team and research topics - lineage-flagship.eu research topics... · team, research topics and work...

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Weizmann Institute of Science, Rehovot (Israel) Team, Research Topics and Work Packages Contact: Prof. Ehud Shapiro [email protected] Country Institute Participants Disciplines Israel Weizmann Institute of Science Ehud Shapiro Coordinator Computer Science, Biology Nava Dekel Fertility Tsvee Lapidot Immune system Elchanan Mossel Mathematical foundations Michal Neeman Vascular system Eldad Tzahor Heart, skeletal muscles David Harel Computer Science and Applied Mathematics Benny Geiger Molecular Cell Biology Austria Universität Wien Peter Steier Carbon dating Walter Kutschera Carbon dating Center for Integrative Bioinformatics Vienna (CIBIV) Arndt von Haeseler Combinatorial approaches and algorithms Belgium Katholieke Universiteit Leuven Luc de Raedt Machine learning algorithms to learn disease status and progression Université de LIège Belgique Louis Wehenkel Ultrascalable anytime machine learning & data mining algorithms for patient similarity computation, classification of disease phenotypes, and inference of their status and progression Canada CHiBi Carl Hansen Microfluidics, Single cell transcriptome University of Toronto John Dick Hematopoietic and immune system Simon Fraser University Cedric Chauve Comparing and coalescing cell lineage trees Denmark Danish Technical University Morten Sommer Biochemistry, Biophysics, Biotechnology Finland Aalto University (Helsinki University of Technology) Harri Lähdesmäki Computational Biology & Bioinformatics, Machine learning Samuel Kaski Computational Biology & Bioinformatics, Machine

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Page 1: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

Team, Research Topics and Work

Packages

Contact: Prof. Ehud Shapiro [email protected]

Country Institute Participants Disciplines

Israel Weizmann Institute of Science

Ehud Shapiro – Coordinator

Computer Science, Biology

Nava Dekel Fertility

Tsvee Lapidot Immune system

Elchanan Mossel Mathematical foundations

Michal Neeman Vascular system

Eldad Tzahor

Heart, skeletal muscles

David Harel Computer Science and Applied Mathematics

Benny Geiger Molecular Cell Biology

Austria Universität Wien Peter Steier Carbon dating

Walter Kutschera Carbon dating

Center for Integrative Bioinformatics Vienna (CIBIV)

Arndt von Haeseler Combinatorial approaches and algorithms

Belgium

Katholieke Universiteit Leuven

Luc de Raedt Machine learning algorithms to learn disease status and progression

Université de

LIège Belgique

Louis Wehenkel Ultrascalable anytime machine learning & data mining algorithms for patient similarity computation, classification of disease phenotypes, and inference of their status and progression

Canada

CHiBi Carl Hansen Microfluidics, Single cell transcriptome

University of Toronto

John Dick Hematopoietic and immune system

Simon Fraser University

Cedric Chauve Comparing and coalescing cell lineage trees

Denmark Danish Technical University

Morten Sommer Biochemistry, Biophysics, Biotechnology

Finland Aalto University (Helsinki University of Technology)

Harri Lähdesmäki Computational Biology & Bioinformatics, Machine learning

Samuel Kaski Computational Biology & Bioinformatics, Machine

Page 2: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

learning

Biomedicum Helsinki, University of Helsinki

Kari Alitalo Vascular system

France CNRS

Nadine Peyriéras Developmental Biology, Cell lineage reconstruction from 3D+time imaging, animal models including zebrafish, mouse, sea urchin and nematode

Jean-Stéphane Joly Cell lineage analysis

Paul Bourgine Complex Systems modelling, Cell lineage reconstruction from 3D+time imaging

