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<strong>Facts</strong> <strong>and</strong> <strong>Figures</strong> <strong>2011</strong><br />
www.embl.org
Contents <strong>Facts</strong> <strong>and</strong> <strong>Figures</strong> <strong>2011</strong><br />
03<br />
07<br />
08<br />
11<br />
Human Resources<br />
Visitors <strong>and</strong><br />
Beamline Users<br />
Finance<br />
<strong>EMBL</strong><br />
Leadership<br />
3 <strong>EMBL</strong> Heidelberg Units<br />
5 <strong>EMBL</strong> Outstations<br />
8 Financial data<br />
9 Member states contributions<br />
10 External funding<br />
11 <strong>EMBL</strong> Council <strong>and</strong><br />
Finance Committee<br />
12 Scientific Advisory Committee<br />
12 Bioinformatics Advisory<br />
Committee<br />
13 Hamburg Priorities Committee<br />
13 <strong>EMBL</strong> Directorate<br />
14 Heads of Units<br />
15 Senior Scientists<br />
16 Faculty <strong>and</strong> Joint Appointments<br />
20 21 24<br />
25<br />
Intellectual Property<br />
<strong>EMBL</strong> International<br />
PhD Programme<br />
Alumni<br />
Publications<br />
20 Granted patents in <strong>2011</strong><br />
21 PhD Theses <strong>2011</strong><br />
2
Human Resources<br />
Categories of Staff<br />
Staff members: Recruited internationally as well as locally. Their tenure is,<br />
in general, limited to a maximum of nine years. Open-ended contracts can<br />
only be awarded in exceptional cases.<br />
Predoctoral <strong>and</strong> postdoctoral fellows: They receive stipends either from<br />
<strong>EMBL</strong> or from external institutions.<br />
Supernumeraries: Employed for a limited time of a maximum of one year.<br />
They are usually temporary replacements.<br />
Ancillaries: Generally recruited from within the local labour market <strong>and</strong><br />
employed to support <strong>EMBL</strong> facilities, for example housekeeping <strong>and</strong><br />
cleaning services.<br />
Employment situation on 31 December <strong>2011</strong>:<br />
1 695 people including 172 visitors.<br />
<strong>EMBL</strong> Heidelberg<br />
Staff at <strong>EMBL</strong> Heidelberg: 788<br />
1 2<br />
Charts 1 – 12 do not include visitors.<br />
3
Human Resources cont.<br />
3<br />
4<br />
5<br />
6<br />
Other Research Activities include, among others, organisational units<br />
(e. g. <strong>EMBL</strong> International PhD Programme, Postdoctoral Programme, International<br />
Relations) <strong>and</strong> extraordinary research projects (e. g. EVIMalaR, BioMalPar, ANTIMAL).<br />
Scientific Support Services include Core Facilities, Laboratory Animal Resources,<br />
IT Services, Photolab, Szilárd Library.<br />
4
Human Resources cont.<br />
<strong>EMBL</strong> Outstations<br />
7<br />
8<br />
9<br />
10<br />
5
Human Resources cont.<br />
11<br />
12<br />
CCO: Course <strong>and</strong> Conference Office<br />
OIPA: Office of Information <strong>and</strong> Public Affairs<br />
13<br />
14<br />
6<br />
Charts 13 <strong>and</strong> 14 include visitors.
Visitors <strong>and</strong> Beamline Users<br />
1<br />
Total number of visitors: 476<br />
Total number of beamline users: 2 724<br />
2<br />
3<br />
<strong>EMBL</strong> Grenoble collaborates with the ESRF to operate beamlines ID14 - ID29.<br />
BM 14 is operated by <strong>EMBL</strong>, ESRF <strong>and</strong> the Indian Department of Biotechnology.<br />
PX = Protein Crystallography<br />
SAXS = Small Angle X-ray Scattering<br />
7
Financial data<br />
<strong>2011</strong><br />
2010<br />
1<br />
2<br />
3<br />
4<br />
8
Member states contributions<br />
Ordinary contributions<br />
See www.embl.de/statistics for more information<br />
Other contributions<br />
Contributions<br />
Pension contribution<br />
<strong>EMBL</strong> budget <strong>2011</strong>: € 171 million<br />
9
External funding<br />
Grants<br />
Other external funding<br />
Grants <strong>2011</strong><br />
Click here for a PDF of the <strong>EMBL</strong> grants <strong>2011</strong><br />
by funding body <strong>and</strong> group leader.<br />
Annual accounts <strong>2011</strong><br />
Click here for a PDF of the complete<br />
accounts for <strong>2011</strong>.<br />
10
<strong>EMBL</strong> Leadership<br />
<strong>EMBL</strong> Council <strong>and</strong> Finance Committee on 31 December <strong>2011</strong><br />
Austria<br />
• Annemarie Frischauf, Delegate<br />
