9 results on '"Le Novère, Nicolas"'
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2. A community-driven global reconstruction of human metabolism
- Author
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Thiele, Ines, primary, Swainston, Neil, additional, Fleming, Ronan M T, additional, Hoppe, Andreas, additional, Sahoo, Swagatika, additional, Aurich, Maike K, additional, Haraldsdottir, Hulda, additional, Mo, Monica L, additional, Rolfsson, Ottar, additional, Stobbe, Miranda D, additional, Thorleifsson, Stefan G, additional, Agren, Rasmus, additional, Bölling, Christian, additional, Bordel, Sergio, additional, Chavali, Arvind K, additional, Dobson, Paul, additional, Dunn, Warwick B, additional, Endler, Lukas, additional, Hala, David, additional, Hucka, Michael, additional, Hull, Duncan, additional, Jameson, Daniel, additional, Jamshidi, Neema, additional, Jonsson, Jon J, additional, Juty, Nick, additional, Keating, Sarah, additional, Nookaew, Intawat, additional, Le Novère, Nicolas, additional, Malys, Naglis, additional, Mazein, Alexander, additional, Papin, Jason A, additional, Price, Nathan D, additional, Selkov, Evgeni, additional, Sigurdsson, Martin I, additional, Simeonidis, Evangelos, additional, Sonnenschein, Nikolaus, additional, Smallbone, Kieran, additional, Sorokin, Anatoly, additional, van Beek, Johannes H G M, additional, Weichart, Dieter, additional, Goryanin, Igor, additional, Nielsen, Jens, additional, Westerhoff, Hans V, additional, Kell, Douglas B, additional, Mendes, Pedro, additional, and Palsson, Bernhard Ø, additional
- Published
- 2013
- Full Text
- View/download PDF
3. Erratum: Corrigendum: The BioPAX community standard for pathway data sharing
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Demir, Emek, primary, Cary, Michael P, additional, Paley, Suzanne, additional, Fukuda, Ken, additional, Lemer, Christian, additional, Vastrik, Imre, additional, Wu, Guanming, additional, D'Eustachio, Peter, additional, Schaefer, Carl, additional, Luciano, Joanne, additional, Schacherer, Frank, additional, Martinez-Flores, Irma, additional, Hu, Zhenjun, additional, Jimenez-Jacinto, Veronica, additional, Joshi-Tope, Geeta, additional, Kandasamy, Kumaran, additional, Lopez-Fuentes, Alejandra C, additional, Mi, Huaiyu, additional, Pichler, Elgar, additional, Rodchenkov, Igor, additional, Splendiani, Andrea, additional, Tkachev, Sasha, additional, Zucker, Jeremy, additional, Gopinath, Gopal, additional, Rajasimha, Harsha, additional, Ramakrishnan, Ranjani, additional, Shah, Imran, additional, Syed, Mustafa, additional, Anwar, Nadia, additional, Babur, Özgün, additional, Blinov, Michael, additional, Brauner, Erik, additional, Corwin, Dan, additional, Donaldson, Sylva, additional, Gibbons, Frank, additional, Goldberg, Robert, additional, Hornbeck, Peter, additional, Luna, Augustin, additional, Murray-Rust, Peter, additional, Neumann, Eric, additional, Reubenacker, Oliver, additional, Samwald, Matthias, additional, van Iersel, Martijn, additional, Wimalaratne, Sarala, additional, Allen, Keith, additional, Braun, Burk, additional, Whirl-Carrillo, Michelle, additional, Cheung, Kei-Hoi, additional, Dahlquist, Kam, additional, Finney, Andrew, additional, Gillespie, Marc, additional, Glass, Elizabeth, additional, Gong, Li, additional, Haw, Robin, additional, Honig, Michael, additional, Hubaut, Olivier, additional, Kane, David, additional, Krupa, Shiva, additional, Kutmon, Martina, additional, Leonard, Julie, additional, Marks, Debbie, additional, Merberg, David, additional, Petri, Victoria, additional, Pico, Alex, additional, Ravenscroft, Dean, additional, Ren, Liya, additional, Shah, Nigam, additional, Sunshine, Margot, additional, Tang, Rebecca, additional, Whaley, Ryan, additional, Letovksy, Stan, additional, Buetow, Kenneth H, additional, Rzhetsky, Andrey, additional, Schachter, Vincent, additional, Sobral, Bruno S, additional, Dogrusoz, Ugur, additional, McWeeney, Shannon, additional, Aladjem, Mirit, additional, Birney, Ewan, additional, Collado-Vides, Julio, additional, Goto, Susumu, additional, Hucka, Michael, additional, Le Novère, Nicolas, additional, Maltsev, Natalia, additional, Pandey, Akhilesh, additional, Thomas, Paul, additional, Wingender, Edgar, additional, Karp, Peter D, additional, Sander, Chris, additional, and Bader, Gary D, additional
