Stuart Pook's Publications

[1]	Nicolas Servant, Julien Roméjon, Pierre Gestraud, Philippe La Rosa, Georges Lucotte, Séverine Lair, Virginie Bernard, Bruno Zeitouni, Fanny Coffin, Gérôme Jules-Clément, Florent Yvon, Alban Lermine, Patrick Poullet, Stéphane Liva, Stuart Pook, Tatiana Popova, Camille Barette, François Prud’homme, Jean-Gabriel Dick, Maud Kamal, Christophe Le Tourneau, Emmanuel Barillot, , and Philippe Hupé. Bioinformatics for precision medicine in oncology: principles and application to the shiva clinical trial. Frontiers in Genetics, 5(152), May 2014. [ bib | PDF | www ] Precision medicine (PM) requires the delivery of individually adapted medical care based on the genetic characteristics of each patient and his/her tumor. The last decade witnessed the development of high-throughput technologies such as microarrays and next-generation sequencing which paved the way to PM in the field of oncology. While the cost of these technologies decreases, we are facing an exponential increase in the amount of data produced. Our ability to use this information in daily practice relies strongly on the availability of an efficient bioinformatics system that assists in the translation of knowledge from the bench towards molecular targeting and diagnosis. Clinical trials and routine diagnoses constitute different approaches, both requiring a strong bioinformatics environment capable of (i) warranting the integration and the traceability of data, (ii) ensuring the correct processing and analyses of genomic data, and (iii) applying well-defined and reproducible procedures for workflow management and decision-making. To address the issues, a seamless information system was developed at Institut Curie which facilitates the data integration and tracks in real-time the processing of individual samples. Moreover, computational pipelines were developed to identify reliably genomic alterations and mutations from the molecular profiles of each patient. After a rigorous quality control, a meaningful report is delivered to the clinicians and biologists for the therapeutic decision. The complete bioinformatics environment and the key points of its implementation are presented in the context of the SHIVA clinical trial, a multicentric randomized phase II trial comparing targeted therapy based on tumor molecular profiling versus conventional therapy in patients with refractory cancer. The numerous challenges faced in practice during the setting up and the conduct of this trial are discussed as an illustration of PM application. Keywords: precision medicine, clinical trial, bioinformatics, sequencing, oncology, SHIVA
[2]	Inna Kuperstein, David PA Cohen, Stuart Pook, Eric Viara, Laurence Calzone, Emmanuel Barillot, and Andrei Zinovyev. Navicell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. BMC Systems Biology, 7(100), October 2013. [ bib | www ] Background: Molecular biology knowledge can be formalized and systematically represented in a computer- readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. Results: NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. Conclusions: NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps. Keywords: Biological network, Comprehensive map of molecular interactions, Google maps, Semantic zooming, Modules in biological networks, Blogging interaction maps
[3]	Isabelle Demeure, Claudie Faure, Eric Lecolinet, Jean-Claude Moissinac, and Stuart Pook. Mobile computing to facilitate interaction in lectures and meetings. In DFMA 2005, pages 359--366, Besançon, France, February 2005. IEEE Computer Society. [ bib | PDF ] The Campus Mobile project explored how PDAs and innovative interfaces can improve interaction during lectures and in small meetings. These mobile computers (small pcs or pdas) are nomad mediators that provide the link between the public space and the users private space. A lecturer uses an augmented whiteboard to annotate her presentation, while the slides and annotations are broadcast in real time to the students pdas. The students can also annotate the presentation. They can then replay the lecture at their leisure. We developed and tested the user interfaces for the interactions on the whiteboard and on the pdas, the data formats to store the annotations and temporal data, and the network protocol for reliable wireless broadcast transmission. Small meetings have a very different interaction pattern. Instead of a lecturer that transmits knowledge, the participants collaborate in modifying documents. We developed groupware services that encourage these interactions and show how the different interaction patterns imply different network usages.
