ISG anagram: Intelligent Systems Group of Basque Country University

Dr. Jose Antonio Fernandes Salvador
(2011) PhD with honours in Probabilistic Methods for Data Mining and Artificial Intelligence (University of Basque Country)
(2003) MSc in Computer Systems Security with honours in Linux Security and Criptography (University of Glamorgan)
(2002) Computer Engineer (Univesidad de Deusto).
(2000) Technical Engineering in Computer Managements (Universidad de Deusto).
(1996) High School in Management and Finances with honours (Instituto Politécnico Jesus Obrero)

	SPAIN: +34 656731025
	UK: +44 (0) 1603456161
	ja.fernandes.sp AT gmail DOT com
Currently, Senior Research Associate at East Anglia University (UEA; Norwich, UK) in the School of Environmental Sciences in collaboration with the Centre for the Environment, Fisheries and Aquaculture Science (CEFAS) working on integrating bioclimate envelope models with other modelling approaches.

Work experience

(2011-currently) Senior Research Associate. East Anglia University. School of Environmental Sciences.
(2011) Researcher. University of Helsinki. Faculty of Biological and Environmental Sciences. FEM group. Modelling of water quality in the Gulf of Finland.
(2007-2010) Researcher. AZTI-Tecnalia Marine Science and Food research fundation. PhD.
(2004-2006) Computer Engineer. Gizerbitek IT Consultancy.
(2000-2004) Systems administrator, web programming and users training. EDEX fundation.
(1999-2000) Server administration, web design and programming. Grant from University of Deusto for Online Catalog of Journals (aurkinet.deusto.es)
(1998-1999) Server administration, web design and programming. Grant from University of Deusto for E-learning system and contends development (elkano.deusto.es)
(1996) Freelance programmer. Bike design program based on morphologic features. Madesa factory.

PhD thesis

Data analysis advances in marine science for fisheries management: Supervised classification applications [dissertation pdf] [presentation pdf]

Refereed JCR-Journals publications

(2012) Evaluation of reaching the targets of the Water Framework Directive in the Gulf of Finland. Jose A. Fernandes, Pirkko Kauppila, Laura Uusitalo, Viivi Fleming, Sakari Kuikka, Heikki Pitkänen. Environ. Sci. Technol. Submitted.
(2012) Supervised pre-processing approaches in multiple class-variables classification for fish recruitment forecasting. Jose A. Fernandes, Jose A. Lozano, Iñaki Inza, Xabier Irigoien, Juan D. Rodríguez, Aritz Pérez. Appl. Soft Comput. Submited. [Java implementation (Instructions in Readme.txt)].
(2012) Robust machine-learning techniques for recruitment forecasting of North East Atlantic fish species. Jose A. Fernandes, Xabier Irigoien, Jose A. Lozano, Iñaki Inza, Aritz Pérez. ICES J. Mar. Sci. Submited. [Java implementation (Instructions in Readme.txt)].
(2012) Improving semi-automated zooplankton classification using an internal control and different imaging devices. Eneko Bachiller, Jose A. Fernandes, Xabier Irigoien. Limnol. Oceanogr.: Methods 10: 1-9.
(2011) Factors determining the distribution and betadiversity of mesozooplankton species in shelf and coastal waters of the Bay of Biscay. Xabier Irigoien, Guillen Chust, Jose A. Fernandes Aitor Albaina, Lucia Zarauz. J. Plankton Res. 33(8): 1163-1181.
(2011) The potential use of a Gadget model to predict stock responses to climate change in combination with Bayesian Networks: the case of the Bay of Biscay anchovy. Eider Andonegi , Jose A. Fernandes, Iñaki Quincoces, Andrés Uriarte, Aritz Pérez, Daniel Howell, Guntar Stefansson. ICES J. Mar. Sci. 68(6): 1257-1269.
(2010) Fish recruitment prediction, using robust supervised classification methods. Jose A. Fernandes, Xabier Irigoien, Nerea Goikoetxea, Jose A. Lozano, Iñaki Inza, Aritz Pérez, Antonio Bode. Ecol. Model. 221(2): 338-352. [Java console implementation].
(2009) Optimizing the number of classes in automated zooplankton classification. Jose A. Fernandes, Xabier Irigoien, Guillermo Boyra, Jose A. Lozano, Iñaki Inza. J. Plankton Res. 31(1): 19-29. [Java implementation (Instructions in Readme.txt)] [Journal link]
(2009) Spring zooplankton distribution in the Bay of Biscay from 1998 to 2006 in relation with anchovy recruitment. Xabier Irigoien, Jose A. Fernandes, Philippe Grosjean, Kevin Denis, Aitor Albaina, Maria Santos. J. Plankton Res. 31(1): 1-17. Featured article.
(2009) Changes in plankton size structure and composition, during the generation of a phytoplankton bloom, in the central Cantabrian sea. Lucia Zarauz, Xabier Irigoien, Jose A. Fernandes. J. Plankton Res. 31(2): 193-207.
(2008) Modelling the influence of abiotic and biotic factors on plankton distribution in the Bay of Biscay, during three consecutive years (2004-06). Lucia Zarauz, Xabier Irigoien, Jose A. Fernandes. J. Plankton Res. 30(8): 857-872.

