Stéphane Joost
EPFL ENAC IIE LASIG
GC D2 398 (Bâtiment GC)
Station 18
CH-1015 Lausanne
EPFL ENAC SSIE-GE
GC D2 398 (Bâtiment GC)
Station 18
CH-1015 Lausanne
Mission
I specialized in the contribution of Geographic Information Science approaches for the analysis and for the management of genetic and health data. Within a small landscape genetics research group at the Laboratory of Geographic Information Systems (LASIG), I apply spatial analysis, spatial statistics, spatial modelling, and geocomputational methods to evolutionary biology and health data. I also make use of environmental engineering monitoring tools (e.g. meteorological stations, airborne sensors) to enhance the quality and the spatial resolution of geo-environmental data used in landscape genomics models.
GIScience : Spatial analysis, Spatial statistics, Geocomputation, Exploratory spatial data analysis
Spatial analysis of genetic (Landscape Genetics, Landscape Genomics, Conservation genetics) and health data (see GIRAPH group)
I currently serve on the editorial boards of BMC Genetics (associate editor), Frontiers in Genetics (associate editor), Frontiers in Ecology and Evolution (review editor), Frontiers in Environmental Informatics (review editor) and of the International Journal of Geomatics and Spatial Analysis (Revue Internationale de Géomatique). I also serve on the standing committee of the Association of American Geographers (AAG) for the attribution of the William L. Garrison award for best dissertation in computational geography.
Media
More news here!
Awards
- Winner of the AAGs first William L. Garrison Award for best dissertation in computational geography
(AAG website) Garrison Award
Biography
2012 Co-founder Geographic Information Research and Analysis in Public Health (GIRAPH)
2008 Co-founder MicroGIS Foundation for Spatial Analysis (MFSA)
1996 Co-founder MicroGIS SA
Researcher ID
-
orcid.org/0000-0002-1184-7501- Researcher ID (Thomson Reuters)
- My citations (Google Scholar)
Projects
HeLP (Health and Land-use Planning)
GIRAPH (Geographic Information Research and Analysis in Public Health)
SAFE FHW Geneva
H2020 IMAGE
BLW GENMON
ADAPTMAP
CLIMGEN
GREENTRACE
URBANGENE
GENESCALE
GIRAPH
NEXTGEN EU
GENOMIC RESOURCES ESF RNP
PIGDIV (Uganda, 2012) and SAVMAP (Namibia, 2014, 2015) CODEV projects
GLOBALDIV EU
ECONOGENE EU
SATW G.de Stael MESSAGE project
MOOCs recorded
Systèmes d'Information Géographique - partie 1
Systèmes d'Information Géographique - partie 2
Ph.D. Thesis
The Geographic Dimension of Genetic Diversity : a GIScience Contribution for the Conservation of Animal Genetic Resources
Commissions and boards
Liens
Orchestre de chambre Da Chiesa
Fields of expertise
Geographic Information Science - Landscape genomics - Seascape genomics - Spatial epidemiology - Geomedicine & Precision population health
Publications
References
. Indication of spatially random occurrence of Chlamydia-like organisms in Bufo bufo tadpoles from ponds located in the Geneva metropolitan area, in New Microbes and New Infections, vol. 27, p. 54-63, 2019-01-31.
. Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae), in Molecular Ecology Resources, vol. Early view, 2019-01-13.
. Landscape Genomics: Understanding Relationships Between Environmental Heterogeneity and Genomic Characteristics of Populations, in Population Genomics: Concepts, Strategies, and Applications, p. 261-322Springer, Cham, 2019.
. Genome-wide SNP profiling of worldwide goat populations reveals strong partitioning of diversity and highlights post-domestication migration routes, in Genetics Selection Evolution, vol. 50, p. 58BMC, London, 2018.
. Signatures of selection and environmental adaptation across the goat genome post-domestication, in Genetics Selection Evolution, vol. 50, p. 57BMC, London, 2018.
