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André Gomes-dos-Santos graduated in Applied Biology in 2015 (Minho University), where he also obtained a Master's degree in Ecology (2017). He concluded his PhD in 2023 at Porto University, which focused on the study of freshwater mussels biology and evolution by applying several NGS approaches to obtain novel mitogenomic, transcriptomic and genomic resources. During his PhD (2018-2023) he specialized in bioinformatics focusing on whole genome assembly and annotations, phylogenomics, populations genomics, and big data management. Among his many contributions to the field of genomics are two 6 whole genomes and 6 transcriptome assemblies (freshwater bivalves and marine invertebrates) and over 70 whole mitogenome assemblies (freshwater bivalves, marine fish, and invertebrates and one land mammal). He also developed new bioinformatic pipelines for mitogenome assembly using PacBio and for assembly of targeted capture regions using whole genome re-sequencing. Over his career, he has been involved in national and international scientific projects. Regularly attends scientific meetings and workshops, gives several presentations, and has been involved in the organization of scientific meetings. He has been a very proficient researcher with 41 ISI-indexed publications in peer-reviewed journals, 17 as the first author, with nearly 100 different co-authors from 25 different countries. His focus of research is the application of genomic sequencing outputs, implemented through computational biology, to understand the evolutionary dynamics and adaptations of freshwater bivalves and other aquatic organisms.
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Identification

Personal identification

Full name
André Manuel Gomes dos Santos

Citation names

  • Santos, André
  • Gomes-dos-Santos, André

Author identifiers

Ciência ID
E717-0CD3-E1E9
ORCID iD
0000-0001-9973-4861
Google Scholar ID
https://scholar.google.com/citations?user=fl7GKIsAAAAJ&hl=en&authuser=1
Scopus Author Id
57208176788

Email addresses

  • asantos@ciimar.up.pt (Professional)

Addresses

  • Centro Interdisciplinar de Investigação Marinha e Ambienta (CIIMAR). Novo Edifício do Terminal de Cruzeiros do Porto de Leixões Avenida General Norton de Matos, 4450-208 , Matosinhos, Porto , Matosinhos, Portugal (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Evolutionary Biology
  • Natural sciences - Biological Sciences - Freshwater Biology
  • Exact Sciences - Computer and Information Sciences - Bioinformatics

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Portuguese (Mother tongue)
Education
Degree Classification
2023/12/11 - 2023/12/15
Concluded
 CAL-AQUA - Laboratory Aquatic Animal Science (Outros)
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2018/10/15 - 2023/04/18
Concluded
 Biologia (Doutoramento)
Major in Sem especialidade
Universidade do Porto Faculdade de Ciências, Portugal
"Margaritiferidae: from “pearls” to genomes" (THESIS/DISSERTATION)
2023/01/13 - 2023/01/13
Concluded
 "Ready for BioData Management?" Day 2 Day Data Management Course (Outros)
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2022/11/10 - 2022/11/10
Concluded
 Course on Grant Proposal writing (Outros)
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2021/01/25 - 2021/01/29
Concluded
 Introduction To Python (Outros)
Freie Universität Berlin, Germany
2020/03/09 - 2020/03/12
Concluded
 De Novo Assembly 2020 (Outros)
Earlham Institute, United Kingdom
2020/01/22 - 2020/01/22
Concluded
 RadCamp 2020 - The Lisbon Edition (Outros)
Universidade de Lisboa Centro de Ecologia Evolução e Alterações Ambientais, Portugal
2019/07/02 - 2019/07/12
Concluded
 Phylogenomics and Population Genomics: Inference and Applications (Outros)
Universitat de Barcelona Facultat de Biologia, Spain
2019/02/21 - 2019/02/21
Concluded
 Workshop on Data and Text processing in Health and Life Sciences, as part of the VIII Bioinformatics Open Days. (Outros)
Universidade do Minho, Portugal
2019/02/11 - 2019/02/15
Concluded
 Assembly And Annotation Of Genomes, Physalia Courses (Outros)
Freie Universität Berlin, Germany
2019/01/14 - 2019/01/16
Concluded
 Gene Prediction And Annotation Of Genomes (Outros)
Universidade do Porto Centro de Investigação em Biodiversidade e Recursos Genéticos, Portugal
2018/02 - 2018/02
Concluded
 Advanced Course Phylogenetics Practical Course¿ (Outros)
Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal
2015/01/10 - 2018/01/10
Concluded
 Ecologia (Mestrado)
Major in Ecologia
Universidade do Minho, Portugal
"Diversity and Distribution of Freshwater Mussels in Morocco" (THESIS/DISSERTATION)
 18 valores
2016 - 2016
Concluded
 Analysis of Data Resulting from Molecular Techniques¿ course (Outros)
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2012/09/01 - 2015/07/24
Concluded
 Licenciatura em Biologia Aplicada (Licenciatura)
Universidade do Minho Escola de Ciências, Portugal
"Curricular Project in the field of Ecology and Conservation of Freshwater Mussels " (THESIS/DISSERTATION)
 16.017
Affiliation

Science

Category
Host institution 		Employer
2017/07/17 - Current Researcher (Research) Centro Interdisciplinar de Investigação Marinha e Ambiental da Madeira, Portugal
Centro Interdisciplinar de Investigação Marinha e Ambiental da Madeira, Portugal
Projects

