C-HPP Workshop schedule of HUPO 2013

Letter of Co-Chairs of the C-HPP Consortium

Dear Colleagues,

As Yokohama congress approaches around the corner, we would like to make update on our workshop schedules which have been finalized very recently (8/3/2013). Based on the recent communications between the interesting groups and Jennifer Watson who is coordinating the HPP initiative program with Yokohama team from the HUPO side, we came up with the final agenda as outlined below. Please make note of this information on your traveling plans where appropriate. If there is any further update on this program, we will keep you posted. The program is available here (updated on 6 September 2013).


Young-Ki, Bill and György
Co-Chairs of the C-HPP Consortium

Program schedule and available presentations

C-HPP Group Break-out session, Saturday, September 14, 9:45 - 11:45 am

1. Young-Ki Paik, Bill Hancock and György Marko-Varga, Co-Chairs of the C-HPP Consortium
1st Year Progress Report of the C-HPP Consortium (Sept 10, 2012-Sept 9, 2013). Presentation is available here.

2. Lydie Lane (SIB, Switzerland)
Progress in Chr 2 Project. Presentation is available here.

3. Joshua Labaer (Arizona State Univ., USA)
Progress in Chr 10 Project. Presenation is available here.

4. Visith Thongboonkerd (Mahidol University , Bangkok, Thailand)
Progress in Chr 12 Project.

5. Charles Lee (Harvard U., USA) and Akhleshi Pandey (Johns Hopkins Univ., USA)
Progress in Chr 22 Project.

6. Christoph Borchers (University of Victoria)
Utilization of MRM Standards in the C-HPP Project. Presentation is available here.

Joint C-HPP session with PSI/ProteomeXchange/KBpC, Sunday, September 15, 8:15 - 9:30 am

1. Eric Deutsch (Institute for Systems Biology, Seattle, WA, USA)
The HUPO Proteomics Standards Initiative Standard Formats and Their Use in Current Software. Presentation is available here.

2. Henning Hermjakob (European Bioinformatics Institute, Cambridge, UK)
Update on ProteomeXchange. Presentation is available here.

3. Lydie Lane (Swiss Institute of Bioinformatics, Geneva, Switzerland)
Integration of Proteomics Data in neXtProt. Presentation is available here

HUPO Plenary Lecture, Monday, September 16, 9:40 - 10:50 am

PL03-02: neXtProt: The Human Protein Knowledge Platform in the Context of HPP, Amos Bairoch (University of Geneva, Switzerland). Presentation in pdf is available here.

C-HPP Group Break-out session, Tuesday, September 17, 8:15 - 9:30 am

Chair: Bill Hancock and Gyögry Marko-Varga

In this session, the C-HPP consortium members from 25 countries will discuss general matters related to protein database, updated status on the missing proteins, integration of both ENCODE and Metabolomics data into the C-HPP scaffold.

1. Siqi Liu (BGI, China) will present the survey results of RNA-Seq service through the C-HPP consortium and give some update on the RNA-Seq database which can be useful for the consortium members.

2. Peter Horvatovich (University of Groningen, Netherlands) will present recent progress in WiKi on the C-HPP. Presentation is available here.

3. Reports from the web browsers (Ed Nice for Rob Goode, Dong Li for Chinese team (presentation is available in pdf here), Andrey Lisita).