• Hemma Bauer, Delegate<br />
Belgium<br />
• Véronique Feys, Delegate<br />
• Vincent Meunier, Adviser<br />
• Marc van Montagu, Delegate<br />
Croatia<br />
• Kresimir Pavelic, Delegate<br />
• Vinko Purgar, Adviser<br />
Denmark<br />
• Troels Tvedegaard Rasmussen, Adviser<br />
• Jørgen Kjems, Delegate<br />
Finl<strong>and</strong><br />
• Kalervo Hiltunen, Adviser<br />
• Riitta Mustonen, Delegate<br />
• Eero Vuorio, Delegate<br />
(Chair of Council)<br />
ˆ<br />
France<br />
• Thierry Meinnel, Delegate<br />
• Annaïg Le Guen, Delegate<br />
• Vincent Geli, Delegate<br />
Germany<br />
• Jan Grapentin, Delegate<br />
• Volker Wiesenthal, Adviser<br />
• Patrick Cramer, Delegate<br />
Greece<br />
• Eftyhia Kolliakou, Delegate<br />
• Charalambos Savakis, Delegate<br />
Icel<strong>and</strong><br />
• Asgerdur Kjartansdottir, Delegate<br />
• Eiríkur Steingrímsson, Delegate<br />
• Katrin Valgeirsdottir, Adviser<br />
Irel<strong>and</strong><br />
• Fergal Cullen, Delegate<br />
• Graham Love, Adviser<br />
• Stephen Simpson, Delegate<br />
Israel<br />
• Mahmoud Taya, Delegate<br />
• Joel Sussman, Delegate<br />
• Yossi Kalifa, Delegate<br />
Italy<br />
• Augusto Cippollone, Adviser<br />
• Glauco P. Tocchini-Valentini, Delegate<br />
Luxembourg<br />
• Josiane Entringer, Delegate<br />
The Netherl<strong>and</strong>s<br />
• Jeannette Ridder-Numan, Delegate<br />
(Chair of Finance Committee)<br />
• Gerrit van Meer, Delegate<br />
Norway<br />
• Jacob Wang, Delegate<br />
• Anders Sundan, Delegate<br />
Portugal<br />
• Maria José Almeida, Delegate<br />
(Finance Committee), Adviser (Council)<br />
• Maria Carmo-Fonseca, Delegate (Council)<br />
• Claúdio Sunkel, Delegate (Council)<br />
(Vice-Chair of Council)<br />
Spain<br />
• Benjamin Sanchez Gimeno, Delegate<br />
(Vice-Chair of Finance Committee)<br />
• Cristina Bauluz, Delegate<br />
• Angela Nieto, Delegate<br />
Sweden<br />
• Dick Heinegård, Delegate<br />
• Maria Thuveson, Delegate<br />
Switzerl<strong>and</strong><br />
• Isabella Beretta, Delegate<br />
• Rolf Zeller, Delegate<br />
United Kingdom<br />
• Mark Palmer, Delegate<br />
• Bruce Minty, Delegate<br />
Associate member: Australia<br />
• Martin Gallagher, Observer<br />
• Richard Larkins, Delegate<br />
<strong>EMBL</strong> Council is composed of delegates from all member states of the laboratory. Each member state is represented by up to two delegates, who may be accompanied by advisers.<br />
<strong>EMBL</strong> Council meets regularly twice a year <strong>and</strong> has occasional extraordinary meetings. One of the main responsibilities of <strong>EMBL</strong> Council is to ensure that the financial requirements set up on the<br />
establishment of <strong>EMBL</strong> are met, <strong>and</strong> that the site agreements with host member states are observed. The Finance Committee assists Council in the financial management <strong>and</strong> governance of <strong>EMBL</strong>.<br />
11
<strong>EMBL</strong> Leadership cont.<br />
Scientific Advisory Committee<br />
The Scientific Advisory Committee gives advice to Council, in particular<br />
with regard to proposals from the Director General on the realisation of the<br />
programme of the laboratory. It is composed of distinguished scientists in<br />
their own right, not as representatives of member states.<br />
Member Country Terms<br />
Siv Andersson Uppsala (S) (2007-2009, 2010-2012)*<br />
Naama Barkai Rehovot (IL) (<strong>2011</strong>-2013)<br />
Konrad Basler Zurich (CH) (2007-2009, 2010-2012)*<br />
Denis Duboule Lausanne (CH) (<strong>2011</strong>-2013)<br />
Roderic Guigo Barcelona (ES) (2012-2014)<br />
Reinhard Jahn Göttingen (D) (2010-2012)** – Vice Chair<br />
Daniel Louvard Paris (F) (2012-2014)<br />
Ron Milligan La Jolla (US) (2012-2014)<br />
Tom Muir Princeton (US) (2010-2012)**<br />
Andrew Murray Harvard (US) (2008-2010, <strong>2011</strong>-2013)<br />
Andrea Musacchio Dortmund (D) (<strong>2011</strong>-2013)<br />
Helen Saibil London (UK) (2007-2009, 2010-2012)*<br />
S<strong>and</strong>ra Schmid La Jolla (US) (2008-2010, <strong>2011</strong>-2013) – Chair<br />
Titia Sixma Amsterdam (NL) (2007-2009, 2010-2012)*<br />
Michael Snyder Stanford (US) (<strong>2011</strong>-2013)<br />
Alfonso Valencia Madrid (ES) (2007-2009, 2010-2012)*<br />
Jean Weissenbach Evry (F) (2012-2014)<br />
Bioinformatics Advisory Committee<br />