Grant

Designation Funders
2023/04/01 - 2025/03/31 MoRePorto - Monitorização e Restauro da Biodiversidade das Zonas Húmidas da Cidade do Porto
MoRe Porto
Researcher
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 EDULOG Fundação Belmiro de Azevedo
Ongoing
2024/11/01 - 2024/11/30 Population genomics of the Portuguese freshwater pearl mussel Margaritifera margaritifera
n/a
Technical development
Collège de France, France
 Instituto Francês de Portugal

Embaixada de França em Portugal
Concluded
2023/03/12 - 2024/09/11 An omics multisensory perspective, how can human activities affect the sensory organs of deep-sea fish?
2022.04750.PTDC
10.54499/2022.04750.PTDC
Researcher
Universidade do Porto Faculdade de Desporto, Portugal

Instituto Español de Oceanografía Centro Oceanográfico de Cádiz, Spain

Universidade de Vigo Facultad de Ciencias, Spain
Fundação para a Ciência e a Tecnologia
Ongoing
2021/03/01 - 2024/05/31 Freshwater Bivalves at the edge: Adaptation genomics under climate-change scenarios
PTDC/CTA-AMB/3065/2020
10.54499/PTDC/CTA-AMB/3065/2020
Researcher
Universidade do Porto Faculdade de Desporto, Portugal

Universidade de Trás-os-Montes e Alto Douro Centro de Investigação e de Tecnologias Agro-Ambientais e Biologicas, Portugal

Universidade do Minho Centro de Biologia Molecular e Ambiental, Portugal

Université de Montréal, Canada

Instituto Politécnico de Bragança, Portugal

Rede de Investigação em Biodiversidade e Biologia Evolutiva, Portugal

Universidade do Minho, Portugal

Universidade de Trás-os-Montes e Alto Douro, Portugal

Universidade do Porto Instituto de Ciências Tecnologias e Agroambiente, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2023/05/01 - 2024/04/30 2DED - 2DBD nuclear receptors as targets for Effective Drugs
UIDB_SEED - 2DED
Researcher
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental
Ongoing
2019/10/10 - 2024/04/04 Conservation of freshwater mussels: a pan-European approach (CONFREMU)
CA18239
 European Cooperation in Science and Technology
Ongoing
2023/04/01 - 2023/09/30 ATLANTIDA - Platform for the monitoring of the North Atlantic Ocean and tools for the sustainable exploitation of the marine resources
2023_033_BI_ATLANTIDA
Integration into Research Grant Fellow
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
Concluded
2022/12/01 - 2023/04/01 Margaritiferidae: from pearls to genomes
COVID/DB/152933/2022
PhD Student Fellow
Fundação para a Ciência e a Tecnologia, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2018/10/01 - 2022/12/01 Margaritiferidae: from pearls to genomes
SFRH/BD/137935/2018
PhD Student Fellow
Fundação para a Ciência e a Tecnologia, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2022/05/08 - 2022/05/28 Short-Term Scientific Mission (STSM) COST Action grant
E-COST-GRANT-CA18239-48f01504
Technical development
Collège de France, France

Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
European Cooperation in Science and Technology
Concluded
2019 - 2019 Junior scientist funding for Theo Murphy meeting (National Science Foundation - NSF)
n/a
Other
National Science Foundation, United States
Concluded
2017/07/17 - 2018/07/31 FRESHCO: Multiple implications of invasive species on Freshwater Mussel decline and coextinction processes (PTDC/AGRFOR/1627/2014)
PTDC/AGR-FOR/1627/2014-BI-2017-007
PTDC/AGRFOR/1627/2014
Research Fellow
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded

Contract

Designation Funders
2024 - 2030 The key to survival: A genomic approach to assess freshwater mussels’ adaptations to a changing world
2023.07625.CEECIND
Principal investigator
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia
2019/01/01 - 2019/12/31 Centro Interdisciplinar de Investigação Marinha e Ambiental
UID/Multi/04423/2019
Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book
  1. Ana Matos; Gomes-dos-Santos, André; Celso Domingos; Diogo Alexandrino; Fernando Pagels; Inês Gregório; Kathleen Abt; et al. Book of Abstracts - Blue Think Conference (2021). Matosinhos, Portugal. 2021.
    Published
  2. Ana Matos; Gomes-dos-Santos, André; Diana Almeida; Diogo Alexandrino; Fernando Pagels; Luana Ramos; Tiago Ribeiro. Book of Abstracts - Blue Think Conference (2020). Matosinhos, Portugal. 2020.
Conference poster
  1. Gomes-dos-Santos, André; Beatriz Silva; Fonseca, Elza; Andre M. Machado; Rui Pinto; Lopes-Lima, Manuel; Luis Filipe C. Castro; Froufe, Elsa. "Genomic Adaptations Associated with Climate Change and Biological Changes in the unionid mussel Unio delphinus (Spengler, 1793)". Paper presented in Conservation Genomics Paris, 2024.
  2. Gomes-dos-Santos, André; Froufe, Elsa; Andre M. Machado; Jasna Latjner; Ján Cernecký; C. Castro, L. Filipe; Lopes-Lima, Manuel. "A PacBio Hi-Fi genome assembly of the Painter's Mussel Unio pictorum (Linnaeus, 1758)". Paper presented in SOCIETY FOR MOLECULAR BIOLOGY AND EVOLUTION - SMBE 2023, 2023.
  3. Fonseca, Elza; Beatriz Silva; Gomes-dos-Santos, André; Andre M. Machado; Rui Pinto; Lopes-Lima, Manuel; C. Castro, L. Filipe; Froufe, Elsa. "Genomic Adaptations Associated with Climate Change and Biological Changes in the unionid mussel Unio delphinus (Spengler, 1793)". Paper presented in SOCIETY FOR MOLECULAR BIOLOGY AND EVOLUTION - SMBE2023, 2023.
  4. Elsa Froufe; Lopes-Lima, Manuel; Teixeira, Amilcar; Gomes-dos-Santos, André; Fonseca, Elza; Martin Österling; Riccardi, Nicoletta; et al. "EdgeOmics - Freshwater Bivalves at the edge: Adaptation genomics under climate-change scenarios". Paper presented in GS8: Genomics in a Changing World: Conservation, Invasive Species, and Climate Change, 2023.
  5. Froufe, Elsa; Lopes-Lima, Manuel; Teixeira, Amílcar; Gomes-dos-Santos, André; Fonseca, E; Österling, Martin; Riccardi, Nicoletta; et al. "Genomics in a Changing World: Conservation, Invasive Species, and Climate Change". Paper presented in SMBE Everywhere series, 2023.
  6. Gomes-dos-Santos, André; Elsa Froufe; Andre M. Machado; Luis Filipe C. Castro; Vincent Prié; Lopes-Lima, Manuel. "The PacBio Hi-Fi genome assembly of the delicate freshwater mussel Unio mancus Lamarck, 1819". Paper presented in Biodiversity Genomics 2022., 2022.
  7. Gomes-dos-Santos, André; Lopes-Lima, Manuel; Andre M. Machado; Amilcar Teixeira; Luis Filipe C. Castro; Elsa Froufe. "The PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus". Paper presented in Biodiversity Genomics 2022., 2022.
  8. Gomes-dos-Santos, André; Lopes-Lima, Manuel; Andre M. Machado; Luis Filipe C. Castro; Thomas Forest; Guillaume Achaz; Amílcar Teixeira; Elsa Froufe. "The Crown Pearl V2: the improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758).". Paper presented in Biodiversity Genomics 2022., 2022.
  9. Gomes-dos-Santos, André; Lopes-Lima, Manuel; Luis Filipe C. Castro; Elsa Froufe. "Molluscan Genomics: The road so far and the way forward". Paper presented in Congress: Pearls of wisdom: synergising leadership and expertise in molluscan genomics. Theo Murphy international scientific meeting, 2019.
Journal article
  1. Lopes-Lima, M.; Geist, J.; Egg, S.; Beran, L.; Bikashvili, A.; Van Bocxlaer, B.; Bogan, A.E.; et al. "Integrative phylogenetic, phylogeographic and morphological characterisation of the Unio crassus species complex reveals cryptic diversity with important conservation implications". Molecular Phylogenetics and Evolution 195 (2024): 108046. http://dx.doi.org/10.1016/j.ympev.2024.108046.
    10.1016/j.ympev.2024.108046
  2. André Gomes-dos-Santos; Elza Fonseca; Nicoletta Riccardi; Mariana Hinzmann; Manuel Lopes-Lima; Elsa Froufe. "The transcriptome assembly of the European freshwater mussel Unio elongatulus C. Pfeiffer, 1825". Scientific Data (2024): https://doi.org/10.1038/s41597-024-03226-y.
    10.1038/s41597-024-03226-y
  3. Machado, André M.; Samico, Rodrigo; Domingues, Marcos; Hagemann, Andreas; Valente, Luísa M.P.; Malzahn, Arne M.; Gomes-dos-Santos, André; et al. "A whole-body transcriptome assembly of the annelid worm Hediste diversicolor". Marine Genomics 74 (2024): 101084. http://dx.doi.org/10.1016/j.margen.2024.101084.
    10.1016/j.margen.2024.101084