. AdaptMap: exploring goat diversity and adaptation, in Genetics Selection Evolution, vol. 50, p. 61BMC, London, 2018.
. Spatial distribution of mammography adherence in a Swiss urban population and its association with socioeconomic status, in Cancer Medicine, vol. 7, num. 12, p. 6299-6307, 2018-10-25.
. Combining Landscape Genomics and Ecological Modelling to Investigate Local Adaptation of Indigenous Ugandan Cattle to East Coast Fever, in Frontiers in Genetics, vol. 9, num. 385, p. 1-16, 2018-10-03.
. Crystal structure evaluation: calculating relative stabilities and other criteria: general discussion, in Faraday Discussions, vol. 211, p. 325-381, 2018-10-01.
. Developing Attitude Measures Based on Respondents’ Representations of Unfamiliar Objects, in Field Methods, p. 1525822X1879728, 2018-09-03.
. Spatial distribution of mammography adherence in a Swiss urban population and its association with socioeconomic status, in BioRxiv preprint, p. 404673, 2018-08-31.
. Indication of spatially random infection of chlamydia-like organisms in Bufo bufo tadpoles from ponds located in the Geneva metropolitan area, submitted in BioRxiv preprint, p. 402487, 2018-08-30.
. Detecting overlapping spatial clusters of high sugar-sweetened beverage intake and high body mass index in a general population: a cross-sectional study, submitted in BioRxiv preprint, p. 2018/08/29/399584, 2018-08-29.
. The Least Cost Path From Landscape Genetics to Landscape Genomics: Challenges and Opportunities to Explore NGS Data in a Spatially Explicit Context, in Frontiers in Genetics, vol. 9, p. 1-4, 2018-06-19.
. Spatial clusters of daytime sleepiness and association with nighttime noise levels in a Swiss general population (GeoHypnoLaus), in International Journal of Hygiene and Environmental Health, p. 1-7, 2018-06-04.
. Population density and water balance influence the global occurrence of hepatitis E epidemics. 16th Annual Ecology and Evolution of Infection Diseases - EEID, Glasgow, Scotland, 2018.
. NTIRE 2018 Challenge on Spectral Reconstruction from RGB Images. IEEE Conference on Computer Vision and Pattern Recognition Workshops 2018, Salt Lake City, USA, 2018.
. Switchable Light Reflectance in Dilute Magneto-Optical Colloids Based on Nickel Ferrite Nanowires, in E-JOURNAL OF SURFACE SCIENCE AND NANOTECHNOLOGY, vol. 16, p. 119-121, 2018.
. Combining landscape genomics and ecological modelling to investigate local adaptation of indigenous Ugandan cattle to East Coast fever, in BioRxiv, p. 1-52, 2018.
. Convergent genomic signatures of domestication in sheep and goats, in Nature Communications, vol. 9:813, num. 1, 2018.
. Some unexpected facets of open access geodata publishing. Noon Talks EPFL Library, Lausanne, Switzerland, 2018.
. Effets de l'environnement urbain sur la santé: l’importance des données géoréférencées au lieu de résidence en géomédecine. 19e Conférence nationale sur la promotion de la santé et 4e Conférence des parties prenantes MNT - Promotion Santé Suisse, Eventfabrik, Berne, 2018.
. Public smoking ban and socioeconomic inequalities in smoking prevalence and cessation: a cross-sectional population-based study in Geneva, Switzerland (1995–2014), in Tobacco Control, vol. 27, num. 6, p. 663-669, 2018.
. Multiscale landscape genomic models to detect signatures of selection in the alpine plant Biscutella laevigata, in Ecology and Evolution, vol. 8, p. 1794–1806, 2018.
. The peatland map of Europe, in Mires and Peat, vol. 19, num. 22, p. 1-17, 2017-11-10.
. Healthy Urban Planning: Body Mass Index association with exposure to night-time noise in the canton of Geneva. GeoMed, Porto, 2017-09-07.
. Modeling the present and future distribution of waterborne Hepatitis E virus. IECID 2017 Impact of Environmental Change on Infectious Diseases, Trieste, Italy, 2017-05-17.