The Bioinformatics Advisory Committee gives advice to the EBI<br />
on scientific strategy, future directions <strong>and</strong> proposals on the<br />
realisation of its programme. It is composed of distinguished<br />
scientists in their own right, not as representatives of member states.<br />
Membership of the Committee is drawn from experts in the field<br />
of bioinformatics <strong>and</strong> other relevant scientific disciplines.<br />
Some are also members of <strong>EMBL</strong>’s Scientific Advisory Committee<br />
<strong>and</strong> Data Resources Advisory Boards.<br />
Member<br />
Anna Tramontano<br />
Roderic Guigo<br />
Tim Hubbard<br />
Olli Kallioniemi<br />
Jonathan Knowles<br />
Philippe Sanseau<br />
Mathias Uhlén<br />
Institution<br />
University of Rome “La Sapienza”, Rome, I – Chair<br />
Centre de Regulació Genòmica, Barcelona, ES<br />
WT Sanger Institute, UK<br />
VTT Medical Biotechnology, Turku, FIN<br />
The Roche Group, Basel, CH<br />
GlaxoSmithKline Plc., UK<br />
Royal Institute of Technology (KTH), Stockholm, S<br />
* Turning over 31 December 2012<br />
**Eligible for re-election in November 2012<br />
12
<strong>EMBL</strong> Leadership cont.<br />
Hamburg Priorities Committee<br />
<strong>EMBL</strong> Directorate<br />
The Hamburg Priorities Committee evaluates project proposals for beamline<br />
access in macromolecular crystallography, small angle X-ray scattering <strong>and</strong><br />
X-ray absorption spectroscopy.<br />
Dino Moras<br />
Maria Armenia Carrondo<br />
Bauke Dijkstra<br />
Ralf Ficner<br />
Mariusz Jaskolski<br />
Jim Naithsmith<br />
Poul Nissen<br />
Gunter Schneider<br />
Patrice Vachette<br />
Bente Vestergaard<br />
Maria Vanoni<br />
IGBMC, Strasbourg, France – Chair<br />
Lisbon, Portugal<br />
Groningen, The Netherl<strong>and</strong>s<br />
University of Göttingen, Germany<br />
Poznan, Pol<strong>and</strong><br />
Saint Andrews, United Kingdom<br />
Aarhus, Denmark<br />
Stockholm, Sweden<br />
Paris, France<br />
Copenhagen, Denmark<br />
University of Milano, Italy<br />
Prof. Iain W. Mattaj, Director General<br />
Ralph Martens, Administrative Director<br />
Prof. Matthias Hentze, Associate Director<br />
Dr. Christian Boulin, Director of Core Facilities <strong>and</strong> Services<br />
Dr. Silke Schumacher, Director International Relations<br />
13
<strong>EMBL</strong> Leadership cont.<br />
Heads of Units<br />
Head of Unit Title Unit Joint Appointments<br />
Iain Mattaj Director General Directors’ Research<br />
Peer Bork Joint Head of Unit Structural <strong>and</strong> Computational Biology<br />
Christian Boulin Director of Core Facilities <strong>and</strong> Services Core Facilities <strong>and</strong> Services<br />
Graham Cameron Associate Director EBI <strong>EMBL</strong>-EBI<br />
Stephen Cusack Head of Outstation <strong>EMBL</strong> Grenoble<br />
Jan Ellenberg Head of Unit Cell Biology <strong>and</strong> Biophysics<br />
Anne Ephrussi Head of Unit / EICAT Coordinator Developmental Biology<br />
Eileen Furlong Joint Head of Unit Genome Biology<br />
Matthias Hentze Associate Director <strong>EMBL</strong> Directors’ Research Genome Biology, Molecular Medicine Partnership Unit<br />
Christoph Müller Joint Head of Unit Structural <strong>and</strong> Computational Biology Genome Biology<br />
Nadia Rosenthal Head of Outstation <strong>EMBL</strong> Monterotondo<br />
Lars Steinmetz Joint Head of Unit Genome Biology<br />
Janet Thornton Director EBI <strong>EMBL</strong>-EBI<br />
Matthias Wilmanns Head of Outstation <strong>EMBL</strong> Hamburg<br />
Heads of Units participate in the collegial leadership of <strong>EMBL</strong> <strong>and</strong> play a critical role in the research direction of their unit.<br />
They lead a research group, mentor younger faculty members <strong>and</strong> ensure the maintenance of world class st<strong>and</strong>ards of research throughout their unit.<br />
14
<strong>EMBL</strong> Leadership cont. – Senior Scientists<br />
Senior Scientist Unit Joint Appointments<br />
Iain Mattaj<br />
Directors’ Research<br />
Rolf Apweiler<br />
<strong>EMBL</strong>-EBI<br />
Detlev Arendt<br />
Developmental Biology<br />
Ewan Birney <strong>EMBL</strong>-EBI Genome Biology<br />
Peer Bork<br />
Structural <strong>and</strong> Computational Biology<br />
Christian Boulin<br />
Core Facilities <strong>and</strong> Services<br />
