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Dr. Nicolas Ray

CV I Publications I Conferences

Citations of my publications are found on Google Scholar Citation

International peer reviewed publications

  1. Lacroix P, Santiago H & N Ray. MASCOT: Multi-criteria Analytical SCOring Tool for ArcGIS Desktop. Submitted to International Journal of Information, Technology and Decision Making
  2. Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, Ray N, Parra MV, Rojas W, DuqueMesa, N, Velez ID, García LF, Triana O, Blair S, Maestre A, Dib JC, Bravi CM, Bailliet G, Corach D, Hünemeier T, Bortolini MC, Salzano F, Petzl-Erler ML, Acuña-Alonzo V, Canizales-Quinteros S, Aguilar-Salinas C, Tusié-Luna T, Riba L, Rodríguez-Cruz M, Lopez-Alarcón M, Coral-Vazquez R, Canto-Cetina T, Silva- Zolezzi I, Fernandez-Lopez JC, Contreras AV, Jimenez-Sanchez G, Gómez-Vázquez MJ, Molina J, Carracedo A, Salas A, Gallo C, Poletti G, Witonsky DB, Alkorta-Aranburu G, Sukernik R, Osipova L, Fedorova S, Vasquez R, Villena M, Moreau C, Hammer M, Barrantes R, Pauls D, Excoffier L, Bedoya G, Rothhammer F, Dugoujon JM, Larrouy G, Klitz W, Labuda D, Kidd J, Kidd K, Di Rienzo A, Freimer NB, Price AL & A Ruiz-Linares. Reconstructing native American population history. Nature, accepted
  3. Arenas M, François O, Currat M, Ray N & L Excoffier. Influence of admixture and Paleolithic range contractions on current European diversity gradients. Submitted to Molecular Biology and Evolution
  4. Mona S, Ray N, Arenas M & L Excoffier. Genetic consequences of habitat fragmentation during a range expansion. Submitted to Journal of Evolutionary Biology
  5. Gorgan D, Bacu V, Mihon D, Stefanut T, Rodila D, Cau P, Abbaspour K, Giuliani G, Ray N & A Lehmann. Software platform interoperability throughout enviroGRIDS portal. Journal of Selected Topics in Applied Earth Observations and Remote Sensing, in press
  6. Kormann U, Gugerli F, Ray N, Excoffier L & K Bollmann. Parsimony-based pedigree analysis and resistance models suggest topography to restrict dispersal and connectivity in the endangered capercaillie. Biological Conservation, in press
  7. Arenas M, Ray N, Currat M & Excoffier L. 2012. Consequences of range contractions and range shifts on molecular diversity. Molecular Biology and Evolution, 29(1): 207-218 [pdf] [suppl. mat.]
  8. Gorgan D, Abbaspour K, Cau P, Bacu V, Mihon D, Giuliani G, Ray N & A Lehmann. 2011. Grid based data processing tools and applications for black sea catchment basin. Proceedings of IDAACS (1) 2011: 223-228 [pdf]
  9. Ray N, Giuliani G, Gorgan D & A Lehmann. 2011. Distributed geocomputation for modeling the hydrology of the Black Sea watershed. Watershed Approach to Environmental Security: Fostering integrated water management in the Azov Sea Basin, ed. Lagutov, V. NATO Science for Peace and Security Series: Environmental Security. Dordrecht, Springer. Pp. 141-158
  10. Yalew SG, van Griensven A, Ray N, Betrie GD & Kokoszkiewicz L. Parallel computing of a large scale SWAT model. Submitted to Environmental Modelling & Software
  11. Giuliani G, Nativi S, Lehmann A & Ray N. WPS mediation: an approach to process geospatial data on different computing backends. Computers and Geosciences, in press [Link to pdf]
  12. Lecca G, Petitdidier M, Hluchy L, Ivanovic M, Kussul N, Ray N & Thieron V. 2011. Grid computing technology for hydrological applications. Journal of Hydrology 403: 186-199 [pdf]
  13. Giuliani G, Ray N, Schwarzer S, de Bono A, Dao H, Peduzzi P, Beniston M, Van Woerden J, Witt R & Lehmann A. 2011. Sharing environmental data through GEOSS. International Journal of Applied Geospatial Research 2(1): 1-17 [pdf]
  14. Giuliani G, Ray N & Lehmann A. 2011. Grid-enabled Spatial Data Infrastructure for environmental sciences: challenges and opportunities. Future Generation Computer Systems 27(3): 292-303 [pdf]