Olivier Gascuel Combinatorial approaches and algorithms

Fabio Pardi Combinatorial approaches and algorithms

Vincent Berry Combinatorial approaches and algorithms

Vincent Ranwez Combinatorial approaches and algorithms

Université de la Méditerranée, Marseille

Robert Kelly Skeletal muscles, Heart

Institut Curie Daniel Louvard Morphogenesis, intracellular signalling

Emmanuel Barillot Inference and classification of health and disease phenotypes from cell lineage data

Sylvie Robine Gastrointestinal tract, including cancer

Jean-Philippe Vert Bioinformatics, statistical learning/classification

Pasteur Margaret Buckingham

Heart and skeletal muscles

Shahragim Tajbakhsh

Skeletal muscles

Fabrice Chrétien Skeletal muscles

ESPCI ParisTech

Patrick Tabeling Microfluidics and biotechnology

École Normale Supérieure

David Bensimon Biochemistry, Biophysics, Biotechnology

Salpetrière hospital

Frederic Relaix Skeletal muscles

Page 3: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

INRIA Claude Kirchner Computer Science

Germany

Fraunhofer Thomas Berlage

EMBL Takashi Hiiragi Embryonic development

Max Planck

Bernhard Herrmann Development

Hans Lehrach Molecular biology and biotechnology

Ralf Herwig Computational Biology & Bioinformatics

Georgia Panopoulou Computational Biology & Bioinformatics

Albert Poustka Computational Biology & Bioinformatics

Ralf Adams Vascular system

Thomas Braun Heart

DKFZ Heidelberg

Hellmut Augustin Vascular system

University of Regensburg

Christoph Klein Dormancy and origin of metastasis / Transcriptome characterization

Universität Jena Sebastian Boecker Combinatorial approaches and algorithms

Heidelberg Institute for Theoretical Studies (HITS gGmbH)

Alexandros Stamatakis

Combinatorial approaches and algorithms

MLL Münchner Leukämielabor GmbH, ELN

Torsten Haferlach Leukemia

High Performance Computing Center Stuttgart (HLRS) of the University of Stuttgart

Stefan Wesner Virtual Laboratory, High Performance Computing and Cloud Integration

Uwe Wössner Data visualization

Deutsche Forschungsgemeinschaft (DFG)

Dorette Breitkreuz Observer

Universität Tübingen

Daniel Huson Combinatorial approaches and algorithms

University of Cologne and Center for Molecular Medicine

Ingo Haase Skin, including melanoma

Page 4: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

University Justus Liebig Giessen

Saverio Bellusci Respiratory system

Helmholtz Zentrum München

Timm Schroeder Hematopoietic system

Heinrich-Heine-University of Duesseldorf

Eckhard Lammert Vascular system

Ireland Queens University Belfast

Alexander Peter Maxwell

Kidney and urinary tract

Israel

Technion Karl Skorecki Kidney and urinary tract

Shlomo Moran Combinatorial approaches and algorithms

Hebrew University

Yuval Dor Pancreas, including pancreatic cancer and diabetes type I & II

Tel Aviv University (TAU)

Dafna Benayahu Stem cells

Benny Chor Bioinformatics, algorithms

Shai Izraeli Paediatric leukaemia

Ron Shamir Data analysis, algorithms

IBM Haim Nelken Clinical and genomic data

Michal Rosen-Zvi Machine learning

Ayal Zaks Compilers

Alex Shulman Storage

Yaron Wolfsthal System and Storage technologies

Dalit Naor Storage

Google Yossi Matias Computer science & systems

Isaac Elias Computer science & systems

Sheba Medical Center

Gidi Rechavi Cancer

Italy

University of Trento

Themis Palpanas Data analysis and mining of massive datasets

Andrea Passerini Machine learning algorithms to learn disease status and progression

Università degli Studi di Firenze

Paolo Frasconi Machine learning algorithms to learn disease status and progression