- Published
- 2012
- Full Text
- View/download PDF
4. The BioPAX community standard for pathway data sharing
- Author
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Demir, Emek, primary, Cary, Michael P, additional, Paley, Suzanne, additional, Fukuda, Ken, additional, Lemer, Christian, additional, Vastrik, Imre, additional, Wu, Guanming, additional, D'Eustachio, Peter, additional, Schaefer, Carl, additional, Luciano, Joanne, additional, Schacherer, Frank, additional, Martinez-Flores, Irma, additional, Hu, Zhenjun, additional, Jimenez-Jacinto, Veronica, additional, Joshi-Tope, Geeta, additional, Kandasamy, Kumaran, additional, Lopez-Fuentes, Alejandra C, additional, Mi, Huaiyu, additional, Pichler, Elgar, additional, Rodchenkov, Igor, additional, Splendiani, Andrea, additional, Tkachev, Sasha, additional, Zucker, Jeremy, additional, Gopinath, Gopal, additional, Rajasimha, Harsha, additional, Ramakrishnan, Ranjani, additional, Shah, Imran, additional, Syed, Mustafa, additional, Anwar, Nadia, additional, Babur, Özgün, additional, Blinov, Michael, additional, Brauner, Erik, additional, Corwin, Dan, additional, Donaldson, Sylva, additional, Gibbons, Frank, additional, Goldberg, Robert, additional, Hornbeck, Peter, additional, Luna, Augustin, additional, Murray-Rust, Peter, additional, Neumann, Eric, additional, Ruebenacker, Oliver, additional, Samwald, Matthias, additional, van Iersel, Martijn, additional, Wimalaratne, Sarala, additional, Allen, Keith, additional, Braun, Burk, additional, Whirl-Carrillo, Michelle, additional, Cheung, Kei-Hoi, additional, Dahlquist, Kam, additional, Finney, Andrew, additional, Gillespie, Marc, additional, Glass, Elizabeth, additional, Gong, Li, additional, Haw, Robin, additional, Honig, Michael, additional, Hubaut, Olivier, additional, Kane, David, additional, Krupa, Shiva, additional, Kutmon, Martina, additional, Leonard, Julie, additional, Marks, Debbie, additional, Merberg, David, additional, Petri, Victoria, additional, Pico, Alex, additional, Ravenscroft, Dean, additional, Ren, Liya, additional, Shah, Nigam, additional, Sunshine, Margot, additional, Tang, Rebecca, additional, Whaley, Ryan, additional, Letovksy, Stan, additional, Buetow, Kenneth H, additional, Rzhetsky, Andrey, additional, Schachter, Vincent, additional, Sobral, Bruno S, additional, Dogrusoz, Ugur, additional, McWeeney, Shannon, additional, Aladjem, Mirit, additional, Birney, Ewan, additional, Collado-Vides, Julio, additional, Goto, Susumu, additional, Hucka, Michael, additional, Le Novère, Nicolas, additional, Maltsev, Natalia, additional, Pandey, Akhilesh, additional, Thomas, Paul, additional, Wingender, Edgar, additional, Karp, Peter D, additional, Sander, Chris, additional, and Bader, Gary D, additional
- Published
- 2010
- Full Text
- View/download PDF
5. Erratum: The Systems Biology Graphical Notation
- Author
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Le Novère, Nicolas, primary, Hucka, Michael, additional, Mi, Huaiyu, additional, Moodie, Stuart, additional, Schreiber, Falk, additional, Sorokin, Anatoly, additional, Demir, Emek, additional, Wegner, Katja, additional, Aladjem, Mirit I, additional, Wimalaratne, Sarala M, additional, Bergman, Frank T, additional, Gauges, Ralph, additional, Ghazal, Peter, additional, Kawaji, Hideya, additional, Li, Lu, additional, Matsuoka, Yukiko, additional, Villéger, Alice, additional, Boyd, Sarah E, additional, Calzone, Laurence, additional, Courtot, Melanie, additional, Dogrusoz, Ugur, additional, Freeman, Tom C, additional, Funahashi, Akira, additional, Ghosh, Samik, additional, Jouraku, Akiya, additional, Kim, Sohyoung, additional, Kolpakov, Fedor, additional, Luna, Augustin, additional, Sahle, Sven, additional, Schmidt, Esther, additional, Watterson, Steven, additional, Wu, Guanming, additional, Goryanin, Igor, additional, Kell, Douglas B, additional, Sander, Chris, additional, Sauro, Herbert, additional, Snoep, Jacky L, additional, Kohn, Kurt, additional, and Kitano, Hiroaki, additional
- Published
- 2009
- Full Text
- View/download PDF
6. A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology
- Author