[4]	Stuart Pook, Eric Lecolinet, Guy Vaysseix, and Emmanuel Barillot. Control menus et vues contextuelles pour les interfaces zoomables. Revue d'Interaction Homme-Machine, 4(1):59--84, 2003. [ bib | PDF ] Les interfaces zoomables constituent un outil intéressant pour visualiser des espaces infor mationnels de grande taille. Cependant, le fait que ces interfaces fournissent généralement peu de contexte peut parfois rendre leur utilisation délicate. Les utilisateurs ont tendance à avoir du mal à se localiser précisément dans l'espace d'infor mation et à déter miner avec certitude la nature de leur point de focus. Nous proposons deux nouvelles aides temporaires transparentes qui facilitent la contextualisation du focus courant dans l'espace d'infor mation. Nous proposons également une représentation hiérarchique qui indique en per manence la structure de l'espace d'infor mation et la position de l'utilisateur dans cette structure. Nous proposons par ailleurs un nouveau type de menu contextuel, appelé « Control menu », qui permet de fluidifier l'interaction en sélectionnant et en contrôlant les opérations en un seul geste. Bien que son utilisation ne soit pas limitée à ce type d'interfaces, ce nouveau type de menu semble particulièrement bien adapté aux interfaces qui nécessitent de fréquentes interactions comme les interfaces zoomables. Deux interfaces zoomables implémentant ces nouvelles techniques peuvent être testées à l'URL http://www.infobiogen.fr/services/zomit/.
[5]	Eric Lecolinet and Stuart Pook. Interfaces zoomables et control menus. techniques focus+contexte pour la navigation interactive dans les bases de données. Les cahiers du numérique, 3(3/2002):191--210, December 2002. [ bib | PDF ]
[6]	Stuart Pook. Interaction and Context in Zoomable User Interfaces. PhD thesis, École Nationale Supérieure des Télécommunications, France, June 2001. [ bib | www ] Many interactive computer systems use menus as an important part of their interface. Menus allow users to select operations but not to control their execution. A second interactor, such as a dialog box, has to be used to control the chosen operation and thus complete the interaction. This decomposition of what is a single action from the user's point of view into two distinct steps slows down interaction with computer systems. This thesis proposes a new contextual pop-up menu, called a Control Menu, that includes proportional control of the chosen operation with immediate feedback. Using this menu gives a more fluid control of complex interfaces and has the advantage of an expert form of use that is very similar to, and thus easily learnt from, the novice usage. Interaction with databases and navigation within large information spaces are important tasks in many applications. Many visualization systems cause user disorientation as users find it difficult to understand their position within the information space and to locate desired information. This thesis proposes several new contextual aids for Zoomable User Interfaces that address these issues. The first aid, a hierarchical view of the information space, helps users understand their current position and the location of the desired information, and accelerates navigation. The second type of aid uses dynamically generated transparent and temporary views that are created and controlled by users in a single gesture. These interactive views overlay the current view of the focus with contextual or historical information which shows users what surrounds the current view or the route taken to arrive at that view. The effective use of these new aids requires a tight coupling between interaction and presentation which is achieved via the use of Control Menus.
[7]	Eric Lecolinet, Jean-Daniel Fekete, and Stuart Pook. Bibliothèques : comparaisons entre le réel et le virtuel en 3D, 2D zoomable et 2D arborescent. In ASTI 2001, pages 24--25, Cité des Sciences et de l'Industrie, Paris, April 2001. Association Française des Sciences et Technologies de l'Information. [ bib | HTML ]
[8]	Stuart Pook, Eric Lecolinet, Guy Vaysseix, and Emmanuel Barillot. Des aides transparentes de navigation et un nouveau type de menu pour les interfaces zoomables. In ERGO-IHM 2000, pages 170--177, Biarritz, France, October 2000. CRT ILS & ESTIA. [ bib | PDF | www ] Le fait que les interfaces zoomables (IZs) fournissent généralement peu de contexte peut parfois rendre leur utilisation difficile. Les utilisateurs ont rapidement tendance à ne plus savoir où ils sont dans l'espace d'information ni ce qu'ils sont en train de regarder. Nous proposons deux aides temporaires et transparentes qui montrent à l'utilisateur sa position dans l'espace d'information. Nous proposons également une représentation hiérarchique qui indique en permanence la structure de l'espace d'information et la position de l'utilisateur dans cette structure. Les IZs soulèvent également un problème d'interaction. Leurs commandes sont fréquemment utilisées et sur une interface changeante : le modèle WIMP est alors trop limité pour un accès rapide à toutes ces commandes sans l'utilisation de nouvelles techniques d'interaction. Nous présentons un nouveau type de menu, nommé control menu, qui facilite l'accès rapide à ces commandes et qui peut être utile dans d'autres types d'applications.