. Des médecins à la direction de l’urbanisme ?. Forum Bâtir et Planifier "Villes en pleine santé", Lausanne, EPFL, Switzerland, 2017.
. Données médicales et génétiques géoréférencées au lieu de résidence pour un service de santé publique de précision. Swiss Public Health Conference 2017, Basel, Switzerland, 2017.
. Systèmes d'Information Géographique 2. Presses Polytechniques et Universitaires Romandes (PPUR), Lausanne, 2017.
. Systèmes d'Information Géographique 1. Presses Polytechniques et Universitaires Romandes (PPUR), Lausanne, 2017.
. Spatial dependence of body mass index and exposure to night-time noise in the Geneva urban area. X international, interdisciplinary conference on spatial statistics, geographical epidemiology and geographical aspects of public health, Porto, Portugal, 2017.
. Open science practices in geospatial education and research. Open Science in Practice Summer School (OSIP2017), EPFL, Lausanne, Switzerland, 2017.
. Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups, in Ecology and Evolution, vol. 7, num. 22, p. 9544–9556, 2017.
. Current challenge in landscape genomics: what about the environmental counterpart of high-throughput genomic data?. ESEB XVI Congress, Groningen, NL, 2017.
. Detecting animals in African Savanna with UAVs and the crowds, in Remote Sensing of Environment -New York-, vol. 200, p. 341–351Elsevier, New York, 2017.
. First quantitative survey delineates the distribution of chimpanzees in the Eastern Central African Republic, in Biological Conservation, vol. 213, p. 84-94Elsevier, Oxford, 2017.
. Integration of the role of climate in the spatial modeling of waterborne hepatitis E virus. Impact of Environmental Changes on Infectious Diseases, International Centre for Theoretical Physics, Trieste, Italy, 2017.
. Spatial dependence of genetic data related to human health and livestock disease resistance: a role for geography to support the One Health approach, in International Journal of Health, Animal science and Food safety, vol. 4, num. 1S, 2017.
. Persistence of butterfly populations in fragmented habitats along urban density gradients: motility helps, in Heredity -London-, vol. 119, p. 328–338Nature Publishing Group, London, 2017.
. Geomedicine: opportunities of using spatial information to move toward more precision in public health - Using geomedicine to identify BMI clusters in Geneva and Lausanne. 2ème congrès de printemps de la Société Suisse de Médecine Interne Générale, Lausanne, Swisstech Convention Center, 2017.
. Geomedicine: opportunities of using spatial information to move toward more precision in public health - spatial approaches and clusters: an introduction for clinicians. 2ème congrès de printemps de la Société Suisse de Médecine Interne Générale, Lausanne, Swisstech Convention Center, 2017.
. A WebGIS platform for the monitoring of Farm Animal Genetic Resources (GENMON), in Plos One, vol. 12, num. 4, p. e0176362Public Library of Science, San Francisco, 2017.
. Simple rules for an efficient use of Geographic Information Systems in molecular ecology, in Frontiers in Ecology and Evolution, vol. 5, p. 33, 2017.
. GenMon-CH : a Web-GIS application for the monitoring of Farm Animal Genetic Resources (FAnGR) in Switzerland. SVT-Tagung 2017 - Swiss Association for Animal Science, Zollikofen, Switzerland, 2017.
. Spatial clustering for district heating integration in urban energy systems: application to geothermal energy, in Applied Energy, num. 15 March 2017, p. 749–763, 2017.
. Spatial variability of potassium in agricultural soils of the canton of Fribourg, Switzerland, in Geoderma, vol. 290, p. 107–121Elsevier, Amsterdam, 2017.
. High performance computation of landscape genomic models including local indicators of spatial association, in Molecular Ecology Resources, vol. 17, num. 5, p. 1072–1089Wiley-Blackwell, Hoboken, 2017.
. Gene-obesogenic environment interactions in the UK Biobank study, in International Journal of Epidemiology, vol. 46, num. 2, p. 559–575Oxford University Press, Oxford, 2017.