Alvis Brazma<br />
<strong>EMBL</strong>-EBI<br />
Graham Cameron<br />
<strong>EMBL</strong>-EBI<br />
Florent Cipriani<br />
<strong>EMBL</strong> Grenoble<br />
Stephen Cusack<br />
<strong>EMBL</strong> Grenoble<br />
Jan Ellenberg<br />
Cell Biology <strong>and</strong> Biophysics<br />
Anne Ephrussi<br />
Developmental Biology<br />
Eileen Furlong<br />
Genome Biology<br />
Anne-Claude Gavin Structural <strong>and</strong> Computational Biology Joint appointment with Genome Biology<br />
Nick Goldman<br />
<strong>EMBL</strong>-EBI<br />
Cornelius Gross <strong>EMBL</strong> Monterotondo Developmental Biology<br />
Matthias Hentze Directors’ Research Genome Biology, Molecular Medicine Partnership<br />
Wolfgang Huber Structural <strong>and</strong> Computational Biology <strong>EMBL</strong>-EBI<br />
Eric Karsenti<br />
Directors’ Research<br />
Victor Lamzin<br />
<strong>EMBL</strong> Hamburg<br />
Christoph Müller Structural <strong>and</strong> Computational Biology Genome Biology<br />
Nadia Rosenthal<br />
<strong>EMBL</strong> Monterotondo<br />
Carsten Schultz<br />
Cell Biology <strong>and</strong> Biophysics<br />
Lars Steinmetz<br />
Genome Biology<br />
Dmitri Svergun<br />
<strong>EMBL</strong> Hamburg<br />
Janet Thornton<br />
<strong>EMBL</strong>-EBI<br />
Matthias Wilmanns<br />
<strong>EMBL</strong> Hamburg<br />
Senior Scientists are a select group, with important statutory responsibilities for advising the Director General on faculty appointments <strong>and</strong> promotions.<br />
They also provide collective advice to the Director General <strong>and</strong> the Heads of Units on matters with significant impact on the scientific life of the laboratory.<br />
15
<strong>EMBL</strong> Leadership cont.<br />
Faculty <strong>and</strong> Joint Appointments on 31 December <strong>2011</strong><br />
Faculty Title Primary appointment Joint appointment<br />
Iain Mattaj Director General Directors’ Research<br />
Claude Antony Team Leader Cell Biology <strong>and</strong> Biophysics<br />
Rolf Apweiler Joint Team Leader <strong>EMBL</strong>-EBI<br />
Detlev Arendt Group Leader Developmental Biology<br />
Alex<strong>and</strong>er Aulehla Group Leader Developmental Biology<br />
Orsolya Barabas Group Leader Structural <strong>and</strong> Computational Biology<br />
Martin Beck Group Leader Structural <strong>and</strong> Computational Biology<br />
Imre Berger Group Leader <strong>EMBL</strong> Grenoble Genome Biology<br />
Paul Bertone Group Leader <strong>EMBL</strong>-EBI Genome Biology, Developmental Biology<br />
Ewan Birney Joint Team Leader <strong>EMBL</strong>-EBI Genome Biology<br />
Peer Bork Joint Head of Unit Structural <strong>and</strong> Computational Biology<br />
Christian Boulin<br />
Director of Core Facilities<br />
<strong>and</strong> Services<br />
Core Facilities <strong>and</strong> Services<br />
Alvis Brazma Senior Team Leader <strong>EMBL</strong>-EBI<br />
John Briggs Group Leader Structural <strong>and</strong> Computational Biology Cell Biology <strong>and</strong> Biophysics<br />
Graham Cameron Associate Director EBI <strong>EMBL</strong>-EBI<br />
Teresa Carlomagno Group Leader Structural <strong>and</strong> Computational Biology Genome Biology<br />
Florent Cipriani Team Leader <strong>EMBL</strong> Grenoble<br />
Guy Cochrane Team Leader <strong>EMBL</strong>-EBI<br />
Stephen Cusack Head of Outstation <strong>EMBL</strong> Grenoble<br />
Stefano De Renzis Group Leader Developmental Biology<br />
Jan Ellenberg Head of Unit Cell Biology <strong>and</strong> Biophysics<br />
Anton Enright Group Leader <strong>EMBL</strong>-EBI <strong>EMBL</strong> Monterotondo<br />
Anne Ephrussi<br />
Head of Unit/EICAT<br />
Coordinator<br />
Developmental Biology<br />
Stefan Fiedler Team Leader <strong>EMBL</strong> Hamburg<br />
Paul Flicek Team Leader <strong>EMBL</strong>-EBI<br />
Members of faculty are<br />
scientists who lead research<br />
groups or the equivalent:<br />
Heads of Unit, group<br />
leaders, team leaders <strong>and</strong><br />
technical team leaders as<br />
well as visiting scientists in<br />
a group leader position.<br />
Many group leaders have<br />
joint appointments with<br />
other Units to promote<br />
interdisciplinary research<br />
<strong>and</strong> to enhance exchange<br />
of information, tools<br />
<strong>and</strong> techniques.<br />
16
