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Ana Paula graduated in Applied Plant Biology (1998) by FCUL and obtained her PhD in Molecular Biology (2010/09) by ITQB NOVA/UNL. Her PhD work on plant stress regulation was conducted at CRAG/IBMB-CSIC in Barcelona (2000-2005) in close collaboration with ITQB NOVA. After a first post-doc at ITQB (2010-2013) she went to Sweden (2013-2015) for a second post-doctoral stay at the Linköping University. In July 2018 (until present) she joined the CCMAR team at the University of Algarve as a researcher of the Welfish Mar2020 project. RESEARCH INTERESTS and EXPERIENCE: 1) Ana Paula is interested on how living organisms adapt to environmental stress at molecular level. This interest settles on the concern with global food/feed security, as environmental constraints severely affect crops and fish/seafood production. During her PhD, she has studied plant abiotic stress responses aiming at the identification of key genes/proteins involved in stress tolerance for further crop improvement. 2) More recently, she has been working on fish stress and nutritional responses towards a sustainable aquaculture production. 3) She is further interested on the regulation of stress-mediated mechanisms at transcriptional, but mostly at translational level, as proteins control virtually all cellular processes. Proteomics and its wide application into distinct biological systems prompted her to join a project on nano-cellular interactions based on mass spectrometry approaches. She contributed to the development of an innovative method for the rapid prototyping and safe-by-design of TiO2 nanoparticles for medical applications (SUSTU). 4) She also pursues an integrated view on the complex regulatory mechanisms beyond cellular-environmental interactions through the application of Bioinformatics and Biostatistical tools. Ana Paula authored/co-authored 20 publications, having received training on Proteomics and Bioinformatics from EMBO, EBI-EMBL, University of Warwick or the Uppsala University, besides being invited as lecturer/instructor of national and international Proteomics courses e.g., at Thailand and Costa Rica. Ciência Vitae most frequent terms in the context of scientific and technological output are: Proteomics; Mass Spectrometry; Multi-Omics; Plant Abiotic Stress; Protein Corona; Fish nutrition; Fish Welfare; Sustainable Aquaculture.
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Identification

Personal identification

Full name
ANA PAULA MARTINS FARINHA RESENDE

Citation names

  • Farinha, Ana Paula
  • Farinha, Ana P
  • Farinha, A
  • F Resende, Paula

Author identifiers

Ciência ID
4312-4B8F-3079
ORCID iD
0000-0003-1455-5958
Google Scholar ID
https://scholar.google.com/citations?user=cY1aKYIAAAAJ&hl=en
Researcher Id
G-5692-2017
Scopus Author Id
54386717500

Email addresses

  • ana.resende@esa.ipsantarem.pt (Professional)

Addresses

  • Dep. Tecnologia Alimentar, Biotecnologia e Nutrição Edifício dos Laboratórios Setor Produção Vegetal e Botânica, Gab. 3. Quinta do Galinheiro – S.Pedro , 2001-904 , Santarém, Santarém, Portugal (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Molecular Biology
  • Agrarian Sciences - Agriculture, Forestry and Fisheries
  • Medical and Health Sciences - Medical Biotechnology - Biomaterials

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Spanish; Castilian Advanced (C1) Advanced (C1) Upper intermediate (B2) Proficiency (C2) Upper intermediate (B2)
Catalan Intermediate (B1) Upper intermediate (B2) Beginner (A1) Advanced (C1) Elementary (A2)
French Elementary (A2) Upper intermediate (B2) Elementary (A2) Upper intermediate (B2) Elementary (A2)
Education
Degree Classification
2021/07
Concluded
 Software for Data Analysis (Postgraduate Certificate)
Universitat de Barcelona, Spain

Universidad Abierta de Cataluña, Spain
Excellent (A)
2017/12
Concluded
 Applied Pharmaceutical Bioinformatics (Postgraduate Certificate)
Uppsala Universitet Farmaceutiska fakulteten, Sweden
 Good (C)
2015/12
Concluded
 Pharmaceutical Bioinformatics (Postgraduate Certificate)
Uppsala Universitet Farmaceutiska fakulteten, Sweden
 Excellent (A)
2010/09
Concluded
 Biology (Doutoramento)
Major in Molecular Biology
Instituto de Biología Molecular de Barcelona, Spain

Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
"Proteomic and transcriptomic approaches to abiotic stress tolerance in rice (Oryza sativa L.)" (THESIS/DISSERTATION)
 Maximum by Unanimity
1998/07
Concluded
 Applied Plant Biology (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Molecular studies on the expression of the maize (Zea mays) PX2 protein in response to water stress" (THESIS/DISSERTATION)
 15/20 final grade and 19/20 diploma thesis
Affiliation

Science

Category
Host institution 		Employer
2018/07/01 - 2021/05/31 Postdoc (Research) Universidade do Algarve, Portugal
Centro de Ciências do Mar, Portugal
2014/06/01 - 2015/05/31 Contracted Researcher (Research) Linköpings Universitet Institutionen för klinisk och experimentell medicin, Sweden
Dep. of Clinical and Experimental Medicine (IKE), Cell Biology, Faculty of Heath Science, Linköping University, Sweden
2013/06/01 - 2014/05/31 Postdoc (Research) Linköpings Universitet Institutionen för klinisk och experimentell medicin, Sweden
Dep. of Clinical and Experimental Medicine (IKE), Cell Biology, Faculty of Heath Science, Linköping University, Sweden
2012/05 - 2013/05 Postdoc (Research) Instituto de Biologia Experimental e Tecnológica, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2010/09/01 - 2012/04/30 Postdoc (Research) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2023/09/01 - Current Invited Adjunct Teacher (Polytechnic Teacher) Instituto Politécnico de Santarém Escola Superior Agrária, Portugal

