About me (Babak Naimi)...
Currently, I am a researcher at the University of Utrecht (QBD: Quantitative Biodiversity Dynamics group), focusing on biodiversity change, particularity employing technological advances in the area of deep/machine learning and remote sensing to address grand challenges related to biodiversity loss and climate change. Previously, I had multiple roles as senior researcher and postdoc at different universities including University of Helsinki, University of Amsterdam (BIOMAC; Daniel Kisling's group), ETH Zurich, Max Planck Institute for Ornithology, Imperial College London, University of Copenhagen (to work in Miguel Araújo’s lab). A full description of my research interests revolve around Remote Sensing of Ecosystem dynamics, Spatio-temporal Statistics, Spatial Modelling, and the interface between Geo-informatics and environmental science. In particular, I am interested in developing new methods for environmental dynamic modelling under climate change and land use change scenarios to improve their ability for understanding of ecological processes associated with the patterns in biodiversity as well as to deal with the challenges in the methods. I have a keen interest to continuing research on understanding and quantifying uncertainties in ensembles of environmental models while focusing on the application of geo-informatics. I am also interested in using temporal remote sensing for exploring ecosystem stability and spatial resilience and model critical transitions in ecosystems in the face of environmental/climate change.
Another area of my interests is scientific software development (either desktop or web-based) specially using open-source technologies. I always do programming joyfully because it allows me to get a maximum level of understanding of problems, enhance my abilities to deal with problems, and furthermore, I can bring something into being that does not exist.
Full CV:
Education & Training:
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PhD (Spatial ecology and Biogeography: Dealing with error and uncertainty) - 2010-2015
Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, The Netherlands
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M.Sc. (GIS & Remote Sensing) - 1998-2001
Department of Geography, Tarbiat Modarres University, Tehran, Iran
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B.Sc. (Natural Resources: Rangeland & Watershed Management) - 1994-1998
Gorgan university of agricultural sciences and natural resources, Gorgan, Iran
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Applied spatio-temporal data analysis with FOSS: R+OSGeo - Geostat 2011, Landau, Germany
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System Analysis and Modelling - 2011, ITC, Netherlands
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Web Technology for GIS and Mapping - 2011, ITC, Natherlands
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Geostatistics and Open-Source Statistical Computing - 2010 - ITC, Netherlands
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Bayesian statistics - 2009 - Wageningen university, Netherlands
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Assessment and Propagation of Uncertainty in Spatially Distributed Environmental Modelling - 2009 - Fiva, Denmark
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Design and Implementation of Database - 2002 - Cybertech, Iran
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Programming skills - 2001 - Cybertech, Iran
Research interest:
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Spatio-temporal Statistics
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Spatial Modelling
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Remote Sensing of Ecosystem Dynamics
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Spatial Resilience, Critical Transitions
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Spatial ecology and biogeography; species distribution modelling
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Global Environmental/Climate Change and its consequence on ecological systems
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Open-source software development
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Web-GIS
Grants and Awards:
Work experience:
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Senior Researcher, University of Utrecht, the Netherlands, 2022-Present
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Senior Researcher, University of Evora, Portugal, 2021-2022
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Senior Researcher, University of Helsinki, the Netherlands, 2019-2021
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Postdoc Researcher, University of Amsterdam, the Netherlands, 2018-2019
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Postdoc Researcher, ETH Zurich, Switzerland, 2017-2018
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Postdoc Researcher, University of Copenhagen, Denmark, 2015-2017
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Research Visitor, Imperial College London, United Kingdom, 2014-2015
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Faculty member, IAU university, Tehran, Iran - 2005-2008
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Project coordinator & Spatial Analyst, SAP consulting engineers Co. Tehran, Iran - 2001-2005
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Spatial Analyst, Remote Sensing Consulting Engineers Co., Tehran, Iran - 2000-2001
Skills:
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GIS & Remote Sensing software: ArcGIS, GRASS GIS, SAGA GIS, ENVI, Imagine ERDAS, Idrisi, Ilwis
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Programming language: R, Python, C++/C, Java script, Visual Basic
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Database Management System: PostgreSQL, PostGIS, MS SQL Server, MS Access, Esri ArcSDE
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Web GIS: MapServer, OpenLayers, NodeJs, JavaScript, HTML, Geo django
Refereed Journal Publications:
- González-Trujillo,J.D., Naimi, B., Assis, J., & Araújo, M. B. (2024). Reshuffling of Azorean Coastal Marine Biodiversity Amid Climate Change. Journal of Biogeography. doi:10.1111/jbi.15008
- Senbeta, A. F., Worku, W., Gayler, S., & Naimi, B. (2024). Unveiling Wheat’s Future Amidst Climate Change in the Central Ethiopia Region. Agriculture, 14(8), 1408.