<strong>EMBL</strong> Leadership – Faculty <strong>and</strong> Joint Appointments – cont.<br />
Faculty Title Primary appointment Joint appointment<br />
Eileen Furlong Joint Head of Unit Genome Biology<br />
Anne-Claude Gavin Group Leader Structural <strong>and</strong> Computational Biology Genome Biology<br />
Toby Gibson Team Leader Structural <strong>and</strong> Computational Biology<br />
Darren Gilmour Group Leader Cell Biology <strong>and</strong> Biophysics Developmental Biology<br />
Nick Goldman Group Leader <strong>EMBL</strong>-EBI<br />
Cornelius Gross Deputy Head of Outstation <strong>EMBL</strong> Monterotondo Developmental Biology<br />
Christian Häring Group Leader Cell Biology <strong>and</strong> Biophysics<br />
Darren Hart Team Leader <strong>EMBL</strong> Grenoble<br />
Marcus Heisler Group Leader Developmental Biology<br />
Matthias Hentze Associate Director <strong>EMBL</strong> Directors' Research<br />
Genome Biology,<br />
Molecular Medicine Partnership Unit<br />
Paul Heppenstall Group Leader <strong>EMBL</strong> Monterotondo Cell Biology <strong>and</strong> Biophysics<br />
Christoph Hermes Group Leader <strong>EMBL</strong> Hamburg<br />
Henning Hermjakob Team Leader <strong>EMBL</strong>-EBI<br />
Takashi Hiiragi Group Leader Developmental Biology<br />
Wolfgang Huber Group Leader Genome Biology <strong>EMBL</strong>-EBI<br />
Lars Hufnagel Group Leader Cell Biology <strong>and</strong> Biophysics Developmental Biology<br />
Sarah Hunter Team Leader <strong>EMBL</strong>-EBI<br />
Martin Jechlinger Group Leader <strong>EMBL</strong> Monterotondo Cell Biology <strong>and</strong> Biophysics<br />
Petteri Jokinen Technical Team Leader <strong>EMBL</strong>-EBI<br />
Marko Kaksonen<br />
Group Leader<br />
Misha Kapushesky Team Leader <strong>EMBL</strong>-EBI<br />
Eric Karsenti Group Leader Directors’ Research<br />
Paul Kersey Team Leader <strong>EMBL</strong>-EBI<br />
Gerard Kleywegt Team Leader <strong>EMBL</strong>-EBI<br />
Maja Köhn Group Leader Genome Biology Cell Biology <strong>and</strong> Biophysics<br />
Jan Korbel Group Leader Genome Biology <strong>EMBL</strong>-EBI<br />
Jeroen Krijgsveld<br />
Team Leader<br />
17
<strong>EMBL</strong> Leadership – Faculty <strong>and</strong> Joint Appointments – cont.<br />
Faculty Title Primary appointment Joint appointment<br />
Victor Lamzin Deputy Head of Outstation <strong>EMBL</strong> Hamburg<br />
Christophe Lancrin Group Leader <strong>EMBL</strong> Monterotondo Developmental Biology<br />
Edward Lemke Group Leader Structural <strong>and</strong> Computational Biology Cell Biology <strong>and</strong> Biophysics<br />
Péter Lénárt Group Leader Cell Biology <strong>and</strong> Biophysics<br />
Nicolas Le Novère Group Leader <strong>EMBL</strong>-EBI <strong>EMBL</strong> Monterotondo<br />
Maria Leptin Director EMBO Directors' Research<br />
Rodrigo Lopez Head of External Services <strong>EMBL</strong>-EBI<br />
Nick Luscombe Group Leader <strong>EMBL</strong>-EBI Genome Biology<br />
John Marioni Group Leader <strong>EMBL</strong>-EBI Developmental Biology<br />
José Márquez Team Leader <strong>EMBL</strong> Grenoble<br />
Maria-Jesus Martin Team Leader <strong>EMBL</strong>-EBI<br />
Andrew McCarthy Team Leader <strong>EMBL</strong> Grenoble<br />
Johanna McEntyre Team Leader <strong>EMBL</strong>-EBI<br />
Rob Meijers Group Leader <strong>EMBL</strong> Hamburg<br />
Christoph Merten Group Leader Genome Biology<br />
Christoph Müller Joint Head of Unit Structural <strong>and</strong> Computational Biology Genome Biology<br />
Jochen Müller-Dieckmann Team Leader <strong>EMBL</strong> Hamburg<br />
François Nédélec Group Leader Cell Biology <strong>and</strong> Biophysics Structural <strong>and</strong> Computational Biology<br />
Pierre Neveu Group Leader Cell Biology <strong>and</strong> Biophysics<br />
Dónal O’Carroll Group Leader <strong>EMBL</strong> Monterotondo Developmental Biology, Genome Biology<br />
Claire O'Donovan Team Leader <strong>EMBL</strong>-EBI<br />
John Overington Team Leader <strong>EMBL</strong>-EBI<br />
Daniel Panne Group Leader <strong>EMBL</strong> Grenoble Genome Biology<br />
Helen Parkinson Team Leader <strong>EMBL</strong>-EBI<br />
Kiran Patil Group Leader Structural <strong>and</strong> Computational Biology<br />
18
<strong>EMBL</strong> Leadership – Faculty <strong>and</strong> Joint Appointments – cont.<br />
Faculty Title Primary appointment Joint appointment<br />