Others

Category
Host institution 		Employer
2021/06/01 - 2023/06/01 External Research Collaborator Universidade do Algarve, Portugal
Centro de Ciências do Mar, Portugal
2009/01/01 - 2009/06/30 Research Technician/Técnic Superior de Suport a la Recerca Universitat Pompeu Fabra, Spain
Parc de Recerca Biomèdica de Barcelona, Spain
2005/01/01 - 2005/12/31 PhD Student (Ministerio Ciencia y Tecnologia, Gobierno de España) Center for Research in Agricultural Genomics, Spain
Consejo Superior de Investigaciones Científicas, Spain
2001/09/01 - 2004/11/30 PhD Student (FCT, Portugal) Center for Research in Agricultural Genomics, Spain
Instituto de Biología Molecular de Barcelona, Spain
2000/12/01 - 2001/08/30 PhD Student (FCT, Portugal) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1999/01/01 - 2000/11/30 Young Researcher Fellow (FCT, Portugal) Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
1998/01/01 - 1998/12/31 Young researcher fellow (FCT, Portugal) Consejo Superior de Investigaciones Científicas, Spain
Consejo Superior de Investigaciones Científicas, Spain
(...)
1997/03 - 1997/10 Erasmus free mover student, Barcelona, Spain Consejo Superior de Investigaciones Científicas, Spain
Centro de Investigación y Desarrollo Josep Pascual Vila, Spain
(...)
Projects

Contract

Designation Funders
2018/07/01 - 2021/05/31 Estabelecimento de biomarcadores de bem-estar em peixe de aquacultura através de uma abordagem proteómica/Establisment of welfare biomarkers in farmed fish through a proteomics approach
MAR-02.05.01-FEAMP-0012 WELFISH
Post-doc Fellow
Universidade do Algarve, Portugal
 European Maritime and Fisheries Fund

Programa Operacional MAR2020
Concluded
2018/07/01 - 2018/12/31 Bases para uma alimentação saudável e sustentável para peixes de aquaculture – ALISSA/Healthy and sustainable feeds for farmed fish
ALG-01-0247-FEDER-003520
Other
Universidade do Algarve, Portugal