Other publications

(2011) Bay of Biscay: Analysis of climate impacts on anchovy and sardine via bottom up processes. Chapter 5 presented by Xabier Irigoien in Deliverable 1.1, Report on analyses of climate-driven processes on farage fish distribution an abundance within each Case Study region (Month 15). In: FACTS project (Forage Dish Interactions), collaborative Research Project on "Sustainable use of seas and oceans: importance of forage fish in the ecosystem". Chapter based on unpublished work by Fernandes J.A., Irigoien X., Lozano J.A., Inza I., Pérez A., Goikoetxea N.
(2011) Escenarios de reclutamiento para la anchoa en 2012 e implicaciones para la toma de decisiones de gestión. Ibaibarriaga L., Boyra E., Fernandes J.A., Uriarte A., Cotano U. Technical report for the Ministry of Agriculture, Fish and Food of Basque Country Government and for the Ministry of Environment of Spanish Government.
(2011) Manuscript on indicators for hard bottom substrata. Germán J., Fernandes J. A., Garmendia J. M., Muxika I., Borja A. Deliverable 4.3-4 of Water bodie in Europe: Integrative Systems to assess Ecological status and Recovery (WISER) project. Collaborative Project (large-scale integrating project), Theme 6: Environment (including Climate Change).
(2011) Spatial structure and nictemeral changes of the zooplankton community along the Garrucha canyon (SW-Spain) as derived from dissecting microscope, ZooImage and FlowCAM analysis. Muñoz M., Reul A., Bautista B., Blanco J. M., Rodríguez J., Fernandes J. A., León P. I., Irigoien X. & Rodríguez V. 5th International Zooplankton Production Symposium Population Connections, Community Dynamics, and Climate Variability. 14-18th March, 2011. Pucon, Chile.
(2011) Zooplankton Image Analysis Manual: automated identification by means of scanner and digital camera as imaging devices. Bachiller E. & Fernandes J. A.. Revista Investigación Marina 18(2) :16-37.
(2010) Use of juvenile abundance indices for the management of the Bay of Biscay. Ibaibarriaga L., Uriarte A., Sanchez S., Fernandes J. A. & Irigoien X. Working document to WGANSA, 24-28 June 2010, Lisbon (Portugal).
(2010) A comparison between digital camera and scanner as imaging devices for semi-automated zooplanktton classification using microscope classification as control. Bachiller E., Fernandes J. A. & Irigoien X. Aquatic Sciences: Global Changes from the Center to the Edge. International Joint Meeting with ASLO & NABS. 6-11 June. Santa Fe, NM, USA.
(2010) Small-scale vertical distribution of zooplankton in the Catalan Sea: Relationships with physical characteristics. Alcaraz M., Saiz E., Lebourges-Dhaussy A., Graña R., Cotano U., Fernandes J. A. , Isari S., Zamora S., Mouriño B. & Irigoien X. Aquatic Sciences: Global Changes from the Center to the Edge. Rapp. Comm. Int. Mer Medit. Vol. 39 - pp. 84. 39th CIESM Congress. 10-14 May, Venice, Italy
(2010) The potential use of a Gadget model to predict stock responses to climate change in combination with Bayesian Networks: the case of the Bay of Biscay anchovy. Andonegi E., Fernandes J. A., Quincoces I., Irigoien X., Pérez A., Howell D. & Stefánsson G. International Symposium “Climate Change Effects on Fish and Fisheries: Forecasting Impacts, Assessing Ecosystem Responses, and Evaluating Management Strategies.” Sendai (Japan), April 26-29.
(2010) UNCOVER: Fish stock recovery strategies - Report from the Bay of Biscay Andonegi E., Quincoces I., Murua H., Fernandes J. A., Uriarte A., Sanchez S., Cerviño S., Velasco F., Huret M., Lehuta S. & Petitgas P.
(2009) Robust approaches to supervised machine learning techniques for seven fish species recruitment prediction in fisheries. Fernandes J. A., Irigoien X., Goikoetxea N., Uriarte A., Lozano J.A. & Inza I. ICES/PICES/UNCOVER Symposium 2009 on Rebuilding Depleted Fish Stocks - Biology, Ecology, Social Science and Management Strategies. Warnemünde/Rostock (Germany), 3-6 November 2009. [poster pdf]. Using latex template by Brian Amberg.
(2009) Anchovy Recruitment Mixed Long Series prediction using supervised classification. Fernandes J. A., Irigoien X., Uriarte A., Ibaibarriaga L., Lozano J.A. & Inza I. Working document to the ICES benchmark workshop on short lived species (WKSHORT) Bergen (Norway), 31 August-4 September 2009.
(2009) FlowCAM/PhytoImage intercalibration exercise. Denis K., Tunin-Ley A., Fernandes J. A., Maurer S., Parent J.-Y., Belin C., Irigoien X. & Grosjean Ph. Third SCOR WG130 meeting. 13-26th May, 2009. Baton Rouge (LA), USA.
(2009) Assesment of the discrimination potential fo bathymetric LIDAR and multispectral imagery for intertidal and subtidal habitats. Grande M., Chust G., Jose A. Fernandes & Galparsoro I. 33rd International Symposium on Remote Sensing of Environment (ISRSE). 4-8 May, 2009. Stresa (Italy)
(2008) Relevance of otolith features for anchovy age classification. Aitor Ascoreca, Jose A. Fernandes, Unai Cotano, Andres Uriarte and Xabier Irigoien. XI international Symposium on Oceanography of the Bay of Biscay. 2-4 April, 2008. Donostia - San Sebastian (Spain).