  4. Gomes-dos-Santos, André; Domingues, Marcos; Ruivo, Raquel; Fonseca, Elza; Froufe, Elsa; Deyanova, Diana; Franco, João N.; C. Castro, L. Filipe. Corresponding author: C. Castro, L. Filipe. "An historical wreck: A transcriptome assembly of the naval shipworm, Teredo navalis Linnaeus, 1978". Marine Genomics 74 (2024): 101097. http://dx.doi.org/10.1016/j.margen.2024.101097.
    10.1016/j.margen.2024.101097
  5. Ana Matos; André Gomes-dos-Santos; Sofia Graça Aranha; Ester Dias; Ana Veríssimo; Alexandra Teodósio; Ivone Figueiredo; L. Filipe C. Castro; Elsa Froufe. "Dataset of the complete mitogenome of the deep-sea sailfin roughshark, Oxynotus paradoxus Frade, 1929". Data in Brief (2024): https://doi.org/10.1016/j.dib.2023.109836.
    10.1016/j.dib.2023.109836
  6. André Gomes-dos-Santos; Nair Vilas-Arrondo; André M. Machado; Esther Román-Marcote; Jose Luís Del Río Iglesias; Francisco Baldó; Montse Pérez; et al. "Mitochondrial replication's role in vertebrate mtDNA strand asymmetry". Open Biology (2023): https://doi.org/10.1098/rsob.230181.
    10.1098/rsob.230181
  7. Alberto Ribes-Navarro; Naoki Kabeya; L. Filipe C. Castro; André Gomes-dos-Santos; Miguel M. Fonseca; Hilke Alberts-Hubatsch; Francisco Hontoria; Juan C. Navarro; Óscar Monroig. "Examination of gammarid transcriptomes reveals a widespread occurrence of key metabolic genes from epibiont bdelloid rotifers in freshwater species". Open Biology (2023): https://doi.org/10.1098/rsob.230196.
    10.1098/rsob.230196
  8. Elsa Froufe; André Gomes-dos-Santos; Ana Matos; Jonathan Wilson; Salman Malakpourkolbadinezhad; Daniel D. Pereira; Randal Singer; L. Filipe C. Castro. "How complex is the hidden species diversity of the teleost Plotosus genus?". Ichthyological Research (2023): http://dx.doi.org/10.1007/s10228-023-00924-2.
    10.1007/s10228-023-00924-2
  9. Sakina Neemuchwala; Nathan A. Johnson; John M. Pfeiffer; Manuel Lopes-Lima; André Gomes-dos-Santos; Elsa Froufe; David M. Hillis; Chase H. Smith. "Coevolution With Host Fishes Shapes Parasitic Life Histories in a Group of Freshwater Mussels (Unionidae: Quadrulini).". Bulletin of the Society of Systematic Biologists (2023): https://doi.org/10.18061/bssb.v2i1.8998.
    10.18061/bssb.v2i1.8998
  10. André Gomes-dos-Santos; Elsa Froufe; André M Machado; Jasna Lajtner; Ján Cernecký; L Filipe C Castro; Manuel Lopes Lima; Laura Katz. "A PacBio Hi-Fi genome assembly of the Painter's Mussel Unio pictorum (Linnaeus, 1758)". Genome Biology and Evolution (2023): https://doi.org/10.1093/gbe/evad116.
    10.1093/gbe/evad116
  11. André Gomes-dos-Santos; Manuel Lopes-Lima; M. André Machado; Amílcar Teixeira; L. Filipe C. Castro; Elsa Froufe. "PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793". Scientific Data (2023): https://doi.org/10.1038/s41597-023-02251-7.
    10.1038/s41597-023-02251-7
  12. André Gomes-dos-Santos; Manuel Lopes-Lima; André M. Machado; Thomas Forest; Guillaume Achaz; Amílcar Teixeira; Vincent Prié; L. Filipe C. Castro; Elsa Froufe. "The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758)". Gigabyte (2023): https://doi.org/10.46471/gigabyte.81.
    10.46471/gigabyte.81
  13. André Gomes-dos-Santos; Elsa Froufe; John M. Pfeiffer; Nathan A. Johnson; Chase H. Smith; André M. Machado; L. Filipe C. Castro; et al. "A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)". Molecular Ecology Resources (2023): https://doi.org/10.1111/1755-0998.13802.
    10.1111/1755-0998.13802
  14. Manuel Lopes-Lima; Joaquim Reis; Maria G. Alvarez; Pedro M. Anastácio; Filipe Banha; Pedro Beja; Paulo Castro; et al. "The silent extinction of freshwater mussels in Portugal". Biological Conservation 285 (2023): 110244-110244. https://www.sciencedirect.com/science/article/pii/S0006320723003452.
    https://doi.org/10.1016/j.biocon.2023.110244
  15. André Gomes-dos-Santos; André M. Machado; L. Filipe C. Castro; Vincent Prié; Amílcar Teixeira; Manuel Lopes-Lima; Elsa Froufe. "The gill transcriptome of threatened European freshwater mussels". Scientific Data (2022): https://doi.org/10.1038/s41597-022-01613-x.
    10.1038/s41597-022-01613-x
  16. Nair Vilas-Arrondo; André Gomes-dos-Santos; Montse Pérez; Francisco Baldó; Ana Veríssimo; Diana Catarino; André M. Machado; et al. "A mitochondrial genome assembly of the opal chimaera, Chimaera opalescens Luchetti, Iglésias et Sellos 2011, using PacBio HiFi long reads". Mitochondrial DNA Part B (2022): https://doi.org/10.1080/23802359.2022.2044403.
    10.1080/23802359.2022.2044403
  17. André M. Machado; André Gomes-dos-Santos; Miguel M. Fonseca; Rute R. da Fonseca; Ana Veríssimo; Mónica Felício; Ricardo Capela; et al. "A genome assembly of the Atlantic chub mackerel (Scomber colias): a valuable teleost fishing resource". Gigabyte (2022): https://doi.org/10.46471/gigabyte.40.
    10.46471/gigabyte.40
  18. André Gomes-dos-Santos; Andreas Hagemann; Luísa Valente; Arne M. Malzahn; Óscar Monroig; Elsa Froufe; L. Filipe C. Castro. "Complete mitochondrial genome of the ragworm annelid Hediste diversicolor (of Müller, 1776) (Annelida: Nereididae)". Mitochondrial DNA Part B 6 10 (2021): 2849-2851. https://doi.org/10.1080/23802359.2021.1970644.