- Kass, J. M., Smith, A. B., Warren, D. L., Vignali, S., Schmitt, S., Aiello‐Lammens, M. E., Arlé, E., Barbosa, A.M., Broennimann, O., Cobos, M.E., Guéguen, M., Guisan, A., Merow, C., Naimi, B., Nobis, M.P., Ondo, I., Osorio-Olvera, L., Owens, H.I., Pinilla-Buitrago, G.E., Sánchez-Tapia, A., Thuiller, W., Valavi, R., Velazco, S.J.E., Zizka, A., & Zurell, D. (2024). Achieving higher standards in species distribution modeling by leveraging the diversity of available software. Ecography, e07346. doi:10.1111/ecog.07346
- Amindin, A., Pourghasemi, H. R., Safaeian, R., Rahmanian, S., Tiefenbacher, J. P., & Naimi, B. (2024). Predicting Current and Future Habitat Suitability of an Endemic Species Using Data-Fusion Approach: Responses to Climate Change. Rangeland Ecology & Managementt, 34, 101149. doi:10.1016/j.rsase.2024.101149
- Taheri,Sh., Naimi, B., & Araújo, M. B. (2024). climetrics: An R package to quantify multiple dimensions of climate change. Ecography. doi:10.1111/ecog.07176
- Li, X., Naimi, B., Gong, P., & Araújo, M. B. (2024). Data error propagation in stacked bioclimatic envelope models. Integrative Zoology. doi:10.1111/1749-4877.12736
- Boali, A., Asgari, H. R., Behbahani, A. M., Salmanmahiny, A., & Naimi, B. (2024). Remotely sensed desertification modeling using ensemble of machine learning algorithms. Remote Sensing Applications: Society and Environment, 34, 101149. doi:10.1016/j.rsase.2024.101149
- Ebrahimi,E., Araújo, M. B., & Naimi, B. (2023). Flood susceptibility mapping to improve models of species distributions. Ecological Indicators. 157, 111250, doi:10.1016/j.ecolind.2023
- Rocchini, D., Tordoni, E., Marchetto, E., Marcantonio, M., Barbosa, A. M., Bazzichetto, M., Beierkuhnlein, C., Castelnuovo, E., Cazzolla Gatti, R., Chiarucci, A., Chieffallo, L., Da Re, D.,Musciano, M., Foody, G., Gabor, L., Garzon-Lopez, C., Guisan, A., Hattab, T., Hortal, J., Kunin, W.E., Jordán, F., Lenoir, J., Mirri, S., Moudrý, V.l Naimi, B., Nowosad, J., Sabatini, F., Schweiger, A., Šímová, P., Tessarolo, G., Zannini, P.& Malavasi, M. (2023). A quixotic view of spatial bias in modelling the distribution of species and their diversity. npj Biodiversity, 2(1), 10.
- Naimi, B., Capinha, C., Ribeiro, J., Rahbek, C., Strubbe, D., Reino, L., & Araújo, M. B. (2022). Potential for invasion of traded birds under climate and land‐cover change. Global Change Biology, 28(19), 5654-5666.