Rainer Pepperkok Team Leader Cell Biology <strong>and</strong> Biophysics<br />
Francesca Peri Group Leader Developmental Biology<br />
Ramesh Pillai Group Leader <strong>EMBL</strong> Grenoble Genome Biology, <strong>EMBL</strong> Monterotondo<br />
Dietrich Rebholz-<br />
Schuhmann<br />
Group Leader<br />
<strong>EMBL</strong>-EBI<br />
Peter Rice Group Leader <strong>EMBL</strong>-EBI<br />
Nadia Rosenthal Head of Outstation <strong>EMBL</strong> Monterotondo<br />
Carsten Sachse Group Leader Structural <strong>and</strong> Computational Biology<br />
Julio Saez-Rodriguez Group Leader <strong>EMBL</strong>-EBI<br />
Ugis Sarkans Technical Team Leader <strong>EMBL</strong>-EBI<br />
Christiane Schaffitzel Team Leader <strong>EMBL</strong> Grenoble<br />
Reinhard Schneider Team Leader Structural <strong>and</strong> Computational Biology<br />
Thomas Schneider Group Leader <strong>EMBL</strong> Hamburg<br />
Carsten Schultz Interdisciplinary Group Leader Cell Biology <strong>and</strong> Biophysics<br />
François Spitz Group Leader Developmental Biology <strong>EMBL</strong> Monterotondo<br />
Christoph Steinbeck Team Leader <strong>EMBL</strong>-EBI<br />
Lars Steinmetz Joint Head of Unit Genome Biology<br />
Dmitri Svergun Group Leader <strong>EMBL</strong> Hamburg<br />
Janet Thornton Director EBI <strong>EMBL</strong>-EBI<br />
Matthias Wilmanns Head of Outstation <strong>EMBL</strong> Hamburg<br />
Weimin Zhu<br />
Head of the Database Research <strong>and</strong><br />
Development Group<br />
<strong>EMBL</strong>-EBI<br />
19
Intellectual Property<br />
In <strong>2011</strong>, 39 invention disclosures were submitted as follows: Cell Biology <strong>and</strong> Biophysics (3), Developmental Biology (2), Genome Biology (4), Structural<br />
<strong>and</strong> Computational Biology (11), Core Facilities (1), Additional Research Activities (1), EBI (2), Interdisciplinary (15).<br />
9 patent applications were applied for in <strong>2011</strong> with the following breakdown according to Research Programmes: Structural <strong>and</strong> Computational Biology (1),<br />
Genome Biology (2), Core Facilities (1), Cell Biology <strong>and</strong> Biophysics (2), Developmental Biology (1), Interdisciplinary (2).<br />
Additionally, 11 software inventions were protected by copyrights during <strong>2011</strong>.<br />
9 patents were granted during the period.<br />
List of all granted patents in <strong>2011</strong>:<br />
Patent number Title Granting date Inventors<br />
CA 2,354,515<br />
Verfahren und Vorrichtung zum Aufbringen von Substanzen auf einen<br />
Träger, insbesondere von Monomeren für die kombinatorische Synthese von<br />
Molekülbibliotheken (Peptidlaserdrucker)<br />
08.03.<strong>2011</strong><br />
Rainer Saffrich, Frank Breitling, Annemarie Poustka,<br />
Karlheinz Gross, Stefan Dübel<br />
CA 2,509,330 Microscope with a viewing direction perpendicular to the illumination direction 21.03.<strong>2011</strong><br />
Ernst Stelzer, Jan Huisken, Steffen Lindeck,<br />
Sebastian Enders, James Swoger<br />
DE 10 2006 042 088 Vorrichtung und Verfahren zum Ausbilden eines Immersionsfilmes 22.03.<strong>2011</strong> Siegfried Winkler, Urban Liebel<br />
EP 1 747 465<br />
Use of novel biomarkers for detection of testicular carcinoma in situ <strong>and</strong> derived<br />
in human samples<br />
23.03.<strong>2011</strong><br />
Wilhelm Ansorge, Ute Wirkner, Christian Schwager,<br />
Jonathon Blake, Kristian Almstrup, Niels Skakkebaek,<br />
Christina Hoi-Hansen, Henrik Leffers, Ewa Rajpert-De Meyts<br />
EP 1 576 404 Microscope with a viewing direction perpendicular to the illumination direction 14.07.<strong>2011</strong><br />
Ernst Stelzer, Jan Huisken, Steffen Lindeck,<br />
Sebastian Enders, James Swoger<br />
AU 2005279000 Method for determining protein solubility 04.08.<strong>2011</strong> Darren Hart<br />
US 7,994,281 Improved cytokine design 09.08.<strong>2011</strong><br />
Luis Serrano, Vincente Tur, Gregorio Fern<strong>and</strong>ez-Ballester,<br />
Almer van der Sloot, Margaret Mullaly, Robbert Cool, Wim Quax,<br />
Eva Szegezdi, Afshin Samali<br />
CN 200910005085.1<br />
Methods <strong>and</strong> compositions for directed cloning <strong>and</strong> subcloning using<br />
homologous recombination<br />
31.08.<strong>2011</strong> Francis Stewart, Youming Zhang, Joep Pieter Muyers<br />