Fondazione San Raffaele Del Monte Tabor, Milano

Giulio Cossu

Skeletal muscles

Japan University of Tokyo

Hiro Nakauchi Immunology

Page 5: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

RIKEN Yokohama Institute

Piero Carninci Turn individual cells into cell data

Yokohama Institute

Alistair Forrest Single Cell Characterization

Netherlands Hubrecht Institute

Hans Clevers Gastrointestinal tract

Stefan Schulte-Merker

Vascular system

Erasmus University Medical Center

Gerard Wagemaker Hematopoietic and immune system

Elaine Dzierzak Hematopoietic and immune system

Riccardo Fodde Gastrointestinal tract, including cancer

Peter van der Spek Cell lineage analysis

Delft University of Technology

Cees Dekker Biophysics, Nanotechnology, nanopores, cells on fluidic chips

Oracle Eric Zwanenburg Computational biology

New Zealand

University of Canterbury

Mike Steel Mathematical foundations

University of Auckland

Alexei Drummond Comparing and coalescing cell lineage trees

University of Otago

David Bryant Combinatorial approaches and algorithms

Slovakia Bratislava University

Karol Mikula Model organisms and controls

Spain

Centro Nacional de Investigaciones Cardiovasculares (CNIC)

Miguel Torres Sanchez

Development

Consejo Superior de investigacion Cientifica (CSIC)

Paola Bovolenta Eye

Jose Juan Sanchez Serrano

VP of International Affairs

Hospital Clinic de Barcelona

Jorge Ferrer Pancreas, including pancreatic cancer and diabetes type I & II

Centre for Genomic Regulation (CRG)

James Sharpe Development, Computer simulations of clonal expansion during organogenesis

Institute for Research in

Eduard Batlle Gastrointestinal tract, including cancer

Page 6: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

Biomedicine (IRB)

Julien Colombelli 3D microscopy

Herbert Auer

Universitat de València

Manuel Díaz-Llopis

Eye

University of Vigo

David Posada Combinatorial approaches and algorithms

Universidad Politecnica de Madrid (UPM)

Andres Santos Model organisms and controls

Sweden

Karolinska Institute

Jonas Frisen Renewal, Carbon dating

Kirsty Spalding Renewal, Fat tissue, Carbon dating

Henrik Druid Renewal, Carbon dating

Patrik Ernfors Brain and nervous system central

Christer Betsholtz Vascular system

Sten Linnarsson Single Cell Characterization

Uppsala University

Mats Nilsson Biochemistry, Biophysics, Biotechnology

Ulf Landegren Biochemistry, Biophysics, Biotechnology

Lena Claesson-Welsh

Vascular system

Royal institute of Technology (KTH)

Joakim Lundeberg Cell lineage analysis centers

Jens Lagergren Computational Biology & Bioinformatics

Linköping University

Jan-Åke Larsson Lineage-dependent transcriptional regulation

Switzerland

University of Geneva

Pedro Herrera Pancreas, including pancreatic cancer and diabetes type I & II

Ecoles Polytechniques Fédérales de Lausanne (EPFL)

Bernard Moret Comparing and coalescing cell lineage trees

Swiss National Research Foundation

Walter Reith Observer

Die Eidgenössische Technische Hochschule Zürich (ETH Zurich)

Rudolf (Ruedi) Aebersold

Biochemistry, Proteomics, Systems Biology

Page 7: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

University of Basel

Georg A. Hollaender Hematopoeitic system

Tecan Group Marc Feiglin Biochemistry, Biophysics, Biotechnology

IBM Alessandro Curioni Computational Biology & Bioinformatics/ Data uncertainty quantification on massive data sets/ New ultrascalable algorithms for classification and clustering

Costas Bekas Computational Biology & Bioinformatics/ Data uncertainty quantification on massive data sets/ New ultrascalable algorithms for classification and clustering

UK

Imperial College Ilpo Huhtaniemi Reproductive system

Andrew de Mello Biochemistry, Biophysics, Biotechnology

Cambridge University

Simon Tavaré Statistical bioinformatics, population genetics, evolutionary cancer genomics

