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hal-01222896v1  Journal articles
Alex Mitchell, Hsin-Yu Chang, Louise Daugherty, Matthew Fraser, Sarah Hunter et al.  The InterPro protein families database: the classification resource after 15 years
Nucleic Acids Research, Oxford University Press, 2015, 43 (D1), pp.D213-D221. ⟨10.1093/nar/gku1243⟩
hal-01605696v1  Journal articles
P. Schlapfer, P. F. Zhang, C. A. Wang, T. Kim, M. Banf et al.  Genome-wide prediction of metabolic enzymes, pathways, and gene clusters in plants
Plant Physiology, American Society of Plant Biologists, 2017, 173 (4), pp.2041-2059. ⟨10.1104/pp.16.01942⟩
hal-00428159v2  Journal articles
Thomas Handorf, Nils Christian, Oliver Ebenhöh, Daniel Kahn. An environmental perspective on metabolism
Journal of Theoretical Biology, Elsevier, 2008, 252 (3), pp.530-537. ⟨10.1016/j.jtbi.2007.10.036⟩
hal-00428358v2  Journal articles
Jean-François Gout, Laurent Duret, Daniel Kahn. Differential retention of metabolic genes following whole-genome duplication
Molecular Biology and Evolution, Oxford University Press (OUP), 2009, 26 (5), pp.1067-1072. ⟨10.1093/molbev/msp026⟩
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hal-00539474v2  Journal articles
Jean-François Gout, Daniel Kahn, Laurent Duret. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution
PLoS Genetics, Public Library of Science, 2010, 6 (5), pp.e1000944. ⟨10.1371/journal.pgen.1000944⟩
hal-01213733v1  Journal articles
O Ebenhöh, T Handorf, Daniel Kahn. Evolutionary changes of metabolic networks and their biosynthetic capacities
Systems Biology, Institution of Engineering and Technology, 2006, 153 (5), pp.354-358. ⟨10.1049/ip-syb:20060014⟩
hal-01213737v1  Journal articles
T Handorf, O Ebenhöh, Daniel Kahn, R Heinrich. Hierarchy of metabolic compounds based on their synthesising capacity
Systems Biology, Institution of Engineering and Technology, 2006, 153 (5), pp.359-363. ⟨10.1049/ip-syb:20060021⟩
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hal-01214141v1  Journal articles
Sarah Hunter, Rolf Apweiler, Teresa K Attwood, Amos Bairoch, Alex Bateman et al.  InterPro: the integrative protein signature database
Nucleic Acids Research, Oxford University Press, 2009, 37 (Database issue), pp.D211-D215. ⟨10.1093/nar/gkn785⟩
hal-00793021v1  Conference papers
Valentina Baldazzi, Delphine Ropers, Yves Markowicz, Daniel Kahn, Hans Geiselmann et al.  The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes
Actes des Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2010), 2010, Montpellier, France. pp.11-12
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inria-00527140v1  Journal articles
Valentina Baldazzi, Delphine Ropers, Yves Markowicz, Daniel Kahn, Johannes Geiselmann et al.  The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes.
PLoS Computational Biology, Public Library of Science, 2010, 6 (6), pp.e1000812. ⟨10.1371/journal.pcbi.1000812⟩
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inria-00593109v1  Reports
Valentina Baldazzi, Delphine Ropers, Johannes Geiselmann, Daniel Kahn, Hidde de Jong. Importance of metabolic coupling for the dynamics of gene expression following a diauxic shift in E. coli
[Research Report] RR-7617, INRIA. 2011
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hal-02652188v1  Journal articles
Sarah Hunter, Philip Jones, Alex Mitchell, Rolf Apweiler, Teresa K. Attwood et al.  InterPro in 2011: new developments in the family and domain prediction database
Nucleic Acids Research, Oxford University Press, 2012, 40 (D1), pp.D306-D312. ⟨10.1093/nar/gkr948⟩
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hal-00793039v1  Journal articles
Sara Berthoumieux, Matteo Brilli, Hidde Jong, Daniel Kahn, Eugenio Cinquemani. Identification of metabolic network models from incomplete high-throughput datasets
Bioinformatics, Oxford University Press (OUP), 2011, 27 (13), pp.i186-i195. ⟨10.1093/bioinformatics/btr225⟩
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hal-00434830v2  Journal articles
Nicola J Mulder, Rolf Apweiler, Teresa K Attwood, Amos Bairoch, Alex Bateman et al.  New developments in the InterPro database
Nucleic Acids Research, Oxford University Press, 2007, 35 (Database issue), pp.D224-D228. ⟨10.1093/nar/gkl841⟩
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hal-00762604v1  Conference papers
Sara Berthoumieux, Daniel Kahn, Hidde de Jong, Eugenio Cinquemani. Structural and practical identifiability of approximate metabolic network models
Proceedings of the 16th IFAC symposium on System Identification, 2012, Brussels, Belgium. ⟨10.3182/20120711-3-BE-2027.00166⟩
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hal-00762620v1  Journal articles
Sara Berthoumieux, Matteo Brilli, Daniel Kahn, Hidde de Jong, Eugenio Cinquemani. On the identifiability of metabolic network models.
Journal of Mathematical Biology, Springer Verlag (Germany), 2013, 67 (6-7), pp.1795-832. ⟨10.1007/s00285-012-0614-x⟩
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inria-00561999v1  Reports
Sara Berthoumieux, Matteo Brilli, Hidde de Jong, Daniel Kahn, Eugenio Cinquemani. Identification of metabolic network models from incomplete high-throughput datasets
[Research Report] RR-7524, INRIA. 2011
hal-00803472v1  Conference papers
Daniel Kahn, Clément Rezvoy, Frédéric Vivien. Parallel large scale inference of protein domain families
ICPADS'2008, the 14th IEEE International Conference on Parallel and Distributed Systems, 2008, Unknown, Australia. pp.72-79, ⟨10.1109/ICPADS.2008.115⟩
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