Sparos Lda, Portugal
European Regional Development Fund

QREN- Quadro de Referência Estratégico Nacional
Concluded
2015 - 2015 Characterisation of TiO2 protein corona in cellular environment: an in vitro approach to nano-bio interactions in keratinocytes and microvascular endothelial cells
QUALITYNANO Grant agreement ID: 262163
Other
University of Birmingham School of Geography Earth and Environmental Sciences, United Kingdom
 QualityNano Research Infrastructure
Concluded
2012/01/01 - 2013/05/31 3to4: Converting C3 to C4 photosynthesis for sustainable agriculture
info:eu-repo/grantAgreement/EC/FP7/289582/EU
Post-doc Fellow
Instituto de Biologia Experimental e Tecnológica, Portugal
 European Commission
Concluded
2010/04/01 - 2012/04/30 Breeding for salinity tolerance in rice and identification of key genes/proteins affecting seed set under salt stress
PTDC/AGR-AAM/099234/2008
Post-doc Fellow
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2005/01/01 - 2005/12/31 Genes regulados por acido abscisico (ABA) y estrés osmotico en plantas
BIO2003-01133
PhD Student Fellow
Consejo Superior de Investigaciones Científicas, Spain
 Gobierno de España Ministerio de Ciencia Innovación y Universidades
Concluded
2000/10/01 - 2004 STUDIES FOR IMPROVEMENT OF RICE PRODUCED IN PORTUGAL AND MOZAMBIQUE
info:eu-repo/grantAgreement/FCT/POCI/33434/PT
PhD Student Fellow
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
1999 - 2000 Towards genetic improvement of Prunus species (almond and peach) through molecular characterisation and genetic transformation techniques
NA
Scientific Initiation Fellow
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Centro de Investigación y Desarrollo Josep Pascual Vila, Spain
Instituto de Cooperação Científica e Tecnológica Internacional/ICCTI
Concluded
1998 - 2000 Saneamento e melhoramento de fruteiras Portuguesas por métodos Biotecnológicos
PRAXIS/3/3.2/Hort/2143/95
PRAXIS/3/3.2/Hort/2143/95
Scientific Initiation Fellow
Instituto de Biologia Experimental e Tecnológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Cerqueira, Marco; de Magalhães, Cláudia Raposo; Schrama, Denise; FARINHA, ANA PAULA; Carrilho, Raquel; Rodrigues, Pedro M.. "Proteomics for Comprehensive Analysis of Seafood Products". In Handbook of Seafood and Seafood Products Analysis. CRC Press, 2024.
    Published
  2. Farinha, Ana Paula; Moreira, Márcio; de Magalhães, Cláudia Raposo; Schrama, Denise; Cerqueira, Marco; Carrilho, Raquel; Rodrigues, Pedro M.. Corresponding author: Farinha, Ana Paula. "Proteomics for Quality and Safety in Fishery Products". In Sustainable Fish Production and Processing, edited by Charis M. Galanakis, 45-78. Elsevier, 2022.
    10.1016/b978-0-12-824296-4.00007-4
  3. Barros, Pedro M.; Martínez-Gómez, P; Kodad, Ossama; FARINHA, ANA PAULA; Oliveira, M.Margarida. "Prunus dulcis syn. Prunus amygdalus Almond". In Biotechnology of Fruit and Nut Crops, edited by Litz; Pliego-Alfaro; Hormaza, 561-580. Wallingford, United Kingdom: CABI, 2020.
    Published • 10.1079/9781780648279.0561
  4. Cerqueira, Marco; FARINHA, ANA PAULA; Schrama, Denise; Moreira, Márcio; Raposo de Magalhães, Cláudia. "Fish". In Proteomics for food authentication, edited by Leo M.L. Nollet; Semih Ötles, 177-202. Boca Raton, United States: CRC Press, Taylor & Francis Group, 2020.
    Published • 10.1201/9780429261923
  5. Duque, Ana Sofia; Almeida, André; Silva, Anabela Bernardes; Silva, Jorge Marques; FARINHA, ANA PAULA; Santos, Dulce; Fevereiro, Pedro; Araújo, Susana Sousa. "Abiotic Stress Responses in Plants: Unraveling the Complexity of Genes and Networks to Survive". In Abiotic Stress - Plant Responses and Applications in Agriculture, edited by Vahdati; Leslie. InTech, 2013.
    Published • 10.5772/52779
  6. FARINHA, ANA PAULA; Lumbreras, Victoria; Pagès, Montserrat. Corresponding author: FARINHA, ANA PAULA. "Molecular responses to drought in rice and maize: towards genetic engineering for stress tolerance". In Genomics for biosafety in plant biotechnology, edited by Nap; Atanassov; Stiekema, 159-169. Amsterdam, Netherlands: IOS Press. NATO Science Series, 2004.
    Published
Conference abstract
  1. Raposo de Magalhães, Cláudia; Blackburn, G; Whitfield, P; FARINHA, ANA PAULA; Carrilho, Raquel; Schrama, Denise; Cerqueira, Marco; Rodrigues, Pedro Miguel. "Integrative proteomics and metabolomics profiling of farmed gilthead seabream hepatic stress response. ORAL COMMUNICATION". Paper presented in 14th International Congress on the Biology of Fish, Montpellier, 2022.
    Accepted
  2. Raposo de Magalhaes, Claudia; FARINHA, ANA PAULA; Carrilho, Raquel; Schrama, Denise; Cerqueira, Marco; Rodrigues, Pedro Miguel. "The promisor role of skin mucus to screen for fish stress biomarkers: a proteomics approach. ORAL COMMUNICATION". Paper presented in Aquaculture 2022 (North America), San Diego, 2022.
    Published
  3. Raposo de Magalhães, Cláudia; FARINHA, ANA PAULA; Carrilho, Raquel; Schrama, Denise; Cerqueira, Marco; Rodrigues, Pedro Miguel. "In search of stress biomarkers: label-free shotgun proteomics analysis of gilthead seabream hepatic and skin mucus proteome. ORAL COMMUNICATION". Paper presented in Aquaculture Europe 2021, Funchal, 2021.
    Published
  4. Raposo de Magalhães, Cláudia; Schrama, Denise; Nakharuthai, Chatsirin; Bunanantanasarn, Surintorn; Revets, Dominique; Kuehn, Annete; Planchon, Sébastien; et al. "Comparative analysis of the stress responsive hepatic proteome and gene expression: identification of stress biomarkers. ORAL COMMUNICATION". Paper presented in Aquaculture Europe 2020, 2020.
    Published
  5. Raposo de Magalhães, Cláudia; Cerqueira, Marco; Schrama, Denise; FARINHA, ANA PAULA; Kuehn, Annete; Revets, Dominique; Boonanuntanasarn, Surintorn; Nakharuthai, Chatsirin; Rodrigues, Pedro Miguel. "Identification of welfare biomarkers in farmed gilthead seabream: integrating multi-omics data. ORAL COMMUNICATION". Paper presented in L’Acqua 2019. Latin American & Caribbean Aquaculture, San José, 2019.
    Published
  6. Carrasco del Amor, A; Kumar, A; Berlin, E; Hurtado, J; Kuruvilla, J; FARINHA, ANA PAULA; Fresnedo, O; Ochoa, B; Cristobal, S. "Designing patient-specific nanodrug-protein corona. ORAL COMMUNICATION". Paper presented in Nano2Clinic, 1st COST Action CA17140 Conference, Riga, 2019.
    Published