Fiona Watt Skin, including skin cancer

Florian Markowetz Computational biology: data integration and network models

Bill Harris Eye, lineage investigation in the zebrafish retina

Juan-Jose Ventura Respiratory system

The University of Oxford

Robert Griffiths Population genetics

Eirik Jacobsen Hematopoietic system

European Bioinformatics Institute

Nick Goldman Computer science, Mathematics & Statistics

Guy Cochrane Computing and data infrastructure

The Wellcome Trust Sanger Institute

Seth Grant Neuroscience, Genes to Cognition

Microsoft Research

Stephen Emmott Computational biology

King's College London

Peter Zammit Skeletal muscles

Science and David Giaretta Cell lineage data system

Page 8: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

Technology Facilities Council (STFC)

Neil Geddes eScience, Cell lineage data system

Institute of Cancer Research

Mel Greaves Pediatric Leukemia

Beatson Institute

Owen Sansom Gastrointestinal tract, including cancer

University of Manchester

Simon Whelan Combinatorial approaches and algorithms

Newcastle University

Tom Kirkwood Aging

University College London

Adam Giangreco Respiratory system

Sam Janes Respiratory system

Medical Research Council (MRC)

Stephen Holgate

Respiratory system

University of Southampton

Donna Davies Respiratory system

Hywel Morgan Biotechnology

Phillip Ball Science Writer

USA

Stanford University

Stephen Quake Biotechnology, Microfluidics

University of California, Berkeley

John Huelsenbeck Population genetics

University of California, Davis (UC Davis)

Bruce Rannala Population genetics

University of

California San

Francisco

Carlo Maley Gastrointestinal tract, Cancer, Human hematopoietic system

Iowa State University

Oliver Eulenstein Comparing and coalescing cell lineage trees

Harvard Medical School

Connie Cepko Eye

University of California Los Angeles

Shimon Weiss

Biophysics

University of Southern California (USC)

Darryl Shibata DNA Methylation and epigenetic markers

Page 9: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

Umass Medical School

Stephen Lyle Skin, including melanoma

University of California, San Diego (UCSD)

Trey Ideker Computational Biology & Bioinformatics

University of Wisconsin

David Page Machine learning algorithms to learn disease status and progression

Juvenile Diabetes Research Foundation (JDRF)

Adrianne Wong Diabetes

Illumina Mostafa Ronaghi Biochemistry, Biophysics, Biotechnology

Nobel Laureate Sydney Brenner Liaison to scientific societies

Altogether up to now there are 168 scientists from 105 institutions in 19 countries.

Page 10: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

Team Organizaton and Work Packages

[Section leader names below are in bold italics]

{Consortium participant responsible for the travel budget}

1. Project Management

2. Scientific leadership, coordination, and integration

2.1. Edit the Human Cell Lineage Flagship Roadmap Book [Ehud Shapiro,

Philip Ball]

3. Development of the Cell Lineage Analysis & Information

Platform

3.1. Turn individual cells into cell data (Biochemistry, Biophysics,

Computer Systems) [Stephen Quake, Hans Lehrach, Simon Tavaré,

Patrick Tabeling, Morten Sommer, Mostafa Ronaghi, Mats Nilsson, Ulf

Landegren, Christoph Klein, Carl Hansen, David Bensimon, Cees Dekker,

Aebersold Rudolf, Andrew de Mello, Marc Feiglin, Hywel Morgan, Joakim

Lundeberg, Piero Carninci] {UU}

3.1.1. Single Cell Capture (2D and 3D laser capture, microfluidics single-cell

sorting) [Julien Colombelli]

3.1.2. Single Cell DNA amplification (whole genome, haploid, and selective

amplification)

3.1.3. Reading single-cell genomic signatures for lineage information

(sequencing, microsatellite fragment information, DNA arrays)

