Annual Report 2010

Imprint

Institute of Science and Technology Austria Am Campus 1, 3400 Klosterneuburg Tel.: +43 (0)2243–9000 [email protected] www.ist.ac.at

Editor: Lisa Cichocki

Texts: IST Austria

Graphic design: Starmühler Agentur & Verlag Schellinggasse 1, 1010 Wien www.starmuehler.at Christine Starmühler Barbara Kaiser Katharina Krizsanits

Photography: Lisa Cichocki Roland Ferrigato Göran Gnaudschun (Portrait Peter Fratzl) Christian Jungwirth (Portrait Beatrix Karl) Oliver Lehmann Rita Newman Lukas Schaller Jürgen Skarwan

Print: Gerin

Paper: Munken Polar 300g, 150g

Copyright: Institute of Science and Technology Austria, 2010 Contents forewords Foreword by the President 03 Foreword by the Chair of the Scientific Board 04 Tennis Courts the institute Soccer Field Fire Station

IST Austria at a Glance 06 Kindergarten The IST Graduate School 08 Donating the Future 10 Museum Gallery Bertalanffy The Bertalanffy Foundation Building 12 Raiffeisen Foundation Building Lecture Hall Central Building research Church Current Research at IST Austria 14 Nick Barton Group 16

Jonathan P. Bollback Group 18 Laboratory Building 2 in construction Tobias Bollenbach Group 20 Residential Units Krishnendu Chatterjee Group 22 Sylvia Cremer Group 24

Herbert Edelsbrunner Group 26 Memorial Călin Guet Group 28 Heating Plant Carl-Philipp Heisenberg Group 30 Thomas A. Henzinger Group 32 Peter Jonas Group 34 Facility Management Main Entrance voestalpine Christoph Lampert Group 36 Building Michael Sixt Group 38 IST Austria Professors 2011 40 Faculty Recruiting 41 Publications & Grants 2010 42 organization Boards & Administration 44 Scientific Service Units 46 events IST Lectures 48 Communicating Science 50 Location & Directions 52

Klosterneuburg S40 | Bus 239 Kierling BYPASS Maria Gugging Tulln Bus 239 B14

Weidling

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IST Austria scientists (January 1, 2011)

Professors (by last appointment before IST Austria) Postdocs (by institution of PhD degree) PhD students (by nationality) 1 Nick Barton University of Edinburgh, UK 17 Itaru Arai University of Freiburg, Germany 47 Hande Acar Turkey 2 Jonathan Bollback University of Edinburgh, UK 18 Paul Bendich Duke University, Durham, USA 48 Simon Aeschbacher Switzerland 3 Tobias Bollenbach Harvard Medical School, Boston, USA 19 Pavol Cerný University of Pennsylvania, Philadelphia, USA 49 Vanessa Barone Italy 4 Krishnendu Chatterjee University of California, Santa Cruz, USA 20 Chao Chen Rensselaer Polytechnic Institute, Troy, USA 50 Martin Behrndt Germany 5 Sylvia Cremer University of Regensburg, Germany 21 Julien Compagnon Paris Diderot, France 51 Pedro Campinho Portugal 6 Jozsef Csicsvari University of Oxford, UK 22 Rodrigo Fernandes Redondo Universidade Federal de Minas Gerais, Belo Horizonte, Brazil 52 Ines Cristo Portugal 7 Herbert Edelsbrunner Duke University, Durham, USA 22 Jian Gan University of Glasgow, UK 53 Alexander Eichner Germany 8 Călin Guet Harvard University, Cambridge, USA 23 Jose Guzman University of Leipzig, Germany 54 Tom Ellis UK 9 Carl-Philipp Heisenberg Max-Planck Institute, Dresden, Germany 25 Michael Kerber Max-Planck Institute, Saarbrücken, Germany 55 Brittany Fasy USA 10 Thomas Henzinger EPFL, Lausanne, Switzerland 26 Simon Frederick Gabriel Krens University of Leiden, Netherlands 56 Sarit Goswami India 11 Harald Janovjak LMU Munich, Germany 27 Janina Kowalski University of Freiburg, Germany 57 Sooyun Kim USA 12 Peter Jonas University of Freiburg, Germany 28 Anne Kupczok University of Vienna, Austria 58 Matthias Konrad Germany 13 Christoph Lampert Max-Planck Institute, Tübingen, Germany 29 Dejan Ničković Verimag Laboratory, Grenoble, France 59 Rajiv Mishra India 14 Michael Sixt Max-Planck Institute, Martinsried, Germany 30 Ferran Palero University of Barcelona, Spain 60 Jean-Léon Maître France 15 Gašper Tkačik University of Pennsylvania, Philadelphia, USA 31 Alejandro Pernia-Andrade Venezuelan Institute for Scientific Research, Caracas, Venezuela 61 Arjun Radhakrishna India 16 Chris Wojtan Georgia Institute of Technology, Atlanta, USA 32 Jitka Polechová University of Prague, Czech Republic 62 Johannes Reiter Austria 33 Keisuke Sako Osaka University, Japan 63 Viktoriia Sharmanska Ukraine 34 Philipp Schmalhorst Hannover Medical School, Germany 64 Magdalena Steinrück Austria 35 Ali Szegin University of Utah, Salt Lake City, USA 65 Miriam Stock Germany 36 Vasu Singh EPFL, Lausanne, Switzerland 66 Ruby Tandon India 37 Michael Smutny University of Vienna, Austria 67 Anmol Tomar India 38 Yvonne Stickler Technical University of Vienna, Austria 68 Simon Tragust Italy 39 Mathieu Tracol University of Paris 11, France 69 Murat Tugrul Turkey 40 Line V. Ugelvig University of Copenhagen, Denmark 70 Damien Zufferey Switzerland 41 Harold Paul Vladar University of Groningen, Netherlands 42 Meghan Vyleta Oregon Health and Science University, Portland, USA 43 Nick Vyleta Oregon Health and Science University, Portland, USA 44 Michele Weber University College London, UK 45 Daniel Weissman Stanford University, Palo Alto, USA 46 Thomas Wies University of Freiburg, Germany Foreword

Growing Up Thomas A. Henzinger » President, IST Austria

I began my term as first president of IST Austria on September 1, in science happens where traditionally separate disciplines 2009. The past sixteen months have been a period of rapid meet, they will be well-positioned to help bring about the sci­ growth for the Institute, which recently surpassed 100 employ­ entific break-throughs of the future. ees and 100 scientific publications. As IST Austria aims to become a beacon of scientific excel­ › In October 2010, we opened the Bertalanffy Foundation Build­ lence, there is always the underlying question of how one ob­ ing for experimental research in the life sciences. The name of jectively measures quality in basic research. In recent years,­ the building, which is the first laboratory building of IST Aus­ the awards of the European Research Council (ERC) have tria, honors a donation of ten million Euro that was given to become a key indicator for research excellence in Europe. By the Institute in support of basic research. As science without that measure, we are on the right path. Three professors of IST experiments remains speculation, and a research institute Austria–the evolutionary biologist Nick Barton, the neuroscien­ without a laboratory building remains a think tank, the opening ­ tist Peter Jonas, and myself, a computer scientist–have been of the Bertalanffy Foundation Building marks a critical mile­ awarded ERC Advanced Grants. The ERC Starting Grant of stone on the way of IST Austria towards entering the first Sylvia Cremer brings the total number of ERC funded re­searchers league of international institutions for basic science. at IST Austria to four. Together we receive more than eight million Euro of research funding from the European Union, in addition to › At the end of 2010, twelve research groups were at work on about two million Euro from other funding agencies.­ campus, and four additional professors were scheduled to arrive in the first months of 2011. There are already four I want to use this opportunity to thank Mag. Peter Bertalanffy scientific fields in which IST Austria has obtained international for his singular generosity and show of confidence in IST Aus­ visibility: evolutionary biology; the interface of cell biology and tria. I would like to thank also all other friends of the Institute– biophysics; neuroscience; and computer science. The Insti­ in science, in industry, in government, in the local community, tute is committed to further strengthen these four areas and and in the public–for their support, without which we cannot aims to hire also professors in the physical and mathematical succeed. I especially thank the Federal Minister for Science sciences in the coming years. and Research, Dr. Beatrix Karl, the governor of the province of Lower Austria, Dr. Erwin Pröll, and the president of the › In September 2010, the first students of the IST Graduate Federation of Austrian Industry, Dr. Veit Sorger, for their con­ School arrived on campus. They represent eleven nationali­ stant commitment to IST Austria. Last but not least, I thank the ties and pursue a multidisciplinary PhD program that brings entire administrative team of IST Austria, led by Gerald Murauer, together biology and computer science. Every new student is for its hard work. Any growth spurt brings with it considerable required to work with three different research groups before stress, and it is a great relief for me to be able to rely on such a The Bertalanffy Foundation Building. choosing a supervisor. This way we will train a new generation dedicated and efficient staff. The structure of the facade was of researchers that will be able to approach a scientific ques­ used as design element for the cover of the Annual Report 2010. tion from several different angles. As much of the innovation Thomas A. Henzinger

Annual Report 2010 3 Foreword

The Blueprint Becomes Alive Kurt Mehlhorn » Trustee and Chairman, Scientific Board of IST Austria

Director, Max-Planck Institute for Computer Science, Saarbrücken, Germany

IST Austria has been built following the blueprint written by Haim collaborations purely on the basis of scientific merit, maximizing Harari, Olaf Kübler, and Hubert Markl. Back in 2006 this inter­ the benefits for the scientific community in Austria. IST Austria national committee looked at successful scientific institutions offers a modern tenure-track system for assistant professors. around the world and selected key elements that they believed Recently, the Max-Planck Society has also started to offer such would fit together to create a unique new institution fitting for opportunities to young researchers. Austria. For six years, I served as Vice President of the Max- Planck Society. Therefore I am pleased to see that many of these Last but not least, IST Austria and the Max-Planck Institutes are elements resemble the principles of my own institution. Other evaluated regularly and rigorously through international peers. aspects, of course, differ from the Max-Planck Society as IST Independent evaluations are an indispensable tool to maintain Austria has to meet its own specific requirements. quality in science. To organize and oversee these evaluations was one of my main duties as Vice President of the Max-Planck Similar to the Max-Planck Society, the freedom of research and Society, as it is now in my new function as Chairman of the Sci­ the primacy of the scientist–rather than predefined topics, pro­ entific Board of IST Austria. The first evaluation of IST Austria will grams, or projects–is one of the basic principles at IST Austria. take place in 2011 and the members of the Scientific Board are The commitment to basic research at the world-class level is as looking forward to the report by the international review panel. fundamental to this Institute as it is to all Max-Planck Instit­utes. While a Max-Planck Institute usually deals with one scientific Finally, I would like to use this occasion to say that I am im­ area and its various aspects, IST Austria is set up as a single pressed–impressed that Austria is committed to the important institution with different scientific fields present on one campus. enterprise of establishing a world-class research institute for ba­ I look forward to scientific advances in this environment which sic science. And I am impressed by the achievements that have will cross the borders of traditional disciplines. been accomplished so far by President Tom Henzinger and the employees–scientists as well as non-scientists–of IST Austria. I As Max-Planck Institutes cannot award PhD degrees they always would also like to thank my colleagues on the Board of Trustees work in close collaboration with universities. IST Austria has its and the Scientific Board. The international scientific community own Graduate School with the right to grant PhD degrees. Ex­ has been enriched, and the visibility of basic research in Austria cellent PhD training lays the foundation for a scientific career enhanced, through the establishment of IST Austria. The blue­ and provides the backbone for a dynamic research institution. print has become alive! The bridge connecting the modern Bertalanffy Foundation Building and the Art Yet it does not discourage the Institute from setting up close Nouveau Central Building; connecting collaborations with universities, but allows it to pursue research Kurt Mehlhorn theoreticians with experimental scientists.

4 Annual Report 2010 Annual Report 2010 5 the institute IST Austria at a Glance

Nationalities of Scientists at IST Austria 2 % each: Brazil, Czech Republic, Hungary, Luxemburg, Netherlands, Germany 25 % Portugal, Rumania, Serbia, Slovak Republic, Slovenia, Spain, Ukraine, Venezuela (24 %)

UK 4 %

Italy 4 % Austria 11 %

USA 5 %

Turkey 5 % India 11 %

Switzerland 5 % France 6 %

The Institute of Science and Technology Austria (IST Austria) stitute owns the rights to all scientific discoveries and is com­ is a PhD granting institution located in the city of Kloster­ mitted to promote their use. The long-term financial health Donations neuburg, 18 km from the center of Vienna. The Institute is of the Institute will rely on four diverse sources of funding: dedicated to basic research in the natural and mathematical public funding, peer-reviewed research grants, technology li­ Donor Category sciences. Its international graduate school educates aspiring censing, and donations. For the period until 2016 the federal young scientists in an English-language environment. government of Austria will provide up to 290 million Euro in Invicta Foundation 10'000'000 € Raiffeisen consortia (Agrana Beteiligungs-AG, 1'500'000–4'999'000 € Established jointly by the federal government of Austria and operational funds, of which 195 million Euro are guaranteed. IST Employees 2010 Leipnik-Lundenburg Invest Beteiligungs-AG, the provincial government of Lower Austria, the Institute was The payment of the remaining 95 million Euro is conditioned Head Count Raiffeisen Holding Niederösterreich-Wien GmbH, inaugurated in 2009. By the end of 2009 the Institute had 37 on the Institute raising an equal amount of third-party funds. Scientists 52 Raiffeisen Zentralbank Österreich AG, employees. With the opening of the first laboratory building, By the end of 2010 IST Austria has received 17 million Euro P r o f e s s o r s 12 STRABAG AG, UNIQA Versicherungen AG) the Bertalanffy Foundation Building, in October 2010 the first in donations and almost 10 million Euro in research grants, Postdocs 19 voestalpine AG (voestalpine, Böhler- experimental research groups moved to campus. Together bringing the current third-party total to 27 million Euro. The PhD Students 20 Uddeholm AG) with the arrival of the first doctoral students and the estab­ province of Lower Austria contributes to the Institute the bud­ Staff Scientists 1 MONDI (Mondi Business Paper Services AG, 500'000–1'499'000 € lishment of the first Scientific Service Units, IST Austria grew get for construction and campus maintenance, so far in the Scientific Support 24 Mondi Packaging AG) to 12 professors and 105 employees by the end of 2010. The amount of approximately 140 million Euro. Administration 29 OMV AG planned campus development will allow a growth to 40–50 Total 105 Miba AG 250'000–499'000 € professors and 500–600 employees by 2016. Independent Leadership Oberbank AG The scientists of IST Austria are organized into independent The governance and management structures of IST Austria Berndorf AG 100'000–249'000 € Prinzhorn Holding GmbH research groups, each led by a Professor or tenure-track guarantee its independence and freedom from political and Research Grants Assistant Professor. The Institute recruits its scientists–from commercial influences. The Institute is headed by the Presi­ Schoeller Bleckmann Oilfield Equipment AG W. Hamburger GmbH doctoral students to postdoctoral fellows and professors–in dent, who is appointed by the Board of Trustees and advised ERC European Research Council 8'080'000 € Alcatel-Lucent Austria AG 10'000–99'000 € the whole world, based exclusively on their research excel­ by the Scientific Board. The Institute is evaluated periodically FWF Austrian Science Fund 900'000 € Gebrüder Weiss GmbH lence and promise. Currently the scientists of IST Austria re­ by an international panel of external scientists. The first Presi­ DFG Deutsche Forschungsgemeinschaft 480'000 € Kapsch AG present 22 nationalities. dent of IST Austria is Thomas Henzinger, a leading computer European Commission Framework Program 7 310'000 € Total 17'000'000 € scientist and former professor of the University of California NSF National Science Foundation 120'000 € Sources of Funding at Berkeley and the EPFL in Lausanne, Switzerland. The ad­ Total 9'890'000 € While IST Austria is dedicated to the principle of basic re­ ministration of the Institute is led by the Managing Director, search, driven solely by the curiosity of the scientist, the In­ Gerald Murauer.

