Bibliography

Major publications by the team in recent years

• 1R. Barriot, D. J. Sherman, I. Dutour.
  How to decide which are the most pertinent overly-represented features during gene set enrichment analysis, in: BMC Bioinformatics, 2007, vol. 8. [ DOI : 10.1186/1471-2105-8-332 ]
  http://hal.inria.fr/inria-00202721/en/
• 2G. Blandin, P. Durrens, F. Tekaia, M. Aigle, M. Bolotin-Fukuhara, E. Bon, S. Casaregola, J. de Montigny, C. Gaillardin, A. Lépingle, B. Llorente, A. Malpertuy, C. Neuvéglise, O. Ozier-Kalogeropoulos, A. Perrin, S. Potier, J.-L. Souciet, E. Talla, C. Toffano-Nioche, M. Wésolowski-Louvel, C. Marck, B. Dujon.
  Genomic Exploration of the Hemiascomycetous Yeasts: 4. The genome of Saccharomyces cerevisiae revisited, in: FEBS Letters, December 2000, vol. 487, n^o 1, pp. 31-36.
• 3E. Bon, A. Delaherche, E. Bilhère, A. De Daruvar, A. Lonvaud-Funel, C. Le Marrec.
  Oenococcus oeni genome plasticity is associated with fitness, in: Applied and Environmental Microbiology, 2009, vol. 75, n^o 7, pp. 2079-90.
  http://hal.inria.fr/inria-00392015/en/
• 4J. Bourbeillon, S. Orchard, I. Benhar, C. Borrebaeck, A. De Daruvar, S. Dübel, R. Frank, F. Gibson, D. Gloriam, N. Haslam, T. Hiltker, I. Humphrey-Smith, M. Hust, D. Juncker, M. Koegl, Z. Konthur, B. Korn, S. Krobitsch, S. Muyldermans, P.-A. Nygren, S. Palcy, B. Polic, H. Rodriguez, A. Sawyer, M. Schlapshy, M. Snyder, O. Stoevesandt, M. J. Taussig, M. Templin, M. Uhlen, S. Van Der Maarel, C. Wingren, H. Hermjakob, D. J. Sherman.
  Minimum information about a protein affinity reagent (MIAPAR), in: Nature Biotechnology, 07 2010, vol. 28, n^o 7, pp. 650-3. [ DOI : 10.1038/nbt0710-650 ]
  http://hal.inria.fr/inria-00544750/en
• 5A. B. Canelas, N. Harrison, A. Fazio, J. Zhang, J.-P. Pitkänen, J. Van Den Brink, B. M. Bakker, L. Bogner, J. Bouwman, J. I. Castrillo, A. Cankorur, P. Chumnanpuen, P. Daran-Lapujade, D. Dikicioglu, K. Van Eunen, J. C. Ewald, J. J. Heijnen, B. Kirdar, I. Mattila, F. I. C. Mensonides, A. Niebel, M. Penttilä, J. T. Pronk, M. Reuss, L. Salusjärvi, U. Sauer, D. J. Sherman, M. Siemann-Herzberg, H. Westerhoff, J. De Winde, D. Petranovic, S. G. Oliver, C. T. Workman, N. Zamboni, J. Nielsen.
  Integrated multilaboratory systems biology reveals differences in protein metabolism between two reference yeast strains, in: Nature Communications, 12 2010, vol. 1, n^o 9, 145 p. [ DOI : 10.1038/ncomms1150 ]
  http://hal.inria.fr/inria-00562005/en/