3.1.4. Single Cell Characterization (genome, transcriptome, proteome,

metabolome) [Christoph Klein, Carl Hansen, Herbert Auer, Hans

Lehrach, Sten Linnarsson, Georgia Panopoulou, Alistair Forrest, Albert

Poustka]

3.2. Turn cell data into information on cell lineage trees (Computer science,

Mathematics & Statistics) [Nick Goldman] {EBI}

3.2.1. Mathematical foundation [Mike Steel, Elchanan Mossel, Sebastian

Boecker]

3.2.2. Phylogenetics; combinatorial and statistical approaches and

algorithms [Olivier Gascuel, Benny Chor, Fabio Pardi, Shlomo Moran,

Daniel Huson, Vincent Berry, Vincent Ranwez, Arndt von Haeseler,

Alexandros Stamatakis, Simon Whelan, David Posada, David

Bryant]{CNRS}

3.2.3. Population genetics; statistical approaches and algorithms [Simon

Tavaré, John Huelsenbeck, Bruce Rannala, Robert Griffiths] {CRUK}

Page 11: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

3.2.4. Massive scale quantification of data uncertainty [Costas Bekas,

Alessandro Curioni]{IBM}

3.3. Turn information on cell lineage trees into biological and medical

knowledge (Computational Biology & Bioinformatics) [Ralf Herwig, Ron

Shamir, Stephen Emmott, Samuel Kaski, Harri Lähdesmäki, Themis

Palpanas, Michal Rosen-Zvi, Trey Ideker, Emmanuel Barillot, Eric

Zwanenburg] {MPG}

3.3.1. Comparing and coalescing cell lineage trees [Jens Lagergren, Cedric

Chauve, Alexei Drummond, Oliver Eulenstein, David Bryant, Bernard

Moret]

3.3.2. Machine learning algorithms for the analysis of cell lineage trees

[Paolo Frasconi, Andrea Passerini, David Page, Luc de Raedt]

3.3.3. Ultrascalable algorithms for classification and clustering [Costas

Bekas, Alessandro Curioni]

3.3.4. Understanding health vs. disease and disease progression

[Emmanuel Barillot, Jean-Philippe Vert, Samuel Kaski, Paolo Frasconi,

Michal Rosen-Zvi ]

3.3.5. Understanding lineage-dependent transcriptional regulation [Ron

Shamir, Jan-Åke Larsson]

3.3.6. Dissecting the dynamics of molecular interactions [Trey Ideker]

3.3.7. Test case development – specification of further domains for applying

cell lineage trees [Ralf Herwig]

3.4. Development of computing and data platform (Computer Systems)

[Yaron Wolfsthal] {STFC}

3.4.1. Cell lineage data entry, taxonomy, UI and visualization [David

Giaretta, Haim Nelken, Yaron Wolfsthal, Stefan Wesner, Yossi Matias,

Isaac Elias, Neil Geddes]

3.4.2. Cell lineage Open Data Management Store [Yossi Matias, Isaac

Elias, Michael Wilpaner, Haim Nelken, Eric Zwanenburg]

3.4.3. Computer systems technologies [Stefan Wesner, Yossi Matias, Isaac

Elias,Yaron Wolfsthal, Neil Geddes, Guy Cochrane]

4. Deployment and operation of the Cell Lineage Analysis &

Information Platform {UStutt}

4.1. Cell lineage analysis and information centers [Joakim Lundeberg,

Herbert Auer, Shimon Weiss, Hans Lehrach, Bernhard Herrmann, Fiona

Watt, Florian Markowetz, Peter van der Spek, Gidi Rechavi, Jean-Stéphane

Joly, Nadine Peyriéras]

4.1.1. Interface with research groups (obtaining cells and DNA, delivering

analysis results)

4.1.2. Operating procedures

Page 12: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

4.1.3. Interface with data and computing cloud (delivering data and analysis

results)