6 Annual Report 2010 Annual Report 2010 7 the institute The IST Graduate School Starting a Scientific Career

The international Graduate School of IST Austria offers doctoral studies as a first step into a scientific career in the fields of Bio­ logy, Computer Science, Neuroscience, and interdisciplinary areas. Students with a background in related disciplines, such as physics and mathematics, are also encouraged to apply. The language of research and instruction at IST Austria is English.

A Multidisciplinary PhD Program The length of the doctoral studies, which lead to a PhD degree, depends on previous degrees and individual progress, and will Application on average last four to five years. The Graduate School offers › BS or MS or equivalent degree a single joint program for all scientific fields represented at IST › Academic CV and Statement of Purpose Austria, underlining the interdisciplinary spirit of the Institute. In › Official university transcripts this way we expect to train a new generation of researchers › Contact addresses for three reference letters › GRE and TOEFL scores optional that will be able to approach a scientific question from several different angles.

During the first phase of the doctoral program, which normally lasts one year, a student takes advanced courses and works with three different research groups. The student uses this pe­ riod to identify a thesis supervisor and a thesis topic. At the end tive salary and full Austrian social-security coverage. Depen­ of the first phase, the student prepares a thesis proposal and ding on availability, accommodations on campus can be rented passes a qualifying examination. During the second phase of for a period of one year from arrival. the doctoral program, the student focuses on research towards Admission to the IST Graduate School a doctoral thesis. The progress of the student is monitored The deadline for the first call for students was January 15, 2010. › Annual call through regular reviews by the entire faculty. After a successful Ninety-nine applications were received from 28 different coun­ › Online application open November 15 (www.ist.ac.at) thesis defense, the student receives the PhD degree. tries and 21 applicants were invited to campus for interviews. › Open day for prospective students in November The Graduate School made eleven offers, of which seven were › Application deadline January 15 Annual Calls for PhD Students accepted. These seven–among them two Austrians–joined the › Visit day for chosen candidates in March All interested students must apply by January 15 in order to en­ Institute as PhD students in September 2010. Together with (travel expenses reimbursed) › Deadline for accepting an offer April 15 ter the PhD program of IST Austria in the subsequent Septem­ the PhD students who moved to IST Austria from other insti­ › Program start September 15 ber. The applicants need not identify a potential supervisor, but tutions as members of the research groups of newly recruited are evaluated by all IST faculty. All admitted PhD students are professors, 24 students from eleven countries currently work offered employment contracts with an internationally competi­ at the Institute.

8 Annual Report 2010 Annual Report 2010 9 Outstanding research is a necessary foundation to stay innovative in the future. IST Austria and its researchers have already accomplished a lot in a short period of time. I am convinced that education and research at the highest international level will be important cornerstones for the future. IST Austria contributes substantially to the strengthening of Austria as a prime location for research.

Dr. Beatrix Karl » Federal Minister of Science and Research

The opening of the Bertalanffy Foundation Building was celebrated only 500 days after the official Campus opening in 2009. This ceremony marked a milestone for Lower Austria–and for Austria as a whole–with respect to its international visibility as a location for cutting-edge research.

Dr. Erwin Pröll » Governor of Lower Austria the institute

Inaugurating the Bertalanffy Foundation Building

The opening ceremony of the Bertalanffy Foundation Build­ stitutions in Austria.” The Governor of Lower Austria, Erwin ing in October 2010 marked the beginning of experimental Pröll, underlined the importance of the Institute for the pro- research at IST Austria. It also afforded the Institute the op- vince: ”Lower Austria will continue on its forward-looking path portunity for a gesture of profound gratitude towards Peter in science policy, especially in difficult economic times.” Pröll Bertalanffy, the successful entrepreneur whose Invicta Foun- concluded: ”Where there is research, there is the future.” dation donated 10 million Euro to IST Austria, by naming the new building in recognition of his great contribution to the On the way from the ceremonial inauguration act in the Raiff- Invicta Foundation Institute. eisen Lecture Hall to the Bertalanffy Foundation Building, the dignitaries performed the groundbreaking for the second Representing Minister Karl, Department Head Elisabeth laboratory building on the campus of IST Austria, which is Freismuth of the Federal Ministry of Science and Research to be completed in 2012. Thereafter, they took a tour of the (BMWF) emphasized that ”IST Austria is a key project for the newly inaugurated Bertalanffy Foundation Building. Musical BMWF. If IST Austria is successful, this will increase also the interludes­ by the Big Band of the BRG Klosterneuburg com- Donating the Future attractiveness of the universities and of all other research in- pleted the festive ceremony.

In 2010 the Invicta Foundation of Peter Bertalanffy donated However, donations from companies and individuals can 10 million Euro to IST Austria. This donation is the largest never replace but only complement the public funding of ba- single gift given to a scientific institution in Austria for at least sic research, be it direct funding by the government or peer- I like the idea behind this institute: a century. It is also remarkable for another reason: that of truly reviewed funding through institutions such as the Austrian altruistic generosity. Adhering to the Institute’s basic principle Science Fund (FWF). In addition to 17 million Euro in dona­ The aim to bring some of the to let its scientists pursue their research driven solely by their tions,–which include the gift by the Invicta Foundation,–the best researchers in the world to own curiosity, the donor cannot influence the research topics scientists of IST Austria have, so far, obtained approximately or strategy of IST Austria, nor profit from the Institute‘s scientific 10 million Euro in research grants, from the FWF and, mostly, Austria, the complete independence from results. In recognition of the donor‘s contribution the Institute from the European Research Council (ERC). all political and economic interests, may–in accordance with international customs–name a buil- ding, a room, a professorial chair, or a student fellowship after Third-party funds are to IST Austria not only welcome finan­ and the professional exploitation of the donor. The gift by the Invicta Foundation was honored in cial support and visible signs of recognition, but they form an scientific discoveries; I think this way through the naming of the Institute‘s first laboratory integral part of the Institute‘s funding philosophy. One third building, as “Bertalanffy Foundation Building”. of the promised federal funding until 2016–and therefore one all of these are essential half of the expected growth to 400–500 scientists by 2016 cornerstones for a world-class While philanthropy is one of the prime sources of funding for uni- –depend on the acquisition of 95 million Euro in third-party versities and research institutions elsewhere, the private support funds, through research grants and donations. IST Austria institute of basic research.

of basic research does not have a strong tradition in Austria. The has taken some big first steps toward that ambitious goal– Mag. Peter Bertalanffy » IST Austria Donor; Grantor of the Invicta Foundation gift by the Invicta Foundation shows that the opportunities for but it must hope that the visionary example set by previous supporting world-class science, in addition to public funding and donors will convince others to contribute to the growth and apart from commercial interests, are increasingly recognized prospering of the Institute. also in Austria. With the incessant help of the Austrian Federation of Industry (IV), IST Austria tries to establish a culture of investing in the future by giving to science, in Austria and in Europe. the institute The Bertalanffy Foundation Building

The Bertalanffy Foundation Building can be seen as a symbol spaces for microscopy and an IT security cell for servers and for the interdisciplinary culture at IST Austria. The modern la­ a computer cluster. The building is linked to an underground boratory building–the first one on campus–is connected with col­lector that serves all campus buildings for maintenance, the renovated Central Building from the nineteenth century by supply, and disposal purposes. a bridge. Just as the bridge connects the offices in the Art Nouveau Central Building to the state-of-the-art laboratories in The interior spaces of the building are designed for maximum the Bertalanffy Foundation Building, it brings together theoreti­ flexibility and can be configured according to the needs of the cal and experimental research groups. scientists. The individual laboratories differ in size as also the research groups vary in size, type of research, and demand for The challenge for the architects (ARGE Maurer–Neumann & interaction. While some of the groups prefer smaller rooms for Partners) was to design a functional and attractive building specialized work and equipment, other groups benefit from a that harmonizes with the Central Building and the Raiffeisen more communicative, open laboratory layout. Lecture Hall. The project supervision was managed by NÖ Real-Consult GmbH (formerly NÖ Hypo Bauplan). It took only The bridge from the second floor to the Central Building is de­ two and a half years of planning and construction to complete signed as a lounge: a large, yet comfortable space for informal the Bertalanffy Foundation Building. By comparison, the Max- communication inviting the theoretical scientists from the Cen­ Planck Society usually estimates four years for similar con­ tral Building to meet and exchange ideas with the experimental struction projects. scientists from the laboratory building. A spiral staircase leads to the second deck of the bridge, where the central node of the The Architecture Institute's library is located. The gross floor area of the four levels comprises 4'300 m2. The ground floor houses several common services, including The facade of the Bertalanffy Foundation Building is made a washing room for laboratory equipment, areas for the pre­ of vertical glass fins that follow the curved footprint of surrounding forest and points to the flexibility of the interior lay­ Jonathan Bollback studies seemingly simple organisms like paration of biological media, and space for image processing. the complex. The glass fins–alternating tinted out. The glass curtain enables the entry of glare-free daylight microbes in the context of evolution. Tobias Bollenbach uses The first floor is the home of four research groups working on sunscreens and reflective panels–cause the while at the same time offering optimal sun protection during methods of physics to understand the information processing topics in evolutionary biology and biophysics. Three groups in building to blend into its green environ­ all seasons, without hindering natural ventilation. In winter, the within cells. Sylvia Cremer investigates the astounding so­cial cell and systems biology have moved into the second floor. The ment. The random scattering of the space between the glass shell and the wall serves as a climatic abilities of ants. Călin Guet explores questions of systems third floor is dedicated to neuroscience. The building services vertical elements repeats the buffer, modulating the temperature range and thus reducing biology by designing networks under synthetic conditions. are on the roof level and in the basement, which contains also irregular appearance of the heating costs. Carl-Philipp Heisenberg studies quantitative aspects of the development of cells into an organism. Michael Sixt investi­ On the north and east sides, the building is surrounded by gates problems of cell biology and immunology, such as how a ring road for deliveries. To the south, the Bertalanffy Foun­ cells change their form. Neuroscientist Peter Jonas researches dation Building faces the site of the next laboratory building: how signals pass through synapses. a 5'800 m2 complex that will accommodate up to twelve re­ Construction period 18 months search groups by 2012. Starting in 2011, Jozsef Csicsvari will combine aspects of neuroscience with computing techniques in order to analyze 2 Gross floor space 4’300 m The Scientists the activities of certain types of neurons. And Harald Janovjak Floors (including basement) 5 Shortly after the opening in October 2010, seven research will develop optical methods to control the behavior of cells. groups started to work in the building, and two more groups The building has room for one or two additional groups, mean­ Scientists (approx.) 100 will follow in the first months of 2011. Their work focuses on ing that in total ten or eleven research groups will have their different aspects of biology and neuroscience. home in the Bertalanffy Foundation Building.

12 Annual Report 2010 Annual Report 2010 13 Research Current Research at IST Austria

Gašper Tkačik Jozsef Csicsvari Peter Jonas

Călin Guet Carl-Philipp Heisenberg Michael Sixt Bertalanffy Raiffeisen Lecture Hall Foundation Building

Guest House Neuroscience Neuroscience

Restaurant & Cafeteria computer science Cell Biology

Mondi Seminar Center Evolutionary Biology Evolutionary Biology Biophysics

Krishnendu Chatterjee Herbert Edelsbrunner Tom Henzinger To foster inter- and multidisciplinarity, research at IST Austria is not organized into departments. The theoretical research Christoph Lampert Tobias Bollenbach groups–currently representing Evolutionary Biology, Computer Science, and Neuroscience–are located in the Central Building; Chris Wojtan Harald Janovjak the experimental groups–currently Evolution, Biophysics, Cell Biology, and Neuroscience–reside in the Bertalanffy Foundation Building. Both buildings are connected through a bridge containing common areas that encourage interaction. Nick Barton Jonathan Bollback Sylvia Cremer Research GroupsResearch

Nick Barton Mathematical models of evolution How do new species emerge from a single population? Why do so many organisms reproduce sexually, despite the obvious costs? How quickly can species adapt to changing conditions? The Barton Group uses mathematical models of genetic change to better understand such fundamental Studies of hybridisation between red- and yellow- flowered Antirrhinum in questions about evolution. the Pyrenees tell us about the process of speciation.

We study diverse topics in evolutionary accelerating adaptation. The challenge genetics, but focus on the evolution of is to find how recombination is favored, populations that are distributed through given that selection acts on a very large space, and that experience natural selec­ number of genes. We are analyzing a va­ tion on many genes. Understanding how riety of stochastic models of selection on species adapt, and how they split into new multiple recombining loci. species, requires understanding of spatial subdivision, whilst interactions between Limits to Selection genes are important in species forma­ How can the development of extraordi­ tion, and in the response to selection. narily complex morphologies and behav­ The recent flood of genomic data makes iors be guided by a functional genome of analysis of the interactions amongst large ~10 8 bases–much less information than is numbers of genes essential. held in a personal computer? This issue is relevant not only to natural selection, Current Projects but also to evolutionary computation, in Spatially Continuous Populations which selection is used to evolve better Career Selected Publications Classical models assume that individuals algorithms. We are studying the relation CV 2008 Professor, IST Austria P 1. Barton NH. 2009. Why sex and recombination? reproduce and disperse independently, between information, entropy, and fit­ 1990– Reader/Professor, University of Edinburgh, UK Cold Spring Harbor Symposia Quant. Biol. 74. and so miss many features of real popula­ ness. 1982–1990 Lecturer/Reader, University College London, UK 2. Barton NH, de Vladar HP. 2009. Statistical tions. Correlations between genes reveal 1980–1982 Demonstrator, Cambridge University, UK mechanics and the evolution of polygenic traits. their shared history, patterns may extend Statistical Mechanics and the Evolu­ 1979 PhD, University of East Anglia, Norwich, UK Genetics 181: 997-1011. over very large spatial scales, and diver­ tion of Quantitative Traits 3. Barton NH, Briggs DEG, Eisen JA, Goldstein DB, sity is often lower than expected from the We have formalized an analogy between Selected Distinctions Patel NH. 2007. Evolution. Cold Spring Harbor number of individuals. I am working with statistical mechanics and population ge­ ISI Highly Cited Researcher Laboratory Press. Alison Etheridge (Oxford) on a model of netics; the results are applied to study the 2009 Linnean Society Darwin-Wallace Medal long-range extinction and recolonisation evolution of quantitative traits, allowing for 2009 ERC Advanced Grant that includes these features. arbitrary interaction effects. 2006 Royal Society Darwin Medal 2001 President, Society for the Study of Evolution Team Evolution of Sex and Recombination We also study several other topics in evo­ 1998 American Society of Naturalists President's Award T Simon Aeschbacher, PhD student Why do almost all eukaryotes reproduce lutionary genetics, including the genetics 1995 Fellow, Royal Society of Edinburgh Ferran Palero, Postdoc sex­ually? The most plausible explanation of hybrid zones, limits to a species’ range, 1994 Fellow, Royal Society of London Jitka Polechová, Postdoc is that recombination helps to bring to­ models of sympatric speciation, and me­ 1994 David Starr Jordan Prize Harold P. de Vladar, Postdoc gether favorable gene combinations, thus thods for inferring population structure. Daniel Weissman, Postdoc