• 6B. Dujon, D. J. Sherman, G. Fischer, P. Durrens, S. Casaregola, I. Lafontaine, J. De Montigny, C. Marck, C. Neuvéglise, E. Talla, N. Goffard, L. Frangeul, M. Aigle, V. Anthouard, A. Babour, V. Barbe, S. Barnay, S. Blanchin, J.-M. Beckerich, E. Beyne, C. Bleykasten, A. Boisramé, J. Boyer, L. Cattolico, F. Confanioleri, A. De Daruvar, L. Despons, E. Fabre, C. Fairhead, H. Ferry-Dumazet, A. Groppi, F. Hantraye, C. Hennequin, N. Jauniaux, P. Joyet, R. Kachouri-Lafond, A. Kerrest, R. Koszul, M. Lemaire, I. Lesur, L. Ma, H. Muller, J.-M. Nicaud, M. Nikolski, S. Oztas, O. Ozier-Kalogeropoulos, S. Pellenz, S. Potier, G.-F. Richard, M.-L. Straub, A. Suleau, D. Swennen, F. Tekaia, M. Wésolowski-Louvel, E. Westhof, B. Wirth, M. Zeniou-Meyer, I. Zivanovic, M. Bolotin-Fukuhara, A. Thierry, C. Bouchier, B. Caudron, C. Scarpelli, C. Gaillardin, J. Weissenbach, P. Wincker, J.-L. Souciet.
  Genome evolution in yeasts, in: Nature, 07 2004, vol. 430, n^o 6995, pp. 35-44. [ DOI : 10.1038/nature02579 ]
  http://hal.archives-ouvertes.fr/hal-00104411/en/
• 7P. Durrens, M. Nikolski, D. J. Sherman.
  Fusion and fission of genes define a metric between fungal genomes, in: PLoS Computational Biology, 10 2008, vol. 4. [ DOI : 10.1371/journal.pcbi.1000200 ]
  http://hal.inria.fr/inria-00341569/en/
• 8A. Goëffon, M. Nikolski, D. J. Sherman.
  An Efficient Probabilistic Population-Based Descent for the Median Genome Problem, in: Proceedings of the 10th annual ACM SIGEVO conference on Genetic and evolutionary computation (GECCO 2008), Atlanta United States, ACM, 2008, pp. 315-322.
  http://hal.archives-ouvertes.fr/hal-00341672/en/
• 9M. Nikolski, D. J. Sherman.
  Family relationships: should consensus reign?- consensus clustering for protein families, in: Bioinformatics, 2007, vol. 23. [ DOI : 10.1093/bioinformatics/btl314 ]
  http://hal.inria.fr/inria-00202434/en/
• 10D. J. Sherman, T. Martin, M. Nikolski, C. Cayla, J.-L. Souciet, P. Durrens.
  Genolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes, in: Nucleic Acids Research (NAR), 2009, D p. [ DOI : 10.1093/nar/gkn859 ]
  http://hal.inria.fr/inria-00341578/en/
• 11J.-L. Souciet, B. Dujon, C. Gaillardin, M. Johnston, P. Baret, P. Cliften, D. J. Sherman, J. Weissenbach, E. Westhof, P. Wincker, C. Jubin, J. Poulain, V. Barbe, B. Ségurens, F. Artiguenave, V. Anthouard, B. Vacherie, M.-E. Val, R. S. Fulton, P. Minx, R. Wilson, P. Durrens, G. Jean, C. Marck, T. Martin, M. Nikolski, T. Rolland, M.-L. Seret, S. Casaregola, L. Despons, C. Fairhead, G. Fischer, I. Lafontaine, V. Leh Louis, M. Lemaire, J. De Montigny, C. Neuvéglise, A. Thierry, I. Blanc-Lenfle, C. Bleykasten, J. Diffels, E. Fritsch, L. Frangeul, A. Goëffon, N. Jauniaux, R. Kachouri-Lafond, C. Payen, S. Potier, L. Pribylova, C. Ozanne, G.-F. Richard, C. Sacerdot, M.-L. Straub, E. Talla.
  Comparative genomics of protoploid Saccharomycetaceae, in: Genome Research, 2009, vol. 19, pp. 1696-1709.
  http://hal.inria.fr/inria-00407511/en/