- Lemes, P., Barbosa, F. G., Naimi, B., & Araújo, M. B. (2022). Dispersal abilities favor commensalism in animal-plant interactions under climate change. Science of The Total Environment, 835, 155157.
- Claude A. Garcia, Sini Savilaakso, René W. Verburg, Natasha Stoudmann, Philip Fernbach, Steven A. Sloman, Garry D. Peterson, Miguel B. Araújo, Jean-François Bastin, Jürgen Blaser, Laurence Boutinot, Thomas W. Crowther, Hélène Dessard, Anne Dray, Scott Francisco, Jaboury Ghazoul, Laurène Feintrenie, Etienne Hainzelin, Fritz Kleinschroth, Babak Naimi, Ivan P. Novotny, Johan Oszwald, Stephan A. Pietsch, Fabien Quétier, Brian E. Robinson, Marieke Sassen, Plinio Sist, Terry Sunderland, Cédric Vermeulen, Lucienne Wilmé, Sarah J. Wilson, Francisco Zorondo-Rodríguez & Patrick O. Waeber (2022). Strategy games to improve environmental policymaking. Nature Sustainability, pp.1-8.
- Tehrani, N.A., Naimi, B. & Jaboyedoff, M. (2022). A data-integration approach to correct sampling bias in species distribution models using multiple datasets of breeding birds in the Swiss Alps. Ecological Informatics, 69, p.101501.
- Peterson, A.T., Aiello-Lammens, M., Amatulli, G., Anderson, R., Cobos, M., Diniz-Filho, J.A., Escobar, L., Feng, X., Franklin, J., Gadelha, L. Georges, D., Naimi, B. et al. (2022). ENM2020: A Free Online Course and Set of Resources on Modeling Species’ Niches and Distributions. Biodiversity Informatics, 17.
- Askaripour, N., Ashrafi, S., Ara, S. R., & Naimi, B. (2022). Understanding the summer roosting habitat selection of the greater mouse-tailed bat (Rhinopoma microphyllum) and the small mouse-tailed bat (Rhinopoma muscatellum) in Iran. Mammal Research, 67(4), 483-497.
- Taheri, S., Naimi, B., Rahbek, C., & Araújo, M. B. (2021). Improvements in reports of species redistribution under climate change are required. Science Advances, 7(15),
eabe1110.
- Thorup, K., Pedersen, L., Da Fonseca, R.R., Naimi, B., Nogués-Bravo, D., Krapp, M., Manica, A., Willemoes, M., Sjöberg, S., Feng, S. and Chen, G. (2021). Response of an Afro-Palearctic bird migrant to glaciation cycles. Proceedings of the National Academy of Sciences, 118(52).
- Harisena, N. V., Groen, T. A., Toxopeus, A. G., & Naimi, B. (2021). When is variable importance estimation in species distribution modelling affected by spatial correlation?. Ecography, 44(5), 778-788.
- Rocchini D, Thouverai E, Marcantonio M, Iannacito M, Daniele, RD, Torresani M, Bacaro G, Bazzichetto M, Bernardi A, Foody GM, Furrer R., Kleijn, D., Larsen, S., Lenoir,J., Malavasi, M., Marchetto, E., Messori, F., Montaghi, A., Moudrý, V., Naimi, B., Ricotta, C., Rossini, M., Santi, F., Santos, MJ., Schaepman, ME., Schneider, FD, Schuh, L., Silvestri, S., Ŝímová, P., Skidmore, AK, Tattoni, C., Tordoni, E., Vicario, S., Zannini, P., Wegmann, M. (2021) rasterdiv—An Information Theory tailored R package for measuring ecosystem heterogeneity from space: To the origin and back. Methods in Ecology and Evolution, 12(6), 1093-1102
- Sales, L. P., Kissling, W. D., Galetti, M., Naimi, B., & M Pires, M. (2021). Climate change reshapes the eco‐evolutionary dynamics of a Neotropical seed dispersal
system. Global Ecology and Biogeography, 30(5), 1129-1138.