  7. FARINHA, ANA PAULA; Cerqueira, Marco; Schrama, Denise; Colen, Rita; Engrola, Sofia. "Effects of amino acid supplementation on the performance of Sparus aurata using metabolic fingerprinting, proteomics and western blot techniques. ORAL COMMUNICATION". Paper presented in 3rd AquaImprove Aquaculture research workshop, Porto, 2018.
    Published
  8. Kuruvilla, Jacob; FARINHA, ANA PAULA; Rueda, Yuri; Fresnedo, Olatz; Cristobal, Susana. "Surface proteomics on nanoparticles, from rapid prototyping of nanodrugs to precision medicine. ORAL COMMUNICATION". Paper presented in XIXth EuroAnalysis 2017, Europe’s Analytical Chemistry Meeting, Stockholm, 2017.
    Published
  9. Kuruvilla, Jacob; FARINHA, ANA PAULA; Bayat, Narges; Cristobal, Susana. "Surface proteomics, a step to simplify the rapid prototyping of nanodrugs. ORAL COMMUNICATION". Paper presented in Multi-target paradigm for innovative ligand identification in the drug discovery process (MuTaLig) COST Action CA15135. First WG Meeting 2016, Budapest, 2016.
    Published
  10. FARINHA, ANA PAULA; Kuruvilla, Jacob; Ochoa, Begoña; Cristobal, Susana. "Proteomics tools to predict nanoparticles targeting and uptake capability. ORAL COMMUNICATION". Paper presented in HUPO 2015 - 14th Human Proteome Organization World Congress, Vancouver, 2015.
    Published
  11. FARINHA, ANA PAULA; Alexandre, Bruno; Abreu, Isabel A. "Post-translational modifications. Converting C3 to C4 photosynthesis for sustainable agriculture. ORAL COMMUNICATION". Paper presented in 3to4 Meeting/ C4 CAM Meeting, Urbana-Champaign, 2013.
    Published
  12. FARINHA, ANA PAULA; Irar, Sami; Pagès, Montserrat; Oliveira, M.Margarida. "Proteomic analysis of rice varieties (Oryza sativa L.) with contrasting sensitivity to abiotic stress. ORAL COMMUNICATION". Paper presented in 8th Plant Genomics European Meeting, Lisboa, 2009.
    Published
  13. FARINHA, ANA PAULA. "Proteomic analysis of rice varieties with distinct sensitivity to abiotic stress. ORAL COMMUNICATION". Paper presented in 18th Franco-Catalan Meeting, IBMB/CSIC-IRTA, St. Hilari Sacalm, 2004.
Conference paper
  1. Goday, Adela; Lumbreras, Victoria; Riera, Marta; Gendra, Elisenda; Nieva, Cláudia; FARINHA, ANA PAULA; Saleh, Abdelaty; Moreno, Alicia; Pagès, Montserrat. "Resistant genes to abiotic stress". Paper presented in Science and Environment. Second Scientific Conference on Environment of the CCMA (Center for Environment Sciences) - CSIC (Spanish Council for Scientific Research), 2002.
    Published
Conference poster
  1. Carrilho, Raquel; FARINHA, ANA PAULA; Raposo de Magalhães, Cláudia; Moreira, Márcio; Rodrigues, Pedro; Cerqueira, Marco. "Thermal and nutritional strategies as alternatives to antibiotics in aquaculture.". Paper presented in Aquaculture 2022 (North America), 2022.
  2. Raposo de Magalhães, Cláudia; Cerqueira, Marco; Schrama, Denise; F RESENDE, PAULA; Kuehn, Annete; Revets, Dominique; Boonanuntanasarn, Surintorn; Nakharuthai, Chatsirin; Rodrigues, Pedro M. "Welfare biomarkers for farmed Gilthead Seabream (Sparus aurata): integrating multi-omics data". Paper presented in 18th Human Proteome Organization World Congress. HUPO 2019, 2019.
  3. FARINHA, ANA PAULA; Cerqueira, Marco; Schrama, Denise; Raposo de Magalhães, Cláudia; Colen, Rita; Engrola, Sofia; Rodrigues, Pedro Miguel. "Effects of methionine supplementation on the performance of European seabass using a shotgun proteomics approach". Paper presented in Proteomic Forum 2019, XIII Annual Congress of the European Proteomics Association, Potsdam, Germany, 2019.
  4. FARINHA, ANA PAULA; Cerqueira, Marco; Schrama, Denise; Raposo de Magalhães, Cláudia; Silva, Tomé; Conceição, Luis; Engrola, Sofia; Rodrigues, Pedro Miguel Leal. "Dietary effects of methionine in atlantic seabass analysed by shotgun proteomics". Paper presented in L’Acqua 2019. Latin American & Caribbean Aquaculture, San José, Costa Rica, 2019.
  5. Cerqueira, Marco; Schrama, Denise; FARINHA, ANA PAULA; Rodrigues, Pedro. "The effects of dietary creatine on muscle quality and allergen parvalbumin modulation of Dicentrarchus labrax". Paper presented in Aquaculture Europe 19, Berlin, Germany, 2019.
  6. Raposo de Magalhães, Cláudia; Cerqueira, Marco; Schrama, Denise; FARINHA, ANA PAULA; Revets, Dominique; Kuehn, Annete; Boonanuntanasarn, Surintorn; Nakharuthai, Chatsirin; Rodrigues, Pedro Miguel Leal. "Using an integrated multi-omics approach to validate more robust welfare biomarkers in gilthead seabream". Paper presented in Multiomics to Mechanisms - Challenges in Data Integration, EMBO|EMBL Symposia, EMBL Heidelberg, Germany, 2019.
  7. Raposo de Magalhães, Cláudia; Cerqueira, Marco; Schrama, Denise; FARINHA, ANA PAULA; Kuehn, Annete; Revets, Dominique; Boonanuntanasarn, Surintorn; Nakharuthai, Chatsirin; Rodrigues, Pedro Miguel Leal. "Establishment of farmed fish welfare biomarkers; a multi-omics approach". Paper presented in Proteomic Forum 2019, XIII Annual Congress of the European Proteomics Association, Potsdam, Germany, 2019.
  8. Cerqueira, Marco; Schrama, Denise; Silva, Tomé; Colen, Rita; Conceição, Luis; Engrola, Sofia; Rodrigues, Pedro Miguel Leal; FARINHA, ANA PAULA. "The effects of dietary tryptophan in the liver proteome of gilthead seabream". Paper presented in L’Acqua 2019. Latin American & Caribbean Aquaculture, San José, Costa Rica, 2019.
  9. Schrama, Denise; FARINHA, ANA PAULA; Cerqueira, Marco; Colen, Rita; Engrola, Sofia; Silva, Tomé; Rodrigues, Pedro Miguel. "Effects of methionine supplementation on the performance of European seabass using a shotgun proteomics approach". Paper presented in 3rd AquaImprove Aquaculture research workshop, CIIMAR, Porto, Portugal, 2018.
  10. Farinha, Ana Paula; Ochoa, Begoña; Cristobal, Susana. "Evolution of nanoparticle-protein corona, learning lessons from quantitative proteomics for nanosafety". Paper presented in SETAC Europe, 25th Society of Environmental Toxicology and Chemistry Annual Meeting, Barcelona, Spain, 2015.
  11. Farinha, Ana Paula; Ochoa, Begoña; Cristobal, Susana. "Proteomic characterisation of TiO2 nanoparticle-protein corona formation in vitro". Paper presented in NANOTOX 2014, 7th International Nanotoxicology Congress, Antalaya,Turkey, 2014.
  12. Alexandre, Bruno; FARINHA, ANA PAULA; Oliveira, M.Margarida; Saibo, Nelson; Abreu, Isabel Alexandra; Farinha, Ana Paula; Luis, Inês. "Identification of New Phosphorylation Sites in Key C4 Maize Enzymes - A Proteomics Approach". Paper presented in Plant Biology Europe FESPB/EPSO Congress, Dublin, Ireland, 2014.