16 Annual Report 2010 Annual Report 2010 17 Research

Jonathan P. Bollback Micro- bial Experimental Evolution and Statistical Genomics Microbes are everywhere: in our gut, on our skin, and at the source of many diseases. The Bollback Group studies the abilities of seemingly simple organisms in the context of Evolutionary Biology. One of the questions: Why sex may not be needed (at least for microbes)? Career CV 2010 Assistant Professor, IST Austria 2008–2010 Postdoc, Interdisciplinary Centre for Human and Avian Influenza Research, University of Edinburgh, UK 2004–2008 Postdoc, University of Copenhagen, Denmark Microbes–viruses, bacteria, archaea, fore, only one beneficial mutation can fix A cluster of 2004 PhD, University of Rochester, USA Escherichia coli. and protists–account for half of all the at a time, and all other beneficial muta­ biomass and the majority of organismal tions are lost in a process called clonal Selected Distinctions diversity on planet earth. Microbes gave interference. As a result, asexual popu­ 2007–2009 Forskningsrådet for Natur og Univers, rise to higher organisms and have left lations suffer a slower rate of adaptation FNU Grant their genomic calling cards in the form relative to their sexual counterparts: in 2007 Featured in Aktuel Naturvidenskab nr 3 of organ­elles, genes, and so called junk sexual populations recombination can (Current Science) DNA. Microbes are the source of the quickly bring competing mutations to­ 2006 Forskningsrådet for Sundhed og Sygdom, majority of human diseases. For these gether accelerating the rate of adapta­ FSS Grant reasons alone microbes are worthy of tion. It has been shown experimentally 1995–1998 Predoctoral Fellow, Smithsonian scientific study. Yet, they are also im­ that in large asexual populations with Institution, USA portant in another way: they are an high mutation rates, mutation alone can extra­ordinarily powerful model system provide a recombination-like benefit by for understanding in very fine detail how bringing together the two competing mu­ Selected Publications evolution works. Our research focuses tations. Our group is using experimental P 1. Bollback JP, Huelsenbeck JP. 2009. Parallel genetic on microbial evolution, evolutionary in­ evolution to understand the mutational evolution within and among bacteriophage species of varying teractions between hosts and parasites, dynamics and rates of adaptation in degrees of divergence. Genetics 181: 225–234. and the evolution of bacterial immunity. (i) purely asexual populations, (ii) asexual ­ 2. Bollback JP, Huelsenbeck JP. 2007. Clonal interference To accomplish this we use experimen­ populations with recurrent mutation, is alleviated by high mutation rates in large populations. tal evolution, population genetics, and and (iii) sexual populations with recom­ Molecular Biology and Evolution 24(6):1397–1406. statis­tical modeling. bination. 3. Bollback JP. 2002. Bayesian model adequacy and choice code viral information into their immune this unique immune system evolves by in phylogenetics. Molecular Biology and Evolution 19 (7): Current Projects The Evolution of an Adaptive system conferring immunity, and then monitoring the dynamics of wild popula­ 1171-1180. The Rate of Adaptive Evolution in Heritable Immune System in Bacteria pass this immunity onto daughter cells. tions of soil bacteria and their viruses, by Sexual and Asexual Populations Bacteria and archaea have independent­ While we are beginning to understand developing statistical evolutionary mo­ In the absence of recombination, bene­ ly, from multicellular organisms, evolved functional aspects of how this system dels, and by genomic sequence analysis Team ficial mutations appearing on different an adaptive heritable immune system works, we know little if anything about of Staphylococcus pseudintermedius in T Flávia Gama Gomes Leite, Technical assistant genetic backgrounds cannot fix simulta­ called CRISPR. In this system infected the evolutionary dynamics of the system. collaboration with Ross Fitzgerald (Royal Anne Kupczok, Postdoc neously in a population together. There­ bacteria identify the infecting virus, en­ My group is working to understand how Infirmary, Edinburgh). Rodrigo A. F. Redondo, Postdoc Annual Report 2010 19

18 Annual Report 2010 Annual Report 2010 19 Research Tobias Bollenbach Physical and Systems Biology of Cell Signaling Cells respond to signals by altering the expression of their genes. But how are such signals processed inside cells? And how are cellular responses controlled? The Bollenbach Group uses methods of biological physics and systems biology to gain a better understanding of these processes. Career CV 2010 Assistant Professor, IST Austria 2006–2010 Postdoc, Department of Systems Biology, Harvard Medical School, Boston, USA 2005–2006 Postdoc, Max-Planck Institute, Dresden, Germany Cells ranging from those in the tissues of Current Projects defined, and experimentally accessible developmental mechanisms to under­ 2005 Guest scientist, University of Tokyo, Japan multi-cellular organisms to single-celled › Cells are often faced with the simulta­ functional goal. stand the key properties and limitations 2005 PhD, Max-Planck Institute, Dresden, Germany microbes respond to signals in the envi­ neous presence of multiple signals that › We are further interested in cell diffe­ of these mechanisms. We collaborate ronment by modifying the expression of individually elicit opposite gene expres­ rentiation, communication between cells with developmental biology groups at Selected Distinctions their genes. While recent technological sion responses. How do cells resolve by secreted signaling molecules, and IST Austria and elsewhere to quantify the 2007–2009 Feodor Lynen Fellowship, Alexander von advances have enabled us to measure such gene regulatory conflicts? As a first other key processes in the development key parameters of animal development Humboldt-Foundation and manipulate such gene expression step, we use fluorescent transcriptional of animals such as fruit flies, mice, and and thus improve our understanding of 2005 REES Fellowship, Japan International Science responses genome-wide, i.e. across all report­ers, time-lapse microscopy, and fish. Our work employs quantitative data these fascinating phenomena. and Technology Exchange Center genes of an organism, little is known a state-of-the-art robotic system to re­ analysis and theoretical descriptions of 2000–2005 Student and PhD Fellowships, German National about the high-level capabilities and veal how the bacterium Escherichia coli Scholarship Foundation limit­­ations of the cellular machinery that responds to combinations of antibiotics. controls these responses. Our long-term Antibiotics are important drugs for the goal is to gain a deeper, more quantitative treatment of infectious diseases and of­ Selected Publications understanding of the relation between the ten used in combination, making this a P 1. Bollenbach T, Quan S, Chait R, Kishony R. 2009. Nonoptimal signals present in the cell’s environment particularly relevant example. We will ex­ microbial response to antibiotics underlies suppressive drug and the information processing and other tend these studies to cover other model interactions. Cell 139: 707-718. events, which they trigger inside cells. In organisms and a broad range of different 2. Bollenbach T*, Pantazis P*, Kicheva A*, Bökel C, particular, we aim to identify general prin­ signals. González-Gaitán M, Jülicher F. 2008. Precision of the Dpp ciples that capture key properties of gene › Optimality has been suggested to be gradient. Development 135: 1137-1146. regulatory responses. To this end, we a key design principle of biological sys­ 3. Kicheva A*, Pantazis P*, Bollenbach T*, Kalaidzidis Y, Bittig combine quantitative experiments, often tems. But to what extent are cellular re­ T, Jülicher F, González-Gaitán M. 2007. Kinetics of morphogen based on fluorescence measurements sponses optimized for a functional goal? gradient formation. Science 315: 521-525. in single cells or entire populations, with To address this question, we systemati­ *equal contribution theoretical approaches from physics. Our cally measure and synthetically manip­ emphasis is on quantitative approaches, ulate gene expression responses. We i.e. whenever possible we measure and currently focus on single-celled bacteria Green Fluorescent Protein in bacteria (left) and mouse embryos interpret numbers, rather than pictures or and fungi where the maximization of cell (image courtesy N. Plachta). qualitative effects. survival and growth is a plausible, clearly

20 Annual Report 2010 Annual Report 2010 21 Research Krishnendu Chatterjee Computer-aided Verification, Game Theory Life is a game – at least in theory. This has a number of implications for the verification of software but also on the trustworthiness of Wikipedia articles. The Chatterjee Group contributes to the comprehension of the theoretical foundations of central questions in Computer Science.

Our main research interest is in the systems. Last year we obtained several and robust systems, and present a new theoretical foundations of formal veri­ important results: for example, we have theoretical framework for the formal ve­ fication and game theory. Our current established optimal complexity results rification of systems. Last year we have Career Selected Publications research focuses on stochastic game for one-player stochastic games with obtained results that show that there CV 2009 Assistant Professor, IST Austria P 1. Chatterjee K., Henzinger, M. 2011 (To appear) theory, prob­abilistic model checking, partial information, and improved the exists a class of quantitative specifica­ 2008–2009 Postdoc, University of California, Faster and dynamic algorithms for maximal logic and au­tomata theory, and quanti­ algorithms related to probabilistic veri­ tion language that is robust and also Santa Cruz, USA end-component decomposition and related graph tative theories of verification. In addition, fication and we now have the fastest decidable. 2007 PhD, University of California, Berkeley, USA problems in probabilistic verification. ACM we are also inter­ested in algorithms for algorithms for the verification of pro­ Symposium on Discrete Algorithms (SODA). developing robust reputation and trust babilistic systems with omega-regular Reputation and Trust Management Selected Distinctions 2. Chatterjee K. 2007. Concurrent games with tail management systems for Wikipedia. specifications. Systems 2008 Ackerman Award, best thesis worldwide objectives. Theoretical Computer Science In this work we study how to design ro­ in Computer Science Logic 388:181-198. Current Projects Quantitative Verification bust algorithms for automatically com­ 2007 David J. Sakrison Prize, best thesis in 3. Chatterjee K. 2005. Two-player non-zero sum Game Theory in Verification The classical Boolean theory of verifica­ puting the reputation of authors and the EECS, University of California, Berkeley, USA omega-regular games. Concurrency Theory This project involves the algorithmic tion has a wide range of applications. trust of text of an article in Wikipedia. 2001 President of India Gold Medal, best IIT Lecture Notes in Computer Science 3653. anal­ysis of various forms of games How­ever, there are a lot of applications Our algorithms are based on the con­ student of the year Springer, 413-427. played on graphs. Automatically ob­ where a more quantitative approach tent evolution of Wikipedia articles, and taining correct systems from specifi­ is neces­sary. For example in the case are completely automatic. The algo­ Team cations (synthesis) as well as many im­ of embedded systems, along with the rithms we have devel­oped are now im­ T Mathieu Tracol, Postdoc portant questions in computer science Boolean specification, a quantitative plemented and soon our results will be Johannes Reiter, PhD student can be analyzed effectively in the broad specification related to resource con­ available as a tool that can be used in framework of games on graphs. In this straints must be satisfied. In this work Wikipedia. project we work on theoret­ical aspects we have been developing a framework for the better understanding of games, to specify quantitative properties and Software developing new algorithms, as well as to answer the quantitative questions Several new efficient algorithms that we practical applications of game solving. related to the classical Boolean theory have developed have also been imple­ The results present the theoretical foun­ of verification. The results of this pro­ mented by us to obtain research tools dations for the formal verification of ject are useful for the design of correct like ALPAGA and GIST for the study of

22 Annual Report 2010 Annual Report 2010 23 Research Sylvia Cremer Cooperative disease defense in insect societies Ants live together in high densities tightly cramped together. Even if this lifestyle should favour disease spread, ants Career CV 2010 Assistant Professor, IST Austria rarely fall ill. If one ant contracts an infection, others take these helpers do not necessarily run the 2006–2010 Group Leader, University of Regensburg, care of it and a breakout of the disease is prevented. The risk of contracting the disease them­ Germany selves, but can even receive an immune­ 2006 Junior Fellow, Institute of Advanced Studies, Cremer Group uses an Evolutionary Biology perspective protection by “social vaccination”. We Berlin, Germany to investigate this Social Immunity in ants and its general currently try to understand both the mo­ 2002–2006 Postdoc, University of Copenhagen, Denmark lecular mechanisms and the effects for 2002 PhD, University of Regensburg, Germany impact on disease management in societies. the society structure of this social vac­ cination. Selected Distinctions 2010 Habilitation Pathogen Detection Abilities 2009 ERC Starting Grant Ants show the amazing feature of being 2008 Member, German Young Academy of Sciences Like other societies, the colonies of social­ able to detect the presence of pathogens Leopoldina and Berlin Brandenburg insects also face the problem of a high in their colonies even before these could 2004–2006 Marie Curie Intra-European Fellowship and risk of disease transmission among the implement an infection. We study the Reintegration Grant members of their social group. This is due pathogen detection abilities of ants and 2003–2004 Feodor Lynen Fellowship, Alexander von to their close social interactions and high determine how these are affected by re­ Humboldt Foundation densities they live in. Despite this risk, duction in the genetic diversity of colo­ 2000 Diploma thesis award, German Life Sciences epidemics occur extremely rarely in the nies by e.g. inbreeding effects. Association colonies of social insects (e.g. bees, ants, termites), as they have evolved coopera­ Host-Parasite Coevolution tive anti-pathogen defenses that comple­ Parasites and pathogens can quickly Selected Publications ment the individual immune systems of adapt to their hosts, which–on the other P 1. Ugelvig LV, Kronauer DJC, Schrempf A, Heinze J, Cremer S. 2010. group members. This “social immunity” hand–develop better defense strategies. Rapid anti-pathogen response in ant societies relies on high genetic comprises a) hygiene behaviors, such We are interested in the dynamics of diversity. Proceedings of the Royal Society B: Biological Sciences, as mutual allogrooming, b) joint physio­ these­ coevolutionary arms races in social 277: 2821-2828. logical defenses, as the production and hosts such as ants. 2. Ugelvig LV , Cremer S. 2007. Social prophylaxis: group interaction pro- application of antimicrobial substances, motes collective immunity in ant colonies. Current Biology 17: 1967-1971. and c) the modulation of interaction types Epidemiology 3. Cremer S, Armitage SAO, Schmid-Hempel P. 2007. Social Immunity. and frequencies upon exposure of group Disease spread occurs along routes of Current Biology 17: R693-R702. members to pathogens. In my group, we­ high numbers of interactions and can Ant networks. study all aspects of social immune thus be modeled by e.g. traffic networks. Drawing by Eva Sixt defenses ­in ants to learn more about dis­ We use the social interaction networks Team ease management in societies. of ants to both apply and further devel­ T Matthias Konrad, PhD student op epidemiological models of disease Barbara Mitteregger, Technical assistant Current Projects spread. This joint approach combining Miriam Stock, PhD student Social Vaccination experimental work and theoretical mod­ Simon Tragust, PhD student When individual ants get sick, their nest­ eling is used to gain insight into disease Line V. Ugelvig, Postdoc mates take care of them. We found that spread in societies. Meghan Vyleta, Postdoc