    10.1080/23802359.2021.1970644
  19. Fabrizio Ghiselli; André Gomes-dos-Santos; Coen M. Adema; Manuel Lopes-Lima; Joel Sharbrough; Jeffrey L. Boore. "Molluscan mitochondrial genomes break the rules". Philosophical Transactions of the Royal Society B: Biological Sciences 376 1825 (2021): https://doi.org/10.1098/rstb.2020.0159.
    10.1098/rstb.2020.0159
  20. David Barros-García; André Gomes-dos-Santos; André M. Machado; L. Filipe C. Castro; Alejandro de Carlos; Rafael Bañón; Isabel Bruno; Juan C. Arronte; Elsa Froufe. "Complete mitogenome of the Oven's halosaur, Halosaurus ovenii (Elopomorpha; Notacanthiformes)". Mitochondrial DNA Part B 6 4 (2021): 1571-1572. https://doi.org/10.1080/23802359.2021.1914518.
    10.1080/23802359.2021.1914518
  21. Gomes-dos-Santos, André; Lopes-Lima, Manuel; Machado, André M; Marcos Ramos, António; Usié, Ana; Bolotov, Ivan N; Vikhrev, Ilya V; et al. "The Crown Pearl: a draft genome assembly of the European freshwater pearl musselMargaritifera margaritifera(Linnaeus, 1758)". DNA Research 28 2 (2021): http://dx.doi.org/10.1093/dnares/dsab002.
    10.1093/dnares/dsab002
  22. André Gomes-dos-Santos; André M. Machado; Sofia Graça Aranha; Ester Dias; Ana Veríssimo; L. Filipe C. Castro; Elsa Froufe. "The complete mitochondrial genome of the endemic Iberian pygmy skate Neoraja iberica Stehmann, Séret, Costa, & Baro 2008 (Elasmobranchii, Rajidae)". Mitochondrial DNA Part B 6 3 (2021): 848-850. https://doi.org/10.1080/23802359.2021.1884030.
    10.1080/23802359.2021.1884030
  23. André Gomes-dos-Santos; Nair Vilas-Arrondo; André M. Machado; Ana Veríssimo; Montse Pérez; Francisco Baldó; L. Filipe C. Castro; Elsa Froufe. "Shedding light on the Chimaeridae taxonomy: the complete mitochondrial genome of the cartilaginous fish Hydrolagus mirabilis (Collett, 1904) (Holocephali: Chimaeridae)". Mitochondrial DNA Part B (2021): https://doi.org/10.1080/23802359.2020.1870887.
    10.1080/23802359.2020.1870887
  24. Lopes-Lima, M.; Gürlek, M.E.; Kebapçi, Ü.; Sereflisan, H.; Yanik, T.; Mirzajani, A.; Neubert, E.; et al. "Diversity, biogeography, evolutionary relationships, and conservation of Eastern Mediterranean freshwater mussels (Bivalvia: Unionidae)". Molecular Phylogenetics and Evolution 163 (2021): http://www.scopus.com/inward/record.url?eid=2-s2.0-85111485498&partnerID=MN8TOARS.
    10.1016/j.ympev.2021.107261
  25. Spitsyn, V.M.; Kondakov, A.V.; Froufe, E.; Gofarov, M.Y.; Gomes-Dos-Santos, A.; Teiga-Teixeira, J.; Spitsyna, E.A.; et al. "Complete mitochondrial genome of an Arctic Collared Lemming subspecies endemic to the Novaya Zemlya Archipelago, Russia". Ecologica Montenegrina 40 (2021): 133-139. http://www.scopus.com/inward/record.url?eid=2-s2.0-85107434330&partnerID=MN8TOARS.
    10.37828/em.2021.40.12
  26. Zieritz, Alexandra; Froufe, Elsa; Bolotov, Ivan; Gonçalves, Duarte V; Aldridge, David C; Bogan, Arthur E; Gan, Han Ming; et al. "Mitogenomic phylogeny and fossil-calibrated mutation rates for all F- and M-type mtDNA genes of the largest freshwater mussel family, the Unionidae (Bivalvia)". Zoological Journal of the Linnean Society (2020): http://dx.doi.org/10.1093/zoolinnean/zlaa153.
    10.1093/zoolinnean/zlaa153
  27. Steven J. Weiss; Duarte V. Gonçalves; Giulia Secci-Petretto; Gernot K. Englmaier; André Gomes-Dos-Santos; Gael P. J. Denys; Henri Persat; et al. "Global systematic diversity, range distributions, conservation and taxonomic assessments of graylings (Teleostei: Salmonidae; Thymallus spp.)". Organisms Diversity & Evolution (2020): https://doi.org/10.1007/s13127-020-00468-7.
    10.1007/s13127-020-00468-7
  28. Fonseca, Elza; Machado, André M.; Vilas-Arrondo, Nair; Gomes-dos-Santos, André; Veríssimo, Ana; Esteves, Pedro; Almeida, Tereza; et al. "Cartilaginous fishes offer unique insights into the evolution of the nuclear receptor gene repertoire in gnathostomes". General and Comparative Endocrinology 295 (2020): 113527. http://dx.doi.org/10.1016/j.ygcen.2020.113527.
    10.1016/j.ygcen.2020.113527
  29. "The complete mitochondrial genome of Thymallus thymallus (Linnaeus, 1758) (Actinopterygii, Salmonidae) obtained by long range PCRs and double multiplexing". (2020): http://sfi-cybium.fr/fr/complete-mitochondrial-genome-thymallus-thymallus-linnaeus-1758-actinopterygii-salmonidae-obtained.
    10.26028/CYBIUM/2020-442-001
  30. Nair Vilas Arrondo; André Gomes-dos-Santos; Esther Román Marcote; Montse Pérez; Elsa Froufe; L. Filipe C. Castro. "A new gene order in the mitochondrial genome of the deep-sea diaphanous hatchet fish Sternoptyx diaphana Hermann, 1781 (Stomiiformes: Sternoptychidae)". Mitochondrial DNA Part B 5 3 (2020): 2859-2861. https://doi.org/10.1080/23802359.2020.1790325.