  13. FARINHA, ANA PAULA; Gonçalves, Nuno; Oliveira, M.Margarida; Negrão, Sónia. "Rice proteome under salt stress at the reproductive stage". Paper presented in 5th Congress of the Spanish Proteomics Society, Barcelona, Spain, 2013.
  14. FARINHA, ANA PAULA; Alexandre, Bruno; Rodrigues, S.; Oliveira, M.Margarida; Saibo, Nelson; Coelho, Ana Varela. "Post-translational modifications in key C4 maize enzymes- analysis of PEP1, PPDK and NADH-ME phosphorylation". Paper presented in The 2013 International Symposium on C4 and CAM Plant Biology, Urbana-Champaign, USA, 2013.
  15. FARINHA, ANA PAULA; Gonçalves, Nuno; Oliveira, M.Margarida; Negrão, Sónia. "Anther multi-omics approach to study salt stress response at the reproductive stage in contrasting rice genotypes". Paper presented in XIII Portuguese-Spanish Congress of Plant Physiology, Lisboa, Portugal, 2013.
  16. FARINHA, ANA PAULA; Gonçalves, Nuno; Oliveira, M.Margarida; Negrão, Sónia. "Rice proteome under salt stress at the reproductive stage". Paper presented in SEB (Society Experimental Biology) Annual Meeting, Salzburg, Austria, 2012.
  17. FARINHA, ANA PAULA; Negrão, Sónia; Bahcevandziev, kiril; Oliveira, M.Margarida. "Rice towards stress: using anthers as a target to improve salt tolerance". Paper presented in International Plant & Animal Genome XX, San Diego, CA, USA, 2012.
  18. FARINHA, ANA PAULA; Negrão, Sónia; Bahcevandziev, kiril; Oliveira, M.Margarida. "Rice anthers: a challeging target to improve salt tolerance". Paper presented in 4th International Workshop - Plant Abiotic Stress -COST ACTION FA0605, Cyprus, 2011.
  19. FARINHA, ANA PAULA; Irar, Sami; Oliveira, M.Margarida; Pagès, Montserrat. "A Proteomic approach to unravel abiotic stress tolerance in rice". Paper presented in Proteomics and Pathology Joint congress of the Spanish Proteomics Society and the European Proteomics Association. Valencia, Spain, 2007.
  20. Irar, Sami; Caparrós, David; FARINHA, ANA PAULA; Fornale, Silvia; Lumbreras, Victoria; Vicient, CM.; Romera, M.; et al. "Proteomic platform at the Centre de Recerca en Agrigenomica in Barcelona.". Paper presented in Proteomics and Pathology Joint congress of the Spanish Proteomics Society and the European Proteomics Association, 2007.
  21. FARINHA, ANA PAULA; Irar, Sami; Oliveira, M.Margarida; Pagès, Montserrat. "A Proteomic approach to unravel abiotic stress tolerance in rice". Paper presented in 4th International Rice Functional Genomics Symposium. Montpellier, France, 2006.
  22. FARINHA, ANA PAULA; Oliveira, M.Margarida; Pagès, Montserrat. "Proteomic analysis of rice varieties with distinct sensitivity to abiotic stress". Paper presented in 2nd EPSO Conference. Interactions in Plant Biology: cells, plants and communities. Ischia, Italy, 2004.
  23. FARINHA, ANA PAULA; Goday, Adela; Lumbreras, Victora; Pagès, Montserrat. "Functional analysis of a novel Maize ABA-inducible gene". Paper presented in VII Reunion de Biologia Molecular de Plantas, 2004.
  24. Goday, Adela; FARINHA, ANA PAULA; Talano, Melina; López, Cristina; Lumbreras, Victoria; Dominguez, Eva; Pagès, Montserrat. "Maize px2, an ABA responsive gene: characterization of PX2 protein". Paper presented in 7th International Congress on Plant Molecular Biology. Barcelona, Spain, 2003.
  25. FARINHA, ANA PAULA; Goday, Adela; Pagès, Montserrat; Oliveira, M. Margarida. "Molecular responses to abiotic stress in tolerant and sensitive rice varieties". Paper presented in 7th International Congress on Plant Molecular Biology. Barcelona, Spain, 2003.
  26. FARINHA, ANA PAULA; Oliveira, M.Margarida; Pagès, Montserrat. "Molecular characterization of tolerant and sensitive rice varieties under abiotic stress". Paper presented in International congress entitled: In the wake of the double helix: from the green revolution to the gene revolution. Bologna, Italy, 2003.
  27. FARINHA, ANA PAULA; Oliveira, M.Margarida; Pagès, Montserrat. "Molecular characterization of tolerant and sensitive varieties in response to abiotic stress". Paper presented in EUCARPIA/ XIX International Conference on Maize and Sorghum. Barcelona, Spain, 2003.
  28. Saleh, Abdelaty; FARINHA, ANA PAULA; Nieva, Cláudia; Pagès, Montserrat. "Regulación de genes inducidos en respuesta al ABA y al estrés hidrico en el maiz.". Paper presented in XV Reunión de la Sociedad Española de Fisiologia Vegetal - VIII Congreso Hispano-Luso de Fisiologia Vegetal., 2003.
  29. FARINHA, ANA PAULA; Oliveira, M. Margarida; Pagès, Montserrat. "Molecular studies of rice gene expression under abiotic stress.". Paper presented in XIII Congresso Nacional de Bioquimica., 2002.
  30. FARINHA, ANA PAULA; Oliveira, M.Margarida. "Silver-staining of AFLP markers in Almond species". Paper presented in 27th Meeting of the Federation of European Biochemical Societies (FEBS). Lisbon, Portugal, 2001.
Journal article
  1. Cláudia Raposo de Magalhães; Kenneth Sandoval; Ferenc Kagan; Grace McCormack; Denise Schrama; Raquel Carrilho; Ana Paula Farinha; Marco Cerqueira; Rodrigues, PM. "Transcriptomic changes behind Sparus aurata hepatic response to different aquaculture challenges: An RNA-seq study and multiomics integration". PLOS ONE (2024): http://dx.doi.org/10.1371/journal.pone.0300472.
    10.1371/journal.pone.0300472
  2. João L. Saraiva; Filippo Faccenda; María J. Cabrera-Álvarez; Michele Povinelli; Peter C. Hubbard; Marco Cerqueira; Ana Paula Farinha; et al. "Welfare of rainbow trout at slaughter: Integrating behavioural, physiological, proteomic and quality indicators and testing a novel fast-chill stunning method". Aquaculture (2024): https://publons.com/wos-op/publon/64934937/.
    10.1016/J.AQUACULTURE.2023.740443
  3. Raposo de Magalhães, Cláudia; Farinha, Ana Paula; Carrilho, Raquel; Schrama, Denise; Cerqueira, Marco; Rodrigues, Pedro M.. Corresponding author: Farinha, Ana Paula. "A new window into fish welfare: A proteomic discovery study of stress biomarkers in the skin mucus of gilthead seabream (Sparus aurata)". Journal of Proteomics 281 (2023): 104904. http://dx.doi.org/10.1016/j.jprot.2023.104904.
    Published • 10.1016/j.jprot.2023.104904
  4. Márcio Moreira; Benjamín Costas; Pedro M. Rodrigues; Cátia Lourenço-Marques; Rui Sousa; Denise Schrama; Cláudia Raposo de Magalhães; Ana Paula Farinha; Florbela Soares. "Amyloodiniosis in aquaculture: A review". Reviews in Aquaculture (2023): https://publons.com/wos-op/publon/61861013/.
    10.1111/RAQ.12883
