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From August 2002 to 2008 he took part in the bioinformatic group of the University of Aveiro, in which he was involved in several projects of genetic information analysis. One of the developed projects had as its primary goal the study of the primary structure of the mRNA, having produced several scientific studies. He has also developed a neonatal screening system of metabolic diseases in cooperation with the Porto Medical Genetic Institute (IGM), which analyses statistically and stores the information that comes from the mass spectrometer (MS/MS). This system is in its full use, analysing daily 600 newborns and screening approximately 30 disorders in Portugal. NeoScreen is also being used at 3 hospitals in Spain, Porto Rico and Colombia. In 2014, he developed a new version of this software to integrate new statistical functionalities. From 2008 until 2012 he started working in the Bioinformatic unit of Biocant (Cantanhede) developing and improving data analysis pipelines, in the fields of assembly, genome annotation, metagenomic and transcriptomic with data from a 454 sequencer, property of this unit. He had developed a pipeline, in perl, for the annotation of transcriptomics. He also developed a web site for the visualization of information supported in a mySQL database. This pipeline was, successfully, applied in Bathymodiolus azoricus mussel transcriptome, which inhabits deep-sea hydrothermal vents in the Azorean waters, as well as other transcriptomes sequenced by this unit. With this pipeline was possible to analyse several samples sequenced by 454 and conduct to several scientific papers. He also developed a pipeline to metagenomics analysis applied to several projects in Biocant. Several data also produced by 454 was analysed, and again, two scientific papers were published. Several advanced courses were realized in BioCant and he was responsible for the Bioinformatic lectures. Biocant is a Biotechnology Innovation Center that has several facilities which one of them is a sequencing facility (www.biocant.pt) From November of 2012 until July of 2015 he worked in the University of St Andrews, in the Medical department, developing a new bioinformatic unit. We start from scratch, buying servers in first place, configure all the equipment and start presenting the bioinformatic services to the Medical department. Other departments also joined the facility, like Biology and Marine Biology. During this period we have produced three scientific papers and others in submission. From September of 2015 until January of 2018 worked in Ophiomics, a start-up focused in precision medicine having the cancer its target. He has developed all the pipeline of annotation and report generation for germline and somatic panels, analysing the NGS data that are produced by an Ion Proton, owned by Ophiomics. All the data is produced by panels targeting a specific type of cancers. From February of 2018 he started working in iBiMED, in a bioinformatics group. The main duties are to pass the knowledge of several years of experience in next generation sequencing (NGS) to the students and present the right tools/best technological options to get the best answer of the data. From 2012 on he is giving support to the microbiology bioinformatic group of Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA) create/improving algorithms, also developing the INSaFLU (https://insaflu.insa.pt/) a service for surveillance of influenza virus. This project has already produced an article, published in a revised magazine, several participations in congress and present in the guidelines of the European Center for Disease Prevention and Control (ECDC) as an analysis tool for the flu virus. This pipeline is also used in SARS-CoV-2 by INSA. In total, he published 27 papers in ISI indexed journals, including Nature Microbiology (IF=14), Genome Biology (IF=13), Clinical Infectious Diseases (IF=8) and others
Identification

Personal identification

Full name
Miguel Pinheiro

Citation names

  • Pinheiro, Miguel

Author identifiers

Ciência ID
4E11-D0EC-05E4
ORCID iD
0000-0002-6601-7513
Google Scholar ID
ZkaJ--MAAAAJ
Researcher Id
K-6572-2017

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Exact Sciences - Computer and Information Sciences - Computer Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Education
Degree Classification
2005/09/01 - 2010/04/01
Concluded
Bioinformatics (Doutoramento)
Universidade de Aveiro, Portugal
"Sistema computacional para o estudo e redesenho de genes" (THESIS/DISSERTATION)
Aprovado
2005
Concluded
Mestrado em Electrónica e telecomunicações (Mestrado)
Universidade de Aveiro, Portugal
"Sistema de rastreio de doenças metabólicas" (THESIS/DISSERTATION)
.
2002/07
Concluded
Engineering in electronics and telecommunications (Licenciatura)
Universidade de Aveiro, Portugal
13
Affiliation