4.2. Computing and data platform [Stefan Wesner, David Giaretta, Yossi

Matias, Isaac Elias, Yaron Wolfsthal, Haim Nelken, Uwe Wossner, Neil

Geddes, Guy Cochrane, Alexandros Stamatakis]

5. Application of the Cell Lineage Analysis and Information

Platform to uncover the Human Cell Lineage Tree in health

and in disease {EMC}

5.1. Organs and systems: Development, growth, renewal, aging, and

pathology [Fiona Watt]

5.1.1. Hematopoietic system (including auto-immune diseases) [Gerard

Wagemaker, Hiro Nakauchi, Tsvee Lapidot, Carlo Maley, Joakim

Lundeberg, Timm Schroeder, Elaine Dzierzak, Georg A. Hollaender,

Sten Eirik Jacobsen]

5.1.2. Heart [Thomas Braun, Margaret Buckingham, Eldad Tzahor]

5.1.3. Vascular System [Hellmut Augustin, Ralf Adams, Kari Alitalo, Lena

Claesson-Welsh, Eckhard Lammert, Stefan Schulte-Merker, Michal

Neeman, Christer Betsholtz]

5.1.4. Respiratory system, including lung cancer [Emma Rawlins, Saverio

Bellusci, Adam Giangreco, Sam Janes, Juan-Jose Ventura, Stephen

Holgate, Donna Davies]

5.1.5. Kidney and Urinary tract [Karl Skorecki, Alexander Peter Maxwell]

5.1.6. Pancreas, including pancreatic cancer and diabetes type I & II [Jorge

Ferrer, Pedro Herrera , Yuval Dor] {CRG}

5.1.7. Gastrointestinal tract, including cancer [Hans Clevers, Owen

Sansom, Riccardo Fodde, Sylvie Robine, Eduard Batlle, Daniel Louvard,

Carlo Maley] {IC}

5.1.8. Bones and Cartilage, Connective tissue [James Sharpe, Dafna

Benayahu] {CRG}

5.1.9. Skeletal Muscles [Shahragim Tajbakhsh, Eldad Tzahor, Robert

Kelly, Frederic Relaix, Giulio Cossu, Peter Zammit, Fabrice Chrétien,

Margaret Buckingham]

5.1.10. Endocrinology and metabolism

5.1.11. Reproductive system [Ilpo Huhtaniemi, Nava Dekel]

5.1.12. Skin, including melanoma [Fiona Watt, Florian Markowetz, Ingo

Haase, Stephen Lyle] {CRUK}

5.1.13. Fat tissue [Kirsty Spalding, Henrik Druid]

5.1.14. Brain and nervous system central [Patrik Ernfors, Jonas Frisén,

Seth Grant] {UU}

5.1.15. Eye [Paola Bovolenta, Connie Cepko, Manuel Díaz-Llopis, Bill

Harris] {CRG}

Page 13: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

5.1.16. Embryonic Development: preimplantation, early patterning and

organogenesis [Bernhard Herrmann, Miguel Torres Sanchez, James

Sharpe, Takashi Hiiragi] {MPG}

5.1.17. Renewal [Jonas Frisén, Kirsty Spalding]

5.1.18. Aging [Tom Kirkwood]

5.2. Cancer [Hans Lehrach, Simon Tavaré, Gidi Rechavi, Carlo Maley] {MPG}

5.2.1. Cancer Stem Cells [John Dick, Tsvee Lapidot, Hans Clevers,

Riccardo Fodde]

5.2.2. Oncogenomics

5.2.3. Dormancy and origin of metastasis [Christoph Klein, Riccardo

Fodde]

5.2.4. Origin of relapse

5.2.5. Clonal heterogeneity

5.2.6. Resistance to therapy

5.2.7. Leukemia

5.2.7.1. Adult Leukemia [Torsten Haferlach]

5.2.7.2. Pediatric Leukemia [Mel Greaves, Shai Izraeli]

5.3. Model organisms and controls {CNRS}

[Note: Mouse model is included in all topics above]

