimensionality reduction


-
clustering


-
decision trees


-
maximum entropy


-
Bayes’ Rule

and its applications


Algorithms, Models, and Proc
esses


-
Stochastic Processes (Poisson
,

Markov
,
Random Walks
)


-
Maximum Likelihood, Likelihood Ratios
,

and Sequential Analysis


-
Gibbs Sampler


-
Boo
t
strap Estimation


Biological Applications


-
pairwise and multiple sequence alignment


-
gen
e and protein classification


-
phylogenetic tree construction.


-
h
igh
d
imension
f
unctional
g
enomics
d
ata


-
g
ene and
m
otif
f
inding


Programming in R
, Perl

Topics in Law and Ethics


Departments: Law, Bioinformatics


-
property rights

-
privacy and d
iscrimination

-
the federal regulatory role

-
self
-
regulatory safeguards

-
liability implications for individual/organizational behavior

-
policy responses to societal concerns in the U.S. and abroad


C
ases

studies


-
gene therapy


-
cloning


-
biomateri
als in the medical and health sector


-
farming and crop modifica
tion in the agricultural sector



Universities where Syllabi were Collected


Boston University

George Mason University

George Washington University

Michigan State University

Northeastern U
niversity

Northern Illinois University

Oregon Health and Science University

Rochester Institute of Technology

Stanford University

University of California Santa Cruz

University of Idaho

University of Illinois at Chicago

University of Iowa

University of Mic
higan

University of Minnesota

University of North Carolina at Chapel Hill

University of Tennessee at Knoxville

University of Texas at El Paso

University of the Sciences in Philadelphia