    10.1080/23802359.2020.1790325
  31. João Teiga-Teixeira; Elsa Froufe; André Gomes-dos-Santos; Arthur E. Bogan; Alexander Y. Karatayev; Lyubov E. Burlakova; David C. Aldridge; et al. "Complete mitochondrial genomes of the freshwater mussels Amblema plicata (Say, 1817), Pleurobema oviforme (Conrad, 1834), and Popenaias popeii (Lea, 1857) (Bivalvia: Unionidae: Ambleminae)". Mitochondrial DNA Part B 5 3 (2020): 2977-2979. https://doi.org/10.1080/23802359.2020.1791008.
    10.1080/23802359.2020.1791008
  32. André Gomes-dos-Santos; Nair Vilas Arrondo; André M. Machado; Ana Veríssimo; Montse Pérez; Esther Román; L. Filipe C. Castro; Elsa Froufe. "The complete mitochondrial genome of the deep-water cartilaginous fish Hydrolagus affinis (de Brito Capello, 1868) (Holocephali: Chimaeridae)". Mitochondrial DNA Part B (2020): https://doi.org/10.1080/23802359.2020.1749154.
    10.1080/23802359.2020.1749154
  33. David Barros-García; André Gomes-dos-Santos; André M. Machado; L. Filipe C. Castro; Alejandro de Carlos; Rafael Bañón; Isabel Bruno; Juan C. Arronte; Elsa Froufe. "Complete mitogenome of the shortfin spiny eel, Notacanthus bonaparte (Elopomorpha; Notacanthiformes)". Mitochondrial DNA Part B (2020): https://doi.org/10.1080/23802359.2020.1736672.
    10.1080/23802359.2020.1736672
  34. André Gomes-dos-Santos; Manuel Nande; Luis A. Espinoza-Ramos; Renzo G. Pepe-Victoriano; Zumilda Contreras-Mamani; Jordan I. Huanacuni; J. Miguel Quispe-Mayta; et al. "Constructing the mitochondrial genome of the Peruvian grunt Anisotremus scapularis Tschudi, 1846 (Lutjaniformes: Haemulidae) using RNA-seq data". Mitochondrial DNA Part B (2020): https://doi.org/10.1080/23802359.2020.1754950.
    10.1080/23802359.2020.1754950
  35. Klunzinger, M. W.; Lopes-Lima, Manuel; Gomes-dos-Santos, Andre; Froufe, Elsa; Lymbery, A. J.; Kirkendale, L.. "Phylogeographic study of the West Australian freshwater mussel, Westralunio carteri, uncovers evolutionarily significant units that raise new conservation concerns". Hydrobiologia (2020): http://dx.doi.org/10.1007/s10750-020-04200-6.
    10.1007/s10750-020-04200-6
  36. Denys, Gaël P.J; Giulia Secci-Petretto; Gomes-dos-Santos, André. "Genome announcement The complete mitochondrial genome of Thymallus thymallus ( Linnaeus , 1758 ) ( Actinopterygii , Salmonidae ) obtained by long range PCRs and double multiplexing by". Cybium 44 2 (2020): 91-94. http://sfi-cybium.fr/fr/complete-mitochondrial-genome-thymallus-thymallus-linnaeus-1758-actinopterygii-salmonidae-obtained.
    Published
  37. Gomes-dos-Santos, André; Lopes-Lima, Manuel; Castro, L. Filipe C.; Froufe, Elsa. "Molluscan genomics: the road so far and the way forward". Hydrobiologia (2019): http://dx.doi.org/10.1007/s10750-019-04111-1.
    10.1007/s10750-019-04111-1
  38. Gomes-dos-Santos, André; Froufe, Elsa; Gonçalves, Duarte V.; Sousa, Ronaldo; Prié, Vincent; Ghamizi, Mohamed; Benaissa, Hassan; et al. "Freshwater conservation assessments in (semi-)arid regions: Testing river intermittence and buffer strategies using freshwater mussels (Bivalvia, Unionida) in Morocco". Biological Conservation 236 (2019): 420-434. http://dx.doi.org/10.1016/j.biocon.2019.05.038.
    10.1016/j.biocon.2019.05.038
  39. Lopes-Lima, Manuel; Burlakova, Lyubov; Karatayev, Alexander; Gomes-dos-Santos, André; Zieritz, Alexandra; Froufe, Elsa; Bogan, Arthur E.. "Revisiting the North American freshwater mussel genus Quadrula sensu lato (Bivalvia Unionidae): Phylogeny, taxonomy and species delineation". Zoologica Scripta 48 3 (2019): 313-336. http://dx.doi.org/10.1111/zsc.12344.
    10.1111/zsc.12344
  40. Gomes-dos-Santos, André; Froufe, Elsa; Amaro, Rafaela; Ondina, Paz; Breton, Sophie; Guerra, Davide; Aldridge, David C.; et al. "The male and female complete mitochondrial genomes of the threatened freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) (Bivalvia: Margaritiferidae)". (2019): http://hdl.handle.net/10198/20075.
    10.1080/23802359.2019.1598794
  41. Sousa, Ronaldo; Teixeira, Amílcar; Santos, André; Benaissa, Hassan; Varandas, Simone; Ghamizi, Mohamed; Prié, Vincent; Froufe, Elsa; Lopes-Lima, Manuel. "Oued Bouhlou: A new hope for the Moroccan pearl mussel". Aquatic Conservation: Marine and Freshwater Ecosystems 28 1 (2017): 247-251. http://dx.doi.org/10.1002/aqc.2825.
    10.1002/aqc.2825
Report
  1. IUCN. 2022. The conservation status of freshwater species and habitats in Key Biodiversity Areas at the Douro river basin. https://portals.iucn.org/library/node/50663.
Thesis / Dissertation
  1. "Margaritiferidae: from pearls to genomes". PhD, Universidade do Porto Faculdade de Ciências, 2023. https://hdl.handle.net/10216/149074.
  2. "Diversity and distribution of freshwater mussels in Morocco". Master, Universidade do Minho, 2017. https://hdl.handle.net/1822/55560.