  5. Cláudia Raposo de Magalhães; Ana Paula Farinha; Gavin Blackburn; Phillip D. Whitfield; Raquel Carrilho; Denise Schrama; Marco Cerqueira; Pedro M. Rodrigues. "Gilthead Seabream Liver Integrative Proteomics and Metabolomics Analysis Reveals Regulation by Different Prosurvival Pathways in the Metabolic Adaptation to Stress". International Journal of Molecular Sciences 23 23 (2022): 15395. https://doi.org/10.3390/ijms232315395.
    Open access • Published • 10.3390/ijms232315395
  6. Schrama, Denise; Raposo de Magalhães, Cláudia; Cerqueira, Marco; Carrilho, Raquel; Farinha, Ana Paula; Rosa da Costa, Ana M.; Gonçalves, Amparo; et al. "Effect of creatine and EDTA supplemented diets on European seabass (Dicentrarchus labrax) allergenicity, fish muscle quality and omics fingerprint". Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 41 (2022): 100941. http://dx.doi.org/10.1016/j.cbd.2021.100941.
    Published • 10.1016/j.cbd.2021.100941
  7. Cláudia Raposo de Magalhães; Denise Schrama; Chatsirin Nakharuthai; Surintorn Boonanuntanasarn; Dominique Revets; Sébastien Planchon; Annette Kuehn; et al. "Metabolic Plasticity of Gilthead Seabream Under Different Stressors: Analysis of the Stress Responsive Hepatic Proteome and Gene Expression". Frontiers in Marine Science 8 (2021): 469. https://publons.com/publon/45217083/.
    Open access • Published • 10.3389/FMARS.2021.676189
  8. Moreira, Marcio; Schrama, Denise; Farinha, Ana Paula; Cerqueira, Marco; Raposo de Magalhaes, Claudia; Carrilho, Raquel; Rodrigues, Pedro. "Fish Pathology Research and Diagnosis in Aquaculture of Farmed Fish; a Proteomics Perspective". Animals 11 1 (2021): 125. https://publons.com/publon/36343122/.
    Published • 10.3390/ANI11010125
  9. Farinha, Ana Paula; Schrama, Denise; Silva, Tome; Conceicao, Luis E. C.; Colen, Rita; Engrola, Sofia; Rodrigues, Pedro; Cerqueira, Marco. Corresponding author: Farinha, Ana Paula. "Data on European seabass fed with methionine-enriched diets obtained through label free shotgun proteomics". Data in Brief 34 (2021): 106675. https://publons.com/publon/36343125/.
    Published • 10.1016/J.DIB.2020.106675
  10. Farinha, Ana Paula; Schrama, Denise; Silva, Tome; Conceicao, Luis E. C.; Colen, Rita; Engrola, Sofia; Rodrigues, Pedro; Cerqueira, Marco. Corresponding author: Farinha, Ana Paula. "Evaluating the impact of methionine-enriched diets in the liver of European seabass through label-free shotgun proteomics". Journal of Proteomics 232 (2021): 104047-104047. https://publons.com/publon/36343124/.
    Published • 10.1016/J.JPROT.2020.104047
  11. Raposo de Magalhães, Cláudia; Schrama, Denise; Farinha, Ana Paula; Revets, Dominique; Kuehn, Annette; Planchon, Sébastien; Rodrigues, Pedro Miguel; Cerqueira, Marco. "Protein changes as robust signatures of fish chronic stress: a proteomics approach to fish welfare research". BMC Genomics 21 1 (2020): http://dx.doi.org/10.1186/s12864-020-6728-4.
    Open access • Published • 10.1186/s12864-020-6728-4
  12. Cerqueira, Marco; Schrama, Denise; Silva, Tome S.; Colen, Rita; Engrola, Sofia A. D.; Conceicao, Luis E. C.; Rodrigues, Pedro M. L.; Farinha, Ana Paula. "How tryptophan levels in plant-based aquafeeds affect fish physiology, metabolism and proteome". Journal of Proteomics (2020): https://publons.com/publon/34996225/.
    10.1016/J.JPROT.2020.103782
  13. Kuruvilla, J.; Farinha, Ana Paula; Bayat, N.; Cristobal, S.. "Surface proteomics on nanoparticles: A step to simplify the rapid prototyping of nanoparticles". Nanoscale Horizons 2 1 (2017): 55-64. http://www.scopus.com/inward/record.url?eid=2-s2.0-85035340133&partnerID=MN8TOARS.
    10.1039/c6nh00162a
  14. Campos, A.; Danielsson, G.; Farinha, A.P.; Kuruvilla, J.; Warholm, P.; Cristobal, S.. "Shotgun proteomics to unravel marine mussel (Mytilus edulis) response to long-term exposure to low salinity and propranolol in a Baltic Sea microcosm". Journal of Proteomics 137 (2016): 97-106. https://publons.com/publon/8295088/.
    Published • 10.1016/J.JPROT.2016.01.010
  15. Abreu, I.A.; Farinha, Ana Paula; Negrão, S.; Gonçalves, N.; Fonseca, C.; Rodrigues, M.; Batista, R.; Saibo, N.J.M.; Oliveira, M.M.. "Coping with abiotic stress: Proteome changes for crop improvement". Journal of Proteomics 93 (2013): 145-168. http://www.scopus.com/inward/record.url?eid=2-s2.0-84888030942&partnerID=MN8TOARS.
    10.1016/j.jprot.2013.07.014
  16. Farinha, Ana Paula; Irar, S.; de Oliveira, E.; Oliveira, M.M.; Pagès, M.. "Novel clues on abiotic stress tolerance emerge from embryo proteome analyses of rice varieties with contrasting stress adaptation". Proteomics 11 12 (2011): 2389-2405. http://www.scopus.com/inward/record.url?eid=2-s2.0-79958131076&partnerID=MN8TOARS.
    10.1002/pmic.201000570
  17. Martins, Madalena; Farinha, Ana Paula; Ferreira, E.; Cordeiro, V; Monteiro, A; Tenreiro, Rogério; Oliveira, M.Margarida. "MOLECULAR ANALYSIS OF THE GENETIC VARIABILITY OF PORTUGUESE ALMOND COLLECTIONS". Acta Horticulturae 546 60 (2001): 449-452. https://publons.com/publon/8295086/.
    Published • 10.17660/ACTAHORTIC.2001.546.60
Thesis / Dissertation
  1. Resende, Ana Paula Martins Farinha. "Proteomic and Transcriptomic Approaches to Abiotic Stress Tolerance in Rice (Oryza sativaL.)". PhD, 2010. http://hdl.handle.net/10362/9757.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2019/11 Fundamentals in mass spectrometry based proteomics Workshop: Proteomics and its application for aquaculture
Universidad Nacional Costa Rica (UNA) (San José, Costa Rica)
2019/11 Brief considerations about statistics and data analysis in Proteomics Workshop: Proteomics and its application for aquaculture
Universidad Nacional Costa Rica (UNA) (San José, Costa Rica)
2019/11 Proteomics applied to Aquaculture - Fish nutrition Workshop: Proteomics and its application for aquaculture
Universidad Nacional Costa Rica (UNA) (San José, Costa Rica)
2018/11 Fundamentals in mass spectrometry based proteomics Proteomics Workshop
Suranaree University of Technology (Nakhon Ratchasima, Thailand)
2015/02 Evolution of nanoparticle-protein corona, learning lessons from quantitative proteomics for nanosafety ABA’s People Meeting. https://www.cragenomica.es/sites/default/files/programa.pdf
Centre for Research in Agricultural Genomics (CRAG) (Barcelona, Spain)
2012/06 Rice contrasting genotypes: what can they tell us about abiotic stress tolerance? A proteomics approach Proteomics Course: gel based protein separation by two-dimensional gel electrophoresis and protein characterization by MALDI-TOF/TOF mass spectrometry
CIIMAR; IPATIMUP; FCUP (Porto, Portugal)