- Tehrani, N. A., Naimi, B., & Jaboyedoff, M. (2021). Modelling current and future species distribution of breeding birds as regional essential biodiversity variables (SD EBVs): a bird perspective in Swiss Alps. Global Ecology and Conservation, e01596.
- Davar, L., Griggs, G., Danehkar, A., Salmanmahini A., Azarnivand, H. & Naimi, B. (2021). A Spatial Integrated SLR Adaptive Management Plan Framework (SISAMP) toward Sustainable Coasts. Water, 13 (16), p2263.
- Firozjaei, M.K., Sedighi, A., Firozjaei, H.K., Kiavarz, M., Homaee, M., Arsanjani, J.J., Makki, M., Naimi, B. & Alavipanah, S.K. (2021). A historical and future impact as-
sessment of mining activities on surface biophysical characteristics change: A remote sensing-based approach. Ecological Indicators, 122, p.107264.
- Araujo, M. B., Mestre, F., & Naimi, B. (2020). Ecological and epidemiological models are both useful for SARS-CoV-2. Nature Ecology & Evolution, doi:10.1038/s41559020-1246-y
- Alibakhshi, S., Naimi, B., Hovi, A., Crowther, T. W., & Rautiainen, M. (2020). Quantitative analysis of the links between forest structure and land surface albedo on a global scale. Remote Sensing of Environment, 246, 111854.
- Alibakhshi, S., Crowther, T. W., & Naimi, B. (2020). Land surface black-sky albedo at a fixed solar zenith angle and its relation to forest structure during peak growing season based on remote sensing data. Data in Brief, 105720.
- Araujo, M. B., & Naimi, B. (2020). Spread of SARS-CoV-2 Coronavirus likely to be constrained by climate. medRxiv. doi:10.1101/2020.03.12.20034728
- Garcia, C.; Savilaakso, S.; Sassen, M.; Stoudmann, N.; Verburg, R.W.; Quétier, F.; Araújo, M.B.; Bastin, J.; Boutinot, L.; Dessard, H.; Dray, A.; Fernbach, P.; Francisco, S.; Ghazoul, J.; Feintrenie, L.; Naimi, B.; Oszwald, J.; Pietsch, S.A.; Robinson, B.E.; Sist, P.; Sloman, S.A.; Sunderland, T.; Vermeulen, C.; Wilmé, L.; Wilson, S.J.; Waeber, P.O. (2020). To Bend the Curve of Terrestrial Biodiversity, Place Agency Centre Stage. Preprints, 2020100609 (doi: 10.20944/preprints202010.0609.v1).
- Garcia, C.A.; Savilaakso, S.; Verburg, R.W.; Gutierrez, V.; Wilson, S.J.; Krug, C.B.; Sassen, M.; Robinson, B.E.; Moersberger, H.; Naimi, B.; Rhemtulla, J.M.; Dessard, H.; Gond, V.; Vermeulen, C.; Trolliet, F.; Oszwald, J.; Quétier, F.; Pietsch, S.A.; Bastin, J.; Dray, A.; Araujo, M.B.; Ghazoul, J.; Waeber, P.O.(2020). The Global Forest Transition is a Human Affair. One Earth 2.5 (2020): 417-428.
- Kourosh Niya, A., Huang, J., Kazemzadeh-Zow, A., Karimi, H., Keshtkar, H., & Naimi, B. (2020). Comparison of three hybrid models to simulate land use changes: a case study in Qeshm Island, Iran. Environmental Monitoring and Assessment, 192, 1-19.
- Amini Tehrani, N., Naimi, B., & Jaboyedoff, M. (2020). Toward community predictions: Multi‐scale modelling of mountain breeding birds’ habitat suitability, landscape preferences, and environmental drivers. Ecology and Evolution.
