(Journal Club)
CMU course number 02-701
Pitt course number MSCBIO/CMPBIO 2060
Time: Monday from
Location: 411 Mellon Institute
Spring 2009 organized by Ge
Yang
Organizer contact
information:
Email: geyang at andrew dot cmu dot edu
Phone: 412-268-3186
Office: Mellon Institute 403
Office hours: appointment by email
Assignment schedule
|
Date |
Group member 1 |
Group member 2 |
Group member 3 |
Comment |
|
|
Presented by organizer |
|
|
|
|
|
MARTIN LUTHER KING DAY |
|
|
CANCELLED |
|
|
Anindita Dutta |
Yuefeng Lin |
Timothy Travers |
Group 1 |
|
|
Keith Callenberg |
John Sekar |
David Mowrey |
Group 2 |
|
|
Yevgeniya Monisova |
|
Guy Zinman |
Group 3 |
|
|
Andrej Savol |
Kyaw Myint |
Karim Benbourenane |
Group 4 |
|
|
Shan Zhong |
Ying Ding |
Jun Ma |
Group 5 |
|
|
Joshua Kangas |
Chao Ma |
Armaghan Naik |
Group 6 |
|
|
SPRING BREAK |
|
|
CANCELLED |
|
|
Virginia Burger |
|
|
Group 7 |
|
|
Ross Curtis |
Grace Huang |
Ming-Chi Tsui |
Group 8 |
|
|
Anindita Dutta |
Yuefeng Lin |
Timothy Travers |
Group 1 |
|
|
Keith Callenberg |
John Sekar |
David Mowrey |
Group 2 |
|
|
Yevgeniya Monisova |
|
Guy Zinman |
Group 3 |
|
|
Andrej Savol |
Kyaw Myint |
Karim Benbourenane |
Group 4 |
|
|
Shan Zhong |
Ying Ding |
Jun Ma |
Group 5 |
|
*** |
Joshua Kangas |
Chao Ma |
Armaghan Naik |
Group 6 |
|
*** |
Virginia Burger |
|
|
Group 7 |
|
*** |
Ross Curtis |
Grace Huang |
Ming-Chi Tsui |
Group 8 |
***:
General Guidelines on Paper Selection
(1) We will focus on recently published research
articles only. No review articles will be considered for this class.
(2)
Unless there are really strong justifications, we will not go back to read old
articles as a class.
(3)
Biology papers are strongly preferred over method papers.
(4)
Each group should send a list of 2~3 suggested papers to the course organizer
two weeks in advance, no later than the Wednesday of that week.
Presentation Format (Revised)
(1)
Each group is formed by three students.
(2)
The first student should give a brief introduction to the background of the
paper to be presented. This introduction
should be brief, preferably less than 10 minutes.
(3)
The second and third students should give a critical review of the paper. It is up to you to decide how to
structure this part of the presentation.
Class Attendance Requirement
To
ensure due diligence and fairness and respect to your fellow students, you are
expected to attend the class on time.
If
there are situations that prevent you from attending the class, you are
required to notify the instructor before the class.
If
under rare circumstances you can not notify the instructor before the class,
you need to communicate with the instructor immediately after the class.
Class
attendance will start to be recorded from
Weekly Course Announcements
|
Week |
Announcement |
|
Week 1 ( |
(1) We will read the following paper “Cancer Cells Display Profound Intra- and Interline Variation following Prolonged Exposure to Antimitotic Drugs,” K. E. Gascoigne and S. S. Taylor, Cancer Cell, 14:111-122, 2008. Ge Yang will present. Since we are still in the process of requesting CMU library to add subscription to this journal, please download from here the main text, the supplementary material, and the preview article. Starting the second week, a group of students will be assigned to present one paper every week. A sign-up sheet will be handed out in the class and then posted online. (2) You are required to come prepared by reading the selected paper each week and suggest papers you would like to read in the following week. Before each class, each group needs to send your suggestions to Ge Yang by email. The course organizers will coordinate this process and make a final selection each week. |
|
Week 2 ( |
(1) Monday of Week 2 (i.e. Jan-19) is Dr. Martin Luther King Day.