CZ 302719 RNA interference mediating small RNA molecules 16.09.<strong>2011</strong><br />
Thomas Tuschl, Sayda Elbashir, Winfried Lendeckel,<br />
Matthias Wilm, Reinhard Lührmann<br />
20
<strong>EMBL</strong> International PhD Programme<br />
PhD theses <strong>2011</strong><br />
In <strong>2011</strong>, the student body comprised 199 students<br />
from 38 countries.<br />
In <strong>2011</strong>, the following 43 students defended their theses:<br />
Junaid Akhtar<br />
Towards underst<strong>and</strong>ing transcriptional regulation in the context<br />
of Drosophila embryogenesis<br />
Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Tugce Aktas MusD transposable elements <strong>and</strong> their impact on endogenous gene regulation Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Samuel Bader Proteomic Analysis of Systematic Perturbations in a Minimal Organism University of Zurich<br />
Thorsten Brach Early endocytic pathway in Saccharomyces cerevisiae Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Ludovic Brun Search <strong>and</strong> Capture Model in different segregation processes Université Paris 7 – Denis Diderot<br />
Florence Cavalli A computational study of transcriptional regulation in eukaryotes on a genomic scale University of Cambridge<br />
Thomas Conrad Chromatin regulation by the histone acetyltransferase MOF in Drosophila Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Sara Cuylen Condensin’s mode of structuring mitotic chromosomes Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Manuela Delvecchio Mechanism of regulation of the p300/CBP acetyltransferase University of Grenoble <strong>and</strong> <strong>EMBL</strong><br />
Heidi Dvinge Time-resolved analysis of transcription factor induction <strong>and</strong> cell differentiation University of Cambridge<br />
Stephanie Eckhardt The MILI/mHEN1 complex <strong>and</strong> functional studies of DrTDRD1 <strong>and</strong> DrMOV10L University of Grenoble <strong>and</strong> <strong>EMBL</strong><br />
Marco Faini Structural studies of COPI-coated vesicle assembly by 3D electron microscopy Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Andreia Denise Lopes Ribeiro<br />
Feijao<br />
The role of phosphorylation in the Schizosaccharomyces pombe EB1 homolog mal3p Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Julia Fischer<br />
Characterisation, Classification <strong>and</strong> Conformational Variability of Organic Enzyme<br />
Cofactors<br />
University of Cambridge<br />
Markus Fritz Exploiting high throughput DNA sequencing data for genomic analysis University of Cambridge<br />
Mirjam Geibel Defining the role of TrkB signalling in CCK-expressing neurons Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
21
<strong>EMBL</strong> International PhD Programme – PhD theses <strong>2011</strong> – cont.<br />
Xavier Heiligenstein<br />
Electron microscopy <strong>and</strong> new technological approaches to investigate structural<br />
elements of the mitotic apparatus in Saccharomyces cerevisiae <strong>and</strong> Xenopus laevis<br />
Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Jaqueline Hess Evolution of Transcription Factor Repertoires in the Saccharomycotina University of Cambridge<br />
Christian Hörner<br />
The role of collective cell dynamics <strong>and</strong> primary cilia in tissue differentiation <strong>and</strong> tissue<br />
homeostasis<br />
ETH Zurich<br />
Ibrahim Ilik A biochemical study of roX2 interacting proteins Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Moritz Mall Lipin triggers rate-limiting steps during mitotic Lamin phosphorylation <strong>and</strong> disassembly ETH Zurich<br />
Michele Mattioni<br />
Integration of computer simulations of biochemical <strong>and</strong> electrical signalling in the medium<br />
spiny neuron of the striatum<br />
University of Cambridge<br />
Hubert Mayerhofer Structural studies of the Arabidopsis thaliana ethylene signal transduction pathway Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Katarzyna Mleczko-Sanecka<br />
Identification of hepcidin regulators using an unbiased, high-throughput siRNA screening<br />
approach<br />
Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Francesca Moretti Translational regulation by microRNAs: positional effects <strong>and</strong> their mechanistic basis Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Andrea Murachelli Structural Studies on ASAP, a Conserved, EJC-associated Complex Ludwig-Maximilians-University Munich<br />
