NOTE! This is a read-only copy of the ENCODE2 wiki.
Please go to the ENCODE3 wiki for current information.

ENCODE working groups

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Contact information for the working group participants can be found at Contacts. Conference calls for the working groups are scheduled on the Calendar. If call minutes are taken, they should be added or uploaded to the Calls page.


Broad Peak Calling

Goal:Provide a best-practices recommendation to ENCODE and modENCODE on identifying regions enriched for broadly distributed biochemical features. This will require identifying the best way to determine the boundaries of broadly distributed biochemical features, and determining what marks are broad, narrow, or mixed. This may result in a publication, for example comparing how well different peak callers perform with broad marks.

Contacts: Peter Park, Mike Pazin, Leslie Adams

Teleconference: Alternate Mondays, 1PM Eastern

Dial-In Information: Domestic: (866) 448-5431 International: (303) 330-0440, then room number (8664485431)

No passcode To mute and unmute use *# (star pound)

Hg19 Migration

Click on "Hg19 Migration" above for additional information.

Goal: To discuss issues related to migrating ENCODE to the new human genome assembly, and to generate a plan and timeline.

Chairs: Kate Rosenbloom, Ian Dunham

Members:

  • Kate Rosenbloom (co-chair)
  • Ian Dunham (co-chair)
  • Joel Rozowsky
  • Terry Furey
  • Ali Mortazavi
  • Richard Sandstrom

Any interested parties, please add your name.

Resources

Click on the "resources and terms" heading on the left for information about common resources.

Goal: To address issues related to the use of common reagents and resources by members of the ENCODE Consortium.

Chairs: Brad Bernstein & Peggy Farnham

Members:

  • Brad Bernstein (co-chair)
  • Peggy Farnham (co-chair)
  • Ewan Birney
  • Carrie Davis
  • Tim Dreszer
  • Chuck Epstein
  • Luiz Penalva
  • John Stamatoyannopoulos
  • Scott Tenenbaum
  • Sherman Weissman
  • Barbara Wold


Analysis

Click on the "Analysis" heading on the left (under "projects") for information about ENCODE analyses.

Goal: To plan and coordinate data analyses, identify gaps in expertise and recommend additional outside groups and datasets, and develop Consortium manuscripts

Chair: Rick Myers

Members: The Analysis Working Group is open to all members of the ENCODE Consortium.


Sequencing Technology

This working group is shared between ENCODE and modENCODE.

Goal: To address issues related to new sequencing technologies, including the evaluation of existing platforms and protocols, the development of experimental protocol/data standards, and new developments in this quickly-evolving field.

Chair: Barbara Wold

Members:

  • Barbara Wold (chair)
  • Ewan Birney
  • Piero Carninci
  • Greg Crawford
  • Carrie Davis
  • Marc Domanus
  • Michael Dorschner
  • Paul Flicek
  • Terry Furey
  • Mark Gerstein
  • Brenton Graveley
  • Phil Green
  • Greg Hannon
  • Rachel Harte
  • Roger Hoskins
  • Vishy Iyer
  • Peter Kharchenko
  • Eric Lai
  • Jane Landolin
  • Soohyun Lee
  • Shirley Liu
  • Dave MacAlpine
  • Larry Meyer
  • Tarjei Mikkelsen
  • Peter Park
  • Mike Pheasant
  • Nicolas Robine
  • Kate Rosenbloom
  • Joel Rozowsky
  • Parantu Shah
  • Mike Snyder
  • Scott Tenenbaum
  • Michael Tolstorukov
  • Ting Wang
  • Steven Wilder
  • Zheng Zha


Data Release

Goal: To address issues related to the release of ENCODE data, including the development of a data release policy for the scale-up of the ENCODE Project.

Chair: Rick Myers

Members:

  • Rick Myers (chair)
  • Stylianos Antonarakis
  • Brad Bernstein
  • Greg Crawford
  • Rachel Harte
  • Jim Kent
  • Jane Lin
  • Kate Rosenbloom
  • John Stamatoyannopoulos
  • Scott Tenenbaum
  • Sherman Weissman


PI Group

Click on "PI Group" above for information about the monthly ENCODE PI calls.