[9]	Stuart Pook, Eric Lecolinet, Guy Vaysseix, and Emmanuel Barillot. Context and interaction in zoomable user interfaces. In AVI 2000, pages 227--231 & 317, Palermo, Italy, May 2000. ACM Press. [ bib | PDF | www ] Zoomable User Interfaces (ZUIs) are difficult to use on large information spaces in part because they provide insufficient context. Even after a short period of navigation users no longer know where they are in the information space nor where to find the information they are looking for. We propose a temporary in-place context aid that helps users position themselves in ZUIs. This context layer is a transparent view of the context that is drawn over the users' focus of attention. A second temporary in-place aid is proposed that can be used to view already visited regions of the information space. This history layeris an overlapping transparent layer that adds a history mechanism to ZUIs. We complete these orientation aids with an additional window, a hierarchy tree, that shows users the structure of the information space and their current position within it. Context layers show users their position, history layers show them how they got there, and hierarchy trees show what information is available and where it is. ZUIs, especially those that include these new orientation aids, are difficult to use with standard interaction techniques. They provide a large number of commands which must be used frequently and on a changing image. The mouse and its buttons cannot provide a rapid access to all these commands without new interaction techniques. We propose a new type of menu, a control menu that facilitates the use of ZUIs and which we feel can also be useful in other types of applications.
[10]	Stuart Pook, Eric Lecolinet, Guy Vaysseix, and Emmanuel Barillot. Contexte et interaction dans les interfaces zoomables. In RJC-IHM 2000, pages 57--60, L'Île de Berder, France, May 2000. Laboratoire VALORIA (Université de Bretagne-Sud). [ bib | PDF | www ] Les interfaces zoomables (IZs) sont difficiles à utiliser sur un grand espace d'information, en partie parce qu'elles ne fournissent pas suffisamment de contexte à l'utilisateur. Même après une courte période d'utilisation, les utilisateurs ne savent plus où ils sont dans l'espace d'information ni ce qu'ils sont en train de regarder. Nous proposons deux nouvelles aides temporaires, une couche de contexte et une couche historique, qui aident les utilisateurs à se situer dans l'espace d'information. Elles sont transparentes et sont dessinées sur le focus de telle sorte que l'aide et le focus sont visibles. La couche de contexte contient une vue du contexte et aide l'utilisateur à se situer dans l'espace d'information. Avec la couche historique l'utilisateur peut revisiter le chemin parcouru dans l'espace d'information. Nous complétons ces aides avec une fenêtre supplémentaire qui montre à tout moment la structure de l'espace d'information et la position de l'utilisateur dans cet espace. De plus, il est difficile d'interagir avec des IZs avec des modèles classiques d'interaction. Les IZs fournissent des commandes qui doivent être utilisées souvent sur une image très changeante. La souris et ses boutons sont trop limités pour un accès rapide à toutes ces commandes sans l'utilisation de nouvelles techniques d'interaction. Nous présentons un nouveau type de menu, un control menu, qui facilite l'accès rapide à ces commandes. Notre IZ inclut ces nouvelles techniques et peut être testée à l'URL http://www.infobiogen.fr/services/zomit/.
[11]	Stuart Pook, Eric Lecolinet, Guy Vaysseix, and Emmanuel Barillot. Control menus: Execution and control in a single interactor. In CHI 2000 Extended Abstracts, pages 263--264, The Hague, The Netherlands, April 2000. ACM Press. [ bib | PDF | www ] We propose a new type of contextual pop-up menu called a control menu. These menus combine the selection of an operation and the control of this operation. They integrate up to two scroll bars or spin-boxes and thus allow users to keep their attention focused on the menu during the operation. Control menus can have sub-menus, and also retain the novice and expert modes of use found in marking menus. We describe control menus and how they are useful in different types of user interfaces. A program incorporating our control menus can be tested at http://www.infobiogen.fr/services/zomit/.