Publications of the year

Doctoral Dissertations and Habilitation Theses

• 12N. Golenetskaya.
  Adressing scaling challenges in comparative genomics, Université Sciences et Technologies - Bordeaux I, September 2013.
  http://hal.inria.fr/tel-00865840

Articles in International Peer-Reviewed Journals

• 13R. Assar, D. J. Sherman.
  Implementing biological hybrid systems: Allowing composition and avoiding stiffness, in: Applied Mathematics and Computation, August 2013.
  http://hal.inria.fr/hal-00853997
• 14W. Dyrka, M. M. Bartuzel, M. Kotulska.
  Optimization of 3D Poisson-Nernst-Planck model for fast evaluation of diverse protein channels, in: Proteins: Structure, Function, and Bioinformatics, August 2013. [ DOI : 10.1002/prot.24326 ]
  http://hal.inria.fr/hal-00857213
• 15W. Dyrka, J.-C. Nebel, M. Kotulska.
  Probabilistic grammatical model for helix-helix contact site classification, in: Algorithms for Molecular Biology, 2013, vol. 8, 31 p. [ DOI : 10.1186/1748-7188-8-31 ]
  http://hal.inria.fr/hal-00923291
• 16T. Gabaldón, T. Martin, M. Marcet-Houben, P. Durrens, M. Bolotin-Fukuhara, O. Lespinet, S. Arnaise, S. Boisnard, G. Aguileta, R. Atanasova, C. Bouchier, A. Couloux, S. Creno, J. Almeida Cruz, H. Devillers, A. Enache-Angoulvant, J. Guitard, L. Jaouen, L. Ma, C. Marck, C. Neuvéglise, E. Pelletier, A. Pinard, J. Poulain, J. Recoquillay, E. Westhof, P. Wincker, B. Dujon, C. Hennequin, C. Fairhead.
  Comparative genomics of emerging pathogens in the Candida glabrata clade, in: BMC Genomics, September 2013, vol. 14, n^o 1, 623 p. [ DOI : 10.1186/1471-2164-14-623 ]
  http://hal.inria.fr/inserm-00871184
• 17A. Romano, H. Trip, H. Campbell-Sills, O. Bouchez, D. D. Sherman, J. S. Lolkema, P. M. Lucas.
  Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines, in: Genome Announcements, January 2013, vol. 1, n^o 1, 12 p. [ DOI : 10.1128/genomeA.00097-12 ]
  http://hal.inria.fr/hal-00863284
• 18A. Sarkar, M. Nikolski, P. Durrens.
  The family based variability in protein family expansion, in: International Journal of Bioinformatics Research and Applications, 2013, vol. 9, n^o 2, pp. 121-33. [ DOI : 10.1504/IJBRA.2013.052473 ]
  http://hal.inria.fr/hal-00857374
• 19A. Zhukova, D. J. Sherman.
  Knowledge-based generalization of metabolic models, in: Journal of Computational Biology, 2014.
  http://hal.inria.fr/hal-00925881
• 20A. Zhukova, D. J. Sherman.
  Knowledge-based generalization of metabolic networks: a practical study, in: Journal of Bioinformatics and Computational Biology, 2014.
  http://hal.inria.fr/hal-00906911

Invited Conferences

• 21D. J. Sherman.
  Taming the complexity of 'n-ary' relations in comparative genomics, in: 9th International Conference on Genome Biology and Bioinformatics, Atlanta, Georgia, United States, M. Borodovsky (editor), Georgia Tech and Emory University, November 2013.
  http://hal.inria.fr/hal-00938262

International Conferences with Proceedings

• 22A. Zhukova, D. J. Sherman.
  Knowledge-based zooming for metabolic models, in: JOBIM, Toulouse, France, July 2013.
  http://hal.inria.fr/hal-00859437

Conferences without Proceedings

• 23A. Zhukova, D. J. Sherman.
  Knowledge-based generalization of metabolic networks: An applicational study, in: Moscow Conference on Computational Molecular Biology, Moscow, Russian Federation, July 2013.
  http://hal.inria.fr/hal-00859440
• 24A. Zhukova, D. J. Sherman.
  What is the optimal representation of a generalized metabolic model using SBML and SBGN?, in: COMBINE 2013, Paris, France, September 2013.
  http://hal.inria.fr/hal-00867373

Scientific Books (or Scientific Book chapters)

• 25P. Durrens.
  Phylogénie moléculaire des champignons, in: Mycologie médicale, C. Ripert (editor), Tech & Doc, Lavoisier, 2013, pp. 49-54.
  http://hal.inria.fr/hal-00833960

Other Publications

• 26A. Zhukova.
  Metabolic Model Generalization, in: International Course in Yeast Systems Biology, Gothenburg, Sweden, June 2013, International Course in Yeast Systems Biology.
  http://hal.inria.fr/hal-00859442