Science

Category
Host institution
Employer
2018/03/01 - Current Principal Investigator (Research) Universidade de Aveiro Instituto de Biomedicina, Portugal
2015/09/01 - 2018/01/31 Auxiliary Researcher (Research) Ophiomics, Portugal
2012/11/01 - 2015/08/01 Auxiliary Researcher (Research) University of St Andrews, United Kingdom
2008/09/01 - 2012/11/01 Auxiliary Researcher (Research) Biocant Associação de Transferência de Tecnologia, Portugal
2002/09/01 - 2008/07/31 Auxiliary Researcher (Research) Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
Projects

Grant

Designation Funders
2014 - 2015 High-performance computing in the search for the Tree of Life
STFC-ST/M000435/1-2014/2015
Researcher
University of St Andrews Biomedical Sciences Research Complex, United Kingdom
2001 - 2004 Development of new methodologies for genome analysis
POCTI/2001/BME/39030
Researcher
Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
Concluded

Contract

Designation Funders
2008 - 2011 The indigenous microbiome of Portuguese wine fermentations
PTDC/AGR-ALI/098292/2008
Researcher
Biocant Associação de Transferência de Tecnologia, Portugal
2008 - 2011 Transcriptomic and proteomic approach for understanding the molecular basis of Bursaphelenchus xylophilus pathogenicity
PTDC/AGR-CFL/098916/2008
Researcher
Biocant Associação de Transferência de Tecnologia, Portugal

Other

Designation Funders
2001 - 2004 INFOGENMED
IST-2001-39013
Researcher
Universidade de Aveiro Instituto de Engenharia Eletrónica e Informática de Aveiro, Portugal
Concluded
Outputs

