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| This is the domain interaction team wiki page. There is a Google group mailing list (interactionTeam@googlegroups.com) for disseminating news and announcements. New members must be invited to join the mailing list but any existing members can initiate an invitation as long as they have a Google account (Simply log into your Google account and access your googlegroup service). | This is the domain interaction team public wiki page mainly for all members to view the latest schedule, related public resources and news. Members can access other info [[InteractionTeam| here]]. There is a Google group mailing list (interactionTeam@googlegroups.com) for disseminating news and announcements. New members must be invited to join the mailing list but any existing members can initiate an invitation as long as they have a Google account (Simply log into your Google account and access your googlegroup service). |
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| || '''Name'''||'''Research Project/Interests''' || '''Lab Project Page''' || || Chris Tan ||Network Evolution || [:ChrisTan/thesis/PDZtracing:PDZ Domain Tracing]|| || Gary Bader || Biological network analysis and pathway information resources || [http://www.baderlab.org Bader Lab] || || Shirley Hui || Domain specificity prediction || [:DomainSpecificityPredictionProject:Domain Specificity Prediction] || || David Gfeller || Specificity and robustness in PDZ networks || || || Raffi Tonikian || Protein domain experimental specificity mapping || || || Xiaofeng Xin ||Protein domain interaction experimental mapping|| || |
|| '''Name'''||'''Research Project/Interests''' || || Andreas Ernst || || || Chris Tan || Signaling network evolution || || Dev Sidhu || || || David Gfeller || Specificity and robustness in PDZ networks || || Gary Bader || Biological network analysis and pathway information resources || || Nisa Dar || || || Mark Sun || || || Philip Kim || || || Shirley Hui || Domain specificity prediction || || Raffi Tonikian || Protein domain experimental specificity mapping || || Xiaojian Shao || Quantitative interaction prediction || || Xiaofeng Xin || Protein domain interaction experimental mapping || |
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| || '''Name'''||'''Research Project/Interests''' || '''Lab Project Page''' || || Ioana Ivan || Membrane interactions with PDZ domains || [:PDZMembraneProject:PDZ Membrane Protein Interaction Project] || || Stacy Hung || Protein interaction prediction || [:BRAINProject:BRAIN Project], [:WWProject:WW Project] || || Lianet Lopez ||Protein domain interaction experimental mapping|| || || Monica Raj (UBC, Vancouver) || Protein interaction prediction || ["PDZProteinInteractionProject"] || || Moyez Dharsee || Protein interaction prediction || [:BRAINProject:BRAIN Project], [:SequenceLogoTool:Sequence Logo Tool] || |
|| '''Name'''||'''Research Project/Interests''' || || Ioana Ivan || Membrane interactions with PDZ domains || || Stacy Hung || Protein interaction prediction || || Lianet Lopez ||Protein domain interaction experimental mapping|| || Monica Raj (UBC, Vancouver) || Protein interaction prediction || || Moyez Dharsee || Protein interaction prediction || |
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| 1. Meeting every 2 weeks 1. Brief WIP by everyone every alternate meeting |
1. Meeting every 2 weeks, alternating between journal club and Work-in-Progress (WIP) meeting 1. The WIP serves for members to update each other on their latest endeavor or research in a casual setting. However, any member can do a formal representation during WIP to get feedback on their work in a timely manner. |
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| From Fall 2007 onward '''Time''': Monday, 4.00 pm (unless indicated) '''Place''': CCBR, 6th floor meeting room (unless indicated) |
* From Nov 2 2009 till end of Dec 2009 '''Time''': Monday, 11.00 am (unless otherwise) '''Place''': CCBR, 6th floor meeting room (unless otherwise) |
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| === 2008 === || '''Date'''||'''Presenter''' || '''Time/Location''' || '''WIP Presentation''' || || Jan 14 || || Cancelled || || || Jan 28 || Raffi || ||1. [http://www.sciencemag.org/cgi/content/full/317/5845/1732 Free-Solution, Label-Free Molecular Interactions Studied by Back-Scattering Interferometry] 2. [http://www.sciencemag.org/cgi/content/full/317/5845/1749 Multicolor Super-Resolution Imaging with Photo-Switchable Fluorescent Probes] || || Feb 11 || WIP || || || || Feb 25 || Shirley || || || || Mar 10 || WIP || 4:00 - 6:00 PM || || || Mar 24 || Chris || 4:00 - 6:00 PM || || || Apr 7 || WIP || 4:00 - 6:00 PM || || || Apr 21 || David || || || || May 5 || WIP || || || || May 19 || Victoria Day?? || || || || Jun 2 || Chris || || || || Jun 16 || WIP || || || || Jun 30 || - || || || || Jul 14 || Shirley || || || || Jul 28 || WIP || || || || Aug 11 || Andreas || || || || Aug 25 || David+Chris || || || || Sep 8 || WIP || || || || Sep 22 || Chris || || || || Oct 6 || WIP || || || || Oct 20 || Rafi || || || || Nov 3 || WIP || || || || Nov 17 || David || || || || Dec 1 || WIP || || || || Dec 15 || Andreas || || || || Dec 29 || WIP || || || |
* From 2010 onward '''Time''': Monday, 4.00 pm (unless otherwise) '''Place''': CCBR, 6th floor meeting room (unless otherwise) |
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| || Jan 12 || Shirley || || || || Jan 26 || WIP || || || || Feb 9 || Xiaojian || || || |
|| '''Date'''||'''Presenter''' || '''Time/Location''' || '''Presentation Title''' || || Nov 2 || Shobhit || || || || Nov 16 || WIP || || || || Nov 30 || X || || || || Dec 14 || ? || || || || Dec 28 || || || || === 2010 === || '''Date'''||'''Presenter''' || '''Time/Location''' || '''Presentation Title''' || || Jan 11 || || || || || Jan 25 || WIP || || || || Feb 8 || Shirley || || || |
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| || Mar 9 || Shobhit || || || | || Mar 8 || Xiaojian || || || || Mar 22 || WIP || || || || Apr 5 || Chris || || || || Apr 19 || WIP || || || || May 3 || Shobhit || || || || May 17 || || || || || May 31 || || || || || June 14 || || || || || June 28 || || || || |
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=== 2007 === || '''Date'''||'''Presenter''' || '''Time/Location''' || '''WIP Presentation''' || || Sep 17 || ? || - || - || || June 18 ||Chris || 11:30 AM, CCBR 8th floor meeting room ||[attachment:InteractionTeam_Chris_18thJune.ppt WIP: Research Directions, Current and Planned Projects] || || June 26 ||Shirley ||5:00 PM, CCBR 8th floor meeting room ||[attachment:WIP_Domain_Specificity_Prediction_MI_Shirley_2007.ppt WIP: Domain Specificity Prediction using Mutual Information]|| || July 2 || CANADA DAY || NO MEETING || - || || July 13 || Moyez ||11:00 AM, CCBR 8th floor meeting room ||attachment:InteractionTeam_wip_20070713.ppt|| || July 16 ||Stacy || 11:00 AM, CCBR 6th floor meeting room ||attachment:stacy_WIP_0716.ppt|| || July 23 ||Ioana || 11:00 AM, CCBR 8th floor meeting room ||WIP attachment|| || July 30 ||Chris || - ||[attachment:PDZSpecificityMouse.ppt Paper discussion: PDZ Domain Binding Selectivity Is Optimized Across the Mouse Proteome]|| || Aug 6 || CIVIC HOLIDAY || NO MEETING || -|| || Aug 13 ||Moyez || Cancelled ||-|| || Aug 20 ||Shirley || 11:00 AM, CCBR 6th floor meeting room ||attachment:WIP-ShirleyHui.ppt|| || Aug 27 ||Moyez ||Cancelled||-|| || Sep 03 ||LABOR DAY|| - ||-|| || Sep 07 || Moyez || 1:30 PM || - || || Sep 10 || Cancelled || Cancelled || - || || Sep 17 || Organization meeting || - || - || || Oct 29 || Shirley/Gary || - || PDZ discussion || || Nov 12 || Everyone || - || Team WIP || || Nov 26 || Chris || - || Discussion Topic TDB || || Dec 10 || Everyone || - || Team WIP || || Dec 24 || Holiday || No meeting || - || = Discussion Topics = Complete paper list is available at http://www.connotea.org/user/DIT * To add papers, you need to log in (p: baderlab) == Papers by category == * [http://www.connotea.org/user/DIT/tag/DomainSpecificityPrediction Domain/Network Specificity] * [http://www.connotea.org/user/DIT/tag/NetworkEvolution Domain/Network Evolution] * [http://www.connotea.org/user/DIT/tag/ProteinInteractionPrediction Protein Interaction Prediction] * [http://www.connotea.org/user/DIT/tag/InteractionData Experimental methods or data for domain interactions] * Domain biology: * [http://www.connotea.org/user/DIT/tag/DomainPDZ PDZ Domains] * [http://www.connotea.org/user/DIT/tag/DomainSH3 SH3 Domains] * [http://www.connotea.org/user/DIT/tag/DomainWW WW Domains] == Tentative discussion list == 1. Detecting Coevolution in and among Protein Domains 1. Forbidden penta-peptides |
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| 1. 3-4 papers discussed per journal club, related to a specific topic. | 1. 1-2 papers discussed per journal club, related to a specific topic. |
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== Presentations == * attachment:2008_Mar28_Carleton.ppt - Presentation of the PDZ domain work circa March 2008. Useful resource for slides about the project background/motivation/significance. == Grants == * We have a CIHR grant to fund this research. attachment:DomainInteractionTeamGrantProposalCIHR-Mar1.pdf (confidential - only for distribution within the Bader Lab). |
== Papers by category == * [[http://www.connotea.org/user/DIT/tag/DomainSpecificityPrediction|Domain/Network Specificity]] * [[http://www.connotea.org/user/DIT/tag/NetworkEvolution|Domain/Network Evolution]] * [[http://www.connotea.org/user/DIT/tag/ProteinInteractionPrediction|Protein Interaction Prediction]] * [[http://www.connotea.org/user/DIT/tag/InteractionData|Experimental methods or data for domain interactions]] * Domain biology: * [[http://www.connotea.org/user/DIT/tag/DomainPDZ|PDZ Domains]] * [[http://www.connotea.org/user/DIT/tag/DomainSH3|SH3 Domains]] * [[http://www.connotea.org/user/DIT/tag/DomainWW|WW Domains]] |
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| * [http://cbm.bio.uniroma2.it/~manuela/ Manuela Helmer-Citterich] * [http://www.uniroma2.it/dottorato/CESARENI.htm Giovanni Cesareni] |
* [[http://cbm.bio.uniroma2.it/~manuela/|Manuela Helmer-Citterich]] * [[http://www.uniroma2.it/dottorato/CESARENI.htm|Giovanni Cesareni]] |
Contents
Introduction
This is the domain interaction team public wiki page mainly for all members to view the latest schedule, related public resources and news. Members can access other info here. There is a Google group mailing list (interactionTeam@googlegroups.com) for disseminating news and announcements. New members must be invited to join the mailing list but any existing members can initiate an invitation as long as they have a Google account (Simply log into your Google account and access your googlegroup service).
Members
Present
Name
Research Project/Interests
Andreas Ernst
Chris Tan
Signaling network evolution
Dev Sidhu
David Gfeller
Specificity and robustness in PDZ networks
Gary Bader
Biological network analysis and pathway information resources
Nisa Dar
Mark Sun
Philip Kim
Shirley Hui
Domain specificity prediction
Raffi Tonikian
Protein domain experimental specificity mapping
Xiaojian Shao
Quantitative interaction prediction
Xiaofeng Xin
Protein domain interaction experimental mapping
Alumni
Name
Research Project/Interests
Ioana Ivan
Membrane interactions with PDZ domains
Stacy Hung
Protein interaction prediction
Lianet Lopez
Protein domain interaction experimental mapping
Monica Raj (UBC, Vancouver)
Protein interaction prediction
Moyez Dharsee
Protein interaction prediction
Meetings
Organization
- Meeting every 2 weeks, alternating between journal club and Work-in-Progress (WIP) meeting
- The WIP serves for members to update each other on their latest endeavor or research in a casual setting. However, any member can do a formal representation during WIP to get feedback on their work in a timely manner.
Schedule
- From Nov 2 2009 till end of Dec 2009
Time: Monday, 11.00 am (unless otherwise) Place: CCBR, 6th floor meeting room (unless otherwise)
- From 2010 onward
Time: Monday, 4.00 pm (unless otherwise) Place: CCBR, 6th floor meeting room (unless otherwise)
2009
Date
Presenter
Time/Location
Presentation Title
Nov 2
Shobhit
Nov 16
WIP
Nov 30
X
Dec 14
?
Dec 28
2010
Date
Presenter
Time/Location
Presentation Title
Jan 11
Jan 25
WIP
Feb 8
Shirley
Feb 22
WIP
Mar 8
Xiaojian
Mar 22
WIP
Apr 5
Chris
Apr 19
WIP
May 3
Shobhit
May 17
May 31
June 14
June 28
Meeting Guide
Journal Club Guide
These are good practices agreed by members
- 1-2 papers discussed per journal club, related to a specific topic.
- Paper(s) should be sent out one week before meeting, together with length of expected discussion time e.g. 5,15,30 minutes. Very important papers may take up the entire discussion session, however less important papers should be covered rapidly.
- Paper(s) selected should be relevant to your own work, and preferably of general interest to members.
- Include a brief introduction on the paper(s) and why you selected it (e.g. a landmark paper, of general interest, a technological advance, important discoveries, thought-provoking)
- Summarize the paper at a high level.
More information is available at http://baderlab.org/Intranet/JournalClubGuidelines
Chairperson Guide
Mission: To ensure meetings are conducted smoothly. This includes preparing the room (e.g. meeting room, projector, markers)
Before Meeting
- Remind the presenter of the next meeting (that it is her/his turn).
- Send reminder to team members on date, time and venue of the next coming meeting (especially if there is change in the original schedule).
- Ensure meeting room is available. CCBR meeting rooms are normally not locked. If not, get the key from Gary (he has keys to all CCBR meeting rooms). If Gary is not around, get the key from administration office at CCBR level 2.
- Prepare projector if it is needed. Check with Gary. If not, get it from administration office at CCBR level 2. Laptop needed will be prepared by presenter.
- Ensure markers and whiteboard eraser is available.
During Meeting
- Prepare and introduce agenda. It may be advisable to list "administrative issues" before a presentation or discussion.
- Keep meeting on track (in term of agenda)
- Keep meeting to the scheduled duration if time is a constraint
- Moderate discussion and manage the group dynamics
- Try not to let one person dominate. Ask for other opinions. If some people are silent, draw them out by asking for their thoughts.
- Decide when to end debate on each topic.
- Give a short summary or recap before going on to the next topic.
After Meeting
- Update wiki
- Return projector
Booking a meeting room in CCBR
The availability of CCBR meeting rooms can be found at http://tdccbr.med.utoronto.ca under "Seminar & Calender" menu.
To book a meeting room, email CCBR <CCBR.Info@utoronto.ca>. Cancel a booking via the same email address.
Resources
Papers by category
- Domain biology:
Other Groups and Researchers