24 Annual Report 2010 Annual Report 2010 25 Research Herbert Edelsbrunner Career CV 2009 Professor, IST Austria Algorithms, Computational 2007–2008 Visiting Professor, Berlin Mathematical School, Germany 2007 Visiting Professor, Ecole Normale Supérieure, Geometry and Topology Paris, France 2006 Moore Distinguished Scholar, Caltech, Pasadena, USA Finding the needle in a haystack seems, in comparison, an 2004– Professor for Mathematics, Duke University, easy mission. Uncovering fundamental shapes in a sea of Durham, USA Selected Publications 2002 Visiting Professor, Lawrence Livermore National P 1. Edelsbrunner H, Harer JL. 2010. Computational occurrences is a central task in Computational Geometry Laboratory, USA Topology. An Introduction. American Mathematical and Topology. The Edelsbrunner Group drives the frontiers 1999– Professor for Computer Science, Duke University, Society, Providence, Rhode Island. Durham, USA 2. Edelsbrunner H. 2001. Geometry and Topology in this constantly reshaping field of science. 1996– Founder, Principal, and Director, Raindrop Geomagic for Mesh Generation. Cambridge University Press, 1994–1995 Visiting Professor, Hong Kong University of Science Cambridge, England. and Technology 3. Edelsbrunner H. 1987. Algorithms in Combinatorial 1985–1999 Assistant, Associate, and Full Professor, Geometry. Springer-Verlag, Heidelberg, Germany. University of Illinois, Urbana-Champaign, USA 1981–1985 Assistant, Graz University of Technology, Austria 1982 PhD, Graz University of Technology, Austria Team Selected Distinctions T Paul Bendich, Postdoc ISI Highly Cited Researcher Chao Chen, Postdoc 2010 ERC Advanced Grant Brittany Fasy, PhD student 2009 Member, Academia Europaea Michael Kerber, Postdoc The core of our research is a combination Current Projects 2008 Member, German Academy of Sciences Leopoldina Ying Zheng, PhD student of mathematics and computer science, › Genome-wide analysis of root traits. 2006 Honorary Doctorate, Graz University of Technology always driven by relevant questions in This NSF-funded project, lead by Philip­ 2005 Member, American Academy of Arts and Sciences applications. During a past shift from Benfey,­ aims at relating the phenoty­ 1991 Alan T. Waterman Award, National Science Foundation geometry to topology (which are related pes of agri­cultural root systems with subjects without clear separation), we their gen­otypes. The work in our group noticed an increase in relevant appli­ focuses on capturing and describing cation questions we could address. phenotypes. The challenging steps These include questions in scientific are the recon­struction of the shape of visualiza­tion, structural molecular bio­ a root system from 2D images, the de­ a multi-scale description of the shape of computational topology. Indeed, the logy, systems biology, but also geome­ velopment of geometric and topological the points sample. pervasive concept of a filtration was first try processing, medical imaging, and descriptors that char­acterize the intrin­ › A productive branch of development perceived as a nested sequence of alpha A small selection from the 180 triangulated tubes created as orthodontics. The common theme is sic and extrinsic shape of roots, and the took alpha shapes into the world of shapes. a first application of the Geomagic the importance of shape and the recog­ exploration of changes through growth. molec­ular structures, in particular pro­ › In industry, the Geomagic Wrap soft­ Wrap software in 1996. nition, matching, and classification teins and nucleic acids. The alpha ware was motivated by the Alpha Shape of shape. Topology is the area within Software shapes provide the mathematical and software but needed a major new idea math­ematics whose methods most › We developed the 3D Alpha Shapes computa­tional foundation for the fastest to lead to reliable surface reconstruction, dire­ctly speak to that need. Algorithms software some 20 years ago, and see and most accurate volume, area, and a problem that arises in many areas of and computer software are need­ed to it now as the origin of a number of dif­ derivative computations we have today. man­ufacturing and medical modeling. make mathematical insights useful in ferent developments, in industry as well › Another development leads from alpha That new idea is a discrete geometric applications, which is the motivation to as in academic research. The software shapes to persistent homology, which flow on a simplicial complex, an idea that study in topology and also geometry takes as input a finite set of points with is the most important innovation that combines geometric and topological from a computational point of view. x-, y-, and z-coordinates, and produces has yet emerged from the young field aspects and is eminently computable.

26 Annual Report 2010 Annual Report 2010 27 Research Caˇlin Guet Systems and Synthetic Biology of Genetic Networks Colonies of Escherichia coli Networking is important on any level and in any performing Boolean logic computations with two chemical Career inputs and green fluorescent environment – genes and proteins do it in bacteria. But protein (GFP) as the output state. CV 2010 Assistant Professor, IST Austria which rules, if at all, do they follow? The Guet Group 2009 Postdoc, Harvard University, Cambridge, USA explores these questions of Systems and Synthetic 2005 Postdoc, University of Chicago, USA Biology by analyzing natural and synthetic networks. 2004 PhD, Princeton University, USA Selected Distinctions 2005-2007 Yen Fellow, Institute for Biophysical Dynamics, University of Chicago, USA 1 9 9 7 Sigma XI Membership

Selected Publications P 1. Kinkhabwala A, Guet CC. 2008. Uncovering cis regulatory codes using synthetic promoter shuffling. PLoS ONE 3: e2030. 2. Guet CC, Bruneaux L, Min TL, Siegal-Gaskins D, Figueroa I, Emonet T, Cluzel P. 2008. Minimally invasive determination of mRNA concentration in single living bacteria. Nucleic Acids Research 36: e73. 3. Guet CC, Elowitz MB, Hsing WH, Leibler S. 2002. Combinatorial synthesis of genetic networks. Science 296: 1466-1470. Our scientific curiosity is centered on ed in microbial genetic systems given­ tion from diverse cellular sources is in­ understanding systems of interacting their relative simplicity and powerful tegrated at the promoter level in order genes and proteins that constitute experimental genetic tools available. An to produce a mostly binary response: themselves into genetic networks in emphasis is placed on understanding gene activation or gene repression. bacteria. These bio-molecular networks the molecular biology and physiology Nat­ural promot­ers have been shaped by are involved in a constant process of of the single cell, since often population evolutionary processes and reveal only decision-making and computation that level measurements mask the behavior a subset of all possible information pro­ takes place over various time scales: of the individual cell. cessing capa­bilities. By building synthe­ from seconds to the division time of an To this end we use and develop in vivo tic promoters we aim to understand the gram-neg­ative bacteria. Several genes organism and beyond. techniques that are minimally invasive in constraints imposed by the molecular that are components of the wider mar By studying existing networks or by order to quantitatively characterize the hardware on the information processing regulon integrate a variety of intra- and constructing networks de novo in living temporal dynamics of gene expression. potential of bacterial promoters. extracellular signals. We are interested cells using synthetic biology approach­ in a systems-level description of the mar es, we aim to uncover universal rules Current Projects Systems Biology of the Mar Regulon regulon at the level of the single cell, in that govern biological genetic net­ Information Processing at The multiple antibiotic resistance or order to gain a deeper understanding works. Complex Promoters mar operon, as the name suggests, is of how resistance towards a variety of We use Escherichia coli as our favorite Promoters perform very basic informa­ an important genetic locus responsi­ different chemicals emerges in natural model system and are generally interest­ tion processing: physiological informa­ ble for multiple antibiotic resistance in settings.

28 Annual Report 2010 Annual Report 2010 29 Research

Carl-Philipp Heisenberg A B Morphogenesis in development

Why do fish develop fins? And not arms? Understanding C the transformation of a bunch of cells into a highly Career CV 2010 Professor, IST Austria structured embryo is a core problem of Cell and 2001–2010 Group Leader, Max-Planck Institute, Dresden, Developmental Biology – and a central task of the Germany 1997–2000 Postdoc, University College London, UK Heisenberg Group. 1993–1996 PhD, Max-Planck Institute, Tübingen, Germany

Selected Distinctions 2000 Emmy Noether Junior Professorship 1998 Marie Curie Postdoctoral Fellowship 1997 EMBO Postdoctoral Fellowship A: Surface cells of an ectoderm explant with Actin (red) and plasma membrane (green) B: Confocal section through the germ ring margin of a gastrulating zebrafish embryo. Cells are labelles with membrane-anchored and cytoplasmic GFP C: Gastrulating zebrafish embryo containing transplanted donor cells labelled in red and blue. The non-transplanted cells are labelled in green (GFP). Selected Publications P 1. Diz-Muñoz A, Krieg M, Bergert M, Ibarlucea-Benitez I, Muller D, Paluch E, Heisenberg CP. 2010. Control of directed cell migration in vivo by membrane-to-cortex attachment. PLoS Biology, 8(11), e1000544. 2. Krieg M, Arboleda-Estudillo Y, Puech PH, Käfer J, Graner F, Müller DJ, We are studying the molecular and cel­ biological, biochemical and biophysical those experiments to study more com­ and biophysical/imaging tools to alter Heisenberg CP. 2008. Tensile forces govern germ-layer organization in lular mechanisms by which vertebrate techniques. Utilizing these different ex­ plex adhesive cell interactions taking and analyze cell properties implicated in zebrafish. Nature Cell Biology 10(4): 429-436. embryos take shape. To obtain insights perimental tools, we are deciphering place in primary cell/tissue culture and migration, such as cell adhesion, polari­ 3. Heisenberg CP, Tada M, Rauch GJ, Saúde L, Concha ML, Geisler R, into critical processes in vertebrate key effector mechanisms mediating the the gastrulating embryo. zation, and motility. Stemple DL, Smith JC, Wilson SW. 2000. Silberblick/Wnt11 mediates morphogenesis, such as cell adhesion, processes by which vertebrate embryos convergent extension movements during zebrafish gastrulation. Nature migration, and polarization, we focus take shape. Cell Movements Cell Polarization 405(6782): 76-81. on gastrulation movements in zebra­ The movement of cells is an integral part The generation of embryo polarity (e.g. fish. Gastrulation is a highly conserved Current Projects of embryo morphogenesis. Cells can head-to-tail) depends on the ability of in­ morphogenetic process describing the Cell Adhesion move individually (single cell migration), dividual cells to polarize. Cell polarization transformation of a seemingly unstruc­ The ability of cells to adhere to each or as part of larger groups of cells (cell influences the way cells move, interact and Team tured blastula into a highly organized other is a central feature in the develop­ intercalation, collective cell migration). assemble into tissues. We study the role of T Vanessa Barone, PhD student gastrula-stage embryo composed of the ment of all multi-cellular organisms. We We are studying the role of these diffe­ cell polarization in tissue morphogenesis Martin Behrndt, PhD student three germ layers ectoderm, mesoderm are studying the role of cell adhesion in rent cell movement modes in embryo during gastrulation. Specifically, we ana­ Pedro Campinho, PhD student and endoderm. Zebrafish is an ideal or­ gastrulation by a reductionist approach. morphogenesis during gastrulation. In lyze how cell polarization influences cell Julien Compagnon, Postdoc ganism to study gastrulation movements We first analyze the molecular and cel­ particular, we are analyzing how the in­ adhesion, movement, and proliferation. We Ines Cristo, PhD student as embryos develop ex-utero and are lular processes determining adhesion of terplay between autonomous and non- address the function of cell polarization in Gabby Krens, Postdoc easily accessible for both experimental individual primary cells taken from dif­ autonomous cell properties influences these processes by using genetic and mo­ Jean-Leon Maitre, PhD student and genetic manipulations. To analyze ferent parts of the gastrulating embryo the movement of cell groups and tissues. lecular techniques to alter cell polarity and Keisuke Sako, Postdoc gastrulation movements, we have cho­ with a combination of genetic, molecu­ To address this interplay we have devel­ high resolution microscopy to characterize Philipp Schmalhorst, Postdoc sen a multi-disciplinary approach em­ lar, and biophysical/imaging techniques. oped different cell movement assays and the effects of polarity changes on tissue Michael Smutny, Postdoc ploying a combination of genetic, cell We then use the information gained from use a combination of genetic, molecular, morphogenesis during gastrulation. Ruby Tandon, PhD student

30 Annual Report 2010 Annual Report 2010 31 Research Thomas A. Henzinger Design and Analysis of Concurrent and Embedded Systems Humans and computers can be surprisingly similar: Inter- action between two actors can be simple but gets more complex with every actor added. With more and more things controlled by software in our everyday life, this fact has an enormous impact on computers – and on humans. The Henzinger Group strives to solve this problem with the methods of Computer Science. Career CV 2009 Professor, IST Austria 2005– Adjunct Professor, University of California, Berkeley, USA 2004–2009 Professor, EPFL, Lausanne, Switzerland 1999–2000 Director, Max-Planck Institute, Saarbrücken, Germany 1998–2005 Professor, University of California, Berkeley, USA Selected Publications 1997–1998 Associate Professor, University of California, My group is interested in mathematical challenges of computer science today. Some of these models can be used also P 1. Guerraoui R, Henzinger TA, Singh V. 2010. Berkeley, USA methods for improving the quality of soft­ Concurrent software is extremely error- to mimic certain biological systems, ma­ Model checking transactional memories. 1996–1997 Assistant Professor, University of California, ware. More and more aspects of our lives prone because of the very large number king the field inherently interdisciplinary. Distributed Computing 22:129-145. Berkeley, USA are controlled by software and over 90 % of different interactions that are possible Computational models of, say, a living 2. Henzinger TA. 2008. Two challenges in embedded 1992–1995 Assistant Professor, Cornell University, Ithaca, USA of the computing power is in places you between parallel processes. They cannot cell are different from mathematical systems design: Predictability and robustness. 1991 Postdoc, University of Grenoble, France wouldn’t expect, such as cell phones, be exhausted by testing the system, and equations as they can be executed on a Philosophical Transactions of the Royal Society A 1991 PhD, Stanford University, Palo Alto, USA kitchen appliances, and pacemakers. concurrency bugs sometimes show up computer and used to study the causal 366:3727-3736. Computer software has, at the same time, after many years of flawless operation of relationships between different events in 3. Fisher J, Henzinger TA. 2007. Executable cell Selected Distinctions become one of the most complicated the system. the cell. This new field of research has biology. Nature Biotechnology 25:1239-1249. ISI Highly Cited Researcher artifacts produced by man. It is therefore been dubbed “Executable Biology.” 2010 ERC Advanced Grant unavoidable that software contains bugs, An embedded system is a software sys­ 2009 Corresponding Member, Austrian Academy of Sciences and dealing with these bugs is a major tem that interacts with the physical world, Current Projects 2006 ACM Fellow technical challenge. such as the electronic components in a › Quantitative modeling and analysis of Team 2006 IEEE Fellow car or aircraft. For such embedded sys­ reactive systems T Pavol Cerny, Postdoc 2006 Member, Academia Europaea We focus on concurrent software and on tems, the main technical challenge is to › Interfaces and contracts for compo­ Dejan Nickovic, Postdoc 2005 Member, German Academy of Sciences Leopoldina embedded software. A concurrent system get the software to react in real time. For nent-based hardware and software de­ Arjun Radhakrishna, PhD student 1995 ONR Young Investigator Award consists of many parallel processes that a flight control system it is not only criti­ sign Ali Sezgin, Postdoc 1995 NSF Faculty Early Career Development Award interact with one another, whether in a glo­ cal that the software computes the right › Predictability and robustness for real- Vasu Singh, Postdoc bal network or on a single chip. Hardware results, but also that it does so suffi­ time and embedded systems Anmol Tomar, PhD student manufacturers pack an ever increasing ciently fast. › Modern concurrency paradigms such Thomas Wies, Postdoc number of microprocessors on one chip, as software transactional memory and Damien Zufferey, PhD student generating massive parallelism inside each Our tools for building more reliable soft­ cloud computing computer. These systems are difficult ware are mathematical logic, automa­ › Model checking biochemical reaction to program, creating one of the biggest ta theory, and models of computation. networks