  15. Ray N, Currat M, Foll M. & Excoffier L. 2010. SPLATCHE2: a spatially-explicit simulation framework for complex demography, genetic admixture and recombination. Bioinformatics 26(23): 2993-2994 [pdf]
  16. Yang NN, Mazières S, Bravi C, Ray N, Wang S, Burley M-W, Bedoya BG, Rojas W, Parra MV, Molina JA, Gallo C, Poletti G, Hill K, Hurtado AM, Petzl-Erler ML, Tsuneto LT, Klitz W, Barrantes R, Llop E, Rothhammer F, Labuda D, Salzano FM, Bortoloni M, Excoffier L, Dugoujon JM & Ruiz-Linares A. 2010. Contrasting patterns of nuclear and mtDNA diversity in Native American populations. Annals of Human Genetics 74(6): 525-38 [pdf]
  17. Ray N & Excoffier L. 2010. A first step toward inferring levels of long distance dispersal during past expansions. Molecular Ecology Resources 10(5): 902-914 [pdf]
  18. Estoup A, Baird SJE, Ray N, Currat M, Cornuet J-M, Santos F, Beaumont M A & Excoffier L. 2010. Combining genetic, historical and geographic data to reconstruct the dynamics of the bioinvasion of cane toad Bufo marinus. Molecular Ecology Resources 10(5): 886-901 [pdf]
  19. François O, Currat M, Ray N, Han E, Excoffier L & J Novembre. 2010. Principal Component Analysis under population genetic models of range expansion and admixture. Molecular Biology and Evolution 27(6): 1257-1268 [pdf]
  20. Ray N, Wegmann D, Fagundes NJR, Ruiz-Linares A & Excoffier L. 2010. A statistical evaluation of models for the initial settlement of the American continent emphasizes the importance of gene flow with Asia. Molecular Biology and Evolution 27(2): 337–345 [pdf] [suppl. info.]
  21. Ray N & Excoffier L. 2009. Inferring past demography using spatially-explicit population genetic models. Human Biology 81(2-3): 141-157 [pdf]
  22. Janin A, Léna J-P, Ray N, Delacourt C, Allemand P & Joly P. 2009. Assessing landscape connectivity with calibrated cost-distance modelling: predicting common toad distribution in a context of spreading agriculture. Journal of Applied Ecology 46(4): 833-841 [pdf]
  23. Hofer T, Ray N, Wegmann D & Excoffier L. 2009. Large allele frequency differences between human continental groups are more likely to have occurred by drift during range expansions than by selection. Annals of Human Genetics 73: 95-108 [pdf]
  24. Ray N & Ebener S. 2008. AccessMod 3.0: computing geographic coverage and accessibility to health care services using anisotropic movement of patients. International Journal of Health Geographics 7: 63 [pdf]
  25. Excoffier L & Ray N. 2008. Surfing during population expansions promotes genetic revolutions and structuration. Trends in Ecology and Evolution 23(7): 347-351 [pdf]
  26. Excoffier L, Ray N & Currat M. 2008. Where was Paradise? A simulation study of the spread of early modern humans in heterogeneous environments. In Simulations, Genetics and Human Prehistory edited by Matsumura S, Forster P & Renfrew C. (McDonald Institute Monographs.) Cambridge: McDonald Institute for Archaeological Research. Pp. 9-18 [pdf]
  27. Ray N, Currat M & Excoffier L. 2008. Incorporating environmental heterogeneity in spatially-explicit simulations of human genetic diversity. In Simulations, Genetics and Human Prehistory edited by Matsumura S, Forster P & Renfrew C. (McDonald Institute Monographs.) Cambridge: McDonald Institute for Archaeological Research. Pp. 103-117 [pdf]
  28. Currat M, Ray N & Excoffier L. 2008. Genetic simulations of population interactions during past human expansions in Europe. In Simulations, Genetics and Human Prehistory edited by Matsumura S, Forster P & Renfrew C. (McDonald Institute Monographs.) Cambridge: McDonald Institute for Archaeological Research. Pp. 37-47 [pdf]