- Khosravifard, S., Skidmore, A. K., Naimi, B., Venus, V., Muñoz, A. R., & Toxopeus, A.G. (2020). Identifying birds’ collision risk with wind turbines using a multidimensional utilization distribution method. Wildlife Society Bulletin, (doi: 10.1002/wsb.1056).
- Allahbakhshi, H., Conrow, L., Naimi, B., Weibel, R. (2020) Using Accelerometer and GPS Data for Real-Life Physical Activity Type Detection. Sensors, 20, 588.
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Naimi, B., Hamm, N.A.S., Groen, T.A., Skidmore, A.K., Alibakhshi, S. (2019) ELSA: entropy-based local indicators for spatial association.
Spatial Statistics, 29, 66-88.
- Araújo, M.B., Anderson, R.P., Márcia Barbosa, A., Beale, C., Dormann, C., Early, R., Garcia, R., Guisan, A., Maiorano, L.,
Naimi, B., O'Hara, B., Zimmermann, N., Rahbek, C. (2019) Standards for distribution models in biodiversity assessments.
Science Advances, 5(1), eaat4858.
- Hosseinzadeh, M.S., Qomi, M.F.,
Naimi, B., Rodder, D., Kazemi, S.M. (2018) Habitat suitability and modelling the potential distribution of Ophiomorus nuchalis (Sauria: Scincidae) on the Iranian Plateau.
North-Western Journal of Zoology, 14 (1): 60-63.
- Alibakhshi, S., Groen, T.A, Rautiainen, M.,
Naimi, B. (2017) Remotely sensed early warning signals of a critical transition in a wetland ecosystem.
Remote Sensing, 9 (4): 352, doi:10.3390/rs9040352
- Taheri, Sh.,
Naimi, B., Araujo, M.B. (2016) Did British breeding birds move north in the late 20th Century?.
Climate Change Responses. 3 (5), doi:
10.1186/s40665-016-0020-5
- Naimi, B., Araujo, M.B. (2016), sdm: a reproducible and extensible R framework for species distribution modelling. Ecography 39 (4), 368-375 , doi: 10.1111/ecog.01881 (Cover paper)
Mokhtari, S., Hosseini, S.M, Danehkar, A., Azad, M.T., Kadlec, J., Jolma, A.
Naimi, B. (2015) Inferring spatial distribution of oil spill risks from proxies: Case study in the north of the Persian Gulf.
Ocean & Coastal Management, 116, 504-511.
- Martnez-Lpez, J.,Martnez-Fernndez, J., Naimi, B., Carreo, M.F., & Esteve, M.A. (2014) An open-source spatio-dynamic wetland model of plant community responses to hydrological pressures. Environmental modelling & Software.In press.
- Salati. S., Ruitenbeek, F.V., var der Meer, F.,Naimi, B. (2014) Detection of Alteration Induced by Onshore Gas Seeps from ASTER and WorldView-2 Data. Remote Sensing. 6(4), 3188-3209.
- Naimi, B. Hamm, N.A.S., Groen, T.A., Skidmore, A.K., Toxopeus, A. (2014) Where is positional uncertainty important for species distribution modelling? Ecography, 37 (2), DOI: 10.1111/j.1600-0587.2013.00205.x
- Gholamalifard, M., Esmaili-Sari, A., Abkar, A., & Naimi, B. (2013). Bathymetric Modeling from Satellite Imagery via Single Band Algorithm (SBA) and Principal Components Analysis (PCA) in Southern Caspian Sea. International Journal of Environmental Research, 7(4), 877-886.
- Gholamalifard, M., Kutser, T., Esmaili-Sari, A., Abkar, A., & Naimi, B. (2013). Remotely Sensed Empirical Modeling of Bathymetry in the Southeastern Caspian Sea. Remote Sensing, 5(6), 2746-2762.
- Gholamalifard, Mehdi, Esmaili-Sari, A., Abkar, A., Naimi, B. and Tiit Kutser (2013). Influence of vertical distribution of phytoplankton on remote sensing signal of Case II waters: southern Caspian Sea case study. Journal of Applied Remote Sensing 7(1): 073550-073550.
