Curriculum Vitae
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Department of Computer Science
Department of Computer Science Content Research Overview of the Computer Science Department This brochure gives an overview of the ongoing research activities at the Department of Computer Science of ETH Zurich. It is a collection of the two-page research summaries given by every professor of the Department. The following pages are in alphabetical order of the names of the professors. Gustavo Alonso Information and Communication Systems Research Group Armin Biere Formal Methods for Solving Complexity and Quality Problems Walter Gander From Numerical Analysis to Scientific Computing Gaston Gonnet Computational Biochemistry and Computer Algebra Markus Gross Computer Graphics Laboratory Thomas Gross Laboratory for Software Technology Jürg Gutknecht Program Languages and Runtime Systems Petros Koumoutsakos Computational Sciences Friedemann Mattern Ubiquitous Computing Infrastructures Ueli Maurer Information Security and Cryptography Bertrand Meyer Chair of Software Engineering Kai Nagel Modeling and Simulation Jürg Nievergelt Algorithms, Data Structures, and Applications Moira Norrie Constructing Global Information Spaces Hans-Jörg Schek Realizing the Hyperdatabase Vision Bernt Schiele Perceptual Computing and Computer Vision Robert Stärk Computational Logic Thomas Stricker Parallel- and Distributed Systems Group Roger Wattenhofer Distributed Computing Group Emo Welzl Theory of Combinatorial Algorithms Peter Widmayer Algorithms, Data Structures, and Applications Carl August Zehnder Development and Application Group The most up-to-date research summaries can be found under Û research in the Web presentation of the Department. This version is as of June 12, 2002. Information and Communication Systems Research Group Information Systems Prof. Gustavo Alonso http://www.inf.ethz.ch/department/IS/iks/ [email protected] Figure 1 to 4 BiOpera, a develop- ment and run time environment for cluster and grid computing The motivation behind our research uted at a large scale and heterogeneous. -
A Phylogenomic Study of Human, Dog, and Mouse
A Phylogenomic Study of Human, Dog, and Mouse Gina Cannarozzi, Adrian Schneider, Gaston Gonnet* Institute of Computational Science, ETH Zurich, Zurich, Switzerland In recent years the phylogenetic relationship of mammalian orders has been addressed in a number of molecular studies. These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships. For example, the relative placement of primates, rodents, and carnivores has differed in various studies. Here, we attempt to resolve this phylogenetic problem by using data from completely sequenced nuclear genomes to base the analyses on the largest possible amount of data. To minimize the risk of reconstruction artifacts, the trees were reconstructed under different criteria—distance, parsimony, and likelihood. For the distance trees, distance metrics that measure independent phenomena (amino acid replacement, synonymous substitution, and gene reordering) were used, as it is highly improbable that all of the trees would be affected the same way by any reconstruction artifact. In contradiction to the currently favored classification, our results based on full-genome analysis of the phylogenetic relationship between human, dog, and mouse yielded overwhelming support for a primate–carnivore clade with the exclusion of rodents. Citation: Cannarozzi G, Schneider A, Gonnet G (2007) A phylogenomic study of human, dog, and mouse. PLoS Comput Biol 3(1): e2. doi:10.1371/journal.pcbi.0030002 Introduction Long branch attraction (LBA) may occur when an ingroup has a faster rate of evolution, thereby promoting migration of A correct interpretation of the direction of evolution in the long branch with accelerated evolution toward the long basal parts of the mammalian tree has important implications branch of the outgroup. -
Fundamentación De La Propuesta De Otorgar El T´Itulo De Doctor Honoris Causa De La Facultad De Ingenier´Ia Al Dr. Gaston Go
