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1

The Systems Biology Graphical Notation

Novère, Nicolas Le, Hucka, Michael, Mi, Huaiyu, Moodie, Stuart, Schreiber, Falk, Sorokin, Anatoly, Demir, Emek, Wegner, Katja, Aladjem, Mirit I, Wimalaratne, Sarala M

Journal:

Nature Biotechnology

Year:

2009

Language:

english

File:

PDF, 1.03 MB

english, 2009

2

Computational Systems Neurobiology || XPPAUT

Year:

2012

Language:

english

File:

PDF, 480 KB

english, 2012

3

Designing and encoding models for synthetic biology

Endler, L., Rodriguez, N., Juty, N., Chelliah, V., Laibe, C., Li, C., Le Novere, N.

Journal:

Journal of The Royal Society Interface

Year:

2009

Language:

english

File:

PDF, 501 KB

english, 2009

4

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation

Touré, Vasundra, Le Novère, Nicolas, Waltemath, Dagmar, Wolkenhauer, Olaf, Ouellette, Francis

Journal:

PLoS Computational Biology

Year:

2018

Language:

english

File:

PDF, 1.26 MB

english, 2018

5

10.1038/19756

Changeux, Jean-Pierre, Marubio, Lisa M., Arroyo-Jimenez, Maria del Mar, Cordero-Erausquin, Matilde, Léna, Clément, Novère, Nicolas Le, d'Exaerde, Alban de Kerchove, Huchet, Monique, Damaj, M. Imad

Journal:

Year:

1999

Language:

english

File:

PDF, 458 KB

english, 1999

6

Erratum: The Systems Biology Graphical Notation

Le Novère, Nicolas, Hucka, Michael, Mi, Huaiyu, Moodie, Stuart, Schreiber, Falk, Sorokin, Anatoly, Demir, Emek, Wegner, Katja, Aladjem, Mirit I, Wimalaratne, Sarala M

Journal:

Nature Biotechnology

Year:

2009

Language:

english

File:

PDF, 65 KB

english, 2009

7

Nicotinic Receptors at the Amino Acid Level

Corringer, Pierre-Jean, Novère, Nicolas Le, Changeux, Jean-Pierre

Journal:

Annual Review of Pharmacology

Year:

2000

Language:

english

File:

PDF, 418 KB

english, 2000

8

Quantitative and logic modelling of molecular and gene networks

Le Novère, Nicolas

Journal:

Nature Reviews Genetics

Year:

2015

Language:

english

File:

PDF, 581 KB

english, 2015

9

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

Sorokin, Anatoly, Le Novère, Nicolas, Luna, Augustin, Czauderna, Tobias, Demir, Emek, Haw, Robin, Mi, Huaiyu, Moodie, Stuart, Schreiber, Falk, Villéger, Alice

Journal:

Journal of Integrative Bioinformatics

Year:

2015

Language:

english

File:

PDF, 2.53 MB

english, 2015

10

Epicardial cells derived from human embryonic stem cells augment cardiomyocyte-driven heart regeneration

Bargehr, Johannes, Ong, Lay Ping, Colzani, Maria, Davaapil, Hongorzul, Hofsteen, Peter, Bhandari, Shiv, Gambardella, Laure, Le Novère, Nicolas, Iyer, Dharini, Sampaziotis, Fotios, Weinberger, Florian,

Journal:

Nature Biotechnology

Year:

2019

Language:

english

File:

PDF, 4.16 MB

english, 2019

11

LibSBGN: Electronic Processing of SBGN maps

Demir, Emek, Dogrusoz, Ugur, Le Novère, Nicolas, Matsuoka, Yukiko, Sorokin, Anatoly, Funahashi, Akira, Mi, Huaiyu, Kitano, Hiroaki, Aladjem, Mirit, van Iersel, Martijn, Blinov, Michael, Boyd, Sarah, V

Journal:

Bioentrepreneur

Year:

2010

File:

PDF, 1.38 MB

2010

12

Localization of [3H]nicotine, [3H]cytisine, [3H]epibatidine, and [125I]α-bungarotoxin binding sites in the brain of Macaca mulatta

Zhi-Yan Han, Michele Zoli, Ana Cardona, Jean-Pierre Bourgeois, Jean-Pierre Changeux, Nicolas Le Novère

Journal:

The Journal of Comparative Neurology

Year:

2003

Language:

english

File:

PDF, 556 KB

english, 2003

13

The diversity of subunit composition in nAChRs: Evolutionary origins, physiologic and pharmacologic consequences

Nicolas Le Novère, Pierre-Jean Corringer, Jean-Pierre Changeux

Journal:

Developmental Neurobiology

Year:

2002

Language:

english

File:

PDF, 229 KB

english, 2002

14

Localization of nAChR subunit mRNAs in the brain of Macaca mulatta

Zhi-Yan Han, Nicolas Le Novère, Michele Zoli, Joseph A. Hill Jr, Nicolas Champtiaux, Jean-Pierre Changeux

Journal:

European Journal of Neuroscience

Year:

2000

Language:

english

File:

PDF, 1.73 MB

english, 2000

15

Acute and long-term changes in the mesolimbic dopamine pathway after systemic or local single nicotine injections

R. Ferrari, N. Le Novère, M. R. Picciotto, J. P. Changeux, M. Zoli

Journal:

European Journal of Neuroscience

Year:

2002

Language:

english

File:

PDF, 358 KB

english, 2002

16

Enhanced Hemicholinium Binding and Attenuated Dendrite Branching in Cognitively Impaired Acetylcholinesterase-Transgenic Mice

R. Beeri, N. Le Novère, R. Mervis, T. Huberman, E. Grauer, J. P. Changeux, H. Soreq

Journal:

Journal of Neurochemistry

Year:

1997

Language:

english

File:

PDF, 1.69 MB

english, 1997

17

New Otx2 mRNA isoforms expressed in the mouse brain

Virginie Courtois, Gilles Chatelain, Zhi-Yan Han, Nicolas Le Novère, Gilbert Brun, Thomas Lamonerie

Journal:

Journal of Neurochemistry

Year:

2003

Language:

english

File:

PDF, 452 KB

english, 2003

18

Software that goes with the flow in systems biology

Michael Hucka, Nicolas Le Novère

Journal:

Year:

2010

Language:

english

File:

PDF, 258 KB

english, 2010

19

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

Chen Li, Marco Donizelli, Nicolas Rodriguez, Harish Dharuri, Lukas Endler, Vijayalakshmi Chelliah, Lu Li, Enuo He, Arnaud Henry, Melanie I Stefan, Jacky L Snoep, Michael Hucka, Nicolas Le Novère, Cami

Journal:

BMC Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.71 MB

english, 2010

20

DARPP-32: molecular integration of phosphorylation potential

N. Le Novère, L. Li, J.-A. Girault

Journal:

Cellular and Molecular Life Sciences

Year:

2008

Language:

english

File:

PDF, 392 KB

english, 2008

21

Looking inside the box: bacterial transistor arrays

Thomas S. Shimizu, Nicolas Le Novère

Journal:

Molecular Microbiology

Year:

2008

Language:

english

File:

PDF, 179 KB

english, 2008

22

Neuronal Nicotinic Receptor a6 Subunit mRNA is Selectively Concentrated in Catecholaminergic Nuclei of the Rat Brain

Nicolas Le Novere, Michele Zoli, Jean-Pierre Changeux

Journal:

European Journal of Neuroscience

Year:

1996

Language:

english

File:

PDF, 3.43 MB

english, 1996

23

10.1038/35041030

Bray, Dennis, Simon Shimizu, Thomas, Le Novère, Nicolas, Daniel Levin, Matthew, Beavil, Andrew J., Sutton, Brian J.

Journal:

Nature Cell Biology

Year:

2000

Language:

english

File:

PDF, 576 KB

english, 2000

24

10.1038/78124

Rogner, Ute C., Spyropoulos, Demetri D., Le Novère, Nicolas, Changeux, Jean-Pierre, Avner, Philip

Journal:

Nature Genetics

Year:

2000

Language:

english

File:

PDF, 1.01 MB

english, 2000

25

Minimum information requested in the annotation of biochemical models (MIRIAM)

Novère, Nicolas Le, Finney, Andrew, Hucka, Michael, Bhalla, Upinder S, Campagne, Fabien, Collado-Vides, Julio, Crampin, Edmund J, Halstead, Matt, Klipp, Edda, Mendes, Pedro

Journal:

Nature Biotechnology

Year:

2005

Language:

english

File:

PDF, 216 KB

english, 2005

26

Novel pharmacological targets for the treatment of Parkinson's disease

Schapira, Anthony H. V., Bezard, Erwan, Brotchie, Jonathan, Calon, Frédéric, Collingridge, Graham L., Ferger, Borris, Hengerer, Bastian, Hirsch, Etienne, Jenner, Peter, Novère, Nicolas Le

Journal:

Nature Reviews Drug Discovery

Year:

2006

Language:

english

File:

PDF, 655 KB

english, 2006

27

63 Predicted secondary structure of a nicotinic acetylcholine receptor subunit. Incorporation of predicted solvent accessibility and experimental data into a two dimensional representation

N. Le Novère, P.J. Corringer, J.P. Changeux

Journal:

Journal of Physiology-Paris

Year:

1998

Language:

english

File:

PDF, 109 KB

english, 1998

28

SysBioMed report: Advancing systems biology for medical applications

Wolkenhauer, O., Fell, D., De Meyts, P., Bluthgen, N., Herzel, H., Le Novere, N., Hofer, T., Schurrle, K., van Leeuwen, I.