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2023/06 - 2023/06 EMBO practical course “Quantitative proteomics: strategies and tools to probe biology”.
Other
European Molecular Biology Laboratory, Germany
2021/01/20 - 2021/01/22 Training in Experimental Design and Analysis of Data for Research with Animals. Online course format. Course in Experimental Design and Analysis of Data for Research with Animals.
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal
2020/09/07 - 2020/09/18 Training in Laboratory Animal Science (Mouse, Rat, Zebrafish and Fish) for FELASA C accreditation (Functions A, B and D) Laboratory Animal Science Course
Universidade do Porto Instituto de Investigação e Inovação em Saúde, Portugal

Universidade do Porto Instituto de Biologia Molecular e Celular, Portugal
2019/02/12 - 2019/02/15 EMBL- EBI Course “Introduction to Multi-Omics Data Integration”. Introduction to MultiOmics Data Integration
European Bioinformatics Institute (EMBL-EBI) , United Kingdom
2018/12/17 - 2018/12/21 Training in laboratory aquatic animal's practices for FELASA B accreditation 14th Cal-Aqua | Laboratory Aquatic Animal Sciences Course
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2015/03/25 - 2015/03/27 Mass spectrometry training: MALDI Essential Training Course (Bruker) Introductory Course to the high performance UltraflexXtreme MALDI system by Bruker
Mass Spectrometry Core Facility, Linköping University, Sweden
2014/04/07 - 2014/04/10 Training on Proteome Bioinformatics Training School on Proteome Bioinformatics. COST Action FA1002
Swiss Institute of Bioinformatics, Switzerland
2013 - 2014 Farm animal Proteomics- FAProteomics. COST Action FA1002
Other
 FAProteomics. COST Action FA1002
European Cooperation in Science and Technology, Belgium
2013/12/10 - 2013/12/12 Training on mass spectrometry based Proteomics Practical Proteomics Course
University of Warwick School of Life Sciences, United Kingdom
2011/03/06 - 2011/03/13 Training on mass spectrometry and Proteomics EMBO practical course “Mass Spectrometry and Proteomics”
Syddansk Universitet, Denmark
1999 - 1999 Training on Molecular Taxonomy Theoretical and Practical Course on Molecular Microbial Taxonomy
Universidade de Lisboa Faculdade de Ciências, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2021/01 - Current Animal Feed Science and Technology (0377-8401) Elsevier
2019 - Current Comparative Biochemistry and Physiology Part B Biochemistry and Molecular Biology (1096-4959) Elsevier
2018 - Current Journal of Proteomics (1874-3919) Elsevier
2011 - Current Journal of Agricultural and Food Chemistry (1520-5118) American Chemistry Society (ACS)