References in notes

• 27R. Assar, A. Garcia, D. J. Sherman.
  Modeling Stochastic Switched Systems with BioRica, in: Journées Ouvertes en Biologie, Informatique et Mathématiques JOBIM 2011, Paris, France, Institut Pasteur, July 2011, pp. 297–304.
  http://hal.inria.fr/inria-00617419/en
• 28R. Assar, A. V. Leisewitz, A. Garcia, N. C. Inestrosa, M. A. Montecino, D. J. Sherman.
  Reusing and composing models of cell fate regulation of human bone precursor cells, in: BioSystems, April 2012, vol. 108, n^o 1-3, pp. 63-72. [ DOI : 10.1016/j.biosystems.2012.01.008 ]
  http://hal.inria.fr/hal-00681022
• 29R. Assar, M. A. Montecino, D. J. Sherman.
  Stochastic Modeling of Complex Systems and Systems Biology: From Stochastic Transition Systems to Hybrid Systems, in: XII Latin American Congress of Probability and Mathematical Statistics, Viña del Mar, Chile, March 2012.
  http://hal.inria.fr/hal-00686072
• 30R. Assar, F. Vargas, D. J. Sherman.
  Reconciling competing models: a case study of wine fermentation kinetics, in: Algebraic and Numeric Biology 2010, Austria Hagenberg, K. Horimoto, M. Nakatsui, N. Popov (editors), Research Institute for Symbolic Computation, Johannes Kepler University of Linz, 08 2010, pp. 68–83.
  http://hal.inria.fr/inria-00541215/en
• 31R. Assar, F. Vargas, D. J. Sherman.
  Reconciling competing models: a case study of wine fermentation kinetics, in: Algebraic and Numeric Biology 2010, Hagenberg, Austria, K. Horimoto, M. Nakatsui, N. Popov (editors), Lecture Notes in Computer Science, Springer, 2012, vol. 6479, pp. 68–83. [ DOI : 10.1007/978-3-642-28067-2_6 ]
  http://hal.inria.fr/inria-00541215
• 32A. Athane, E. Bilhère, E. Bon, P. Lucas, G. Morel, A. Lonvaud-Funel, C. Le Hénaff-Le Marrec.
  Characterization of an acquired-dps-containing gene island in the lactic acid bacterium Oenococcus oeni, in: Journal of Applied Microbiology, 2008, Received 22 October 2007, revised 8 April 2008 & Accepted 8 May 2008 (In press).
  http://hal.inria.fr/inria-00340058/en/
• 33R. Barriot, J. Poix, A. Groppi, A. Barre, N. Goffard, D. J. Sherman, I. Dutour, A. De Daruvar.
  New strategy for the representation and the integration of biomolecular knowledge at a cellular scale, in: Nucleic Acids Research (NAR), 2004, vol. 32, pp. 3581-9. [ DOI : 10.1093/nar/gkh681 ]
  http://hal.inria.fr/inria-00202722/en/
• 34E. Bon, C. Granvalet, F. Remize, D. Dimova, P. Lucas, D. Jacob, A. Groppi, S. Penaud, C. Aulard, A. De Daruvar, A. Lonvaud-Funel, J. Guzzo.
  Insights into genome plasticity of the wine-making bacterium Oenococcus oeni strain ATCC BAA-1163 by decryption of its whole genome, in: 9th Symposium on Lactic Acid Bacteria, Egmond aan Zee Netherlands, 2008.
  http://hal.inria.fr/inria-00340073/en/
• 35L. Bourgeade, T. Martin, E. Bon.
  PSEUDOE: A computational method to detect Psi-genes and explore PSEUDome dynamics in wine bacteria from the Oenococcus genus, in: JOBIM2012- 13ème Journées Ouvertes en Biologie, Informatique et Mathématiques, Rennes, France, D. T. François Cost (editor), SFBI, Inria, July 2012, pp. 435-436.
  http://hal.inria.fr/hal-00722968
• 36L. Bourgeade, T. Martin, A. Goulielmakis, A. Lonvaud-Funel, P. Lucas, E. Bon.