Journal:

IET Systems Biology

Year:

2009

Language:

english

File:

PDF, 172 KB

english, 2009

29

Ranked retrieval of Computational Biology models

Ron Henkel, Lukas Endler, Andre Peters, Nicolas Le Novère, Dagmar Waltemath

Journal:

BMC Bioinformatics

Year:

2010

Language:

english

File:

PDF, 1.57 MB

english, 2010

30

The Molecular Pages of the mesotelencephalic dopamine consortium (DopaNet)

Nicolas Le Novère, Marco Donizelli

Journal:

BMC Bioinformatics

Year:

2004

Language:

english

File:

PDF, 277 KB

english, 2004

31

SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML)

Nicolas Rodriguez, Marco Donizelli, Nicolas Le Novère

Journal:

BMC Bioinformatics

Year:

2007

Language:

english

File:

PDF, 490 KB

english, 2007

32

Model storage, exchange and integration

Nicolas Le Novère

Journal:

BMC Neuroscience

Year:

2006

Language:

english

File:

PDF, 1.75 MB

english, 2006

33

The long journey to a Systems Biology of neuronal function

Nicolas Le Novère

Journal:

BMC Systems Biology

Year:

2007

Language:

english

File:

PDF, 215 KB

english, 2007

34

MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology

Camille Laibe, Nicolas Le Novère

Journal:

BMC Systems Biology

Year:

2007

Language:

english

File:

PDF, 799 KB

english, 2007

35

Molecules for memory: modelling CaMKII

Melanie Stefan, Nicolas Le Novere

Journal:

BMC Systems Biology

Year:

2007

Language:

english

File:

PDF, 138 KB

english, 2007

36

Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters

Melanie I Stefan, Stuart J Edelstein, Nicolas Le Novère

Journal:

BMC Systems Biology

Year:

2009

Language:

english

File:

PDF, 464 KB

english, 2009

37

Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

Dominic P Tolle, Nicolas Le Novère

Journal:

BMC Systems Biology

Year:

2010

Language:

english

File:

PDF, 1.56 MB

english, 2010

38

Brownian diffusion of AMPA receptors is sufficient to explain fast onset of LTP

Dominic P Tolle, Nicolas Le Novère

Journal:

BMC Systems Biology

Year:

2010

Language:

english

File:

PDF, 2.09 MB

english, 2010

39

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Dagmar Waltemath, Richard Adams, Frank T Bergmann, Michael Hucka, Fedor Kolpakov, Andrew K Miller, Ion I Moraru, David Nickerson, Sven Sahle, Jacky L Snoep, Nicolas Le Novère

Journal:

BMC Systems Biology

Year:

2011

Language:

english

File:

PDF, 927 KB

english, 2011

40

Computational Systems Neurobiology Volume 7053 || Reconstructing Models from Proteomics Data

Year:

2012

Language:

english

File:

PDF, 1.05 MB

english, 2012

41

Conformational spread in a ring of proteins: a stochastic approach to allostery

T.A.J. Duke, N. Le Novère, D. Bray

Journal:

Journal of Molecular Biology

Year:

2001

Language:

english

File:

PDF, 2.12 MB

english, 2001

42

Comparative models of P2X2 receptor support inter-subunit ATP-binding sites

Guillaume Guerlet, Antoine Taly, Lia Prado de Carvalho, Adeline Martz, Ruotian Jiang, Alexandre Specht, Nicolas Le Novère, Thomas Grutter

Journal:

Biochemical and Biophysical Research Communications

Year:

2008

Language:

english

File:

PDF, 891 KB

english, 2008

43

Brain nicotinic receptors: structure and regulation, role in learning and reinforcement

Jean-Pierre Changeux, Daniel Bertrand, Pierre-Jean Corringer, Stanislas Dehaene, Stuart Edelstein, Clément Léna, Nicolas Le Novère, Lisa Marubio, Marina Picciotto, Michele Zoli

Journal:

Brain Research Reviews

Year:

1998

Language:

english

File:

PDF, 713 KB

english, 1998

44

Ion Channels, a Practical Approach

Nicolas Le Novère, Lisa Marubio, Clément Léna

Journal:

Trends in Neurosciences

Year:

1996

Language:

english

File:

PDF, 69 KB

english, 1996

45

Computational Systems Neurobiology || NEST by Example: An Introduction to the Neural Simulation Tool NEST

Year:

2012

Language:

english

File:

PDF, 503 KB

english, 2012

46

Computational Systems Neurobiology || Using Chemical Kinetics to Model Neuronal Signalling Pathways

Year:

2012

Language:

english

File:

PDF, 528 KB

english, 2012

47

Computational Systems Neurobiology || Functional Genomics and Molecular Networks Gene Expression Regulations in Complex Diseases: Down Syndrome as a Case Study

Year:

2012

Language:

english

File:

PDF, 466 KB

english, 2012

48

Computational Systems Neurobiology || Spatial Organization and Diffusion in Neuronal Signaling

Year:

2012

Language:

english

File:

PDF, 894 KB

english, 2012

49

Computational Systems Neurobiology || Multi-compartmental Models of Neurons

Year:

2012

Language:

english

File:

PDF, 680 KB

english, 2012

50

Computational Systems Neurobiology || Noise in Neurons and Other Constraints

Year:

2012

Language:

english

File:

PDF, 866 KB

english, 2012