Following university calendar and schedules of previous years, we will not
have class on that day. Instead, we will shift the paper assigned for Week 2
to Week 3. |
|
Week 3 ( |
Following the recommendations from the group of Keith Callenberg, John Sekar,
and David Mowrey (Group 2), we will be reading the following paper for Week 4
(we skipped week 2 following the university calendar). |
|
Week 4 ( |
Following the recommendations from the group of Yevgeniya Monisova, Sabah Kadri, and Guy Zinman (Group 3), we will be reading the following paper for Week 5 Budovskaya, Y.V., Wu, K., Southworth, L.K., Jiang, M., Tedesco, P., Johnson, T.E., and Kim, S.K. (2008). An elt-3/elt-5/elt-6 GATA transcription circuit guides aging in C. elegans. Cell 134, 291-303. |
|
Week 5 ( |
Following the recommendations from the group of Andrej Savol, Kyaw Myint, and Karim Benbourenane (Group 4), we will be reading the following paper for Week 6 Application of a Translational Profiling Approach
for the Comparative Analysis of CNS Cell Types by Joseph P. Doyle et al,
Cell, 135, 749-762. |
|
Week 6 ( |
Following the recommendation by the group of Shan Zong, Ying Ding, and Jun
Ma (group 5), we will be reading the following paper for Week 7: |
|
Week 7 ( |
After consulting with the group of Joshua Kongas, Chao Ma, and Armaghan Naik, I have chosen the following paper for Week 8 Sensing Chromosome Bi-Orientation by Spatial Separation of Aurora B Kinase
from Kinetochore Substrates, by Dan Liu, |
|
Week 8 ( |
After consulting with the group of Joshua Kongas, Chao Ma, and Armaghan Naik, I have chosen the following paper for Week 10: The Native 3D Organization of Bacterial Polysomes, by Forian Brandt, Stephanie Etchells, Julio Ortiz, Adrian Elcock, Ulrich Hartl, and Wolfgan Baumeister, Cell, 136:261-271, 2009 |
|
Week 9 ( |
Following recommendation of the group of Ross Curtis, Ming-Chi Tsai, and Grace Huang, we will be reading the following paper for Week 11: Jun Zhu et al, Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks, Nature Genetics, 40:854-861, 2008 |
|
Week 10 ( |
Following recommendation of the group of Anindita Dutta, Yuefeng Lin, and Timothy Travers, we will be reading the following paper for Week 12: Holt et al, Positive feedback sharpens the anaphase switch, Nature, 454, 353-357, 2008. |
|
Week 11 ( |
Following recommendation of the group of Keith Callenberg, John Sekar, and David Mowre, we will be reading the following paper for Week 13: Real-time |
|
Week 12 ( |
Following recommendation of the group of Yevgeniya Monisova, Sabah Kadri, and Guy Zinman, we will be reading the following paper for Week 14: Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast, Science, 322, 405-410, 2008. |
|
Week 13 ( |
As recommended by the group of Andrej Savol, Kyaw Myint, and Karim Bencourenane, we will read the following paper for Week 15: Activation of tyrosine kinases by mutation of the gatekeeper threonine, by Azam et al, Nat. Struct. Mol. Biol., vol. 15, 1109-1118, 2008 |
|
Week 14 (04/17/09) |
As recommended by the group of Shan Zhong, Ying Ding, and Jun Ma, we will read the following paper for Week 16: Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M. A tunable synthetic mammalian oscillator. Nature. 2009 Jan 15; 457(7227): 309-12. |
List
of papers by week
|
Topic |
Selected Paper |
|
Week 1 (1/12/2009) |
|
|
Week 2 (1/19/2009) |
Class cancelled following university calendar |
|
Week 3 (1/26/09) |
|
|
Week 4 (2/2/09) |
|
|
Week 5 (2/9/09) |
An elt-3/elt-5/elt-6
GATA Transcription Circuit Guides Aging in C. elegans |
|
Week 6 (2/16/09) |
Application of a
Translational Profiling Approach for the Comparative Analysis of CNS Cell
Types |
|
Week 7 (2/23/09) |
Single-RNA
counting reveals alternative modes of gene expression in yeast |
|
Week 8 (03/02/09) |
|
|
Week 9 (03/09/09) |
Spring break; class cancelled |
|
Week 10 (03/16/09) |
|
|
Week 11 (03/23/09) |
|
|
Week 12 (03/30/09) |
|
|
Week 13 (04/06/09) |
|
|
Week 14 (04/13/09) |
Conservation
and rewiring of functional modules revealed by an epistasis map in fission
yeast |
|
Week 15 (04/20/09) |
Activation
of tyrosine kinases by mutation of the gatekeeper threonine |
|
Week 16 (04/27/09) |
Assignment schedule
|
Date |
Group member 1 |
Group member 2 |
Group member 3 |
Comment |
|
1/12/09 |
Presented by organizer |
|
|
|
|
1/19/09 |
MARTIN LUTHER KING DAY |
|
|
CANCELLED |
|
1/26/09 |
Anindita Dutta |
Yuefeng Lin |
Timothy Travers |
Group 1 |
|
2/2/09 |
Keith Callenberg |
John Sekar |
David Mowrey |
Group 2 |
|
2/9/09 |
Yevgeniya Monisova |
Sabah Kadri |
Guy Zinman |
Group 3 |
|
2/16/09 |
Andrej Savol |
Kyaw Myint |
Karim Benbourenane |
Group 4 |
|
2/23/09 |
Shan Zhong |
Ying Ding |
Jun Ma |
Group 5 |
|
3/2/09 |
Joshua Kangas |
Chao Ma |
Armaghan Naik |
Group 6 |
|
3/9/09 |
SPRING BREAK |
|
|
CANCELLED |
|
3/16/09 |
Virginia Burger |
Om Choudhary |
|
Group 7 |
|
3/23/09 |
Ross Curtis |
Grace Huang |
Ming-Chi Tsui |
Group 8 |
|
3/30/09 |
Anindita Dutta |
Yuefeng Lin |
Timothy Travers |
Group 1 |
|
4/6/09 |
Keith Callenberg |
John Sekar |
David Mowrey |
Group 2 |
|
4/13/09 |
Yevgeniya Monisova |
Sabah Kadri |
Guy Zinman |
Group 3 |
|
4/20/09 |
Andrej Savol |
Kyaw Myint |
Karim Benbourenane |
Group 4 |
|
4/27/09 |
Shan Zhong |
Ying Ding |
Jun Ma |
Group 5 |
|
*** |
Joshua Kangas |
Chao Ma |
Armaghan Naik |
Group 6 |
|
*** |
Virginia Burger |
Om Choudhary |
|
Group 7 |
|
*** |
Ross Curtis |
Grace Huang |
Ming-Chi Tsui |
Group 8 |
***: Reading
report assignment, TBD
Previous course organizers: William Cohen and Bino John