João Paulo Rodrigues Machado (CE18-6E56-7947)

Curriculum Vitae

João Paulo Rodrigues Machado

Identification

Personal identification

Full name: João Paulo Rodrigues Machado

Author identifiers

Ciência ID: CE18-6E56-7947

Education

	Degree	Classification
2012/09 - 2016/11 Concluded	Engenharia Informática (Licenciatura) Instituto Politécnico do Porto Instituto Superior de Engenharia do Porto, Portugal
2008/11 - 2014/12/12 Concluded	Ciências do Mar e do Ambiente (Doutoramento) Major in Especialidade: Oceanografia e Ecossistemas Marinhos Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal "Evolutionary characterization of genes involved in development and adaptation in vertebrates under differential environmental conditions of selective pressure " (THESIS/DISSERTATION)
2008/10 - 2014/12 Concluded	Ciências do Mar e do Ambiente (Doutoramento) Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2002/10 - 2007/07 Concluded	Biologia (Licenciatura) Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal

Projects

Grant

	Designation	Funders
2022/08 - 2025/08	FAIR EArth Sciences & Environment services (FAIR-EASE) 10039779	UK Research and Innovation
2019/03 - 2023/08	Providing an open collaborative space for digital biology in Europe 824087	European Commission
2012/05 - 2015/09	Biological warfare: unraveling the genomics of natural venoms and the mechanisms of natural venom-resistance PTDC/AAC-AMB/121301/2010	Ministério da Ciência, Tecnologia e Inovação
2013/05 - 2015/04	The role of glutatione-S-transferase isoenzymes in bivalve's tolerance to microcystins. 131555 Provided by PTCRIS: 131555	Fundação para a Ciência e a Tecnologia, I.P.
2011/03/01 - 2014/02/28	EVOLUTIONARY CHARACTERIZATION OF GENES INVOLVED IN DEVELOPMENT AND ADAPTATION IN VERTEBRATE SPECIES UNDER DIFFERENTIAL ENVIRONMENTAL CONDITIONS OF SELECTIVE PRESSURE SFRH/BD/65245/2009 Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2008/01 - 2011/06	Phenogenetic drift in evolution: insights into the genetic basis of vertebrate developmental genes 69144 Provided by PTCRIS: 69144	Fundação para a Ciência e a Tecnologia, I.P.
2007/04 - 2011/04	Managing effects of global climate on estuarine biodiversity and productivity PT010	European Economic Area Financial Mechanism

Contract

	Designation	Funders
2023/04/01 - 2029/03/31	Sem título CEECINST/00109/2021/CP2800/CT0001 10.54499/CEECINST/00109/2021/CP2800/CT0001	Fundação para a Ciência e a Tecnologia Ongoing
2021/01/01 - 2025/12/31	Centro de Investigação Marinha e Ambiental LA/P/0101/2020 10.54499/LA/P/0101/2020 Universidade do Algarve Centro de Ciências do Mar, Portugal Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018/06/01 - 2022/05/31	Rastreando a carne de animais selvagens: estratégia molecular para investigar o comércio de carne de caça africana e os riscos de doenças emergentes PTDC/BIA-CBI/32130/2017 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Concluded
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
2013/05/01 - 2015/09/30	O papel das isoenzimas glutationa-S-transferase na tolerância dos bivalves às microcistinas. PTDC/MAR-EST/4614/2012 Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2011/01/01 - 2012/12/31	Projecto Estratégico - LA 15 - 2011-2012 PEst-C/MAR/LA0015/2011 Centro de Investigação Marinha e Ambiental, Portugal Universidade do Porto Centro Interdisciplinar de Investigação Marinha e Ambiental, Portugal Universidade do Algarve Centro de Ciências do Mar, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Outputs

