Chemistry 574 / MCB 554


Genomics, Proteomics, and Bioinformation:
A Survey of Modern Bioanalytical Methods

Lecture Schedule, Spring 2005

Tues. & Thurs. 4 to 5:20 pm, 161 Noyes Laboratory

Library Reserves URL:  TBA

WEB CT Environment and Course Support:  http://www.chem.uiuc.edu/clcwebsite/Webcoursespage.html

Note: The outline will evolve slightly as the Course progresses, Please check regularly. 

last updated Jan. 19, 2005

Lecture Date

Topic

Primary  Required Reading

Presentations/
Problem Sets / Exams

Jan. 18

Sign-up, Introduction, Syllabus, Overview 
Genomes of Bacteria, Archaea & Eucarya

Brown ch.1/ /Equipping Scientists for the New Biology /DNA, PCR, Remedial Mol. Biology: technical notes & research briefings Brown  ch. 4

 Semantics

Jan. 20

Genome Shapes and Topology:  chromatin, supercoling, and packaging. 

Brown ch 1.2 , begin Brown ch.2

 Primer Problem Set 1: 
"Molecular Biology 101"
(Brown Chpt.s 1 and 4)

Jan 25

Genetic mapping, polymorphisms 

Brown ch.5.2.2 only (Linkage later)

 

Jan 27

No Lecture

 (Univ. of Wisconsin)

 

Feb. 1

Physical mapping in the Human Genome Project:  Sequence Tagged Sites.

Brown ch.5.3

 

Feb. 3

Physical mapping: STSs

Brown ch. 5.3.2 - 5.3.3

 

Feb. 8

Genome sequencing (Shotgun vs. Directed Shotgun vs. clone contig strategies):  Library construction, Technologies, Assembly, Gap Closure.

Brown ch. 6, Fraser et al.

PS #1   Due

Feb. 10

After a Genome Has Been Sequenced:  Gene Finding and Functional Annotation  (SNPs by DNA Chips)

 Brown, Chapter 7  , through 7.1.2

 PS #2 Assign

Feb. 15

RNA Synthesis, Processing,  and Editing

Brown ch. 10 ; Basics of Eukaryotic RNA processing only 

 ***News Alerts***
(See Kelleher to schedule)

Feb. 17

Guest Lecture:  Hugh Robertson and “sequence gazing”

(NIH Study Section)

 

Feb 22

 Possibly No Lecture ?

(Back from Indianapolis in time?)

 

Feb 24

Genome Arrays and SAGE

Church, 2001 (Nat. Biotechnol.) (Velculescu) 

 1 Unit Students to hand in Paper & Presentation Topics to Prof. Kelleher

Mar 1

Guest Lecture: Mark Band  DNA Chips: RNA Data Handling/Manipulation 

(Pittcon)   Microarrays:  construction and analysis,  tools,

 PS #2 Due

Mar 3

Catch Up Lecture

 

 

Mar 8

Hour Exam 1

(Pittcon) Questions from  Brown  and Required Literature

 Hour Exam 1

Mar 10

Transcriptome Analysis of Escherichia coli and S. cerevisiae

Brown ch. 9 
Velculescu’s 2 papers

Assign PS #3

Mar 15

Do mRNA levels correlate with the protein levels?

Gygi and Washburn

 

Mar 17

The Protein Level: 2D-gels, Densitometry and Classical Methods of Protein Identification, Approaches to Mass Spectrometry-Based Protein Identification.

 Mann  (Nature 2000) , Yates (1999, Nature Biotchnology)

 

Mar 22

Spring Break

(Bremen)

 

Mar 24

Spring Break

 

 

Mar 29

Mass Spectrometry – Fundamentals of ionization and mass/charge analysis of ions

 

PS #3 Due

 

***News Alerts/***

Mar 31

Peptide-Focused Mass Spectrometry

()

 

Apr 5

Functional Proteomics and Characterization of Multi-Protein Complexes.

 

Assign PS #4

Apr 7

Quantitative Proteomics.

point of view (M. Mann) 
ICAT  (Gygi and Aebersold)

 

Apr 12

Forward and Reverse Chemical Genetics.
Guest Lecture: Paul Hergenrother

 

 

Apr 14

Posttranslational Modifications and Mammalian Proteome Projects.
Intact Protein Analysis:  Top Down Proteomics.