5.3.1. Gold standards for the validation of cell lineage reconstruction

methods (C. elegans, Zebrafish) [Nadine Peyrieras, Paul Bourgine,

Jean-Stéphane Joly, Louis Wehenkel, Karol Mikula, Andres Santos]

5.3.2. Mitochondrial DNA

5.3.3. DNA Methylation and epigenetic markers [Darryl Shibata, Simon

Tavaré, Carlo Maley]

5.3.4. Lineage tracing methods (pulse/chase, others) [Miguel Torres

Sanchez, Bernhard Herrmann, Hellmut Augustin, Ralf Adams,

Margaret Buckingham] {CRG}

5.3.5. Carbon dating [Jonas Frisen, Kirsty Spalding, Henrik Druid, Walter

Kutschera, Peter Steier]

6. Dissemination and support {STFC}

6.1. Liaison with national academies, scientific and professional

associations

6.1.1. The Royal Society [Bill Harris, Fiona Watt] {CRUK}

6.1.2. French Academy of Sciences [Daniel Louvard, Margaret Buckingham]

{IC}

6.1.3. Royal Swedish Academy of Sciences [Ulf Landegren]

6.1.4. Dutch Royal Society [Hans Clevers]

6.1.5. Israeli National Academy of Sciences and Humanities [David Harel]

6.1.6. Academy of Medical Sciences [Simon Tavaré, Fiona Watt] {CRUK}

6.1.7. Complex Systems Society (CSS) [Paul Bourgine]

Page 14: Team and Research Topics - lineage-flagship.eu Research Topics... · Team, Research Topics and Work Packages ... their status and progression Canada ... Aebersold Biochemistry, Proteomics,

Weizmann Institute of Science, Rehovot (Israel)

6.1.8. National Network of Complex Systems, France (RNSC), [Paul

Bourgine]

6.1.9. Society for Laboratory Automation and Screening [Marc Feiglin]

6.1.10. Society of Systematic Biologists [Alexandros Stamatakis]

6.1.11. European Society of Cardiology [Robert Kelly]

6.1.12. European Leukemia Net (ELN) [Torsten Haferlach]

6.1.13. Gesellschaft für Informatik [Sebastian Boecker]

6.1.14. Royal Society of New Zealand [Mike Steel]

6.1.15. Nobel Laureate Sydney Brenner

6.2. Liaison with research funding agencies and research foundations

6.2.1. DFG [Dorette Breitkreuz]

6.2.2. Scientific Council of the Dutch Cancer Society [Riccardo Fodde]

6.2.3. Israel Science Foundation (ISF) [Benny Geiger]

6.2.4. Biological Sciences Committee of Cancer Research UK [Simon

Tavaré] {CRUK}

6.2.5. National Cancer Institute (INCA) [Daniel Louvard]

6.2.6. Association Française contre les Myopathies (AFM) [Margaret

Buckingham]

6.2.7. Spanish national research council (Consejo Superior de Investigacion

Cientifica, CSIC) [Jose Juan Sanchez Serrano, Paola Bovolenta]

6.2.8. Science and Technology Facilities Council (STFC) [Neil Geddes]

6.2.9. Swiss National Research Foundation [Walter Reith] –tbc

6.2.10. Biotechnology and Biological Sciences Research Council (BBSRC)

[Stephen Emmott]

6.2.11. Allan Wilson Centre of Molecular Ecology and Evolution [David

Bryant]

6.2.12. Wellcome Trust [Stephen Emmott, Seth Grant]

6.2.13. Medical Research Council (MRC) [Stephen Holgate, Seth Grant]

6.2.14. Juvenile Diabetes Research Foundation [Adrianne Wong]

6.3. Liaison with multi-site research organizations

6.3.1. Fraunhofer [Thomas Berlage]

6.3.2. INRIA [Claude Kirchner]

6.3.3. MPG