Time and Location:
University of Illinois Hospital
1740 W Taylor
Chicago IL. 60612
Room: 1135 (Main Floor)
Meeting time: Tuesday, 12:PM - 12:50PM
Fall Rotation Dates:
September: 10, 17, 24
October: 1, 8, 15, 29
November: 5, 12
Fall 2002 Rotation:
Section I: Probability and Statistical
Inference.
Session
1.1 September
10
Session 1.2 September
17
Session 1.3 September
24
In
this basic module we will discuss the basic
grammar of reasoning with uncertainty. At
the end of the Section, participants will
be able to understand the core of the statistical
grammar (the object of statistical statements),
including the notions of uncertainty, probability
models, interpretation of model parameters,
data simulation, data summary, meaningful
data summaries, the role of sample size,
modes of estimation and hypothesis testing
(from the classical paradigm) and an outline
of the non-classical paradigms such as the
Bayesian formulation for inference.
Suggested readings:
Sections
II and III: Biological Sequences Analysis.
This is an introductory series of lectures
aimed at discussing the basic concepts of
biological (nucleotides and amino acids)
sequence analysis from a probabilistic modeling
perspective. This knowledge will facilitate
the understanding of contemporary and classic
clinical applications of the underlying
probabilistic concepts, including those
illustrated in the selected readings (see
references below).
The probability and statistics background
will be derived from the notions and examples
introduced in the Basic Module (Section
I) of the Rotation, including probability
distributions, entropy, inference, sampling
and estimation of probability from counts.
| Session
2.1 |
October
1: |
Sequence
similarity, homology and alignment |
| Session
2.2 |
October
8: |
Scoring
models for pairwise alignment |
| Session
2.3 |
October
15: |
Markov chains and hidden Markov models |
| Session
3.1 |
October
29: |
Pairwise
alignemnt using HMM |
| Session
3.2 |
November
5: |
Phylogenetic
trees |
| Session
3.3 |
November
12: |
Analysis
and interpretation of microarray data
Invited guest lecture: Borko
Jovanovic, PhD, Northwestern University
|
Suggested
readings and links:
 |
Biological
Sequences: Briefly Annotated Definitions
and Concepts (Part I) (view
article)
Author: Marlos Viana |
|
Biological
sequence analysis: Probabilistic models
of protein and nucleic acids
Authors:
Durbin, R., Eddy S., Krogh A., and
Mitchison, G.
Cambridge
U. Press, 1998 |
|
National
Center for Biotechnolgy Information
(NCBI)
|
|
User's Guide to Human 's Genome
(Links)
|
|
Importance
of purine and pyrimidine content of
local nucleotide sequences (six bases
long) for evolution of the human immunodeficiency
virus type 1.(view
article)
Author: H. Doi, Proc Natl Acad Sci U
S A. 1991 Oct 15;88(20) |
|
A piecewise-homogeneous
Markov chain process of lung transplantation.
(view
abstract)
Authors:
Sharples LD, Taylor GI, Faddy M.
J Epidemiol Biostat 2001;6(4):349-55
|
|
Hidden
Markov models for the onset and progression
of bronchiolitis
obliterans syndrome in lung transplant
recipients. (view
abstract)
Authors:
Jackson CH, Sharples LD.
Stat Med 2002 Jan 15;21(1):113-28 |
|
Profile
hidden Markov models.
(view article) (view
abstract)
Author:
Eddy SR.
Bioinformatics 1998;14(9):755-63 |
|
A
Markov model for analysing cancer markers
and disease states in survival studies.Biometrics.
1986 Dec;42(4):855-65.
(view article) (view
abstract)
Author:
Richard Kay
|
|
Classification,
subtype discovery, and prediction of
outcome in pediatric acute lymphoblastic
leukemia by gene expression profiling.
(view
abstract)
Authors:
Yeoh EJ, Ross ME, Shurtleff SA, Williams
WK, Patel D, Mahfouz R, Behm FG, Raimondi
SC, Relling MV, Patel A, Cheng C, Campana
D, Wilkins D, Zhou X, Li J, Liu H, Pui
CH, Evans WE, Naeve C, Wong L, Downing
JR.
|
Note:
|
The PDF
files in the above links can be viewed
with
|
 |