Other

Dataset
  1. André Gomes-dos-Santos; Elsa Froufe; André Machado; Jasna Lajtner; Ján Cernecký; L Filipe C Castro; Manuel Lopes-Lima. A PacBio Hi-Fi genome assembly of the painter's mussel Unio pictorum (Linnaeus, 1758).
    10.6084/m9.figshare.22203223
  2. André Gomes-dos-Santos; Manuel Lopes-Lima; André Machado; Thomas Forest; Guillaume Achaz; Amílcar Teixeira; Vincent Prié; Luis Filipe Castro; Elsa Froufe. The Crown Pearl V2: an improved genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758).
    10.6084/m9.figshare.22048250
  3. André Gomes-dos-Santos; André M. Machado; Luis Filipe Castro; Vincent Prié; Amílcar Teixeira; Manuel Lopes-Lima; Elsa Froufe. Take Five: The gill transcriptome of threatened European freshwater mussels.
    10.6084/m9.figshare.19787566
  4. André Gomes-dos-Santos; Manuel Lopes-Lima; André Machado; Amílcar Teixeira; Luis Filipe Castro; Elsa Froufe. PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793.
    10.6084/m9.figshare.21878946
  5. Andre M. Machado; Rodrigo Samico; Marcos Domingues; Andreas Hagemann; Valente, Luisa M.P.; Arne M. Malzahn; Gomes-dos-Santos, André; et al. The transcriptome assembly of the annelid worm Hediste diversicolor. figshare.
    https://doi.org/10.6084/m9.figshare.24236311.v1
  6. Giulia Secci-Petretto; Steven J. Weiss; Gomes-dos-Santos, André; Henri Persat; Andre M. Machado; Inês Vasconcelos; C. Castro, L. Filipe; Froufe, Elsa. A multi-tissue de novo transcriptome assembly of the vulnerable freshwater salmonid Thymallus ligericus. figshare.
  7. Andre M. Machado; Gomes-dos-Santos, André; Miguel M. Fonseca; Rute R. da Fonseca; Ana Veríssimo; Felício, Mónica; Ricardo Capela; et al. A draft genome assembly of the Atlantic chub mackerel (Scomber colias) using Illumina and Pacbio Hifi reads. figshare.
    10.6084/m9.figshare.17025506.v4
  8. Gomes-dos-Santos, André; Lopes-Lima, Manuel; Andre M. Machado; Marcos Ramos, António; Usié, Ana; Ivan N Bolotov; Ilya V Vikhrev; et al. Margaritifera margaritifera whole genome assembly and annotation.
    10.6084/m9.figshare.13333841
  9. André Gomes-dos-Santos; Elza Fonseca; Nicoletta Riccardi; Mariana Hinzmann; Manuel Lopes-Lima; Elsa Froufe. The transcriptome assembly of the European freshwater mussel Unio elongatulus C. Pfeiffer, 1825. 2023.
    10.6084/m9.figshare.24422431
  10. André Gomes-dos-Santos; Marcos Domingues; Raquel Ruivo; Elsa Froufe; Diana Deyanova; João N. Franco; Luis Filipe Castro. An historical wreck: a transcriptome assembly of the naval shipworm, Teredo navalis Linnaeus, 1978. 2023.
    10.6084/m9.figshare.24182502
Software
  1. Gomes-dos-Santos, André; Froufe, Elsa; John M. Pfeiffer; Nathan A. Johnson; Chase H. Smith; Andre M. Machado; C. Castro, L. Filipe; et al. "A novel assembly pipeline and functional annotations for targeted sequencing: A case study on the globally threatened Margaritiferidae (Bivalvia: Unionida)". Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental. 2023.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2024/05/28 The path to and challenges of producing freshwater mussels' whole genome assemblies Establishing state-of-the-art mollusc genomics
European Molecular Biology Organization (EMBO) (Namur, Belgium)
2023/05/10 Nuclear receptors and the mussels that "don't get better with butter" IJUP 2023
Universidade do Porto (Porto, Portugal)
2023/04/11 PacBio Hi-Fi genome assembly of the Iberian dolphin freshwater mussel Unio delphinus Spengler, 1793 13th Biennial Freshwater Mollusk Conservation Society Symposium
Freshwater Mollusk Conservation Society (Portland, United States)
2021/09/23 The evolutionary history of the family Margaritiferidae using genomic multilocus approaches. Blue Think Conference 2021. 23-24 September 2021. Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto de Leixões, 4450 Matosinhos, Portugal. Blue Think Conference 2021
Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) (Matosinhos, Portugal)
2021/06/14 The Crown Pearl: a draft genome assembly of the European freshwater pearl mussel Margaritifera margaritifera (Linnaeus, 1758) Annual Meeting of the American Malacological Society