32 Annual Report 2010 Annual Report 2010 33 Research Peter Jonas Synaptic transmission in hippocampal CV Career P Selected Publications 2010 Professor, IST Austria 1. Nörenberg A, Hu H, Vida I, Bartos M, Jonas P. 1995–2010 Professor and Department Head, University of 2010. Distinct non-uniform cable properties microcircuits Freiburg, Germany optimize rapid and efficient activation of fast-spiking 1994–1995 Associate Professor, Technical University of Munich, GABAergic interneurons. Proceedings of the Synapses enable communication between neurons Germany National Academy of Sciences USA 107: 894-899. in the brain. The Jonas Group researches how signals 1990–1994 Research Assistant, Max-Planck Institute, Heidelberg, 2. Bucurenciu I, Bischofberger J, Jonas P. 2010. Germany A small number of open Ca2+ channels trigger pass through these vital interfaces–a major undertaking 1988-1989 Postdoc, University of Giessen, Germany transmitter release at a central GABAergic synapse. in the field of Neuroscience. 1987 PhD, University of Giessen, Germany Nature Neuroscience 13: 19-21. 3. Hu H, Martina M, Jonas P. 2010. Dendritic Selected Distinctions mechanisms underlying rapid synaptic activation 2010 ERC Advanced Grant of fast-spiking hippocampal interneurons. Science 2009 Adolf-Fick-Award, Physicomedical Society, Würzburg, 327: 52-58. Germany 2008 Member, Academy of Sciences, Heidelberg, Germany 2007 Tsungming Tu Award, National Science Council Team Taiwan T Itaru Arai, Postdoc 2006 Szentagothai memorial lecture, University of Jian Gan, Postdoc Understanding the function of neuronal drites, and presynaptic terminals of this California, Irvine, USA Sarit Goswami, PhD student microcircuits is one of the major chal­ key type of GABAergic interneuron, and 2006 Gottfried Wilhelm Leibniz Award, German Research Jose Guzman, Postdoc lenges of life science in the 21st cen­ to directly analyze the resulting functio­ Foundation Sooyun Kim, PhD student tury. The human brain is comprised of nal properties. To achieve this goal, we 2002 Member, German Academy of Sciences Leopoldina Janina Kowalski, Postdoc approximately 10 billions of neurons, will use cutting-edge subcellular patch- 1998–2001 Human Frontiers Science Program Organization Grant Florian Marr, Technical assistant which communicate with each other at clamp recording techniques pioneered 1998 Max-Planck Research Award Rajiv Mishra, PhD student a huge number (~1015) of specialized in my lab. As fast-spiking, GABAergic 1997 Medinfar European Prize in Physiology, Portugal Alejandro Pernía-Andrade, Postdoc sites. These sites of contact and com­ interneurons play a key role in the con­ 1994 Heinz Maier Leibnitz Award, German Ministry for Yvonne Stickler, Postdoc munication between neurons are ter­ trol of the stability of the network and Education and Science Nicholas Vyleta, Postdoc med synapses. Very broadly, synapses­ the generation of rhythmic activity in the 1992 Heisenberg Fellowship, German Research Foundation in the brain fall into two categories: brain, the results will provide insight into 1992 Habilitation excitatory synapses releasing the trans­ the mechanisms underlying dynamic ac­ mitter glutamate and inhibitory synapses tivity of neuronal networks in health and releasing the transmitter -aminobutyric disease. acid (GABA). My research team wants to quantitatively address the mechanisms Functional Analysis of Glutamatergic­ of synaptic signaling at these highly Synaptic Connections between Combined patch-clamp recording and specialized synaptic sites in the brain. Hip­pocampal Pyramidal Neurons learning and memory, the results will be develop computational models of neu­ presynaptic Ca2+ imaging from a fast-spiking GABAergic interneuron. To achieve this, we will use multiple-cell In this project, we will record from en­ important to understand the mechanisms ronal networks based on our experimen­ recording, subcellular patch-clamp tech­ sembles of hippocampal CA3 pyramidal underlying the processing and storage of tal findings. Beyond reproducing experi­ niques, Ca2+ imaging, and modeling. neurons and examine the properties of informa­tion in the hippocampus. mental observations, we anticipate that glutamatergic synaptic connections. modeling will make specific predictions, Current Projects In particular, we want to determine the Development of Realistic Network which can be tested experimentally. The Nanophysiology of Fast-spiking, induction rules of synaptic plasticity, Mo­dels of Hippocampal Microcircuits interdisciplinary research platform of IST GA­BAergic Interneurons including long-term potentiation and Our ultimate goal is to understand how Austria, in particular the presence of sev­ The goal is to completely map the dis­ depression. As the synapses between synaptic properties shape complex net­ eral computer science groups, will greatly tribution of ion channels at soma, den­ CA3 pyramidal neurons play a key role in work functions. To reach this goal, we will facilitate our modeling efforts.

34 Annual Report 2010 Annual Report 2010 35 Research Christoph Lampert but also about their properties. We work Computer Vision and on extending existing image and object representations by attributes. These are characteristic properties of a scene Machine Learning or an object category that can be pre­ dicted from the image information, but Every kid knows how to play "I spy with my little eye", but to also have a semantic interpretation. Our a computer the task of analyzing images and recognizing goal is to show that attribute-­enabled representations can achieve higher­ objects in them is tremendously difficult. The Lampert Group classification accuracy than purely explores these problems with the tools of Computer Vision object-centric ones, that they require Career less training data and that they allow CV 2010 Assistant Professor, IST Austria and Machine Learning. solving new image-related prediction 2007–2010 Senior Research Scientist, Max-Planck tasks, for example for making deci­sions Institute, Tübingen, Germany about the importance of objects in a 2004–2007 Senior Researcher, German Research Center for scene. Artificial Intelligence, Kaiserslautern, Germany 2003 PhD, University of Bonn, Germany Structured Prediction and Learning We s t u d y a n d d e ve l o p s t a t i s t i c a l m a c h i n e­ humans do, enabling them to answer for object localization based on formu­ We are working on extending and Selected Distinctions learning algorithms for computer vision questions like: What objects are visible lating the problem as a regression task im­proving existing techniques for 2008 Main Price, German Society for Pattern applications, in particular for the task of in an images? Where are they located? between structured spaces instead of the prediction of structured objects Recognition (DAGM) natural image understanding. Machine How do they interact? a sequence of classification tasks. This using machine learning techniques, 2008 Best Paper Award, IEEE Conference for learning enables automatic systems to allows the use of global optimization in particular graph labeling prob­ Computer Vision and Pattern Recognition analyze large amounts of high dimen­ Current Projects techniques, such as branch-and-bound, lems. Treating these in a framework (CVPR) sional data with significant between- Efficient Objects and Action instead of the exhaustive search used by of empirical risk minimization allows us 2008 Best Student Paper Award, European feature correlations. This makes it par­ Localization currently dominating sliding window ap­ to develop algorithms that can learn Conference for Computer Vision (ECCV) ticularly suit­able for computer vision The tasks of identifying and locating proaches. prediction functions that are tailored to problems, such as the analysis of digital objects in natural images are crucial the specific prediction tasks and thereby images with re­spect to their contents. In components for any automatic image Attribute-Enabled Representations achieve higher prediction accuracy. In the long run, we are interested in build­ understanding system, and they are in­ Image understanding on a semantic lev­ particular, we work on developing tech­ Selected Publications ing automatic systems that understand herently linked. We work on developing el requires knowledge not only about niques for handling the cases of ambig­ P 1. Lampert CH, Nickisch H, Harmeling S. 2009. Learning images on the same semantic level as fast learning and inference techniques the presence and location of objects, uous input and outputs. to detect unseen object classes by between-class attribute transfer. IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 951–958. Object recognition in natural images: learning-based 2. Lampert CH, Blaschko MB, Hofmann T. 2008. Beyond computer vision techniques can detect objects and describe them semantically. sliding windows: Object localization by efficient subwindow search. IEEE Conference on Computer Vision and Pattern Recognition (CVPR), 1–8. 3. Blaschko MB, Lampert CH.2008. Learning to localize objects with structured output regression. European Conference on Computer Vision (ECCV), 2–15.

Annual Report 2010 37

Team T Novi Quadrianto, Research intern Viktoriia Sharmaska, PhD student Elena Tretyak, Research intern

36 Annual Report 2010 Annual Report 2010 37 Research Michael Sixt Molecular The image shows a snapshot of a video sequence capturing dendritic cells that are about to enter a Mechanics of immune cells lymphatic vessel in the skin. Dendritic cells are labeled in red and position Every answer gives room to new, fascinating questions: in close vicinity of the basement membrane of the lymphatic vessel How does a cell change its form? And what impact does that is labeled in white. it have on the surrounding tissue, which is formed by its likes? The Sixt Group investigates these problems of Cell Biology and Immunology.

The laboratory investigates morphody­ dics. A general aim of the lab is to test in namic processes both at the cellular and vitro findings also in the context of living at the tissue level. We mainly focus on the tissues. To this end we also dev­eloped ex Career selected publications immune system and try to understand the vivo (tissue explant) and in vivo imaging CV 2010 Assistant Professor, IST Austria P 1. Schumann K, Lämmermann T, Bruckner M, molecular and mechanical principles un­ setups that allow us to monitor leuko­ 2008–2010 Endowed Professor, Peter Hans Hofschneider Legler DF, Polleux J, Spatz JP, Schuler G, Förster derlying leukocyte dynamics during pro­ cytes together with their physiological Foundation for Experimental Biomedicine R, Lutz MB, Sorokin L, Sixt M. 2010. Immobilized c­esses such as migration and intercellular environment. Finally we are also interested 2005–2010 Group Leader, Max-Planck Institute, chemokine fields and soluble chemokine gradients communication. We work at the interface in testing the implications of our findings Martinsried, Germany shape migration patterns of dendritic cells. of cell biology, immunology and biophys­ for physiological immune responses. 2003–2005 Postdoc, Institute for Experimental Immunity 32(5):703-713. ics and currently investigate how the cy­ Pathology, Lund, Sweden 2. Renkawitz J, Schumann K, Weber M, Lämmer- toskeleton generates force to deform the Current Projects 2003 MD, University of Erlangen, Germany mann T, Pflicke H, Polleux J, Spatz JP, Sixt M. cell body, how this force is trans­duced › Environmental control of leukocyte mi­ 2002 Full approbation in human medicine 2009. Adaptive force transmission in amoeboid cell to the extracellular environment and gration: We are investigating how dif­ferent migration. Nature Cell Biology 11(12): 1438-1443. how the cells are polarized and guided extracellular constraints like the form of 3. Lämmermann T, Bader BL, Monkley SJ, Worbs within tis­sues. To obtain a holistic view of chemokine presentation, mechanical T, Wedlich-Söldner R, Hirsch K, Keller M, Förster the process we are also studying tissue forces and the geometry and molecular Team R, Critchley DR, Fässler R, Sixt M. 2008. Rapid architecture as well as the distribu­ composition of the extracellular sub­strate, T Alexander Eichner, PhD student leukocyte migration by integrin-independent flowing tion and presentation of guidance affect leukocyte locomotion. Michele Weber, Postoc and squeezing. Nature 453(7191): 51-55. cues (chemokines) within these tis­ › Cellular force generation and transduc­ Ingrid de Vries, Technical assistant sues. We developed a number of in tion: We ask how cytoskeletal activity is vitro tools that allow us to ob­serve cy­ translated into actual locomotion. This toskeletal dynamics in real time using includes transmembrane force coupling different life cell imaging approaches. receptors but also locomotion by other These are all based on advanced light means like physical deformation of the microscopy like total internal reflection, cell body. fast confocal and multiphoton technolo­ › Invasion of tissue barriers: How do gy. We combine these approaches with leukocytes traverse tissue boundaries genetic and pharmacol­ogical interference like endothelial / epithelial layers and ex­ as well as substrate mani­pulations like tracellular matrix barriers like basement surface micropatterning and microflui­ membranes?

38 Annual Report 2010 Annual Report 2010 39 Research

IST Austria Professors Starting in 2011

Applications and nominations 2'286

Evaluated by international experts 304

Invited to campus 117

Offers made 28

information processing in the brain. Harald will join IST Austria Jozsef Csicsvari Offers accepted as Assistant Professor in March 2011. 16 Jozsef Csicsvari graduated with an MS in in­ formatics from the Technical University of Gašper Tkačik Budapest in 1993. He received a PhD in neuroscience under the supervision of Gyor­ Gašper Tkačik is a theoretical physicist study­ gy Buzsaki at Rutgers University, where he finished his thesis in ing information processing in living systems. 1999 and continued as a postdoctoral fellow until 2002. In 2003 He studied mathematical physics at the Uni­ Faculty Recruiting he became a group leader at the MRC Anatomical Neurophar­ versity of Ljubljana and received a PhD in the macology Unit in Oxford. Jozsef’s main research interest lies in group of William Bialek at Princeton University. Since 2008 he has the field of systems neuroscience. He explores neural cell as­ been a postdoc at the University of Pennsylvania. Gašper uses at IST Austria sembly activities in the hippocampus, a brain region that plays tools from the statistical physics of disordered systems and from important roles in long-term memory and spatial navigation. information theory to study biological systems such as networks Coming from a computer background, he pioneered methodo­ of neurons or genes. The unifying hypothesis driving his research The scientific fields of IST Austria are chosen on the basis of the The complete recruiting statistics is shown in the in the figure. logies allowing large-scale cell assembly recordings and their is that information processing networks have evolved or adapted availability of outstanding scientists. The Institute will not enter Until December 31, 2010, IST Austria received 2'286 applica­ computer analysis. Jozsef will join IST Austria as Professor in to maximize the information transmitted from their inputs to their into any field of research unless it can attract professors who tions and nominations. Thereof, 55 % were considered as can­ July 2011. outputs, given the biophysical noise and resource constraints. compete internationally at the forefront of their discipline, and didates for Assistant Professor, 45 % for Professor; 14 % of the Gašper will join IST Austria as Assistant Professor in March 2011. unless it can provide them with an environment that allows the candidates were female; 55 % of the candidates worked in the Harald Janovjak scientists to perform at the highest level. The overall recruiting physical, mathematical, and engineering sciences, 45 % in the Chris Wojtan process requires a coordinated strategy of identifying the best life sciences; 81 % of the candidates applied, 19 % were nomi­ Harald Janovjak works at the interface of available faculty candidates while, at the same time, avoiding nated. The candidates worked in 74 countries: 51 % in Europe, bio­physics and cell biology. He studied Chris Wojtan received a BS in computer sci­ the dangers of scientific isolation, by creating networks of re­ 39 % in North America, and 10 % on other continents. mole­cular biology in Basel, received a PhD ence in 2004 from the University of Illinois in search groups in related fields and around intellectual connec­ from the TU Dresden in 2005, and worked Urbana-Champaign. He then moved to the tions between different disciplines. After an initial screening, the most promising candidates are as a postdoc in the group of Ehud Isacoff at the University of Georgia Institute of Technology for his PhD evaluated in detail by collecting reviews from leading internatio­ California in Berkeley. Harald developed new techniques to studies. Chris’ research is in computer graphics, with a special fo­ IST Austria advertises open positions internationally and invites nal scientists. Fewer than 10 % of the candidates have been in­ study ­the folding and unfolding of single membrane proteins cus on the realistic simulation of physical systems. Using numeri­ both applications and nominations of candidates. The Institute vited to campus to give a scientific lecture and be interviewed using atomic force microscopy. Later he concentrated on the cal techniques, he creates computer animations of physical phe­ also tries to actively identify and approach potential candidates, by the professors of the Institute. Less than 2 % of all candi­ manipulation­ of ion channels using light and established a new nomena like fluids, deformable bodies, or cloth. He combines for example, by tracking Austrian scientists abroad. IST Austria dates have received an offer from IST Austria, and 59 % of the method for the light-induced inhibition of nerve cell activity. mathematical methods from computational physics with geome­ is committed to equality and diversity in hiring. Female scien­ offers have been accepted. Given that the best scientists are Such combinations­ of optical and genetic techniques, called tric techniques from computer graphics. Chris will join IST Austria tists, in particular, are encouraged to apply and the Institute sought after all over the world, similar success rates are seen opto­genetics, are of increasing importance for understanding as Assistant Professor in 2011. actively supports their careers. even at some of the most prestigious institutions.