. Combining genotype, phenotype and environment to infer potential candidate genes: An example using the Loblolly pine (Pinus taeda), in Journal of HeredityOxford University Press, Cary, 2017.
. Single-Cell Transcriptomics Reveals that Differentiation and Spatial Signatures Shape Epidermal and Hair Follicle Heterogeneity, in Cell Systems, vol. 3, num. 3, p. 221-237.e9, 2016-09-28.
. A GIS application to conservation genomics. IDYST Seminars, Faculty of Geosciences and Environment, University of Lausanne, UNIL, Lausanne, Switzerland, 2016.
. Approches spatiales pour une santé publique de précision en milieu urbain. Coloques du Service de la santé publique du canton de Vaud (SSP), Lausanne, Switzerland, 2016.
. Dissolution dynamic nuclear polarization of deuterated molecules enhanced by cross-polarization, in Journal Of Chemical Physics, vol. 145, num. 19, p. 194203Amer Inst Physics, Melville, 2016.
. Selective Trapping of DNA Using Glass Microcapillaries, in Langmuir, vol. 32, num. 33, p. 8525-8532American Chemical Society, Washington, 2016.
. Evidence that low socioeconomic position accentuates genetic susceptibility to obesity, in bioRxiv, 2016.
. Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition), in Autophagy, vol. 12, num. 1, p. 1-222Taylor & Francis Inc, Philadelphia, 2016.
. A role for HOX13 proteins in the regulatory switch between TADs at the HoxD locus, in Genes & Development, vol. 30, num. 10, p. 1172-1186Cold Spring Harbor Laboratory Press, Cold Spring Harbor, 2016.
. Combining Human Computing and Machine Learning to Make Sense of Big (Aerial) Data for Disaster Response, in Big data, vol. 4, num. 1, p. 47-59Mary Ann Liebert, Inc, New Rochelle, 2016.
. Open computational landscape genetics. Open Source Geospatial Research & Education Symposium 2016, Perugia, Italy, 2016.
. Advances in farm animal genomic resources. Frontiers, Lausanne, 2016.
. Spatial Areas of Genotype Probability of Cattle Genomic Variants Involved in the Resistance to East Coast Fever: A Tool to Predict Future Disease-Vulnerable Geographical Regions. Plant & Animal Genome Conference XXIV, San Diego, California, USA, 2016.
. Persistent spatial clusters of high body mass index in a Swiss urban population as revealed by the 5-year GeoCoLaus longitudinal study, in British Medical Journal Open, num. 6, p. e010145Bmj Publishing Group, London, 2016.
. Detecting spatial genetic signatures of local adaptation in heterogeneous landscapes, in Molecular Ecology, vol. 25, num. 1, p. 104–120Wiley-Blackwell, Hoboken, 2016.
. Multi locus genotypic data reveal high genetic diversity and low genetic structure of Iranian sheep, in Animal Genetics, vol. 47, num. 4, p. 463-470Wiley-Blackwell, Hoboken, 2016.
. The Visual Object Tracking VOT2014 Challenge Results. 13th European Conference on Computer Vision (ECCV), Zurich, SWITZERLAND, 2015.
. Chondroitinase gene therapy improves upper limb function following cervical contusion injury, in Experimental Neurology, vol. 271, p. 131-135Elsevier, San Diego, 2015.
. Advances in farm animal genomic resources, in Frontiers in Genetics, vol. 6, p. 333, 2015.
. Very high-resolution digital elevation models for multi-scale analysis in landscape genomics (GENESCALE). Rechalp Symposium, University of Lausanne, 2015.
. Effect of climate change on the spatial distribution of genomic variants involved in the resistance to East Coast Fever in Ugandan cattle. 19th Evolutionary Biology Meeting, Marseilles, France, 2015.
. Combined Optical Coherence and Fluorescence Microscopy to assess dynamics and specificity of pancreatic beta-cell tracers, in Scientific reportsNature Publishing Group, London, 2015.