American Malacological Society (United States)
2020/09/17 Phylogeny of the thick-shelled river mussel Unio crassus Philipsson, 1788 (Bivalvia Unionidae) in the genomic era. Blue Think Conference 2020. 17 September 2020. Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto de Leixões, 4450 Matosinhos, Portugal. Blue Think Conference 2020
Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) (Matosinhos, Portugal)
2019/12/06 Freshwater conservation assessments in (semi-)arid regions: Testing river intermittence and buffer strategies using freshwater mussels (Bivalvia, Unionida) in Morocco Tibe 2019 Biodiversity, Ecology and Evolution in Mediterranean ecosystems
Research Centre in Biodiversity and Genetic Resources (CIBIO), University of Porto (Vila do Conde, Portugal)
2018/11/09 Distribution and Diversity of the freshwater mussels of Morocco CIIMAR Neptune Seminar Series
Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) (Matosinhos, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2023/09/01 - 2024/07/01 Light in the deep: The transcriptome of the deep-sea marine hatchetfish Sternoptyx diaphana, Hermann, 1781
Supervisor
Universidade do Porto Faculdade de Ciências, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2021/09/23 - 2021/09/24 The Blue Think Conference (BTC) 2021 , a meeting organized by the Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) PhD Students Committee. The aim was to gather all students affiliated with CIIMAR in a casual and relaxed environment to share the outputs of our works. Event organisation done in 2021 (2021/09/23 - 2021/09/24)
Conference (Member of the Organising Committee)
 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal
2020/09/17 - 2020/09/17 The Blue Think Conference (BTC) 2020 was the first meeting organized by the Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) PhD Students’ Committee. The aim was to gather all students affiliated with CIIMAR in a casual and relaxed environment to share the outputs of our works. (2020/09/17 - 2020/09/17)
Conference (Member of the Organising Committee)
 Centro Interdisciplinar de Investigação Marinha e Ambiental da Madeira, Portugal
2015/02/17 - 2015/02/18 XVI Jornadas da Biologia Aplicada, 2015 (2015/02/17 - 2017/02/18)
Conference (Member of the Organising Committee)
 Universidade do Minho, Portugal

Ad Hoc journal article review

Journal title (ISSN) Publisher
2024/01/01 - Current Scientific Data Springer Nature
2023 - Current Scientific Reports (2045-2322) Nature
2021 - Current Mitochondrial DNA Part B: Resources (2380-2359) Taylor & Francis
2020 - Current BMC Genomics (1471-2164) Springer
2020 - Current Heredity (1365-2540) Nature

Committee member

Activity description
Role 		Institution / Organization
2019 - 2021 Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) PhD Students Committee.
Member
 Centro Interdisciplinar de Investigação Marinha e Ambiental da Madeira, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2022/06/22 - Current Workshop: Fish Genetics: from Sanger to Next Generation Sequencing. June 20-23rd, 2022. SIBIC 2022 – IX Iberian Congress of Ichthyology. Porto, Portugal. (Outros)

Interview (newspaper / magazine)

Activity description Newspaper / Forum
2021/10/01 CIIMAR alerta para impacto das alterações climáticas na biodiversidade de água doce Notícias Universidade do Porto
2021/09/30 Mértola: UPorto lidera estudo sobre impacto de alterações climáticas em mexilhões de água doce LUSA
2021/04/21 Sequenciado genoma do mexilhão-de-rio conhecido pelas suas pérolas Several

Interview (tv / radio show)

Program Topic
2021/01/11 - 2021/01/11 SIC Notícias Estudar o mexilhão de água doce para medir o impacto das alterações climáticas em Portugal

Mentoring / Tutoring

Topic Student name
2022/09 - 2024/07/19 Identify gene expression profiles in freshwater mussels under thermal stress Beatriz Ferreira da Silva
2021/09 - 2022/06 Phylogeny analyses of Unio genus using Next Generation Sequencing (NGS) from directionally enriched genomic regions Luísa Isabel Sá Portela