40 Annual Report 2010 Annual Report 2010 41 Research

Publications and Research Grants 2010

Publications by IST Members accepted in 2010 (joint › Chatterjee, K. & Henzinger, M., 2010. Faster and Dynamic › Bendich, P., Edelsbrunner, H., Morozov, D. & Patel, › Černý, P., Henzinger, T.A. & Radhakrishna, A., 2010. › Ghosal, A., Iercan, D., Kirsch, C.M., Henzinger, T.A. Lampert Group publications involving several groups are listed multiple times) Algorithms For Maximal End-Component Decomposition A., 2010. Robustness of Level Sets. In: Lecture Notes in Quantitative Simulation Games. In: Lecture Notes in & Sangiovanni-Vincentelli, A., 2010. Separate compilation › Lampert, C.H. & Krömer, O., 2010. Weakly-Paired Maximum And Related Graph Problems In Probabilistic Verification. In: Computer Science 6346. ESA: European Symposium Computer Science 6200. Time For Verification: Essays in of hierarchical real-time programs into linear-bounded Covariance Analysis for Multimodal Dimensionality Reduction Barton Group SODA: Symposium on Discrete Algorithm. Association for on Algorithms. Springer, 1-10. Memory of Amir Pnueli. Springer, 42-60. embedded machine code. Science of Computer and Transfer Learning. In: Lecture Notes in Computer › Barton, N.H., 2010. The role of natural selection in speciation. Computing Machinery, in press. › Berberich, E., Halperin, D., Kerber, M. & Pogalnikova, › Černý, P., Henzinger, T.A. & Radhakrishna, A., 2010. Simulati­ Programming, in press. Science 6311. ECCV: European Conference on Computer Philosophical Transactions of the Royal Society of London. › Chatterjee, K. & Henzinger, T.A., 2010. A survey of stochastic R., 2010. Polygonal Reconstruction from Approximate on Distances. In: Lecture Notes in Computer Science 6269. › Guerraoui, R., Henzinger, T.A. & Singh, V., 2010. Model Vision. Springer, 566-579. Series B, Biological Sciences, 365(1547), 1825-1840. omega-regular games. Journal of Computer and System Offsets. In: Eurocg European Workshop on Computational CONCUR: Concurrency Theory. Springer, 42-60. checking transactional memories. In: Distributed Computing. › Lampert, C.H. & Peters, J., 2010. Real-Time Detection › Barton, N.H., 2010. Mutation and the evolution of recombin­ Sciences, in press. Geometry. TU Dortmund, 12-23. › Černý, P., Radhakrishna, A., Zufferey, D., Chaudhuri, Springer, 129-145. of Colored Objects In Multiple Camera Streams With ation. Philosophical Transactions of the Royal Society of › Chatterjee, K. & Henzinger, T.A. (editors), 2010. FORMATS: › Chatterjee, K., Doyen, L., Edelsbrunner, H., Henzinger, S. & Alur, R., 2010. Model Checking of Linearizability of › Guerraoui, R., Henzinger, T.A., Kapalka, M. & Singh, V., 2010. Off-the-Shelf Hardware Components. Journal of Real-Time London. Series B, Biological Sciences, 365(1544), 1281-1294.­ Formal Modeling and Analysis of Timed Systems. Lecture T.A. & Rannou, P., 2010. Mean-Payoff Automaton Concurrent List Implementations. In: Lecture Notes in Transactions in the Jungle. In: SPAA: Parallel Algorithms and Image Processing, Epub ahead, 1-11. › Barton, N.H., 2010. Estimating multilocus linkage Notes in Computer Science 6246. Springer. Expressions. In: Lecture Notes in Computer Science 6269. Computer Science 6174. CAV: Computer-Aided Architectures. Association for Computing Machinery, 263-272. › Nowozin, S., Gehler, P. & Lampert, C.H., 2010. Learning in disequilibria. In: Heredity, 84 (Pt 3), 373-389. › Chatterjee, K. & Henzinger, T.A., 2010. Probabilistic CONCUR: Concurrency Theory. Springer, 269-283. Verification. Springer, 465-479. › Henzinger, T.A., 2010. From boolean to quantitative notions CRF-based Approaches to Object Class Image Segmen­ › Barton, N.H., 2010. Understanding adaptation in large Automata on Infinite Words: Decidability and Undecidability › Chen, C. & Freedman, D., 2010. Topology noise removal for › Chatterjee, K. & Henzinger, T.A., 2010. A survey of stochastic of correctness. In: POPL: Principles of Programming tation. In: Lecture Notes in Computer Science 6316. ECCV: populations. In: PLoS Genetics, 6(6), e1000987-e1000987. Results. In: Lecture Notes in Computer Science 6252. curve and surface evolution. In: MCV: Medical Computer omega-regular games. Journal of Computer and System Languages. Association for Computing Machinery, 157-158. European Conference on Computer Vision. Springer, 98-111. › Barton, N.H., 2010. Genetic linkage and natural selection. ATVA: Automated Technology For Verification and Analysis. Vision. in press. Sciences, in press. › Henzinger, T.A., Hottelier, T. & Kovács, L., 2010. Aligators for Philosophical Transactions of the Royal Society of London. Springer, 1-16. › Edelsbrunner, H., Michael Kerber, & Paul Bendich,, 2010. › Chatterjee, K. & Henzinger, T.A. (editors), 2010. FORMATS: arrays. In: Lecture Notes in Computer Science 6397. LPAR: Administration Series B, Biological Sciences, 365(1552), 2559-2569. › Chatterjee, K. & Majumdar, R., 2010. Discounting in Games Computing Robustness and Persistence for Images. In: VIS: Formal Modeling and Analysis of Timed Systems. Lecture Logic For Programming, Artificial Intelligence, and Reasoning. › Bergmann, J. & Danowski, P., 2010. Ist Bibliothek 2.0 über­ › Palero, F., Abelló, P., Macpherson, E., Matthee, C. & Pascual, across Time Scales. In: Electronic Proceedings in Theoretical IEEE Conference on Visualization, 16(6). IEEE, 1251-1260. Notes in Computer Science 6246. Springer. Springer, 348-356. haupt noch relevant? – Eine Einleitung in das Handbuch. In: M., 2010. Genetic diversity levels in fishery-exploited Computer Science. GandALF: Games, Automata, Logic, and › Edelsbrunner, H., Morozov, D. & Patel, A.K., 2010. The › Chatterjee, K. & Henzinger, T.A., 2010. Probabilistic Automata › Henzinger, T.A., Hottelier, T.B., Kovács, L. & Voronkov, A., Handbuch Bibliothek 2.0, 5-20. Palinurus spiny lobsters (Decapoda: Achelata). Journal of Formal Verification 2010. EPTCS. stability of the apparent contour of an orientable 2-manifold. on Infinite Words: Decidability and Undecidability Results. In: 2010. Invariant and type inference for matrices. In: Lecture › Bergmann, J. & Danowski, P., 2010. Handbuch Bibliothek Crustacean Biology, 30(4), 658-663. › Chatterjee, K., Alfaro, L.D. & Henzinger, T.A., 2010. Qualitati­ In: Mathematics and Visualization. Topological Data Analysis Lecture Notes in Computer Science 6252. ATVA: Automated Notes in Computer Science 5944. VMCAI: Verification, Model 2.0. Bibliothekspraxis. deGruyter. › Palero, F., González-Candelas, F. & Pascual, M., 2010. ve concurrent parity games. ACM Transactions on and Visualization: Theory, Algorithms and Applications. Technology For Verification and Analysis. Springer, 1-16. Checking, and Abstract Interpretation. Springer, 163-179. › Sabeti -Aschraf, M., Gonano, C., Nemecek, E., Cichocki, MICROSATELIGHT – Pipeline to Expedite Microsatellite Computational Logic, in press. Springer, 27-42. › Chatterjee, K., Alfaro, L.D. & Henzinger, T.A., 2010. › Henzinger, T.A., Jobstmann, B. & Wolf, V., 2010. L. & Schueller-Weidekamm, C., 2010. Intra-operative ultra­ Analysis. Journal of Heredity, in press. › Chatterjee, K., de Alfaro, L., Majumdar, R. & Raman, V., › Fasy, B., 2010. The difference in length of curves in R^n.. Qualitative concurrent parity games. ACM Transactions on Formalisms for specifying Markovian population models. sound facilitates the localization of the calcific deposit during › Palero, F., Guerao G., Clark PF, & Abelló, P., 2010. Scyllarus 2010. Algorithms for Game Metrics. Logical Methods in Acta Sci. Math. Szeged, in press. Computational Logic, in press. International Journal of Foundations of Computer Science, arthroscopic treatment of calcifying tendinitis. Medicine Knee arctus (Crustacea: Decapoda: Scyllaridae) final stage Computer Science, 6(3:13), 1-27. › Kerber, M. & Edelsbrunner, H., 2010. Covering and › Chatterjee, K., Doyen, L. & Henzinger, T.A., 2010. Expres­ in press. Surgery Sports Traumatology Arthroscopy, 18(12), phyllosoma identified by DNA analysis, with morphological › Chatterjee, K., de Alfaro, L., Raman, V. & Sanchez, C., 2010. packing with spheres by diagonal distortion in R^n. siveness and closure properties for quantitative languages. › Henzinger, T.A., Mateescu, M., Mikeev, L. & Wolf, V., 2010. 1792-1794-1794. description. Journal of the Marine Biological Association of Analyzing the Impact of Change in Multi-threaded Programs. In: Rainbow of Computer Science. Springer, in print. Logical Methods in Computer Science, 6(3:10), 1-23. Hybrid numerical solution of the chemical master equation. the United Kingdom, in press. In: Lecture Notes in Computer Science 6013. FASE: › Kerber, M. & Sagraloff, M., 2010. A Note on the › Chatterjee, K., Doyen, L. & Henzinger, T.A., 2010. Qualitative In: Lecture Notes in Bioinformatics. CMSB: Computational › Rosas, U., Barton, N.H., Copsey, L., Barbier de Reuille, Fundamental Approaches To Software Engineering. Springer, Complexity of Real Algebraic Hypersurfaces. Graphs Analysis of Partially-Observable Markov Decision Processes. Methods in Systems Biology. Springer, in press. Peer-reviewed Research Grants acquired P. & Coen, E., 2010. Cryptic variation between species and 293-307. and Combinatorics, in press. In: Lecture Notes in Computer Science 6281. MFCS: Mathe- › Henzinger, T.A., Singh, A.V., Singh, V., Wies, T. & Zufferey, D., or active in 2010 the basis of hybrid performance. PLoS Biology, 8(7), › Chatterjee, K., Doyen, L. & Henzinger, T.A., 2010. matical Foundations of Computer Science. Springer, 258-269. 2010. A Marketplace for Cloud Resources. In: EMSOFT: Em- e1000429-e1000429. Expressiveness and closure properties for quantitative Heisenberg Group › Chatterjee, K., Doyen, L. & Henzinger, T.A., 2010. bedded Software. Association for Computing Machinery, 1-8. Barton Group › Senn, H.V., Swanson, G.M., Goodman, S.J., Barton, languages. Logical Methods in Computer Science, 6(3:10), › Heisenberg, C. & Krens, G., 2010. Cell sorting in Quantitative Languages. ACM Transactions on Computa­ › Henzinger, T.A., Singh, A.V., Singh, V., Wies, T. & Zufferey, › Limits to selection in biology and in evolutionary computation, N.H. & Pemberton, J.M., 2010. Phenotypic correlates of 1-23. development. In: Current Topics in Developmental tional Logic, 11(4:23), 1-38. D., 2010. FlexPRICE: Flexible Provisioning of Resources in a ERC, € 1'975'000, 7/2010 – 6/2015. hybridisation between red and sika deer (genus Cervus). › Chatterjee, K., Doyen, L. & Henzinger, T.A., 2010. Qualitative Biology, in press. › Chatterjee, K., Doyen, L., Edelsbrunner, H., Henzinger, Cloud Environment. In: CLOUD: Cloud Computing. IEEE, Journal of Animal Ecology, 79(2), 414-425. Analysis of Partially-Observable Markov Decision Processes. › Diz-Muñoz, A., Krieg, M., Bergert, M., Ibarlucea-Benitez, I., T.A. & Rannou, P., 2010. Mean-Payoff Automaton 83-90. Chatterjee Group › de Vladar, H.P. & Barton, N.H., 2010. The statistical In: Lecture Notes in Computer Science 6281. MFCS: Mathe- Muller, D., Paluch, E. & Heisenberg, C., 2010. Control of di­ Expressions. In: Lecture Notes in Computer Science 6269. › Jones, K.D., Konrad, V. & Nickovic, D., 2010. Analog › RiSE - Rigorous Systems Engineering, FWF, € 450'000, mechanics of a polygenic character under stabilizing matical Foundations of Computer Science. Springer, 258-269. rected cell migration in vivo by membrane-to-cortex attach­ CONCUR: Concurrency Theory. Springer, 269-283. property checkers: a DDR2 case study. Formal Methods in 3/2011 – 2/2015. selection, mutation and drift. Journal of the Royal Society › Chatterjee, K., Doyen, L. & Henzinger, T.A., 2010. Quantitative ment. In: PLoS Biology, 8(11), e1000544. › Chatterjee, K., Doyen, L., Gimbert, H. & Henzinger, T.A., System Design, 36(2), 114-130. Interface, In press. Languages. ACM Transactions on Computational Logic, › Quesada-Hernández, E., Caneparo, L., Schneider, S., Winkler, 2010. Randomness for Free. In: Lecture Notes in Computer › Kuncak, V., Piskac, R., Suter, P. & Wies, T., 2010. Building a Cremer Group › de Vladar, H.P. & Chela-Flores, J., 2010. Can Multicellularity 11(4:23), 1-38. S., Liebling, M., Fraser, S. & Heisenberg, C., 2010. Stereo­ Science 6281. MFCS: Mathematical Foundations of Calculus of Data Structures. In: Lecture Notes in Computer › Social Vaccines - Social Vaccination in Ant Colonies: from be anticipated in the exploration of the solar system?. In: › Chatterjee, K., Doyen, L., Edelsbrunner, H., Henzinger, typical cell division orientation controls neural rod midline for­ Computer Science. Springer, 246-257. Science 5944. VMCAI: Verification, Model Checking, and Individual Mechanisms to Society Effects, ERC, A. Hanslmeier, S. Kempe, & J. Seckbach. Cellular Origin and T.A. & Rannou, P., 2010. Mean-Payoff Automaton mation in zebrafish. In: Current biology, 21(20), 1966-1972. › Chatterjee, K., Doyen, L., Henzinger, T.A. & Raskin, J., 2010. Abstract Interpretation. Springer, 26-44. € 1'375'000, 11/2010 – 3/2015. Life in Extreme Habitats and Astrobiology. Life in the Universe Expressions. In: Lecture Notes in Computer Science 6269. › Klopper, A., Krens, G., Grill, S. & Heisenberg, C., 2010. Generalized Mean-payoff and Energy Games. In: Leibniz › Mateescu, M., Wolf, V., Didier, F. & Henzinger, T.A., 2010. › Host-Parasite Coevolution, DFG, € 95'000, From the Miller Experiment To the Search For Life on Other CONCUR: Concurrency Theory. Springer, 269-283. Finite-size corrections to scaling behavior in sorted cell International Proceedings in Informatics. FSTTCS: Founda­ Fast adaptive uniformization of the chemical master equation. 11/2010 –12/2011. Worlds, 83-87. › Chatterjee, K., Doyen, L., Gimbert, H. & Henzinger, T.A., aggregates. In: The European Physical Journal E - Soft tions of Software Technology and Theoretical Computer IET Systems Biology, 4(6), 441-452. 2010. Randomness for Free. In: Lecture Notes in Computer Matter and Biological Physics, 33(2), 99-103. Science. Springer, in press. › Nickovic, D. & Piterman, N., 2010. From MTL to Deterministic Edelsbrunner Group Bollback Group Science 6281. MFCS: Mathematical Foundations of › Papusheva, E. & Heisenberg, C.P., 2010. Spatial organization › Chatterjee, K., Henzinger, T.A. & Piterman, N., 2010. Strategy Timed Automata. In: Lecture Notes in Computer Science › Roots Grant, NSF, $ 160'000 , 9/2010 – 12/2011. › Hollatz, C., Vilaca, S., Redondo, R., Marmontel, M., Baker, Computer Science. Springer, 246-257. of adhesion: force-dependent regulation and function in tis­ logic. Information and Computation, 208(6), 677-693. 6246. FORMATS: Formal Modeling and Analysis of Timed C. & Santos, F., 2010. The Amazon River as an ecological › Chatterjee, K., Doyen, L., Henzinger, T.A. & Raskin, J., 2010. sue morphogenesis. In: EMBO Journal, 29(16), 2753-2768. › Chatterjee, K., Henzinger, T.A., Jobstmann, B. & Systems. Springer, 152-167. Heisenberg Group barrier to Pink Dolphin (Inia geoffrensis) marginal populations. Generalized Mean-payoff and Energy Games. In: Leibniz › Carvalho, L. & Heisenberg, C., 2010. The yolk syncytial layer Radhakrishna, A., 2010. Gist: A Solver for Probabilistic › Podelski, A. & Wies, T., 2010. Counterexample-guided focus. › SPP, DFG, € 45'000, 2/2010. Biological Journal of the Linnean Society, in press. International Proceedings in Informatics. FSTTCS: in early, zebrafish development. In: Trends In Cell Biology, Games. In: Lecture Notes in Computer Science 6174. In: POPL: Principles of Programming Languages. Association › ZF Cancer, EC-FP7, € 138'000, 4/2008 – 3/2011. › Kupczok, A., 2010. Consequences of different null models Foundations of Software Technology and Theoretical 20(10), 586-592. CAV: Computer-Aided Verification. Springer, 665-669. for Computing Machinery, 249-260. › SFRH/BD/60401/2009, FCT-PT, € 12'000, 11/2010. on the tree shape bias of supertree methods. Systematic Computer Science. Springer, in press. › Chatterjee, K., Henzinger, T.A., Jobstmann, B. & Singh, R., › Singh, V., 2010. Runtime Verification of Transactional Biology, in press. › Chatterjee, K., Henzinger, T.A. & Piterman, N., 2010. Strategy Henzinger Group 2010. Measuring and Synthesizing Systems in Probabilistic Memories. In: Lecture Notes in Computer Science 6418. Rv Henzinger Group › Pavan, A., Martins, F., Santos, F., Ditchfield, A. & Redondo, logic. Information and Computation, 208(6), 677-693. › Berwanger, D., Chatterjee, K., De Wulf, M., Doyen, Environments. In: Lecture Notes in Computer Science 6174. International Conference on Runtime Verification. Springer, › Combest. EC-FP7, € 107'000, 1/2008 – 12/2010. R., 2010. Patterns of diversification in two species of › Chatterjee, K., Henzinger, T.A., Jobstmann, B. & L. & Henzinger, T.A., 2010. Strategy construction for CAV: Computer-Aided Verification. Springer, 380-395. 421-435. › Artist Design, EC-FP7, € 63'000, 1/2007 –12/2011. short-tailed bats (Carollia Gray, 1838): the effects of historical Radhakrishna, A., 2010. Gist: A Solver for Probabilistic parity games with imperfect information. Information and › Chatterjee, K., Henzinger, T.A. & Prabhu, V.S., 2010. Timed › Wies, T., Zufferey, D. & Henzinger, T.A., 2010. Forward › RiSE - Rigorous Systems Engineering, FWF, € 450'000, fragmentation of Brazilian rainforests. Biological Journal of Games. In: Lecture Notes in Computer Science 6174. CAV: Computation, 208(10), 1206-1220. parity games: Complexity and robustness. Logical Methods Analysis of Depth-Bounded Processes. In: Lecture Notes in 3/2011 – 2/2015. the Linnean Society, in press. Computer-Aided Verification. Springer, 665-669. › Beyer, D., Henzinger, T.A., Théoduloz, G. & Zufferey, D., in Computer Science, in press. Computer Science 6014 . FOSSACS: Foundations of Soft- › Quantitative Reactive Modeling (QUAREM), ERC, › Chatterjee, K., Henzinger, T.A., Jobstmann, B. & Singh, R., 2010. Shape Refinement through Explicit Heap Analysis. › Didier, F., Henzinger, T.A., Mateescu, M. & Wolf, V., 2010. ware Science and Computation Structures. Springer, 94-108. € 2'300'000, 9/2011– 8/2016. Chatterjee Group 2010. Measuring and Synthesizing Systems in Probabilistic In: Lecture Notes in Computer Science 6013. FASE: Approximation of event probabilities in noisy cellular › Wolf, V., Goel, R., Mateescu, M. & Henzinger, T.A., 2010. › Berwanger, D., Chatterjee, K., De Wulf, M., Doyen, Environments. In: Lecture Notes in Computer Science 6174. Fundamental Approaches To Software Engineering. Springer, processes. Theoretical Computer Science, in press. Solving the chemical master equation using sliding windows. Jonas Group L. & Henzinger, T.A., 2010. Strategy construction for CAV: Computer-Aided Verification. Springer, 380-395. 263-277. › Didier, F., Mateescu, M., Wolf, V. & Henzinger, T.A., 2010. BMC Systems Biology, 4:42, 1-19. › DFG/780, DFG/FWF, € 46'000. parity games with imperfect information. Information and › Chatterjee, K., Horn, F. & Löding, C., 2010. Obliging Games. › Blanc, R., Henzinger, T.A., Hottelier, T. & Kovacs, L., 2010. Sabre: A tool for the stochastic analysis of biochemical › Nanophysiology of fast-spiking, parvalbumin-expressing Computation, 208(10), 1206-1220. In: Lecture Notes in Computer Science 6269. CONCUR: ABC: Algebraic bound computation for loops. In: Lecture reaction networks. In: QEST: Quantitative Evaluation of Jonas Group GABAergic interneurons, ERC, € 2'500'000, 7/2011–6/2016. › Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T.A. & Concurrency Theory. Springer. Notes in Computer Science 6355. LPAR: Logic for Systems. IEEE, 193-194. › Guzman, S.J. & Jonas, P., 2010. Beyond TARPs: the growing Jobstmann, B., 2010. Robustness in the Presence of › Chatterjee, K., Horn, F. & Loeding, C., 2010. Obligingness Programming, Artificial Intelligence, and Reasoning. Springer, › Doyen, L., Henzinger, T., Legay, A. & Nickovic, D., 2010. list of auxiliary AMPAR subunits (Review). Neuron, 66(1), 8-10. Sixt Group Liveness. In: Lecture Notes in Computer Science 6174. Games. In: Lecture Notes in Computer Science 6269. CON- 103-118. Robustness of Sequential Circuits. In: ACSD: Application of › Guzman, S.J., Schmidt, H., Franke, H., Krügel, U., Eilers, J., › Zytoskelettdynamik und Kraftgenerierung wandernder CAV: Computer Aided Verification. Springer, 410-424. CUR: Concurrency Theory. Springer, 284-296. › Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T.A. & Concurrency To System Design. IEEE Computer Illes, P. & Gerevich, Z., 2010. P2Y1 receptors inhibit long- Leukozyten, DFG, € 110'000, 11/2010 4/2012. › Chatterjee, K. & Doyen, L., 2010. Energy Parity Games. Jobstmann, B., 2010. Robustness in the Presence of Society, 77-84. term depression in the prefrontal cortex. Neuropharmacology­ , › Einfluss der Chemokinpräsentation auf das Reaktionsmuster In: Lecture Notes in Computer Science 6199. ICALP: Edelsbrunner Group Liveness. In: Lecture Notes in Computer Science 6174. CAV: › Feret, J., Henzinger, T.A., Koeppl, H. & Petrov, T., 2010. 59(6), 406-415. von Leukozyten, DFG, € 117'000, 1/2011 –12/2012. Automata, Languages and Programming. Springer, 599-610. › Bendich, P. & Harer, J., 2010. Persistent Intersection Computer Aided Verification. Springer, 410-424. Lumpability abstractions of rule-based systems. In: › Jonas, P. & Hefft, S., 2010. GABA release at terminals › Role of the WAVE-complex in the haematopoietic › Chatterjee, K. & Doyen, L., 2010. The Complexity of Partial- Homology. Foundations of Computational Mathematics, in › Burckhardt, S., Musuvathi, M. & Singh, V., 2010. Verifying Electronic Proceedings in Theoretical Computer Science. of CCK-interneurons: synchrony, asynchrony and modulation System, DFG, € 70'000, 11/2010 – 12/2011. Observation Parity Games. In: LPAR: Logic For Program- press. Local Transformations on Relaxed Memory Models. In: MECBIC: Membrane Computing and Biologically Inspired by cannabinoid receptors (commentary on Ali & Todorova). ming, Artificial Intelligence, and Reasoning. Springer, 1-14. › Bendich, P., Edelsbrunner, H., Kerber, M. & Patel, A., 2010. Lecture Notes in Computer Science 6011. CC: Compiler Process Calculi. Open Publishing Association, 137-156. The European Journal of Neuroscience, 31(7), 1194-1195. Persistent Homology under Non-uniform Error. In: Lecture Construction. Springer, 104-123. Notes in Computer Science 6281. MFCS: Mathematical Foundations of Computer Science. Springer, 12-23.