  Cracking the Pseudome Code: Inside the "silent" Psi-genes language to reconstruct Oenococcus oeni evolutionary adaptation to wine, in: 18th CBL-Club des Bactéries Lactiques Meeting, Clermont-Ferrand, France, UR CALITYSS - VetAgroSup (editor), May 2012, 82 p.
  http://hal.inria.fr/hal-00722971
• 37M. Cvijovic, H. Soueidan, D. J. Sherman, E. Klipp, M. Nikolski.
  Exploratory Simulation of Cell Ageing Using Hierarchical Models, in: 19th International Conference on Genome Informatics Genome Informatics, Gold Coast, Queensland Australia, J. Arthur, S.-K. Ng (editors), Genome Informatics, Imperial College Press, London, 2008, vol. 21, pp. 114–125, EU FP6 Yeast Systems Biology Network LSHG-CT-2005-018942, EU Marie Curie Early Stage Training (EST) Network “Systems Biology”, ANR-05-BLAN-0331-03 (GENARISE).
  http://hal.inria.fr/inria-00350616
• 38D. Dimova, E. Bon, P. Lucas, R. Beugnot, M. De Leeuw, A. Lonvaud-Funel.
  The whole genome of Oenococcus strain IOEB 8413, in: 9th Symposium on Lactic Acid Bacteria, Egmond aan Zee Netherlands, 2008.
  http://hal.inria.fr/inria-00340086/en/
• 39A. Enache-Angoulvant, J. Guitard, F. Grenouillet, T. Martin, P. Durrens, C. Fairhead, C. Hennequin.
  Rapid Discrimination between Candida glabrata, Candida nivariensis, and Candida bracarensis by Use of a Singleplex PCR, in: Journal of Clinical Microbiology, September 2011, vol. 49, n^o 9, pp. 3375-3379. [ DOI : 10.1128/JCM.00688-11 ]
  http://hal.inria.fr/inria-00625115/en
• 40A. Garcia, D. J. Sherman.
  Mixed-formalism hierarchical modeling and simulation with BioRica, in: 11th International Conference on Systems Biology (ICSB 2010), United Kingdom Edimbourg, 10 2010, Poster.
  http://hal.inria.fr/inria-00529669/en
• 41D. Gloriam, S. Orchard, D. Bertinetti, E. Björling, E. Bongcam-Rudloff, C. Borrebaeck, J. Bourbeillon, A. R. M. Bradbury, A. De Daruvar, S. Dübel, R. Frank, T. J. Gibson, L. Gold, N. Haslam, F. W. Herberg, T. Hiltker, J. D. Hoheisel, S. Kerrien, M. Koegl, Z. Konthur, B. Korn, U. Landegren, L. Montecchi-Palazzi, S. Palcy, H. Rodriguez, S. Schweinsberg, V. Sievert, O. Stoevesandt, M. J. Taussig, M. Ueffing, M. Uhlén, S. Van Der Maarel, C. Wingren, P. Woollard, D. J. Sherman, H. Hermjakob.
  A community standard format for the representation of protein affinity reagents, in: Mol Cell Proteomics, 01 2010, vol. 9, n^o 1, pp. 1-10. [ DOI : 10.1074/mcp.M900185-MCP200 ]
  http://hal.inria.fr/inria-00544751/en
• 42N. Golenetskaya, D. J. Sherman.
  Rethinking global analyses and algorithms for comparative genomics in a functional MapReduce style, in: Algorithmique, combinatoire du texte et applications en bio-informatique (SeqBio 2011), Lille, France, December 2011.
  http://hal.inria.fr/hal-00654797/en
• 43A. Goulielmakis, J. Bridier, A. Barré, O. Claisse, David James. Sherman, P. Durrens, A. Lonvaud-Funel, E. Bon.
  How does Oenococcus oeni adapt to its environment? A pangenomic oligonucleotide microarray for analysis O. oeni gene expression under wine shock, in: OENO2011- 9th International Symposium of Oenology, Bordeaux, France, P. Darriet, L. Geny, P. Lucas, A. Lonvaud, G. de Revel, P. Teissedre (editors), Dunod, Paris, April 2012, pp. 358-363.
  http://hal.inria.fr/hal-00646867
