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Tuesdays, Thursdays,
1:00 to 2:30 PM.
2901 Learning
Resource Center
(under Taubman Library)
For information regarding
upcoming Bioinformatics seminars, please e-mail gradbioinfo@umich.edu
or check
the website link: Bioinformatics
Seminars
Students are
required to participate in lecture meetings and seminar
reading sessions, as noted. Students will be expected to come
to seminar sessions with their own brief written questions
about the paper(s), and one or two students will be designated
beforehand as discussion leaders for the day's discussion. In
addition there will be problem sets and one or more term
projects to be worked out in groups of approximately four
students. More details will be forthcoming soon!
Faculty Participants:
| Phil Andrews |
Biological
Chemistry |
| Nick Bergman |
Bioinformatics |
| Tom Blackwell |
Bioinformatics |
| Dan Burns |
Mathematics |
| Kristina Hakansson |
Chemistry |
| George Michailidis |
Statistics |
| Dr Gil Omenn |
Human Genetics/Internal Medicine/SPH |
|
Dr David States
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Bioinformatics/Human Genetics
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Lecture
Schedule:
Links are to lecture notes
(if available) and related
or required literature reading.
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January 13
2813 Med Sci II
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Phil Andrews
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Protein Separation
Techniques
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January 15
2903 LRC
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Phil Andrews
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An Intro to
Mass Spectrometry (MS)
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January 20
NA
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No Meeeting Today
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January 22
2817 Med Sci II
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Phil Andrews
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Tandem Mass
Spectrometry (MS/MS)
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January 27
2813 Med Sci II*
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Andrews,
Blackwell,
Burns
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Literature Seminar
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January 29
2813 Med Sci II*
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Andrews,
Blackwell,
Burns
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Literature Seminar
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February 5
2813 Med Sci II*
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Kristina Hakansson
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Literature Seminar
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February 12
2813 Med Sci II*
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Kristina Hakansson
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Literature Seminar
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February 19
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*
NO CLASS * |
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March 2
2903 LRC
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Tom Blackwell |
Introduction
to Database Search Methods for MS/MS |
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(1)
M.
Mann and M. Wilm, Error-Tolerant identification of Peptides in
Sequence Databases by Peptide Sequence Tags, Anal. Chem.
66 (1994), 4390-4399
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March 4
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Dr. Hanjo Lim
Dr. Jimmy Song
Aventis Pharmaceuticals
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Multidimensional Protein
Identification Technology ("Mudpit") and Its Applications
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Dr. Hanjo Lim:
Application of MudPIT in
Proteomics
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(1)
A.J.
Link, et al., Direct analysis of protein complexes using mass spectrometry,
Nat. Biotech.17 (1999), 676-682.
(2)
M.J.
MacCoss, et al., Shotgun identification of protein modifications
from protein complexes and lens tissue, PNAS 99 (2002),
pp. 7900-7905.
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March 9
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Tom Blackwell
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March 11
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Dan Burns
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De
Novo Peptide Sequencing Methods
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March 16
2903 LRC
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Dan Burns
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SHERENGA (end)
Literature Seminar
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(1)
Chen,
et al., A dynamic programming qapproach to de novo peptide sequencing
via tandem mass spectrometry, J. Comp. Bio. 8 (2001)
325-338.
(2) Dancik,
et al., De Novo Peptide Sequencing via Tandem Mass Spectrometry,
J. Comp. Bio. 6 (1999) 327-342.
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March 18
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* No
Class *
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Please attend the Bioinformatics
Seminar
4:00 PM
2903 LRC
"Integrated gloabl profiling
of cancer"
Samir Hanash, M.D.,
Ph.D.
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(1) Chad
Creighton, Rork Kuck, David E Misek, David S Rickman, Franck M Brichory,
Jean-Marie Rouillard, Gilbert S Omenn and Samir Hanash, "Profiling
of pathway-specific changes in gene expression following growth
of human cancer cell lines transplanted into mice," Genome
Biology 4 (2003) R46.1-R46.12
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March 23
2903 LRC
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Nick Bergman
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Introduction
to Anthrax biology and life cycle
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March 25
2903 LRC
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Nick Bergman
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Literature Seminar
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(1)
H
Liu, NH Bergman, B Thomason, S Shallom, A Hazen, J Crossno,
DA Rasko, J Ravel, TD Read, SN Peterson, JR Yates III, PC Hanna,
"Formation and composition of the Bacillus anthracis endospore,"
Journal of Bacteriology 186.1 (2004) 164-178.
(uses cookies)
(2)
Ariel, N.,
A. Zvi, K. S. Makarova, T. Chitlaru, E. Elhanany, B. Velan, S. Cohen,
A. M. Friedlander, and A. Shafferman. "Genome-Based Bioinformatic
Selection of Chromosomal Bacillus anthracis Putative Vaccine Candidates
Coupled with Proteomic Identification of Surface-Associated Antigens."
Infection and Immunity 71.8 (2003) 4563-79.
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March 30
2903 LRC
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Dr. Marcin Adamski
States Lab
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Protein Identifications
in the HUPO Plasma Proteome Project
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(1) S.