[12]	Emmanuel Barillot, Stuart Pook, Frédéric Guyon, Christophe Cussat-Blanc, Éric Viara, and Guy Vaysseix. The HuGeMap database: interconnection and visualization of human genome maps. Nucleic Acids Research, 27(1):119--122, 1999. [ bib | PDF | www ] The HuGeMap database stores the major genetic and physical maps of the human genome. HuGeMap is accessible on the Web at http://www.infobiogen.fr/services/Hugemap and through a CORBA server. A standard genome map data format for the interconnection of genome map databases was defined in collaboration with the EBI. The HuGeMap CORBA server provides this interconnection using the interface definition language IDL. Two graphical user interfaces were developed for the visualization of the HuGeMap data: ZoomMap (http://www.infobiogen.fr/services/zomit/ZoomMap.html ) for navigation by zooming and data transformation via magic lenses, and MappetShow (http://www.infobiogen.fr/services/Mappet ) for visualizing and comparing maps.
[13]	Stuart Pook, Guy Vaysseix, and Emmanuel Barillot. Zomit: biological data visualization and browsing. Bioinformatics, 14(9):807--814, October 1998. [ bib | PDF | www ] Motivation: The problems caused by the difficulty in visualizing and browsing biological databases have become crucial. Scientists can no longer interact directly with the huge amount of available data. However future breakthroughs in biology depend on this interaction. We propose a new metaphor for biological data visualization and browsing that allows navigation in very large databases in an intuitive way. The concepts underlying our approach are based on navigation and visualization with zooming, semantic zooming, and portals; and on data transformation via magic lenses. We think that these new visualization and navigation techniques should be applied globally to a federation of biological databases. Results: We have implemented a generic tool, called Zomit, that provides an application programming interface for developing servers for such navigation and visualization, and a generic architecture-independent client (Java applet) that queries such servers. As an illustration of the capabilities of our approach, we have developed ZoomMap, a prototype browser for the Hugemap human genome map database. Availability: Zomit and ZoomMap are available at the URL http://www.infobiogen.fr/services/zomit. Contact: stuart@infobiogen.fr
[14]	Eric Viara, Stuart Pook, Frédéric Guyon, Christophe Cussat-Blanc, Guy Vaysseix, and Emmanuel Barillot. Distributing and visualising biological objects at infobiogen. In Objects in Bioinformatics '98, Hinxton Hall, Cambridge, UK, August 1998. European Bioinformatics Institute. [ bib | HTML ] Our aim is to design a complete object-oriented environment for biological data management. In that respect, Sysra Informatique and Infobiogen first developed an object-oriented database management system EyeDB with funding from Sysra Informatique, ANVAR and the EC BIOTECH program. Then we have implemented a complete Java mapping of the EyeDB object model. We also designed a CORBA layer on top of EyeDB. An ad-hoc compiler can automatically generate an IDL and an ORB server from the database schema. A language allows to define a more elaborate mapping from the database schema to a target IDL. This allows to export different views from the same database. It also permits to target a common IDL from databases with different schemas. We believe that the biological community should now adopt a standard to define the semantic of its objects. With colleagues at EBI (Patricia Rodriguez-Tomé et al), we have defined a standard description for the genome maps in the form of an IDL and we submit it to the bioinformatic community for adoption and comments. This is done through the Life Sciences Research Task Force of the Object Management Group. Biological data now constitutes a huge amount of information with which it is difficult to interact. Particularly it is quite impossible to visualise these large spaces of information with the traditional display techniques. We propose to use new concepts of visualisation and navigation well suited for huge volume of data. We have implemented these new concepts in two applications: a map viewer, (MappetShow) that gives a clear view of very dense maps (several hundreds of markers); it uses the following concepts: (multi-)focus+context techniques, dynamic layout, multi-scaling display. a generic navigator for large information spaces: Zomit. It consists of a generic Java applet client and a C++ library used to develop a server. It has been used to implement a genome browser: ZoomMap. It is based on the concepts of zooming, semantic zooming, portals and magic lenses.