Committee member

Activity description
Role 		Institution / Organization
2014 - 2015 Improving Allergy risk assessment strategy for new food proteins -ImpPARAS. COST action FA1402
Member
 European Cooperation in Science and Technology, Belgium

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2019/11/18 - 2019/11/19 Proteomics and its application for aquaculture Proteomics Universidad Nacional de Costa Rica, Costa Rica
2018/11/22 - 2018/11/23 Proteomics training and Workshop - Proteomics and its application for aquaculture Proteomics Suranaree University of Technology, Thailand
2012/02/27 - 2012/03/01 Proteomics Course: Gel based protein separation by two-dimensional gel electrophoresis and protein characterization by MALDI-TOF/TOF mass spectrometry Proteomics Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal

Mentoring / Tutoring

Topic Student name
2014 - 2015 Titanium dioxide Protein Corona characterization through MS-based proteomics Jacob Kuruvilla
2011/12/01 - 2013/04/01 Rice development and reproduction under salinity stress- a Multi-OMICs integrated approach Nuno Miguel Gonçalves
Distinctions

Other distinction

2013 Carl Tryggers postdoctoral fellowship
Carl Tryggers Stiftelse för Vetenskaplig Forskning, Sweden
1999 Merit award to graduated students with best classification in FCUL
PRODEP II (Programa de Desenvolvimento Educativo para Portugal, 1995-1999)/União Europeia, Portugal