Hanash, "HUPO initiatives relevant to cllinical proteomics",
Mol. Cell. Proteomics, online prepublication Jan 27, 2004
(R400004-MCP200)
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April 1
2903 LRC
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Dr. Chris Taylor
European Bioinformatics Inst.
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MIAPE:
The Minimum Information About A Proteomics Experiment
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Authors: Chris
Taylor, Henning Hermjakob, Kai Runte, Weimin Zhu, Rolf Apweiler [European
Bioinformatics Institute, Hinxton, UK]; HUPO PSI/PPP/BPP/LPP.
Abstract:
The volume
of generated proteome data is rapidly increasing, due both to
the movement towards high-throughput approaches, and to the advent
of new experimental techniques and analyses. However, publicly
available proteomics data is rather limited; sample extraction
and preparation are usually undocumented, and the analytical methods
employed in deriving
conclusions are often absent. There are no widely used databases
of (for example) mass spectrometry data, and those containing
2-DE gel images represent little more than pictorial indexes into
Swiss-prot.
A robust,
future proofed, standard representation of both methods and data
from proteomics experiments is required, analogous to the MIAME/MAGE
system for transcriptomics. To that end we present the MIAPE model,
and associated toolkit. The establishment of such a model as a
standard will bring a number of benefits: it will allow researchers
to quickly establish the provenance and relevance of a dataset,
facilitating information exchange; non-standard searches become
possible, e.g. by technique; and the process of tool and database
development will be greatly simplified.
This wide-ranging
talk will cover the development process for the MIAPE standard,
the role played by the EBI in various of the HUPO projects, and
the future for integrated functional genomics models, and the
ontologies to support them.
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(1)
Chris
F. Taylor, Norman W. Paton, Kevin L. Garwood, Paul D. Kirby, David
A. Stead, Zhikang Yin, Eric W. Deutsch, Laura Selway, Janet Walker,
Isabel Riba-Garcia, Shabaz Mohammed, Michael J. Deery, Julie A.
Howard, Tom Dunkley, Ruedi Aebersold, Douglas B. Kell, Kathryn S.
Lilley, Peter Roepstorff, John R. Yates III, Andy Brass, Alistair
J.P. Brown, Phil Cash, Simon J. Gaskell, Simon J. Hubbard, Stephen
G. Oliver. "A systematic approach to modeling, capturing, and
disseminating proteomics experimental data." Nature Biotechnology,
21.3, (2003) 247-254.
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April 6
6311 Med Sci I*
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Dr. Ron Beavis
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New computational strategies
for database searches with tandem mass spectra |
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(1)
David
Fenyo and Ronald C. Beavis, "A Method for Assessing the Statistical
Significance of Mass Spectrometry-Based Protein Identifications
Using General Scoring Schemes. " Anal. Chem. 75
(2003) 768-774.
(2)
Robertson
Craig, Ronald C. Beavis, "A method for reducing the time required
to match protein sequences with tandem mass spectra" Rapid
Communications in Mass Spectrometry 17.20 (2003) 2310-2316.
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April 8
2813 Med Sci II*
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Dr. Curtis Wilkerson
Michigan State Univ.
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Informatics issues for
high throughput proteomics
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(1)
Tabb
DL, McDonald WH, Yates JR 3rd. "DTASelect and Contrast: tools
for assembling and comparing protein identifications from shotgun
proteomics." J Proteome Res. 1 (2002 ) 21-6
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April 13
2903 LRC
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Dr. Brian Haab
Van Andel Research Inst.
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Quantitative
assays by protein microarrays
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(1)
Wang, Y. X. Wang S.-W. Guo S.
Ghosh, "Conditions to ensure competitive hybridization in two-color
microarray: a theoretical and experimental analysis," BioTechniques
32 (2002):1342-1346.
(2)
Heping Zhou,
Kerri Bouwman, Mark Schotanus, Cornelius Verweij, Jorge A Marrero,
Deborah Dillon, Jose Costa, Paul Lizardi and Brian B Haab, "Two-color,
rolling-circle amplification on antibody microarrays for sensitive,
multiplexed serum-protein measurements," Genome Biology
5 (2004) R28.1 - R28.12
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April 15
2903 LRC
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Dan Burns
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Statistics of Ion Fragmentation |
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(1)
D.L. Tabb, L.L. Smith, L.A. Breci,
V.H. Wysocki, D. Lin, J.R. Yates, III "Statistical Characterization
of Ion Trap Tandem Mass Spectra from Doubly Charged Tryptic Peptides",
Anal. Chem. 75 (2003), 1155-1163.
(2) V.H.
Wysocki, G. Tsaprailis, L.L. Smith, L.A. Breci "Mobile and
Localized Protons: A Framework for Understanding Peptide Dissociation",
J. Mass Spectrom. 35 (2000), 1399-1406.
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April 20
2903 LRC
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Dan Burns
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(1) Literature seminar;
see paper 1 for April 15, above.
(2) De Novo demos (time permitting)
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| For the De
Novo demo we didn't get to in class, go to the class workspace (you
will have to log in), and click for "Resources". Follow
the directions there. There are two De Novo tools and MASCOT: it is
useful to compare the three on the same test peaklist file. This is
set up for you in the workspace. |
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