The phosphoproteome.

***News Alerts/***

Apr 19

Identification of new SNPs, haplotypes, and their high throughput detection; Polymorphisms, multi-genic phenotypes.

Garg et al, 
Haff and Smirnov

Begin Biomedical / Disease Section

Apr 21

Linkage (disequilibrium):  Gene hunting. Environmental vs. Genetic Etiologies.

Brown ch 5 (Genetic Mapping)

 

Apr 26

Cancer Biomarkers by DNA Microarrays:Tumor Classification; Protein-Based Biomarkers

Lander ...(Science '99)
Opitek, Caprioli

PS #4 Due

Apr 28

Selected 30 min student talks /

 

Supplemtary slots for student talks should not be required this year.

May 3

Selected 30 min student talks / / Course Wrap Up

 

 

May X

Reading Day

 

 

May XX

TUES ?, May XXth ;  X-XX PM ; 161 or 100 Noyes Lab

Comprehensive

Final


 

Instructor:

Neil Kelleher

53 RAL

4-3927

kelleher@scs.uiuc.edu

 

Office Hours:  Wed. 2:30-3:30 pm

 

Teaching assistants:

Meagan Mann

66 RAL

333-5098

mkmann@uiuc.edu

 

TA Office Hours:   Mondays 9-10 am


 

Grading

1 midterm exam

150 points

150 points

1 final exam

200 points

200 points

4 problem sets

4 x 75

300 points

paper + oral presentation (extra credit hour)

200

(200) points

news alerts

5 extra points each

maximum 2 presentations/person

TOTAL

 

650 (3 hours) or 850 (4 h)

List of past Guest Lecturers:

Zan Schulten (schulten@scs.uiuc.edu)
Hugh Robertson (hughrobe@uiuc.edu)

Gary Olsen (gary@phylo.life.uiuc.edu)
Carl Woese (carl@ninja.life.uiuc.edu)
Mark Band (markband@ux1.cso.uiuc.edu)
Lila Vodkin (l-vodkin@uiuc.edu)
Eric Jakobsson (jake@ncsa.uiuc.edu )
Paul Hergenrother (hergenro@uiuc.edu)
Bill Metcalf (metcalf@uiuc.edu)

 

Chemistry 574 / MCB 554

Required Reading List (NLK, March 15, 2005)

DNA

THE SNP papers below were on PROBLEM SET #2 , but not Exam #1.  They will become very important in the last quarter of the course !!!

RNA

RNA-Protein Correlations

  • Gygi SP, Rochon Y, Franza BR, Aebersold R. Mol. Cell Biol., 1999, 19(3), 1720-30.
  • Washburn, et al. ‘Protein pathway and complex clustering of correlated mRNA and protein expression analyses in Saccharomyces cerevisiae’ Proceedings of the National Academy of Sciences of the United States of America, 100, 3107-3112, 2003.

 

Protein

Disease Gene Hunting and Biomarkers

  • Haff and Smirnov. 'Single-nucleotide polymorphism identification assays using a thermostable DNA polymerase and delayed extraction MALDI-TOF mass spectrometry' Genome Research, 7, 378-388, 1997.
  • Golub, et al. ‘Molecular Classification of Cancer: Class Discovery and Class Prediction by Gene Expression Monitoring’ Science, 286, 531-537, 2000.
  • Jorde ‘Linkage Disequilibrium and the Search for Complex Disease Genes’ Genome Research, 10,1435–1444, 2000.
  • Pang, et al. ‘Biomarker discovery in urine by proteomics’ Journal of Proteome Research, 1, 161-169, 2002.
  • Chaurand, et al. ‘Imaging mass spectrometry:  a new tool to investigate the spatial organization of peptides and proteins in mammalian tissue sections’ Current Opinion in Chemical Biology, 6, 676-681, 2002.
  • Diamandis ‘Proteomic Patterns in Biological Fluids:  Do They Represent the Future of Cancer Diagnostics?’ Clinical Chemistry, 49, 1272-1278, 2003.