Reviewer for

Teaching

(2011) Guest lecturer in the subject "Machine learning", Computer Engineering Degree. University of Basque Country, San Sebastian (Spain).
(2011) EURO-BASIN Training Workshop on Introduction to statistical modelling tools, for habitat models development: Model Validation, performance measures, models comparison and Weka (open source software for data mining). AZTI-Tecnalia, Pasaia (Spain). [pdf]
(2007-2010) ZooImage software and plankton classification. AZTI-Tecnalia, Pasaia (Spain).
(2008-2009) Flowcam for phytoplankton digitalization and classification. AZTI-Tecnalia, Pasaia (Spain). CMIMA (CSIC), Barcelona (Spain).

Talks & Tutorials

(2011) Data mining in fisheries reseach: from zooplankton automated classification to fish recruitment forecasting. University of East Anglia. Norwich. UK. September.
(2011) Supervised classification in fisheries reseach: from zooplankton automated classification to recruitment forecasting. CEFAS. Lowestoft. UK. September.
(2011) Supervised classification applications in fisheries management. Helsinki Institute for Information Technology. Helsinki. Finland. February.
(2010) New approaches for fish recruitment forecasting: supervised classification, naive Bayes for regression and multi-dimensional classification. Institute of Information Theory and Automation, Academy of Sciences of the Czech Republic. Prague. July.
(2010) IBAM: Evaluation of feasibility of reaching water framework directives objectives (WFD and HELCOM) in the Gulf of Finland. Finnish Environment Institute (SYKE). Helsinki. June.
(2010) New approaches for fish recruitment forecasting: supervised classification, naive Bayes for regression and multi-dimensional classification. University of Helsinki. Helsinki. April.
(2010) New approaches for fish recruitment forecasting. AZTI-Tecnalia. March.
(2010) Supervised pre-processing approaches in multiple class-variables classification for fish recruitment forecasting. Universidad Politécnica de Madrid. March. [pdf]
(2009) JUVENA 2009: Campaña, proyecciones y consecuencias. Irigoien X., Andrés M., Fernandes J. A. AZTI-Tecnalia. November.
(2009) Recruitment prediction, classification, secondary analysis and meta-analysis. AZTI-Tecnalia. June. [pdf]
(2009) Robust approaches to machine learning techniques for recruitment prediction in fisheries. UNCOVER (Barcelona). March. [pdf]
(2009) Robust fish recruitment prediction using supervised classification methods. ECOANCHOA, AZTI-Tecnalia. March. [pdf]
(2008) Problemas de clasificación supervisada en ciencias marinas: de la clasificación de imágenes de plancton a la predicción de reclutamiento. Fernandes J. A., Irigoien X., Lozano J.A, Inza I.. Suficiencia investigadora. 8 November, 2008. UPV-EHU, Donostia - San Sebastian (Spain).