[15]	Eric Viara, Stuart Pook, Bruno Lacroix, Michel Tissot, Laurent Atlan, Annick Cohen-Akenine, Guy Vaysseix, and Emmanuel Barillot. The IDB database system and its use in the human genome project: HUGEMAP. In Interconnection of Molecular Biology Databases, Stanford, CA, USA, August 1994. SRI International Artificial Intelligence Center. only published electronically. [ bib | HTML ]
[16]	Ilya Chumakov, Phillipe Rigault, Sophie Guillou, Pierre Ougen, Alain Billault, Ghislaine Guasconi, Patricia Gervy, Isabelle LeGall, Pascal Soularue, Laurent Grinas, Lydie Bougueleret, Christine Bellanné-Chantelot, Brune Lacroix, Emmanuel Barillot, Philippe Gesnouin, Stuart Pook, Guy Vaysseix, Gerard Frelat, Annette Schmitz, Jean-Luc Sambucy, Assumpcio Bosch, Xavier Estivill, Jean Weissenbach, Alain Vignal, Harold Riethman, David Cox, David Patterson, Kathleen Gardiner, Masahira Hattori, Yoshiyuki Sakaki, Hitoshi Ichikawa, Misao Ohki, Denis Le Paslier, Roland Heilig, Stylianos Antonarakis, and Daniel Cohen. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature, 359:380--387, October 1992. [ bib | www ] A continuous array of overlapping clones covering the entire human chromosome 21q was contructed from human yeast artificial chromosome libraries using sequence-tagged sites as landmarks specifically detected by polymerase chain reaction. The yeast artificial chromosome contiguous unit starts with pericentromeric and ends with subtelomeric loci of 21q. The resulting order of sequence-tagged sites is consistent with other physical and genetic mapping data. This set of overlapping clones will promote our knowledge of the structure of this chromosome and the function of its genes.
[17]	Christine Bellanné-Chantelot, Bruno Lacroix, Pierre Ougen, Alain Billaut, Sandrine Beaufils, Stéphane Bertrand, Isabelle Georges, Fabrice Glibert, Isabelle Gros, Georges Lucotte, Laurent Susini, Jean-Jacques Codani, Philippe Gesnouin, Stuart Pook, Guy Vaysseix, Jennifer Lu-Kuo, Thomas Ried, David Ward, Ilya Chumakov, Denis Le Paslier, Emmanuel Barillot, and Daniel Cohen. Mapping the whole human genome by fingerprinting yeast artificial chromosomes. Cell, 70:1059--1068, September 1992. [ bib | www ] Physical mapping of the human genome has until now been envisioned through single chromosome strategies. We demonstrate that by using the large insert yeast artificial chromosomes (YACs) a whole genome approach becomes feasible. YACs (22,000) of 810 kb mean size (5 genome equivalents) have been fingerprinted to obtain individual patterns of restriction fragments detected by a LINE-1 (L1) probe. More than 1000 contigs were assembled. Ten randomly chosen contigs were validated by metaphase chromosome fluorescence in situ hybridization, as well as by analyzing the inter-Alu PCR patterns of their constituent YACs. We estimate that 15 mainly the L1-rich regions, is already covered with contigs larger than 3 Mb.
[18]	Stuart L. Pook and Jason Catlett. Making sense out of searching. In Proceedings of the Online Information Conference, pages 69--78, Sydney, NSW, Australia, January 1988. Library Association of Australia (Information Science Section). [ bib | PDF ] The trouble with text retrieval using keywords is that English words are imprecise: there may be many words for the entity the user wants, and each of these may also have other (unintended) meanings. To get closer to the dream of `retrieve what I mean, not what I say,' systems need to take into account the sense in which each word is used in the text stored, and to get from the user a more precise and complete statement of the concept sought. Recent research on machine-readable dictionaries and thesauri may soon make this a reality.
[19]	Stuart Leonard Pook. Experiments with machine-readable dictionaries. B.Ec Honour's thesis, Basser Department of Computer Science, The University of Sydney, Australia, December 1987. [ bib | PDF ] Machine-readable dictionaries are just starting to become available to information scientists and lexicographers. Many other databases of machine-readable text such as news wires, library catalogues and collections of scientific papers are also becoming available as well as increasing in size and coverage. New sets of tools are required to efficiently store and access these new sources of information. This thesis explores some of the ways that machine- readable dictionaries and thesauri can be used in the transmission and retrieval of these new databases. A piece of text must first be understood before it can be processed by an intelligent retrieval system. The most basic level of understanding is at the word level; the computer needs to understand in which sense the words in the text are being used. Machine-readable dictionaries and thesauri can be used in this task provided they are first stored in suitable databases. Once the pieces of text have been analysed they must then be classified and transmitted. Then the user of a database must be provided with the tools necessary to retrieve interesting items. Algorithms that can be used to implement new methods of text retrieval and the ways in which they can be used in commercial products are presented.
[20]	Stuart L. Pook. Synthetic portfolios and currency options. B.Ec Honour's thesis, Department of Econometrics, The University of Sydney, Australia, 1986. [ bib | PDF ]

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