Publications

Journal article

Haris Zafeiropoulos; Martin Beracochea; Stelios Ninidakis; Katrina Exter; Antonis Potirakis; Gianluca De Moro; Lorna Richardson; et al. "metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data". GigaScience (2022): https://doi.org/10.1093/gigascience/giad078.
10.1093/gigascience/giad078
Emam M; Machado JP; Antunes A. "Evolutionary genomics of mammalian lung cancer genes reveals signatures of positive selection in APC, RB1 and TP53.". Genomics (2020): http://europepmc.org/abstract/med/32818633.
10.1016/j.ygeno.2020.08.020
Machado JP; Antunes A. "The genomic context of retrocopies increases their chance of functional relevancy in mammals.". Genomics (2020): http://europepmc.org/abstract/med/31981699.
10.1016/j.ygeno.2020.01.013
Borges R; Machado JP; Gomes C; Rocha AP; Antunes A. "Measuring phylogenetic signal between categorical traits and phylogenies.". Bioinformatics (Oxford, England) (2019): http://europepmc.org/abstract/med/30358816.
10.1093/bioinformatics/bty800
Humisto A; Jokela J; Liu L; Wahlsten M; Wang H; Permi P; Machado JP; et al. "The swinholide biosynthetic gene cluster from a terrestrial cyanobacterium Nostoc sp. UHCC 0450.". Applied and environmental microbiology (2017): http://europepmc.org/abstract/med/29150506.
10.1128/aem.02321-17
João Paulo Machado; Siby Philip; Emanuel Maldonado; Stephen J. O’Brien; Warren E. Johnson; Agostinho Antunes. "Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns". Genome Biology and Evolution 8 9 (2016): 2748-2759. https://doi.org/10.1093%2Fgbe%2Fevw200.
10.1093/gbe/evw200
João Paulo Machado; Warren E. Johnson; M. Thomas P. Gilbert; Guojie Zhang; Erich D. Jarvis; Stephen J. O’Brien; Agostinho Antunes. "Bone-associated gene evolution and the origin of flight in birds". BMC Genomics 17 1 (2016): https://doi.org/10.1186%2Fs12864-016-2681-7.
10.1186/s12864-016-2681-7
Vitor Ramos; Daniele Salvi; João Machado; Micaela Vale; Joana Azevedo; Vitor Vasconcelos. "Culture-Independent Study of the Late-Stage of a Bloom of the Toxic Dinoflagellate Ostreopsis cf. ovata: Preliminary Findings Suggest Genetic Differences at the Sub-Species Level and Allow ITS2 Structure Characterization". Toxins 7 7 (2015): 2514-2533. https://doi.org/10.3390%2Ftoxins7072514.
10.3390/toxins7072514
Reis B; Carneiro M; Machado J; Azevedo J; Vasconcelos V; Martins JC. "Transcriptional Responses of Glutathione Transferase Genes in Ruditapes philippinarum Exposed to Microcystin-LR.". (2015): http://europepmc.org/abstract/med/25884330.
10.3390/ijms16048397
Machado, João. "Comparative genomics reveals insights into avian genome evolution and adaptation.". Science (New York, N.Y.) (2014): http://europepmc.org/abstract/med/25504712.
10.1126/science.1251385
João Paulo Machado; Vitor Vasconcelos; Agostinho Antunes. "Adaptive Functional Divergence of the Warm Temperature Acclimation-Related Protein (WAP65) in Fishes and the Ortholog Hemopexin (HPX) in Mammals". Journal of Heredity 105 2 (2013): 237-252. https://doi.org/10.1093%2Fjhered%2Fest087.
10.1093/jhered/est087
Siby Philip; João Paulo Machado; Emanuel Maldonado; Vítor Vasconcelos; Stephen J. O'Brien; Warren E. Johnson; Agostinho Antunes. "Fish Lateral Line Innovation: Insights into the Evolutionary Genomic Dynamics of a Unique Mechanosensory Organ". Molecular Biology and Evolution 29 12 (2012): 3887-3898. https://doi.org/10.1093%2Fmolbev%2Fmss194.
10.1093/molbev/mss194
João Machado; Warren E Johnson; Stephen J O'Brien; Vítor Vasconcelos; Agostinho Antunes. "Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals". BMC Evolutionary Biology 11 1 (2011): 342-342. https://doi.org/10.1186%2F1471-2148-11-342.
10.1186/1471-2148-11-342
José Carlos Martins; João Machado; António Martins; Joana Azevedo; Luís OlivaTeles; Vitor Vasconcelos. "Dynamics of Protein Phosphatase Gene Expression in Corbicula fluminea Exposed to Microcystin-LR and to Toxic Microcystis aeruginosa Cells". International Journal of Molecular Sciences 12 12 (2011): 9172-9188. https://doi.org/10.3390%2Fijms12129172.
10.3390/ijms12129172

Thesis / Dissertation

João Paulo Rodrigues Machado. "Evolutionary characterization of genes involved in development and adaptation in vertebrates under differential environmental conditions of selective pressure". PhD, 2014. https://repositorio-aberto.up.pt/handle/10216/81357.

Other

Dataset

Haris Zafeiropoulos; Martin Beracochea; Stelios Ninidakis; Katrina Exter; Potirakis Antonis; Gianluca De Moro; Lorna Richardson; et al. Supporting data for "metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data". 2023.
10.5524/102443