- Naimi, B. Voinov, A. (2012) StellaR: A software to translate Stella models into R open-source environment. — Environmental modelling & Software. 38: 117-118
- Naimi, B. Skidmore, A.K., Groen, T.A., Hamm, N.A.S. (2011) Spatial Autocorrelation in Predictors Reduces the Impact of Positional Uncertainty in Occurrence Data on Species Distribution Modelling. — Journal of biogeography. 38: 1497-1509
- Abbaspour,M., Mahiny, A.R., Arjmandy, R., Naimi, B. (2011) Integrated approach for land use suitability analysis. — International Agrophysics. 25: 311-318
Conference Publications & Presentations:
- Naimi, B. Hamm, N.A.S., Groen, T.A., Skidmore, A.K., Toxopeus, A. (2013) ELISA: an entropy-based local indicators of spatial assciation. In: Spatial statistics 2013 : Revealing intricacies in spatial and spatio-temporal data with statistics, 4-7 June, 2013, Columbus, Ohio, The USA.
- Naimi, B., Skidmore, A.K., Hamm, N.A.S. and Groen, T.A. (2011) Using local spatial autocorrelation to deal with positional uncertainty of occurence data in species distribution modelling : abstract. In: Spatial statistics 2011 : mapping global change, abstracts for the conference, 23-25 March, 2011, University of Twente, Enschede, The Netherlands / editor A. Stein, , E. Pebesma, , G.B.M. Heuvelink. - Enschede : University of Twente Faculty of Geo-Information and Earth Observation ITC, 2011. 1 p
- Naimi, B., Skidmore, A.K., Groen, T.A. and Hamm, N.A.S. (2011) Spatial autocorrelation in predictors reduces the impact of positional uncertainty in occurrence data on species distribution modelling : abstract. In: Proceedings of the 5th international conference of the International biogeography Society : The advancement of all studies of the geography of nature, 7-11 January, 2011, Irakleion, Crete, Greece. p. 161
- Naimi, B., Skidmore, A.K., Hamm, N.A.S. & Groen, T.A. (2010) Positional error propagation analysis in habitat distribution modelling. In: Proceedings of Accuracy 2010 : 9th International symposium on spatial accuracy assessment in natural resources and envionrmental sciences, 20-23 July, 2010, Leicester, United Kingdom. / ed. by, N.J.Tate and P.F. Fisher. Leicester; University of Leicester on behalf of the International Spatial Accuracy Research Association (ISARA), 2010. pp. 409-412
- Naimi, B., Alimohammadi, A., Rahimipouri, H. (2006) Design and Implementation of Geographic Information Systems for Integrated Coastal Zone Management (ICZM) in Iran, 7th international symposium of ICOPMAS, Tehran, Iran
Other Publications:
- Goljani, R., Kaboli, M., Karami, M., Naimi, B., Shabani, A.A. (2010) Fall habitat suitability modelling of central Alborz wild ship (Ovis gmelini X O. vignei) in Jajrood protected complex, Iran, Journal of natural environment (Iranian Journal of Natural Resources), 63(2):173-186.
- Davar, L., Daneh Kar, A., Riazi, B., Mahiny, A.S., Naimi, B., (2010) Comparison effectiveness of NOAA and IMO methods for identification of environmentally sensitive coastal areas in Sistan and Balochestan Province, Journal of Environmental Sciences and Technology, 12(1): 113-136
- Mahiny, A.S., Riazi, B., Naimi, B., Kafaki, S.B., Larijani, A.J. (2009) Evaluation of ecotourism potential in Behshahr using a multi-criteria evluation method and GIS, Journal of Environmental Sciences and Technology, 11(1): 187-198
- Naimi, B., Alimohammadi, A., (2000) Modelling spatial distribution of floristic biodiversity using landsat TM satellite images (case study: Golestan National Park, Iran), Tarbiat modarres University, Tehran, Iran