Fundamentaci´onde la propuesta de otorgar el t´ıtulode Doctor Honoris Causa de la Facultad de Ingenier´ıaal Dr. Gaston Gonnet. Gaston Henry Gonnet naci´oen Uruguay en setiembre de 1948. En 1968, habiendo concluido sus estudios secundarios, ingres´ocomo do- cente al reci´encreado CECUR (Centro de Computaci´onde la Universidad de la Rep´ublica).Al mismo tiempo, fue estudiante de la nueva carrera de Computador Universitario, habi´endosegraduado en agosto de 1973. A pesar de su juventud, Gonnet ya ten´ıacontacto con las grandes compu- tadoras de esa ´epoca gracias a su trabajo en la empresa IBM en Uruguay. Poco tiempo despu´esde la intervenci´onde la UDELAR en 1973, Gonnet se radic´oen Canad´a. En 1977, se doctor´oen la Universidad de Waterloo transform´andose r´api- damente en un cient´ıficodestacado internacionalmente en el ´areade Algorit- mos y Computabilidad. En 1980, Gonnet co-fund´oel Grupo de Computaci´onSimb´olicaen la Uni- versidad de Waterloo. De ese grupo surgi´oel proyecto Maple, que produjo el conocido Sistema de Algebra Computacional de amplio uso en el ´ambito cient´ıfico-tecnol´ogico.En 2011, Gaston Gonnet y Keith Geddes recibieron el Premio ACM Richard Jenks a la Excelencia en Ingenier´ıade Software apli- cada al Algebra Computacional en el Proyecto Maple. En 1984, Gonnet fue uno de los miembros fundadores del proyecto New Oxford English Dictionary. Este proyecto permiti´ocrear la primer versi´on electr´onicadel Oxford English Dictionary. En 1985, utiliz´osu a~nosab´aticopara retornar al Uruguay y ayudar al Instituto de Computaci´onen su reconstrucci´onluego de la dictadura. -
Curriculum Vitae
Curriculum Vitae 1 Personal Information Name Ricardo Baeza-Yates E-mail [email protected] Personal website http://www.baeza.cl/ 2 Current Activities • Research Professor (half-time) at the Institute for Experiential AI, Northeastern University, since 2021. • Consultant for startups, companies, and venture capital in Brazil, Chile, Mexico, Spain, and USA; as well as for international organizations like United Nations and IADB (BID). • Member of Global Partnership of AI (Data Governance Working Group), Spain’s Advisory Council of AI, Catalonia’s AI Observatory Advisory Board, ACM’s Policy Technology subcommittee in AI and Algorithms, and IABD’s Advisory Committee for fAIr LAC (Fair AI in Latin America and the Caribbean). • Full Professor (part-time) at the Dept. of Information and Communication Technologies of Universitat Pompeu Fabra, Barcelona, Catalonia, Spain, since 2006. • Full Professor (part-time) at the Dept. of Computing Sciences, Universidad de Chile, Santiago, Chile, since 1989. • Corresponding member of the Brazilian Academy of Sciences since 2019. • Founding member of the Chilean Academy of Engineering since 2010. • Corresponding member of the Chilean Academy of Sciences since December 2002. • Member of the advisory board of the National Portuguese Research Lab in CS, INESC, since 2012. • Member of the advisory board of the CSE Department of UC Riverside as well as the Department of Informatics Engineering, University of Porto, Portugal, since 2020. • Member of the Advisory Board of the Professional Association of Computing Professionals of Cat- alonia since 2009. 3 Highlights • World class expert in search, data mining and data science. • Research innovator and team builder with leadership and multitasking skills. -
Computer Science at the University of Waterloo
COMPUTER SCIENCE AT WATERLOO A HISTORY TO CELEBRATE 25 YEARS by Peter J. Ponzo The William G. Davis Centre for Computer Research University of Waterloo COMPUTER SCIENCE at WATERLOO A History to Celebrate 25 Years : 1967 - 1992 Table of Contents Foreword ...................................................................................................................... 1 Prologue: "Computers" from Babbage to Turing .............................................. 3 Chapter One: the First Decade 1957-1967 ............................................................ 13 Chapter Two: the Early Years 1967 -1975 ............................................................ 39 Chapter Three: Modern Times 1975 -1992.............................................................. 52 Chapter Four: Symbolic Computation ..................................................................... 62 Chapter Five: the New Oxford English Dictionary ................................................. 67 Chapter Six: Computer Graphics ........................................................................... 74 Appendices A: A memo to Arts Faculty Chairman ..................................................................... 77 B: Undergraduate Courses in Computer Science .................................................... 79 C: the Computer Systems Group ............................................................................. 80 D: PhD Theses ......................................................................................................... 89 E: Graduate -