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Herrgård, Markus J, primary, Swainston, Neil, additional, Dobson, Paul, additional, Dunn, Warwick B, additional, Arga, K Yalçin, additional, Arvas, Mikko, additional, Blüthgen, Nils, additional, Borger, Simon, additional, Costenoble, Roeland, additional, Heinemann, Matthias, additional, Hucka, Michael, additional, Le Novère, Nicolas, additional, Li, Peter, additional, Liebermeister, Wolfram, additional, Mo, Monica L, additional, Oliveira, Ana Paula, additional, Petranovic, Dina, additional, Pettifer, Stephen, additional, Simeonidis, Evangelos, additional, Smallbone, Kieran, additional, Spasié, Irena, additional, Weichart, Dieter, additional, Brent, Roger, additional, Broomhead, David S, additional, Westerhoff, Hans V, additional, Kürdar, Betül, additional, Penttilä, Merja, additional, Klipp, Edda, additional, Palsson, Bernhard Ø, additional, Sauer, Uwe, additional, Oliver, Stephen G, additional, Mendes, Pedro, additional, Nielsen, Jens, additional, and Kell, Douglas B, additional
- Published
- 2008
- Full Text
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7. The Systems Biology Graphical Notation.
- Author
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Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, and Kitano H
- Subjects
- History, 20th Century, Internet, Computer Graphics history, Software, Systems Biology history
- Abstract
Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.
- Published
- 2009
- Full Text
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8. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.
- Author
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Taylor CF, Field D, Sansone SA, Aerts J, Apweiler R, Ashburner M, Ball CA, Binz PA, Bogue M, Booth T, Brazma A, Brinkman RR, Michael Clark A, Deutsch EW, Fiehn O, Fostel J, Ghazal P, Gibson F, Gray T, Grimes G, Hancock JM, Hardy NW, Hermjakob H, Julian RK Jr, Kane M, Kettner C, Kinsinger C, Kolker E, Kuiper M, Le Novère N, Leebens-Mack J, Lewis SE, Lord P, Mallon AM, Marthandan N, Masuya H, McNally R, Mehrle A, Morrison N, Orchard S, Quackenbush J, Reecy JM, Robertson DG, Rocca-Serra P, Rodriguez H, Rosenfelder H, Santoyo-Lopez J, Scheuermann RH, Schober D, Smith B, Snape J, Stoeckert CJ Jr, Tipton K, Sterk P, Untergasser A, Vandesompele J, and Wiemann S
- Subjects
- Databases as Topic, Internet, Oligonucleotide Array Sequence Analysis standards, Proteomics standards, Vocabulary, Controlled, Guidelines as Topic, Information Dissemination, Research Design standards
- Published
- 2008
- Full Text
- View/download PDF
9. Minimum information requested in the annotation of biochemical models (MIRIAM).
- Author
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Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, and Wanner BL
- Subjects
- Biochemistry standards, Cell Physiological Phenomena, Guidelines as Topic, Information Dissemination methods, Information Storage and Retrieval standards, Biochemistry methods, Databases, Factual, Documentation methods, Documentation standards, Information Storage and Retrieval methods, Models, Biological, Terminology as Topic
- Abstract
Most of the published quantitative models in biology are lost for the community because they are either not made available or they are insufficiently characterized to allow them to be reused. The lack of a standard description format, lack of stringent reviewing and authors' carelessness are the main causes for incomplete model descriptions. With today's increased interest in detailed biochemical models, it is necessary to define a minimum quality standard for the encoding of those models. We propose a set of rules for curating quantitative models of biological systems. These rules define procedures for encoding and annotating models represented in machine-readable form. We believe their application will enable users to (i) have confidence that curated models are an accurate reflection of their associated reference descriptions, (ii) search collections of curated models with precision, (iii) quickly identify the biological phenomena that a given curated model or model constituent represents and (iv) facilitate model reuse and composition into large subcellular models.
- Published
- 2005
- Full Text
- View/download PDF
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