Rosa Chiara Paolicelli<br />
Synaptic pruning by microglia is essential in normal brain development // A new juvenile<br />
chronic social stress paradigm as a model for early maltreatment in mice<br />
University of Milano <strong>and</strong> <strong>EMBL</strong><br />
France Audrey Peltier<br />
Chromosome segregation during meiosis I in a new model organism<br />
Saccharomycodes ludwigii<br />
Université Paris 7 Denis Diderot <strong>and</strong> <strong>EMBL</strong><br />
Mateusz Putyrski Chemically-inducible subunits of heterotrimeric G-proteins Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Sarada Raghavan<br />
Engineering new strategies to improve fluorescent proteins <strong>and</strong> building a<br />
fluorescence based live-cell sensor towards elucidating the role of Fus3 activity<br />
Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
in the yeast mating pathway<br />
Kasper Dindler Rasmussen<br />
The miR-144/451 locus: Functional analysis of a microRNA cluster in murine<br />
hematopoiesis<br />
University of Copenhagen<br />
Dace Ruklisa Large scale genomic association studies in fruit fly <strong>and</strong> human University of Cambridge<br />
Beat Rupp<br />
Studies of microtubule organization <strong>and</strong> dynamics in natural <strong>and</strong><br />
engineered configurations<br />
Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Margot Scheffer The nucleosome organization in native chromatin by 3D Cryo-Electron Tomography Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
22
<strong>EMBL</strong> International PhD Programme – PhD theses <strong>2011</strong> – cont.<br />
Johanna Scheuermann<br />
Identification of PR-DUB - a Polycomb Group Complex with Histone H2A<br />
Deubiquitinase Activity<br />
Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Alex<strong>and</strong>er Shkumatov Methods for Hybrid Modeling of Solution Scattering Data <strong>and</strong> their Applications University of Würzburg<br />
Sebastian Streichan On biophysical aspects of growth <strong>and</strong> dynamics of epithelial tissues University of Saarl<strong>and</strong><br />
Nicholas Taylor Structural <strong>and</strong> biochemical studies of the RNA polymerase III transcription factor IIIC Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Kalliopi Trachana<br />
Evolution of spatiotemporal organization of biological systems: Origins <strong>and</strong> phenotypic<br />
impact of duplicated genes<br />
Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Martina Trokter Reconstitution <strong>and</strong> characterization of the human cytoplasmic dynein complex Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Annelie Wünsche<br />
High-content fluorescence microscopy applied for functional analysis of TOR1AIP1 <strong>and</strong><br />
its automation for comprehensive gene studies<br />
Ruprecht-Karls-University of Heidelberg <strong>and</strong> <strong>EMBL</strong><br />
Jordi Xiol Functional studies on piRNA pathway components MOV10L1 <strong>and</strong> FKBP6 University of Grenoble <strong>and</strong> <strong>EMBL</strong><br />
Judith Zaugg<br />
Computational study of promoter structure <strong>and</strong> transcriptional regulation in yeast on a<br />
genomic scale<br />
University of Cambridge<br />
23
Alumni<br />
<strong>2011</strong><br />
1<br />
Worldwide distribution of <strong>EMBL</strong> Alumni.<br />
2<br />
24
Publications<br />
<strong>EMBL</strong> publications<br />
The scientific output of <strong>EMBL</strong> is best characterised by its publications.<br />
Click on the icon for a list of<br />
peer-reviewed publications in <strong>2011</strong>.<br />
Total number of peer-viewed publications: 384<br />
Internal collaborations<br />
Publications co-authored by more than one <strong>EMBL</strong> group leader.<br />
Click on the icon for a list of<br />
co-authored publications in <strong>2011</strong>.<br />
Total number of co-authored publications: 36<br />
External collaborations<br />
Publications authored by an <strong>EMBL</strong> group leader together with at least<br />
one external collaborator.<br />
Click on the icon for a list of<br />
publications in <strong>2011</strong>.<br />
914 external collaborations of which<br />
77 resulted in publications<br />
25
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