2019 ISCB Overton Prize: Christophe Dessimoz[Version 1; Peer Review
F1000Research 2019, 8(ISCB Comm J):722 Last updated: 05 AUG 2021 EDITORIAL 2019 ISCB Overton Prize: Christophe Dessimoz [version 1; peer review: not peer reviewed] Diane Kovats 1, Ron Shamir1,2, Christiana Fogg3 1International Society for Computational Biology, Leesburg, USA 2Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel 3Freelance Writer, Kensington, USA v1 First published: 23 May 2019, 8(ISCB Comm J):722 Not Peer Reviewed https://doi.org/10.12688/f1000research.19220.1 Latest published: 23 May 2019, 8(ISCB Comm J):722 https://doi.org/10.12688/f1000research.19220.1 This article is an Editorial and has not been subject to external peer review. Abstract Any comments on the article can be found at the Each year the International Society for Computational Biology (ISCB) end of the article. honors the achievements of an early- to mid-career scientist with the Overton Prize. This prize was instituted in 2001 to honor the untimely loss of Dr. G. Christian Overton, a respected computational biologist and founding member of the ISCB Board of Directors. The Overton Prize recognizes early or mid-career phase scientists who have made significant contributions to computational biology or bioinformatics through their research, teaching, and service. In 2019, ISCB recognized Dr. Christophe Dessimoz, Swiss National Science Foundation (SNSF) Professor at the University of Lausanne, Associate Professor at the University College London, and Group Leader at the Swiss Institute for Bioinformatics. Dessimoz receives his award and is presenting a keynote address at the 2019 Joint Intelligent Systems for Molecular Biology/European Conference on Computational Biology held in Basel, Switzerland on July 21-25, 2019. -
Preface of Proceedings of GNOME 2014 ¬タヤ Festschrift for Gaston
Gonnet is Not Only about Molecular Evolution (GNOME) 2014 Festschrift on the Occasion of the Retirement of Prof. Gaston H. Gonnet Preface s t Maria Anisimova1 and Christophe Dessimoz2,3 n i r 1Institute of Applied Simulations, School of Life Sciences and Facility Management, P Zürich University of Applied Sciences, CH-8820 Wädenswil, Switzerland e r 2University College London, Gower St, London WC1E 6BT, United Kingdom P 3Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zurich, Switzerland Email: [email protected], [email protected] It is an immense pleasure to present this Festschrift on the occasion of Professor Gaston H. Gonnet’s retirement. This volume accompanies the associated symposium Gonnet is Not Only about Molecular Evolution (GNOME) on the 4th of July 2014 at ETH Zurich. Born in Uruguay, Gaston completed his undergraduate studies in Montevideo before going to Waterloo, Canada, where he completed his Master’s and, just less than two years later, his PhD degree under the supervision of J. Alan George. Over the course of his career, first at the Pontifical Catholic University of Rio de Janeiro, then later at the University of Waterloo, and since 1990 at ETH Zurich, Gaston H. Gonnet made seminal contributions to at least three fields. First, together with Keith Geddes, he created the Maple computer algebra system whose rapid adoption in the research community led to founding of the Maplesoft software company. The impact of this work is reflected in the thousands of citations to Maple’s various reference books. Second, Gaston made several influential contributions to text analysis and algorithms on strings, culminating with the digitalization of the Oxford English Dictionary and the founding of the Open Text Corporation with Tim Bray and Frank Tompa. -
Comparative Genomics Using Pairwise Evolutionary Distances