Publications

Conference abstract
  1. Pinheiro, Miguel; Borges, Vítor. "INSaFLU-TELE-Vir: an open web-based bioinformatics suite for influenza and SARS-CoV-2 genome-based surveillance". Paper presented in ARPHA Conference Abstracts, 2021.
    Published
Journal article
  1. Ferreira, Margarida; Francisco, Stephany; Soares, Ana R.; Nobre, Ana; Pinheiro, Miguel; Reis, Andreia; Neto, Sonya; et al. "Integration of segmented regression analysis with weighted gene correlation network analysis identifies genes whose expression is remodeled throughout physiological aging in mouse tissues". Aging 13 14 (2021): 18150-18190. http://dx.doi.org/10.18632/aging.203379.
    10.18632/aging.203379
  2. Pereira, Marisa; Ribeiro, Diana R.; Pinheiro, Miguel M.; Ferreira, Margarida; Kellner, Stefanie; Soares, Ana R.. "m5U54 tRNA Hypomodification by Lack of TRMT2A Drives the Generation of tRNA-Derived Small RNAs". International Journal of Molecular Sciences 22 6 (2021): 2941. http://dx.doi.org/10.3390/ijms22062941.
    10.3390/ijms22062941
  3. Borges, Vítor; Pinheiro, Miguel; Pechirra, Pedro; Guiomar, Raquel; Gomes, João Paulo. "INSaFLU: an automated open web-based bioinformatics suite “from-reads” for influenza whole-genome-sequencing-based surveillance". Genome Medicine 10 1 (2018): http://dx.doi.org/10.1186/s13073-018-0555-0.
    10.1186/s13073-018-0555-0
  4. Parcell, B.J.; Oravcova, K.; Pinheiro, M.; Holden, M.T.G.; Phillips, G.; Turton, J.F.; Gillespie, S.H.. "Pseudomonas aeruginosa intensive care unit outbreak: winnowing of transmissions with molecular and genomic typing". Journal of Hospital Infection 98 3 (2018): 282-288. http://dx.doi.org/10.1016/j.jhin.2017.12.005.
    10.1016/j.jhin.2017.12.005
  5. Pinto, Miguel; Borges, Vítor; Antelo, Minia; Pinheiro, Miguel; Nunes, Alexandra; Azevedo, Jacinta; Borrego, Maria José; et al. "Genome-scale analysis of the non-cultivable Treponema pallidum reveals extensive within-patient genetic variation". Nature Microbiology 2 1 (2016): http://dx.doi.org/10.1038/nmicrobiol.2016.190.
    10.1038/nmicrobiol.2016.190
  6. Dias, L.; Caetano, T.; Pinheiro, M.; Mendo, S.. "The lanthipeptides of Bacillus methylotrophicus and their association with genomic islands". Systematic and Applied Microbiology 38 8 (2015): 525-533. http://dx.doi.org/10.1016/j.syapm.2015.10.002.
    10.1016/j.syapm.2015.10.002
  7. Borges, Vítor; Santos, Andrea; Correia, Cristina Belo; Saraiva, Margarida; Ménard, Armelle; Vieira, Luís; Sampaio, Daniel A.; et al. "Helicobacter pullorum Isolated from Fresh Chicken Meat: Antibiotic Resistance and Genomic Traits of an Emerging Foodborne Pathogen". Applied and Environmental Microbiology 81 23 (2015): 8155-8163. http://dx.doi.org/10.1128/aem.02394-15.
    10.1128/aem.02394-15
  8. Pinto, Cátia; Pinho, Diogo; Cardoso, Remy; Custódio, Valéria; Fernandes, Joana; Sousa, Susana; Pinheiro, Miguel; Egas, Conceição; Gomes, Ana C.. "Wine fermentation microbiome: a landscape from different Portuguese wine appellations". Frontiers in Microbiology 6 (2015): http://dx.doi.org/10.3389/fmicb.2015.00905.
    10.3389/fmicb.2015.00905
  9. Cruz, Andreia; Rodrigues, Raquel; Pinheiro, Miguel; Mendo, Sónia. "Transcriptomes analysis of Aeromonas molluscorum Av27 cells exposed to tributyltin (TBT): Unravelling the effects from the molecular level to the organism". Marine Environmental Research 109 (2015): 132-139. http://dx.doi.org/10.1016/j.marenvres.2015.06.017.
    10.1016/j.marenvres.2015.06.017
  10. Borges, Vítor; Pinheiro, Miguel; Antelo, Minia; Sampaio, Daniel A.; Vieira, Luís; Ferreira, Rita; Nunes, Alexandra; et al. "Chlamydia trachomatis In Vivo to In Vitro Transition Reveals Mechanisms of Phase Variation and Down-Regulation of Virulence Factors". PLOS ONE 10 7 (2015): e0133420. http://dx.doi.org/10.1371/journal.pone.0133420.
    10.1371/journal.pone.0133420
  11. Pinheiro, Miguel M.; Ahmed, Md Atique; Millar, Scott B.; Sanderson, Theo; Otto, Thomas D.; Lu, Woon Chan; Krishna, Sanjeev; Rayner, Julian C.; Cox-Singh, Janet. "Plasmodium knowlesi Genome Sequences from Clinical Isolates Reveal Extensive Genomic Dimorphism". PLOS ONE 10 4 (2015): e0121303. http://dx.doi.org/10.1371/journal.pone.0121303.
    10.1371/journal.pone.0121303
  12. Cowart, Dominique A.; Pinheiro, Miguel; Mouchel, Olivier; Maguer, Marion; Grall, Jacques; Miné, Jacques; Arnaud-Haond, Sophie. "Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities". PLOS ONE 10 2 (2015): e0117562. http://dx.doi.org/10.1371/journal.pone.0117562.
    10.1371/journal.pone.0117562
  13. Rocheta, Margarida; Amorim, Maria I.; Ribeiro, Teresa; Pinheiro, Miguel; Egas, Conceição; Morais-Cecílio, Leonor; Costa, Maria M. R.. "Comparative transcriptomic analysis of male and female flowers of monoecious Quercus suber". Frontiers in Plant Science 5 (2014): http://dx.doi.org/10.3389/fpls.2014.00599.
    10.3389/fpls.2014.00599
  14. Gillespie, S. H.; Ling, C. L.; Oravcova, K.; