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| This is the domain interaction team public wiki page mainly for all members to view the latest schedule, related public resources and news. 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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| || Chris Tan || Signaling Network Evolution || | || Andreas Ernst || || || Chris Tan || Signaling network evolution || || Dev Sidhu || || || David Gfeller || Specificity and robustness in PDZ networks || |
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| || David Gfeller || Specificity and robustness in PDZ networks || | |
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| || Xiaojian Shao || Quantitative interaction prediction || | |
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| || Xiaojian Shao || Quantitative interaction prediction || | |
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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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| || '''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 || || || |
|| '''Date'''||'''Presenter''' || '''Time/Location''' || '''Presentation Title''' || || Sep 22 || Chris || || ''Built-in loops allow versatility in domain–domain interactions: Lessons from self-interacting domains'', PNAS Sept 9, 2008 vol. 105 no. 36 13292-13297 || |
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| || Nov 17 || David || || || | || Nov 17 || Andreas || || || |
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| || Dec 15 || Andreas || || || | || Dec 15 || David || || || |
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| || '''Date'''||'''Presenter''' || '''Time/Location''' || '''Presentation Title''' || | |
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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 |
|| Aug 10 || Xiaojian || || || || Aug 24 || WIP || || || || Sept 7 || Shobhit || || || || Sept 21 || WIP || || || || Oct 5 || Someone from Kim lab? || || || || Oct 19 || WIP || || || |
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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
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
- Brief WIP by everyone every alternate meeting
Schedule
- From Fall 2007 onward
Time: Monday, 4.00 pm (unless indicated) Place: CCBR, 6th floor meeting room (unless indicated)
2008
Date
Presenter
Time/Location
Presentation Title
Sep 22
Chris
Built-in loops allow versatility in domain–domain interactions: Lessons from self-interacting domains, PNAS Sept 9, 2008 vol. 105 no. 36 13292-13297
Oct 6
WIP
Oct 20
Rafi
Nov 3
WIP
Nov 17
Andreas
Dec 1
WIP
Dec 15
David
Dec 29
WIP
2009
Date
Presenter
Time/Location
Presentation Title
Jan 12
Shirley
Jan 26
WIP
Feb 9
Xiaojian
Feb 22
WIP
Mar 9
Shobhit
Aug 10
Xiaojian
Aug 24
WIP
Sept 7
Shobhit
Sept 21
WIP
Oct 5
Someone from Kim lab?
Oct 19
WIP
Meeting Guide
Journal Club Guide
These are good practices agreed by members
- 3-4 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