Research Collection Doctoral Thesis Comparative Genomics Using Pairwise Evolutionary Distances Author(s): Dessimoz, Christophe Publication Date: 2009 Permanent Link: https://doi.org/10.3929/ethz-a-005762050 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library Diss. ETH No. 18177 Comparative Genomics Using Pairwise Evolutionary Distances A dissertation submitted to the ETH Zurich for the degree of Doctor of Sciences presented by Christophe Dessimoz Dipl. Natw. ETH born on 21 November 1980 citizen of Conthey (VS) and Vétroz (VS), Switzerland accepted on the recommendation of Prof. Dr. Gaston H. Gonnet, examiner Prof. Dr. Amos Bairoch, co-examiner Prof. Dr. Niko Beerenwinkel, co-examiner Prof. Dr. Jörg Stelling, co-examiner Prof. Dr. Martin Vingron, co-examiner 2009 ii iii Abstract Comparative genomics is the study of genome structure, function, and evolu- tion across species enabled by the recent availability of complete genome se- quences. In this context, and assuming a common origin, one of the fundamen- tal notion is the degree of evolutionary relatedness among sequences. This is usually expressed either as a tree structure, or as the matrix of distances between pairs of sequences. In this thesis, we explore and develop comparative genomics methods that rely on pairwise distances. Part one of the thesis reviews and extends methods to estimate and combine distances between pairs of biological sequences. To estimate distances, the ho- mologous characters must be identified; thus we begin with an evaluation of se- quence alignment methods using simulation and real biological sequences. -
ECCB 2012 Organization
Copyedited by: GS MANUSCRIPT CATEGORY: ECCB Vol. 28 ECCB 2012, pages i306–i310 BIOINFORMATICS doi:10.1093/bioinformatics/bts418 ECCB 2012 Organization CONFERENCE CHAIR Niko Beerenwinkel, SIB and ETHZ, Basel, Torsten Schwede, Biozentrum Universität Basel & SIB Swiss Switzerland Institute of Bioinformatics, Basel, Switzerland D. Databases, Ontologies, and Text Mining CONFERENCE CO-CHAIR Alfonso Valencia, Centro Nacional de Investigaciones Dagmar Iber, ETHZ & SIB Swiss Institute of Bioinformatics, Oncologicas, Madrid, Spain Basel, Switzerland Dietrich Rebholz-Schuhmann, European Bioinformatics Institute (EMBL-EBI) LOCAL ORGANIZING COMMITTEE Torsten Schwede, Biozentrum Universität Basel & SIB Swiss E. Evolution, Phylogeny, and Comparative Genomics Institute of Bioinformatics, Basel, Switzerland Katja Jenni, Biozentrum Universität Basel, Switzerland Nicolas Galtier, CNRS, Université Montpellier 2, France Rita Manohar, Biozentrum Universität Basel, Switzerland Marc Robinson-Rechavi, University of Lausanne & SIB, Sarah Güthe, Biozentrum Universität Basel & SIB Swiss Institute Switzerland of Bioinformatics, Basel, Switzerland Yvonne Steger, Biozentrum Universität Basel, Switzerland F. Macromolecular Structure, Dynamics, and Function Lorenza Bordoli, Biozentrum Universität Basel & SIB Swiss Anna Tramontano, University of Rome ‘La Sapienza’, Italy Institute of Bioinformatics, Basel, Switzerland Torsten Schwede, SIB & Biozentrum, University of Basel, Irene Perovsek, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland Switzerland Jocelyne -
Gaston Gonnet Oral History
An interview with Gaston Gonnet Conducted by Thomas Haigh On 16-18 March, 2005 Zurich, Switzerland Interview conducted by the Society for Industrial and Applied Mathematics, as part of grant # DE-FG02-01ER25547 awarded by the US Department of Energy. Transcript and original tapes donated to the Computer History Museum by the Society for Industrial and Applied Mathematics © Computer History Museum Mountain View, California Gonnet, p. 2 ABSTRACT Born in Uruguay, Gonnet was first exposed to computers while working for IBM in Montevideo as a young man. This led him to a position at the university computer center, and in turn to an undergraduate degree in computer science in 1973. In 1974, following a military coup, he left for graduate studies in computer science at the University of Waterloo. Gonnet earned an M.Sc. and a Ph.D. in just two and a half years, writing a thesis on the analysis of search algorithms under the supervision of Alan George. After one year teaching in Rio de Janeiro he returned to Waterloo, as a faculty member. In 1980, Gonnet began work with a group including Morven Gentleman and Keith Geddes to produce an efficient interactive computer algebra system able to work well on smaller computers: Maple. Gonnet discusses in great detail the goals and organization of the Maple project, its technical characteristics, the Maple language and kernel, the Maple library, sources of funding, the contributions of the various team members, and the evolution of the system over time. He compares the resulting system to MACSYMA, Mathematica, Reduce, Scratchpad and other systems.