• 44H. Hermjakob, L. Montecchi-Palazzi, G. Bader, J. Wojcik, L. Salwinski, A. Ceol, S. Moore, S. Orchard, U. Sarkans, C. von Mering, B. Roechert, S. Poux, E. Jung, H. Mersch, P. Kersey, M. Lappe, Y. Li, R. Zeng, D. Rana, M. Nikolski, H. Husi, C. Brun, K. Shanker, S. Grant, C. Sander, P. Bork, W. Zhu, A. Pandey, A. Brazma, B. Jacq, M. Vidal, D. J. Sherman, P. Legrain, G. Cesareni, I. Xenarios, D. Eisenberg, B. Steipe, C. Hogue, R. Apweiler.
  The HUPO PSI's molecular interaction format–a community standard for the representation of protein interaction data, in: Nat. Biotechnol., Feb. 2004, vol. 22, n^o 2, pp. 177-83.
• 45G. Jean, D. J. Sherman, M. Nikolski.
  Mining the semantics of genome super-blocks to infer ancestral architectures, in: Journal of Computational Biology, 2009.
  http://hal.inria.fr/inria-00414692/en/
• 46N. Loira, T. Dulermo, M. Nikolski, J.-M. Nicaud, D. J. Sherman.
  Genome-scale Metabolic Reconstruction of the Eukaryote Cell Factory Yarrowia Lipolytica, in: 11th International Conference on Systems Biology (ICSB 2010), United Kingdom Edimbourg, 10 2010, Poster.
  http://hal.inria.fr/hal-00652922
• 47N. Loira, D. J. Sherman, P. Durrens.
  Reconstruction and Validation of the genome-scale metabolic model of Yarrowia lipolytica iNL705, in: Journée Ouvertes Biologie Informatique Mathématiques, JOBIM 2010, France Montpellier, 09 2010.
  http://www.jobim2010.fr/?q=fr/node/55
• 48D. J. Sherman, N. Golenetskaya.
  Addressing scaling-out challenges for comparative genomics, in: Moscow Conference on Computational Molecular Biology, Moscow, Russian Federation, July 2011.
  http://hal.inria.fr/hal-00649189/en
• 49D. J. Sherman, P. Durrens, E. Beyne, M. Nikolski, J.-L. Souciet.
  Génolevures: comparative genomics and molecular evolution of hemiascomycetous yeasts, in: Nucleic Acids Research (NAR), 2004, vol. 32, GDR CNRS 2354 “Génolevures”. [ DOI : 10.1093/nar/gkh091 ]
  http://hal.inria.fr/inria-00407519/en/
• 50D. J. Sherman, P. Durrens, F. Iragne, E. Beyne, M. Nikolski, J.-L. Souciet.
  Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts, in: Nucleic Acids Res, 01 2006, vol. 34. [ DOI : 10.1093/nar/gkj160 ]
  http://hal.archives-ouvertes.fr/hal-00118142/en/
• 51D. J. Sherman, N. Loira, N. Golenetskaya.
  High-performance comparative annotation, in: Bioinformatics after next-generation sequencing, Zvenigorod Russian Federation, V. Makeev, G. Kucherov (editors), Russian Academy of Sciences, 06 2010.
  http://hal.inria.fr/inria-00563533/en/
• 52H. Soueidan, M. Nikolski, G. Sutre.
  Qualitative Transition Systems for the Abstraction and Comparison of Transient Behavior in Parametrized Dynamic Models, in: Computational Methods in Systems Biology (CMSB'09), Italie Bologna, Springer Verlag, 2009, vol. 5688, pp. 313–327.
  http://hal.archives-ouvertes.fr/hal-00408909/en/
• 53H. Soueidan, D. J. Sherman, M. Nikolski.
  BioRica: A multi model description and simulation system, in: F0SBE, Allemagne, 2007, pp. 279-287.
  http://hal.archives-ouvertes.fr/hal-00306550/en/
• 54N. Vyahhi, A. Goëffon, D. J. Sherman, M. Nikolski.
  Swarming Along the Evolutionary Branches Sheds Light on Genome Rearrangement Scenarios, in: ACM SIGEVO Conference on Genetic and evolutionary computation, F. Rothlauf (editor), ACM, 2009.
  http://hal.inria.fr/inria-00407508/en/