. Whole genome duplications and recruitment of ecologically relevant genes in alpine Mustards. XVth ESEB Meeting, Lausanne, 2015.
. Prospects and Challenges for the Conservation of Farm Animal Genomic Resources, 2015-2025, in Frontiers in Genetics, vol. 6, p. 314, 2015.
. Very high resolution digital elevation models: are multi-scale derived variables ecologically relevant?, in Methods in ecology and evolution, vol. 6, num. 12, p. 1373–1383Wiley-Blackwell, Hoboken, 2015.
. Genomic diversity and Population Structure of Ugandan Taurine and Zebuine Cattle Breeds. XXI ASPA Congress, Milan, 2015.
. Modeling the spatial distribution of Theileria parva (Theiler 1904), causative agent of East Coast Fever disease in cattle. XXI ASPA Congress, Milan, 2015.
. Relationship between land cover type and Body Mass Index in Geneva. Joint Urban Remote Sensing Event, Lausanne, 2015.
. Characterizing neutral genomic diversity and selection signatures in indigenous populations of Moroccan goats (Capra hircus) using WGS data, in Frontiers in Genetics, 2015.
. Genomic diversity and disease prevalence in Ugandan cattle. Recolad Workshop, Paris, 2015.
. Biodiversity dynamics and the effect of urban environment on the distribution of genetic variation in the Geneva cross-border area. First Annual Meeting in Conservation Genetics – Science and Practice, Birmensdorf, Switzerland, 2015.
. Impact of the urbanization process on connectivity and genetic diversity - a spatially explicit simulation approach. First Annual Meeting in Conservation Genetics – Science and Practice, Birmensdorf, Switzerland, 2015.
. Sustained Delivery of Insulin-Like Growth Factor-1/Hepatocyte Growth Factor Stimulates Endogenous Cardiac Repair in the Chronic Infarcted Pig Heart, in Journal of Cardiovascular Translational Research, vol. 7, num. 2, p. 232-241, 2014.
. Method for hyperpolarization transfer in the liquid state, EP2904414, 2014.
. Adaptations to Climate-Mediated Selective Pressures in Sheep, in Molecular Biology And Evolution, vol. 31, num. 12, p. 3324-3343Oxford Univ Press, Oxford, 2014.
. Biogeoinformatics. Meetings del Comitato Italo-Svizzero per la Geoinformatica, Como, 2014.
. Subsampling as an economic consequence of using whole genome sequence data in landscape genomics: how to maximize environmental information from a reduced number of locations?. Livestock Genomic Resources in a Changing World, Cardiff, UK, 2014.
. Riding the whole-genome data tsunami: a landscape genomic study of local adaptation in Moroccan sheep and goats. Livestock Genomic Resources in a Changing World, Cardiff, UK, 2014.
. Data integration, GIS and multi-criteria decision making for the monitoring of livestock genomic resources. Livestock Genomic Resources in a Changing World, Cardiff, UK, 2014.
. Biogeoinformatics of livestock genomic resources. Livestock genomic resources in a changing world, Cardiff, UK, 2014.
. Microclimatological consequences for plant and microbial composition in Sphagnum-dominated peatlands, in Boreal Environment Research, vol. 19, num. 3, p. 195-208Finnish Environment Inst, Helsinki, 2014.
. The characterization of goat genetic diversity: Towards a genomic approach, in Small Ruminant Research, vol. 121, num. 1, p. 58-72Elsevier, Amsterdam, 2014.
. A participatory WebGIS platform to support biodiversity inventory in the Geneva cross-border area. Third Open Source Geospatial Research & Education Symposium (OGRS 2014), Otaniemi, Espoo, Finland, 2014.
. Genome-wide patterns of adaptation to climate-mediated selective pressures in sheep. The 34th ISAG Conference, Xi’an, China, 2014.
. High performance computation of landscape genomic models integrating local indices of spatial association, in arXiv Quantitative Biology, vol. [q-bio.PE], num. arXiv:1405.7658v1, 2014.