42 Annual Report 2010 Annual Report 2010 43 organization boards of IST Austria

Scientific Board Kurt Mehlhorn, Chair; Director, Max-Planck Institute, Saarbrücken, 01 02 03 04 05 06 Germany (10) Arnold Schmidt, Vice-chair; Former President, Austrian Science Administration Fund FWF (16) Frank Allgöwer, Professor, Managing Director: Gerald Murauer (1) 1 2 3 4 5 6 7 07 08 09 10 11 University of Stuttgart, Germany (17) Angelika Amon, Professor, MIT, Academic Affairs: Laurenz Niel (Head; 2), Cambridge, USA (18) Irene Hetzenauer (Academic Events; 3), Peter Fratzl, Director, Max-Planck Barbara Kunes, Helga Materna, Ulrike Seiss Institute, Potsdam, Germany (19) 8 9 10 11 12 13 14 (Graduate School; 4)

12 13 14 15 16 Tony Heinz, Professor, Columbia University, New York, USA Administrative Assistants for Research (from 2011) (20) Groups: Julia Asimakis, Elisabeth Hacker, Hannah Monyer, Professor, Nicole Hotzy, Eva Kramberger University of Heidelberg, Germany (21) Office of the President: Lisa Cichocki 17 18 19 20 21 22 Martin Nowak, Professor, Harvard Administration (Communications; 5), Martina Doppler, Sabine University, Cambridge, USA (22) Ghobriel, Oliver Lehmann (Media Relations; 6) Board of Trustees Ernst-Ludwig Winnacker, Secretary General, Human Frontiers Science In 2010 the most important milestone the first of which are currently being set Human Resources: Claudia Kernstock Claus J. Raidl*, Chair; CEO, Eric Kandel, Professor, Columbia Program, Strasbourg, France (15) of campus development was the open­ up. In the future the Scientific Service (Head; 7), Bettina Karnolz, Andrea Mühlberger, Böhler Uddeholm AG, Vienna (1) University, New York, USA (8) Anton Zeilinger, Professor, ing of the Bertalanffy Foundation Build­ Units and the support staff for scientists Michaela Stöckel Anton Zeilinger*, Vice-Chair; Professor, Olaf Kübler*, Former President, University of Vienna and IQOQI, ing. On the same day, October 13, the (technicians, administrative assistants) University of Vienna and IQOQI, Austrian ETH Zurich, Switzerland; Vice-Chair, Austrian Academy of Sciences (2) groundbreaking ceremony for the sec­ will grow in parallel with the growth Construction and Maintenance: Stefan Academy of Sciences (2) Executive Committee (9) Hipfinger (Head; 8), Robert Hojski (Deputy Non-Voting Member: ond laboratory building took place. We of the research personnel, while the Catherine Cesarsky, High Commissioner Kurt Mehlhorn, Director, Max-Planck Claus J. Raidl, CEO, BöhlerUddeholm Head; 9), Catalin Mitru, Michael Pletzer, Gertrude expect the second laboratory building admin­istration of the Institute will grow for Atomic Energy, CEA Saclay, Institute, Saarbrücken, Germany (10) AG, Vienna (1) Resch, Michael Rockenschaub, Martin Träxler Gif-sur-Yvette, France (3) Alfred Ötsch*, Wiener Neustadt; (11) to open in the fall of 2012; it will provide only moderately. space for an additional 12 experimental Alice Dautry, President, Institut Pasteur, Wolfgang Ruttenstorfer, CEO, OMV AG, Finance: Leopold Kronlachner (Head; 10), Paris, France (4) Vienna (12) research groups. Our most important goal remains provid­ Barbara Abraham (Grant Office; 11), Haim Harari*, Former President, Elisabeth Stadler, Chairperson, ERGO ing the best possible and most efficient Eva Strieck, Peter Jakubitz (Procurement; 12), Weizmann Institute of Science, Rehovot, Austria International AG, Vienna (13) Over the past year the ratio of admin­ support for creating a prospering scien­ Jasmin Pielorz, Ursula Prandstätter, Israel; Chair, Executive Committee (5) Hansjörg Tengg, Manager, smart istrative personnel to scientists has tific environment. I would like to thank all Bruno Wöran (Grant Office, Controlling; 13) Alexander Hartig, Member of the technologies, Vienna (14) changed noticeably. Our main task has administrative employees for their efforts Management Board, Constantia Ernst-Ludwig Winnacker, Secretary shifted from setting up administrative and achievements and look forward to Hospitality: Martin Rinder (Restaurant, Industries AG, Vienna (6) General, Human Frontiers Science structures to providing service to the our further collaboration at IST Austria. Guest House; 14), Pirkko Määttänen Gisela Hopfmüller*, Freelance journalist, Program, Strasbourg, France (15) scientists. Much of this service is being Vienna; (7) bundled within Scientific Service Units, Gerald Murauer, Managing Director

* Members of the Executive Committee of the Board of Trustees

44 Annual Report 2010 Annual Report 2010 45 organization

Scientific Service Units Supporting the Scientists

Scientific Service Units

Bioimaging Facility: Ekaterina Papusheva 1 2 3 4 5 (Facility Manager; 1), Robert Hauschild