  29. Wang S, Ray N, Rojas W, Parra M V, Bedoya G, Gallo C, Poletti G, Mazzotti G, Hill K, Hurtado A M, Camrena B, Nicolini H, Klitz W, Barrantes R, Molina J A, Freimer N, Bortolini M C, Salzano F M, Petzl-Erler M L, Tsuneto L T, Dipierri J E, Alfaro E L, Bailliet G, Bianchi N O, Llop E, Rothhammer F, Excoffier L & Ruiz-Linares A. 2008. Geographic patterns of genome admixture in Latin American Mestizos. PLoS Genetics 4(3): e1000037 [pdf]
  30. Neuenschwander S, Largiader CR, Ray N, Currat M, Vonlanthen P & Excoffier L. 2008. Colonization history of the Swiss Rhine basin by the bullhead (Cottus gobio): Inference under a Bayesian spatially explicit framework. Molecular Ecology 17(3): 757-772 [pdf]
  31. Fagundes N J R, Ray N, Beaumont M, Neuenschwander S, Salzano F M, Bonatto S L & Excoffier L. 2008. Ancient lineages and assimilation: A reply to Garrigan and Hammer. Proceedings of the National Academy of Sciences USA 105: E4 [pdf]
  32. Wang S, Jakobsson M, Lewis Jr C M, Ramachandran S, Ray N, Bedoya G, Rojas W, Parra M V, Molina J A, Gallo C, Mazzotti G, Poletti G, Hill K, Hurtado A M, Labuda D, Klitz W, Barrantes R, Cátira Bortolini M, Salzano F M, Petzl-Erler M L, Llop E, Rothhammer F, Excoffier L, Feldman M W, Rosenberg N A & Ruiz-Linares A. 2007. Genetic variation and population structure in Native Americans. PLoS Genetics 3(11): e185 [pdf]
  33. Fagundes N J R, Ray N, Beaumont M, Neuenschwander S, Salzano F M, Bonatto S L & Excoffier L. 2007. Statistical evaluation of alternative models of human evolution. Proceedings of the National Academy of Sciences USA 104: 17614-17619 [pdf] [suppl. info.]
  34. Fontaine M C, Baird S J E, Piry S, Ray N, Tolley K A, Duke S, Birkun A Jr, Ferreira M, Jauniaux T, Llavona A, Öztürk B, Öztürk A A, Ridoux V, Rogan E, Sequeira M, Siebert U, Vikingsson G A, Bouquegneau J-M & Michaux J R. 2007. Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters. BMC Biology 5, 30 [pdf]
  35. Ray N & Burgman M A. 2006. Subjective uncertainties in habitat suitability maps. Ecological Modelling 195: 172-186 [pdf]
  36. Broquet T, Ray N, Petit E, Fryxell J M & Burel F. 2006. Genetic isolation by distance and landscape connectivity in the American marten (Martes americana). Landscape Ecology 21(6): 877-889 [pdf]
  37. Currat M, Excoffier L, Maddison W, Otto SP, Ray N, Whitlock MC & Yeaman S. 2006. Comment on "Ongoing Adaptive Evolution of ASPM, a Brain Size Determinant in Homo sapiens" and "Microcephalin, a Gene Regulating Brain Size, Continues to Evolve Adaptively in Humans". Science 313(5784): 172 [pdf]
  38. Ray N. 2005. PATHMATRIX: a GIS tool to compute effective distances among samples. Molecular Ecology Notes 5(1): 177-180 [pdf]
  39. Ray N, Currat M, Berthier P & Excoffier L. 2005. Recovering the geographic origin of early modern humans by realistic and spatially explicit simulations. Genome Research 15(8): 1161-7 [pdf] [suppl. data]
  40. Hamilton G, Currat M, Ray N, Heckel G, Beaumont M & Excoffier L. 2005. Bayesian estimation of recent migration rates after a spatial expansion. Genetics 170: 409-417 [pdf]
  41. Currat M, Ray N & Excoffier L. 2004. SPLATCHE: a program to simulate genetic diversity taking into account environmental heterogeneity. Molecular Ecology Notes 4(1): 139-142 [pdf]
  42. Ray N, Currat M & Excoffier L. 2003. Intra-deme molecular diversity in spatially expanding populations. Molecular Biology and Evolution 20(1): 76-86 [pdf]
  43. Ray N. 2003. Comment on "Population growth, carrying capacity, and conflict". Current Anthropology 44(1): 77-78 [pdf]
  44. Ray N, Lehmann A & Joly P. 2002. Modeling spatial distribution of amphibian populations: a GIS approach based on habitat matrix permeability. Biodiversity and Conservation 11(12): 2143-2165 [pdf]
  45. Ray N & Adams J M. 2001. A GIS-based vegetation map of the world at the Last Glacial Maximum. 25,000-15,000 BP). Internet Archaeology 11 [pdf] [Data sets download page]