4. Updates from Protein atlas and Monash antibody initiative (Ed Nice).

5. Encode update (Kate Rosenbloom and Mike Snyder).

C-HPP poster session, Tuesday, September 17, 14:00 - 15:00 am

Chromosome 1:
Chromosome 2:
Chromosome 3:
Chromosome 4:
Chromosome 5: Chromosome-Centric Human Protein Project: Chromosome 5, Peter Horvatovich, Pei-Jing Pai, Henry Lam, Rainer Bischoff. Poster in pdf is available here.
Chromosome 6:
Chromosome 7:
Chromosome 8:
Chromosome 9:
Chromosome 10:
Chromosome 11:
Chromosome 12:
Chromosome 13:
Chromosome 14:
Chromosome 15:
Chromosome 16: Bioinformatic workflow for Chr16 characterization using proteomic shotgun and transcriptomic RNA-seq experiments
Development of SRM methods for the detection and quantification of chromosome 16 proteins
Dissecting subcellular compartments for deep proteome coverage of chromosome 16 in t cells
Improving Chr-16 proteins coverage with high confidence and MIAPE compliant MS data
Missing proteins in Chromosome 16 - Spanish HPP
Chromosome 17:
Chromosome 18:
Chromosome 19: Integration of Chromosome 19 Transcriptomic and Proteomic Datasets Using Six Glioma Derived Cancer Stem Cell Lines, C.F. Lich, H. Liu, A.S. Shavkunov, E. Mostovenko, E.P. Sulman, R. Ezhilarasan, Q. Wang, R.A. Kroes, J.C. Moskal, D. Fenyö, B.A. Oksuz, C.A. Conrad, F.F. Lang, F.S. Berven, Á. Végvári, M. Rezeli, G. Marko-Varga, S. Hober, C.L. Nilsson. The poster in pdf format is available here.
Chromosome 20:
Chromosome 21:
Chromosome 22:
Chromosome X:
Chromosome Y:
Mitochondrial Chromosome:
CAPER 2.0: An interactive, configurable and extensible workflow-based platform to analyze datasets from C-HPP. D. Wang, Z. Liu, L.H. Diao, F.F. Guo, D. Li, F. He. The poster in pdf format is available here.

HPP Special Parallel Session, Wednesday, September 18, 9:00 - 11:50 am

1. SS-01 9:00-9:15, Vision of Genome-Wide HPP, Young-Ki Paik. Slides of the presentation in pdf format is available here.
2. SS-02 (Keynote) 9:15-9:45, The Strategy, Organization, and Progress of the Human Proteome Project, Gilbert S. Omenn. Slides of the presentation is available here.
3. SS-03 (Keynote) 9:50-10:20, Genome-wide Proteomics: The Role the C-HPP Initiative to Study Cancer Gene Amplicons, and Proteomic Signatures, W. Hancock, G. Omenn, M.Snyder, R. Beavis, Y-K. Paik, Hoguen Kim.
4. SS-04 10:25-10:55, Protein Post-Translational Modifications and their Regulation of Cardiovascular Disease, Melanie Y. White, Benjamin L. Parker, Jana Paulech, Kiersten A. Liddy, Lauren E. Smith, Alistair V.G. Edwards, Stuart J. Cordwell.
5. SS-05 11:00-11:50, Panel of HPP Leaders and General Discussion, William S. Hancock.

The HUPO Initiative Assembly in Kyoto (Uji), September 19, 2013, Kyoto, Japan

Main organizer: Tadashi Yamamoto.

Opening and Messages from HUPO/HPP, 9:30-10:00
Chair: Naoyuki Taniguchi (Japan)

  • HUPO, Pierre Legrain (France)
  • HPP, Gilbert S Omenn (USA)
  • C-HPP, William Hancock (USA). The presentation is available here.
  • B/D-HPP, Jennifer Van Eyk (USA)
  • KBpC, Lydie Lane (Switzerland)
  • MSpC, Bruno Domon (Luxembourg)
  • ABpC, Jochen Schwenk (Sweden)

Pre-existing Initiatives, 10:45-13:00
Chairs: Pierre Legrain & Tadashi Yamamoto

  • HPPP, Mark Baker (Australia)
  • HAI, Jochen Schwenk (Sweden)
  • PSI, Henning Hermjakob (UK)
  • HLPP, Pumin Zhang (USA)
  • HBPP, Young Mok Park (Korea) and Lea T Grinberg (Brazil)
  • HGPI, Hisashi Narimatsu (Japan)
  • HCVI, Peipei Ping (USA)
  • HKUPP, Yutaka Yoshida (Japan)
  • iMOP, Emøke Bendixen (Denmark)

New HPP Initiatives, 14:00-17:00:
Chairs: Gill Omenn & Bill Hancock

  • Eyeome, Richard Semba (USA)(tentative)
  • Network, Amos Bairoch (Switzerland)
  • Epigenetics, Edyta Marcon (Canada)
  • Cancer, Hui Zhang (USA)
  • Chromosome 1, Ping Xu (China)
  • Chromosome 2, Lydie Lane (Switzerland)
  • Chromosome 5, Péter Horvatovich (Netherlands). Presenation is vailable here.
  • Chromosome 6, Christopher M Overall (Canada)
  • Chromosome 7, Mark Becker (Australia)
  • Chromosome 14, French consortium (France) (tentative)
  • Chromosome 18, Alexander Archakov (Russia)
  • Chromosome X, Tadashi Yamamoto (Japan)
  • Chromosome Y, Ghasem Hosseini Salekdeh (Iran)