Information Technology: Franz Schäfer (Facility Manager; 2), Michael Adletzberger, Michael Brandstätter, Alois Schlögl A major challenge in 2010 was the estab­ The following Scientific Service Units are › Library: The library of IST Austria is de­ ment support our scientists in fabricating lishment of several Scientific Service Units, currently being set up: signed as a predominantly electronic library,­ customized laboratory set-ups. Library: Patrick Danowski (3) whose purpose is to provide the scientists › Bioimaging Facility: A number of state- providing electronic access to scholarly with the cutting-edge equipment and pro­ of-the-art microscopes support the work journals, conference proceedings, and A charging system for scientific services Life Sciences Facility: Matthias Nowak fessional services that allow them to per­ of the cell biologists. Currently the facility books. will not only make the resource allocation (Facility Manager; 4), Michael Schunn form research at an internationally compe­ includes two confocal microscopes, an › Life Sciences Facility: In addition to within IST Austria efficient, but will also (Facility Manager; 5), Cornelia Kohl, Günther Reiterer, Eva Schlegl, Melanie titive level. The philosophy of IST Austria is atomic-force microscope, a fluorescent standard research infrastructure for biolo­ allow external partners and companies to Sedlacek, Renate Srsek, Mersija Smailagic to maximize the sharing of equipment and stereo microscope, and a multi-photon gy, such as laminar flow hoods, autoclaves,­ use the facilities on campus. services among multiple research groups, microscope. centrifuges, and fridges, a media kitchen, a Machine Shop: Todor Asenov, in order to avoid a duplication of efforts and › Information Technology: In addition to FACS machine, and services for the neuro­ Mathias Wascher expenses within different groups. The Sci­ standard IT services we offer a cluster of scientists are part of the facility. entific Service Units of IST Austria are cen­ machines for scientific computation as › Machine Shop: A milling machine, a turn­ tral core facilities that can be used by all well as programmers to support the sci­ ing machine, a grinding and buffing ma­ scientists of the Institute. entists in their software needs. chine, and several smaller pieces of equip­

46 Annual Report 2010 events IST Lectures Presenting Distinguished Scientists

6 7

1 Martin Nowak gives the first IST Lecture in the Raiffeisen Lecture Hall.

2 Martin Nowak, Professor of Biology and Mathematics at Harvard University, USA

3 Ada Yonath speaking about ribosomal structure and antibiotics.

4 Audience enjoys refreshments.

4 5 5 Ada Yonath, Martin S. and Helen Kimmel 3 Professor of Structural Biology at the Weizmann Institute, Rehovot, Israel 1 2 6 Jeannette Wing, President's Professor of Computer Science, Head of the Computer Science Department at the Carnegie- Mellon University, Pittsburgh, USA

7 IST Austria President Tom Henzinger and IST Austria actively seeks to educate the public about the im­ the mathematical description of evolutionary processes, includ­ Jeannette Wing portance and impact of basic science–through the IST Lecture ing the evolution of cooperation and human language, and the series, where renowned international scientists are invited to dynamics of virus infections and human cancer. In his lecture give public talks on campus, and through the annual Open Nowak, who is also a member of the Scientific Board of IST Campus Day and Science-Industry Talk. Austria, started by giving an explanation of Darwin’s achieve­ ments. From this, he led the audience to one of his current research The IST Lectures are targeted towards a general audience in­ topics, the “Evolution of Cooperation: From Selfish Genes to terested in current developments in science. The speakers are Supercooperators.” asked to provide sufficient background information for non-ex­ insights contributed decisively to our better understanding of and software engineering. Wing summarizes her vision for the perts and, at the same time, go into detailed explanations of IST Lecture 2: Ada Yonath these molecular engines and to the development of antibiotics twenty-first century as follows: “Computational thinking will be a recent scientific topic. Each talk is followed by a Questions As part of a series of events on the occasion of the Institute’s first targeting ribosomal structures. a fundamental skill used by everyone in the world. To reading, and Answers session. The events are concluded by a social anniversary, Ada Yonath visited IST Austria on June 16, 2010, writing, and arithmetic, we should add computational thinking to get-together offering further possibilities for conversations with to give the second IST Lecture. Yonath, one of the 2009 Nobel IST Lecture 3: Jeannette Wing every child's analytical ability. Teaching computational thinking the speaker. Special public transportation from and to Vienna is laureates for Chemistry, is the Martin S. and Helen Kimmel Pro­ In the third IST Lecture on September 27, 2010, Jeanette Wing can not only inspire future generations to enter the field of com­ usually provided. fessor of Structural Biology at the Weizmann Institute in Israel. introduced the audience to her concept of “Computational Thin­ puter science but benefit people in all fields.” On this first visit to Austria after being awarded the Nobel Prize, king”. Wing, who recently headed the Computer and Informa­ IST Lecture 1: Martin Nowak Yonath lectured about “The Amazing Ribosome, its Origin and tion Science and Engineering Directorate at the US National The IST Lecture series will continue in 2011. The next lecture, Martin Nowak inaugurated the IST Lecture series on November its Tiny Enemies, the Antibiotics”. In the talk she related her per­ Science Foundation, is the President's Professor of Computer –on March 10, 2011–will be given by Angelika Amon, Profes­ 27, 2009. Nowak, a native of Austria, is professor of biology and sonal story of how she got to focus on the mechanism of pro­ Science and head of the Computer Science Department at Car­ sor of Biology at the Massachusetts Institute of Technology and of mathematics at Harvard University and director of Harvard’s tein biosynthesis by investigating the structures and functions negie-Mellon University in Pittsburgh. Her research focuses on member of the Scientific Board of IST Austria. For forthcoming program for Evolutionary Dynamics. His research focuses on of ribosomes–the translators from RNA to proteins. Yonath’s the areas of trustworthy computing, programming languages, events, please visit the Institute's website: www.ist.ac.at.

48 Annual Report 2010 Annual Report 2010 49 events

Scientific Events

January 25, 2010 Communicating Biology meets Physics

May 6–7, 2010 Science Reactive Modeling in Science and Engineering

June 22, 2010 Neuroscience: From Molecules to Code IST Austria friends and neighbors at the Open September 8–10, 2010 Campus Day Formal Modeling and Analysis of Timed Communicating science is a central mission of IST Austria–to ren of all ages a fascination with science and with the role of Scientific Symposia, Conferences, and Talks Systems (Formats) many kinds of different audiences, be it to fellow researchers science in everyday life. The large number of entries showed a Scientific symposia, conferences, and summer schools are plat­ from other institutions within the relative privacy of a seminar remarkable enthusiasm of children and teachers alike. forms for researchers to meet and exchange ideas. In 2010 IST September 28–October 1, 2010 room, or to children and their parents at the Open Campus Austria hosted four symposia (“Biology meets Physics” in January, Introduction to Evolutionary Genetics Day on the lawn next to the pond. The Institute has developed Meeting our Neighbors “Reactive Modeling in Science and Engineering” in April, “Neuro­ a set of different formats in order to satisfy the information de­ Frequent Neighborhood Talks aim at satisfying the curiosity science: From Molecules to Code” in June, and “Condensed November 27, 2010 Open Day for Prospective Students mands of very distinct target groups interested in the activities of the local community about the latest developments at IST Matter Physics and Optics” in December). In September 2010 of the Institute. Austria. Members of the administration regularly inform regio­ the Institute hosted the eighth annual international conference December 20, 2010 nal clubs and associations about the progress at the Institute, on “Formal Modeling and Analysis of Timed Systems”, which Condensed Matter Physics and Optics Open Campus Day and School Competition and in particular, about physical changes on campus. brought together computer scientists from the whole world who The biggest event is the annual Open Campus Day on a week­ study real-time computation. The workshop on “Evolutionary end in late May or early June, celebrating the anniversary of Science-Industry Talk Genetics” held in the same month offered graduate students Public Events the Institute's inauguration on June 1, 2009. In 2010 approxi­ The Science-Industry Talk is an annual event with the goal from 18 countries the opportunity to meet some of the leading mately 750 visitors came to the Open Campus Day, enjoying to foster the interaction between the basic research commu­ researchers in that domain. May 29, 2010 public lectures by faculty members Sylvia Cremer, Carl-Philipp nity–which includes IST Austria–and the business world. The Open Campus Heisenberg, and Thomas Henzinger, a paper plane competi­ event is organized jointly by the Federation of Austrian Indus­ Throughout the year seminar talks link IST Austria to the scienti­ tion, a science tour for kids, and a BBQ for parents. try (IV) and IST Austria. In 2010 the event was devoted to the fic community, both locally and globally. The lectures cover not June 16, 2010 question “What kind of research is needed in Austria?” Af­ only research topics represented at the Institute, but also bring IST Lecture Ada Yonath A central activity at each Open Campus Day is the award ter words of welcome by the Federal Minister of Science and scientists in new fields to the Institute. Over the course of the year ceremony for a school science competition aimed, in three Research, Beatrix Karl, and the President of the Vienna 72 talks by external scientists were held on campus. Sometimes June 21, 2010 different age categories, at elementary and high school stu­ chapter of the IV and chairman of the Kapsch AG, Georg the speakers might be known only to their fellow experts. But this Science-Industry Talk: What Kind of dents from the Klosterneuburg region. In 2010 IST Austria in­ Kapsch, the panel members Thomas Henzinger (IST Austria), can change abruptly. On March 23 Konstantin Novoselov (School Research is Needed in Austria? vited participants from 6 to 19 years to “Show us your world Christian Schilling (CEO, Boehringer Ingelheim RCV GmbH), of Physics and Astronomy, University of Manchester) presented September 27, 2010 of numbers – mathematics in everyday life”. The contributors Edeltraud Stiftinger (Head of Corporate Technology CEE, his findings on “Graphene and its Chemical Derivatives” in room IST Lecture Jeannette Wing were asked for creative ideas on where to find mathematical Siemens AG Österreich), and Georg Winckler (Rector, Univer­ number 3 of the Mondi Seminar Center in the Central Building of concepts–apart from the math lessons in school. With such sity of Vienna) discussed many different aspects of the multi- IST Austria. On October 5 Novoselov was named Nobel Laureate competitions the Institute wants to instill and deepen in child­ faceted relationship between science and industry. in physics – the youngest Nobel Prize winner in 37 years.

Speakers at IST Austria in 2010 Almut Arneth, Lund, SWE I Michalis Averof, Crete, GRE I Nathalie Q. Balaban, Jerusalem, ISR I Claudia Bank, Vienna, AUT I Jiri Barnat/David Safranek, Brno, CZE I Udi Boker, Jerusalem, ISR I Radu Ioan Bot, Chemnitz, GER I Frank Bradke, Martinsried, GER I Brona Brejova, Bratislava, SVK I Pinaki Chakraborty, Urbana-Champaign, USA I Enrico Coen, Colney/Norwich, UK I Otto Cordero, Cambridge, USA I Jozsef Csicsvari, Oxford, UK I Tal Dagan, Düsseldorf, GER I Benoit Delahaye, Cachan, FR I Alexander DeLuna, Cinvestav, MEX I Martin Depken, Amsterdam, NED I Francesco Dinuzzo, Pavia, ITA I Laurent Doyen, Cachan, FR I Santiago F. Elena, València, ESP I Jan Engelstaedter, Zurich, SUI I Dmitry Feichtner- Kozlov, Bremen, GER I Jasmin Fisher, Cambridge, UK I Matthias Fuegger, Vienna, AUT I Carsten Grashoff, Charlottesville, USA I George Haller, Montreal, CAN I Michael Häusser, London, UK I Juergen Heinze, Regensburg, GER I Gerhard Hummer, Bethesda, USA I Harald Janovjak, Berkeley, USA I Fedor Jelezko, Stuttgart, GER I Felicity Jones, Palo Alto, USA I Paul Joyce, Moscow, USA I Satish Babu Korada, Palo Alto, USA I Laura Kovacs, Vienna, AUT I Daniel Kroening , Oxford, UK I Daniel Kronauer, Cambridge, USA I Leslie Lamport, Mountain View, USA I Georg Langs, Cambrigde, USA I Julian McAuley, Canberra, AUS I Dmitri Miroshnychenko, Vienna, AUT I Thomas Moscibroda, Redmond, USA I Konstantin S. Novoselov, Manchester, UK I Pleuni S. Pennings, Cambridge, USA I Peter Rabl, Innsbruck, AUT I Friederike Range, Vienna, AUT I Jean-Francois Raskin, Bruxelles, BEL I Jochen C. Rink, Salt Lake City, USA I Denis Roze, Edinburgh, UK I Andrey Rybalchenko, Munich, GER I Paul Schmid-Hempel, Zurich, SUI I Hinrich Schulenburg, Kiel, GER I Peter Schurtenberger, Fribourg, SUI I Olivier Serre, Paris, FR I Ali Sezgin, Istanbul, TUR I Ana Sokolova, Salzburg, AUT I Federico Sukno, Barcelona, ESP I Sorin Tanase-Nicola, Atlanta, USA I Michael Tautschnig, Vienna, AUT I Gasper Tkacik, Philadelphia, USA I Enrico Tronci, Rome, ITA I Rien van de Weygaert, Groningen, NED I Jeroen S. van Zon, Cambrigde, USA I Alipasha Vaziri, Chevy Chase, USA I Zhikun Wang, Tübingen, GER I Daniel Weissman, Klosterneuburg, AUT I Thomas Wies, Klosterneuburg, AUT I Claus O. Wilke, Austin, USA I Chris Wojtan, Atlanta, USA I Florian Wolschin, Tempe, USA I Yuen-Tsu Yu, Bloomington, USA I Florian Zuleger, Vienna, AUT

50 Annual Report 2010 Annual Report 2010 51 location

Tennis Courts Soccer Field Fire Station location Kindergarten Museum Gallery Bertalanffy Raiffeisen Foundation Building and Directions Lecture Hall Central Building Church

Laboratory Building 2 in construction Residential Units

Memorial Heating Plant

Prague Brno

Facility Management Main Entrance voestalpine Building

Klosterneuburg

IST Austria Linz Bratislava

River Danube

Vienna

Budapest

Graz Schwechat

The city of Klosterneuburg is known for its high quality of Klosterneuburg living. The location between the river Danube and the rolling S40 | Bus 239 Kierling hills of the Vienna Woods, with its vineyards, pastures, and BYPASS forests, provides an exceptional environment that is both Maria Gugging Tulln Bus 239 tranquil and stimulating for studying and recreation. The city B14 offers educational, medical, social, and cultural facilities of the Weidling

highest standard. B14 A22

The historical center of Klosterneuburg is dominated by the

enormous medieval monastery, which was redesigned in NORDBRÜCKE

the early 18th century, in Baroque style, as residence for the Heiligenstadt Austrian emperor. Close to the monastery, the Essl Museum U4 | S40 | Bus 239 is world-famous for its contemporary art. Our immediate Spittelau U4 | U6 neighbor on campus is the internationally renowned Art Brut Airport Center Gugging. Vienna City Center

52 Annual Report 2010 Annual Report 2010

Imprint

Institute of Science and Technology Austria Am Campus 1, 3400 Klosterneuburg Tel.: +43 (0)2243–9000 [email protected] www.ist.ac.at

Editor: Lisa Cichocki

Texts: IST Austria

Graphic design: Starmühler Agentur & Verlag Schellinggasse 1, 1010 Wien www.starmuehler.at Christine Starmühler Barbara Kaiser Katharina Krizsanits

Photography: Lisa Cichocki Roland Ferrigato Göran Gnaudschun (Portrait Peter Fratzl) Christian Jungwirth (Portrait Beatrix Karl) Oliver Lehmann Rita Newman Lukas Schaller Jürgen Skarwan

Print: Gerin

Paper: Munken Polar 300g, 150g

Copyright: Institute of Science and Technology Austria, 2010