(2008) Recruitment prediction, from BNs to DBNs and MDBNs. Basque Country University. October.
(2008) Recruitment prediction using supervised classification methods. AZTI-Tecnalia. September. [pdf]
(2008) Habitat modelling with Bayesian Networks. Basque Country University. April.
(2007) Procesamiento y clasificación automática. AZTI-Tecnalia. November. [pdf]
(2007) Data Mining, problemas de clasificación con Weka. Universidad de Deusto. E-ghost. July. [pdf]

Akcnoledgements to E-ghost group and Borja Sotomayor for training in latex use and providing the base layout for these presentations.

Thesis collaborations

(2009-2011) Influence of the northeastern Atlantic oceano-meteorological variability on the northern hake (Merluccius merluccius), based on the last three-decadal period data (1978-2006). Goikoetxea N. PhD thesis. AZTI-Tecnalia.
(2008-2011) Trophic Ecology of small pelagic species in the Bay of Biscay. Bachiller E. PhD thesis. AZTI-Tecnalia.
(2008-2009) Assessment of the discrimination potential of bathymetric LIDAR and multispectral imagery for intertidal and subtidal habitats. Grande M. European Master of Science in Marine Environment and Resources. AZTI-Tecnalia.
(2007-2008) Feeding behaviour and diet of anchovy juveniles (Engraulis encrasilous L.) in the Bay of Biscay. Bachiller E. European Master of Science in Marine Environment and Resources. AZTI-Tecnalia.
(2007) Description and modelling of plankton biomasa distribution in the Bay of Biscay by means of image analisis-based methods. Zarauz L. PHd thesis. AZTI-Tecnalia.

Thesis supervision

(2010) Análisis automático de señales de atún obtenidas mediante sonar de largo alcance a bordo de buques pesqueros. Ari Urkullu. MSc in Computational Engineering and Expert Systems. University of Basque Country. Supervisors: Yosu Yurramendi, Haritz Arrizabalaga, Jose A. Fernandes.

Basque, Spanish and European projects

WISER: Water bodies in Europe: Integrative Systems to assess Ecological status and Recovery

EURO-BASIN: Basin Scale Analysis, Synthesis and Integration

FACTS: Forage Fish Interactions

K-EGOKITZEN: Cambio Climático Impactos y Adaptación

UNCOVER: UNderstanding the Mechanisms of Stock ReCOVERy

ECOANCHOA by Department of Agriculture, Fisheries and Food of the Basque Country Government.
PERFIL (CTM2006-12344-C02-02) from the Spanish Ministry of Education and by the Department of Agriculture, Fisheries and Food of the Basque Country Government.
Theme 6 of the EC Seventh Framework program, through the Marine Ecosystem Evolution in a Changing Environment (MEECE No 212085) Collaborative Project.
Collaborator in the SeaLifeBase

Oceanographic surveys

(2009) Perfil at Mediterranean Sea. Flowcam. June.
(2008) Perfil at Cantabrian Sea. Flowcam. July.
(2008) Bioman at Cantabrian Sea. Pairovet and Flowcam. May.
(2007) Bioman at Cantabrian Sea. Cufes and Flowcam. May.