Thesis

  1. Ray N. 2003. Modélisation de la démographie des populations humaines préhistoriques à l‘aide de données environnementales et génétiques PhD thesis. Université de Genève, Genève [online thesis].
  2. Ray N. 1999. Etude de la migration des amphibiens et de la connectivité à l‘aide d‘un Système d‘Information Géographique Master thesis (DESSNE). Université de Genève/Université de Lausanne, Genève [online thesis]

Other publications

  1. Lehmann A, Giuliani G, Ray N, Allenbach K, Charvat K, Gorgan D, Gvilava M, Bakuradze T. Sözen S, Goksel C & the enviroGRIDS consortium. 2009. The Black Sea Catchment Observation System built on a grid-enabled Spatial Data Infrastructure. INSPIRE, GMES and GEOSS activities, methods and tools towards a single Information Space in Europe for the environment, eds. Charvat, K., Alberts, M. & Horajova, S. Wirelessinfo Tehnologiju attistibas forums, Riga, pp. 42-58 [pdf]
  2. Giuliani, G., Ray, N., Lehmann, A. and K. Charvat. 2009. EnviroGRIDS interoperability guidelines. 92 pages
  3. Gorgan, D., Bacu, V., Ray, N. and A. Maier. 2009. EnviroGRIDS data storage guidelines. 67 pages
  4. Lehmann, A., Ray, N., Kideys, A., Weller, P. and M. Gvilava. 2009. Connecting the enviroGRIDS Black Sea Catchment Observation System to ICZM. Proceedings of the ninth International Conference on the Mediterranean Coastal Environment, MEDCOAST 09, Sochi, Russia, Volume 1, pp. 115-126 [pdf]
  5. Ebener S, Ray N, Black M & El Morjani Z. 2005. Physical Accessibility to health care: from isotropy to anisotropy. GIS Development 9(6): 34-36 [pdf]
  6. Ray, N. and S. Ebener. Physical Accessibility to Health Care and Population coverage Modeling - AccessMod© 3.0. Training and user guide. WHO. 51 pages
  7. Ray N & Adams J. 2002. Present-potential vegetation maps of the world. A GIS-based reconstruction using altitudinal zone [link and download]
  8. Ray, N. 2000. Training Guide for the use of GEO-3 Core Data Sets On-Line and the preparation of spatial data sets. United Nations Institute for Training and Research/Training Programme for the Application of the new Information and Communication Technologies, Geneva
  9. Levine JS, Bobbe T, Ray N, Singh A & RG Witt. 1999. Wildland Fires and the Environment: a Global Synthesis. UNEP-Technical and Assessment Report 99(1) [pdf]

Software

  1. Ray N, Currat M, Foll M. & Excoffier L. 2010. SPLATCHE2: a spatially-explicit simulation framework for complex demography, genetic admixture and recombination. [link and download]
  2. Ray, N. 2008. ACCESSMOD 3.0: a GIS tool to compute accessibility to health care based on environmental constraints to movement. [link and download]
  3. Ray, N. 2004. PATHMATRIX: a GIS tool to compute effective distances among samples. [link and download]
  4. Currat, M., Ray, N., Excoffier, L. 2004. SPLATCHE: A program to simulate genetic diversity based on environment heterogeneity. [link and download]
  5. Ray, N. 2002. CORRELATOR. A program for the exploration of correlation among a high number of sampling locations. LGB/University of Geneva
  6. Ray, N. 2002. G.SERVER LINK 1.0. Extension to ArcView 3.x enabling GIS information layers to be extracted and displayed from an IBM DB2-powered G.server. Geotask, Basel, Switzerland
  7. Ray, N. and L. Excoffier. 2002. MANTELN. A program for the computation of correlation and Mantel test on an arbitrary number of matrices. LGB/University of Geneva
  8. Ray, N. 2002. GEODIST. A program to compute matrices of geographic distances. LGB/University of Geneva
  9. Ray, N. 2001. GRID2TEXT and TEXT2GRID. Translator tools between ESRI grid format and regular text files using GRIDIO api. LGB/University of Geneva

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