. The open source dynamics in geospatial research and education, in Journal of Spatial Information Science, num. 8, p. 67-71, 2014.
. Large-Scale Chondroitin Sulfate Proteoglycan Digestion with Chondroitinase Gene Therapy Leads to Reduced Pathology and Modulates Macrophage Phenotype following Spinal Cord Contusion Injury, in Journal Of Neuroscience, vol. 34, num. 14, p. 4822-4836Society for Neuroscience, Washington, 2014.
. Objective comparison of particle tracking methods, in Nature Methods, vol. 11, num. 3, p. 281-289Nature Publishing Group, London, 2014.
. A comparison of body mass index spatial dependence among adults and children in a Swiss general population, in Nutrition & Diabetes, num. 4, p. e111Nature Publishing Group, London, 2014.
. Assessing the spatial dependence of adaptive loci in 43 European and Western Asian goat breeds using AFLP markers, in Plos One, vol. 9, num. 1, p. e86668Public Library of Science, San Francisco, 2014.
. Investigation of genetic diversity of domestic C. hircus breeds reared within an early goat domestication area in Iran, in Genetics Selection Evolution, vol. 46, p. 27EDP Sciences, London, 2014.
. Spatial variability of soil phosphorus in the Fribourg canton, Switzerland, in Geoderma, vol. 217-218, p. 26-36, 2014.
. Quantitative single-cell RNA-seq with unique molecular identifiers, in Nature Methods, vol. 11, num. 2, p. 163-166, 2013-12-22.
. A Fast pH-Switchable and Self-Healing Supramolecular Hydrogel Carrier for Guided, Local Catheter Injection in the Infarcted Myocardium, in Advanced Healthcare Materials, vol. 3, num. 1, p. 70-78, 2013.
. Sustained Delivery Of Insulin-Like Growth Factor-1/Hepatocyte Growth Factor Promotes Endogenous Cardiac Repair And Regeneration In The Chronic Ischemic Heart. 62nd Annual Scientific Session of the American College of Cardiology, San Francisco, CA, 2013.
. Method and device for rapid dnp, US9329245, 2013.
. Analyse spatiale de la conflictualité, exploration par la régression géographiquement pondérée, in Canadian Journal of Regional Science, num. 36, p. 37-54, 2013.
. Geocomputational approaches for the analysis of Next-Generation Sequencing (NGS) and multi-scale data in landscape genomics. 11th Swiss Geoscience Meeting, Lausanne, 2013.
. A multiscale landscape genomics analytical framework to identify local adaptive variation in the Buckler Mustard. The IALE 2013 European Congress, Manchester, UK, 2013.
. SamBada in Uganda: landscape genomics study of traditional cattle breeds with a large SNP dataset. The IALE 2013 European Congress, Manchester, UK, 2013.
. Integrating landscape genomics and spatially explicit approaches to detect loci under selection in clinal populations, in Evolution -Lawrence Kansas-, vol. 67, num. 12, p. 3455–3468Wiley-Blackwell, Hoboken, 2013.
. eAtlas du Valais. , 2013.
. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics, in Molecular Ecology, vol. 22, num. 14, p. 3659-3665Wiley-Blackwell, Hoboken, 2013.
Teaching & PhD
Teaching
- Environmental Sciences and Engineering,
PhD Programs
- Doctoral Program in Civil and Environmental Engineering
PhD Students
Bosch Padros Martí
Gaillard Solange Catherine
Ladoy Anaïs Laurence
Rochat Estelle
Salmi Andrea
Stucki Sylvie ...
Gaillard Solange Catherine
Ladoy Anaïs Laurence
Rochat Estelle
Salmi Andrea
Past PhD Students
Leempoel Kevin ...Stucki Sylvie ...
Courses
Exploratory data analysis and geovisualization
This course teaches how to apply spatial exploratory approaches and processing methods and to apply them to georeferenced datasets relevant to the fields of environmental engineering, urban planning and spatial epidemiology. 