Schedule (approx) Topic (relates to book)

hordeprobableBiotechnology

Oct 4, 2013 (3 years and 10 months ago)

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Welcome to 458

Bioinformatics

Fall 2010















Times:

(1:30 PM R)





Instructors:
Wayne
Smith


Stuart Gordon




Richardon

129


Lassiter 102


X8194




X8405


wasmith@presby.edu


sggordon@presby.edu


Schedule
(approx)

Topic (relates to book)

Task (due date)

August

Course Syllabus



Course intro

Biological Problems in Need of Solutions



September

Review of Molecular Genetics



Genome Projects



Gene Calling



Sequence Similarity: Local Sequence Alignments



October

BLAST



more BLAST and other tools



maximizing BLAST



Multiple Sequence Alignments



November

HMM and Domain
-
level analysis



Phylogenetic

trees



Transcriptomics

&

Personalized Medicine (
pharmacogenomics
)



Comparative Genomics



December

Metagenomics



student presentations



Course Homepage:
http://web.presby.edu/~wasmith/newcourses/458bioinformatics/

Evaluation


Paper Discussions




10%


Participation





10%


Midterm Exam




20%


Project Phase One




15%


Project Phase Two




15%


Project Presentation (part of final)


5%


Final Exam





20%

Why Bioinformatics?


First off: What is bioinformatics?


Bioinformatics arises from the interaction of biology, computer science, math, and
statistics. It deals with the staggering amount of biological information, mainly in the
form of DNA and protein sequences, and tries to find ways to organize, sort, compare,
and decode these sequences to find underlying similarities and patterns that are
biologically relevant.

Right time, Right place

October 2011, 11003 projects



“The generation of genomic data will have
[has had!] little value without corresponding
phenotypic information about individuals'
observable characteristics, and computational
tools for linking the two.” Craig Venter


“The consequences for clinical medicine,
however, have thus far been modest.” Francis
Collins

It is Sequenced, What’s Next?


Tracing Phylogeny


Finding family relationships between species by
tracking similarities between species.


Gene Annotation (cooperative genomics)


Comparison of similar species.


Determining Regulatory Networks


The variables that determine how the body reacts
to certain stimuli.


Proteomics


From DNA sequence to a folded protein.


Figure 4. The change in
misannotation

over time in the NR database for the 37 families investigated.

Schnoes

AM, Brown SD,
Dodevski

I, Babbitt PC (2009) Annotation Error in Public Databases:
Misannotation

of Molecular Function in Enzyme
Superfamilies
.
PLoS

Comput

Biol

5(12): e1000605. doi:10.1371/journal.pcbi.1000605

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000605

Modeling


Modeling biological processes tells us if we
understand a given process


Because of the large number of variables that
exist in biological problems, powerful
computers are needed to analyze certain
biological questions

Protein Modeling


Quantum chemistry imaging algorithms of active sites
allow us to view possible bonding and reaction
mechanisms


Homologous protein modeling is a comparative
proteomic approach to determining an unknown
protein’s tertiary structure


Predictive tertiary folding algorithms are a long way off,
but we can predict secondary structure with ~80%
accuracy.


The most accurate online prediction tools:




PSIPred



PHD

Regulatory Network Modeling


Micro array experiments allow us to compare
differences in expression for two different
states


Algorithms for clustering groups of gene
expression help point out possible regulatory
networks


Other algorithms perform statistical analysis
to improve signal to noise contrast

Systems Biology Modeling


Predictions of whole cell interactions.


Organelle processes, expression modeling



Currently feasible for specific processes (eg.
Metabolism in E. coli, simple cells)


Flux Balance Analysis



The future…


Bioinformatics is still in it’s infancy


Much is still to be learned about how proteins
can manipulate a sequence of base pairs in
such a peculiar way that results in a fully
functional organism.


How can we then use this information to
benefit humanity without abusing it?