Research visits to research institutions

(2010) University of Helsinki, Finland. Sakari Kuikka and Laura Uusitalo. Financed by Spanish Ministry of Education. Fellowships for European PhDs. Thee months.
(2009) Ifremer, France. Alina Tunin Ley and Daniele Maurer. Financed by AZTI-Tecnalia. One week.
(2008) Mons-Hainaut University, Belgium. Philippe Grosjean and Kevin Denis. Financed by AZTI-Tecnalia. Two weeks.
(2007) Mons-Hainaut University, Belgium. Philippe Grosjean and Kevin Denis. Financed by AZTI-Tecnalia. One week.

Organized events

(2011-2012) Every two weeks "Fish club coffee of UEA", a serie of informal meetings/talks to gather multidisciplinar proffesors, postdocs and PhD students that work on issues related to Fisheries.

ZooImage training and counseling

ZooImage (http://www.sciviews.org/zooimage/) is a tool for automated classification of plankton images. It can be used for scanned samples and for FlowCam images, or for any other divice images if they have a uniform background. This tool has been used in some of my research projects and I have been providing training to people of several countries:

(2011) Chile: Karen Manríquez, Nicolás Bralic (COPAS Center-Universidad de Concepción).
(2010) France: Delphine Bonnet and Juliette Balavoine (CNRS-Université Montpellier II).
(2010) Taiwan: Elise Marquis (National Taiwan University).
(2009) Spain: Sonia Romero Romero (Universidad de Cádiz).
(2009) Spain: Cristina Garcia Muñoz (CSIC).
(2008-2009) Spain: María Lidia Nieves (Universidad de las Palmas).
(2008-2009) Spain: Pablo León (Universidad de Málaga).
(2008-2009) Spain: Enric Saiz (CMIMA), CSIC.
(2008) France: Serge A. Poulet (INRS).
(2008) Greece: Nikolaos Nikolioudakis (University of Crete).
(2008) South Africa: Fabienne Cazassus (MA-RE Institute, UCT).
(2007) Portugal: María Manuel Angelico (IPIMAR).

Our manuals and course materials can be downloaded:

Flowcam training and counseling:

(2009) Spain: Course in CMIMA (CSIC). Barcelona. June.
(2009) Spain: Courses in AZTI-Tecnalia. San Sebastian. May, June and July.
(2008) Spain: Courses in AZTI-Tecnalia. San Sebastian. May and July.

Television and newspaper: Divulgative Science

Itsasnet: El portal del mar Software para predecir el reclutamiento de peces (Recruitment Forecasting Software) November 2011. A new about a software I developed during my thesis freely available now.
Diario Vasco newspaper. Azti-Tecnalia publica un manual sobre el estudio del zooplacton en imágenes March 2011. A new about a technical manual written by Eneko Bachiller and me for semi-automatic zooplankton classification.
ETB1 channel. Kresala program. February 2010. Eneko Bachiller comments our work in semi-automatic zooplankton classification.
ETB1, ETB2 and ETB3 channels. Teknopolis program. 'Tras la pista de la anchoa'. November 2009. Xabier Irigoien comments our work studing relationships between anchovy and climate.

Weka

Supervised version of Cmean missing values imputation filter based on the non-supervised version provided in weka. Download.

Favourite cites

"Luck is what happens when preparation meets opportunity." Seneca Roman dramatist, philosopher and politician (5 BC - 65 AD).

Other interests

Dancing: Salsa (combining Cuban style with other styles) and Argentine Tango. Teacher of salsa at "Keseakava" salsa bar (Bilbao, Spain), in the dance schools "Pasos de Baile" (Bilbao, Spain), "Estudio Rosa Mari" (Bilbao, Spain) and Chilli con Salsa (Norwich, UK).
Theater: Colaborations with La hAceria (El bosque encantado). Amateur groups: Cuerpo Escena (Temple and Cuadros Insolitos) and Uyu-Yui (Crimenes Ejemplares).
Martial arts: Penkat Silat (Indonesian and Malasian). Scottish and Auchi Jiu-Jitsu. Wing-chung. Budocan Karate. Viet vo dao. Aikido. Capoeira Gerais.

Old pre-researcher curriculums

Spanish curriculum. Last update June 2007.
American format curriculum. Last update November 2006.
Artistic curriculum. Photos Book. Last update September 2007.

Mendeley
Researcher ID: B-8985-2009
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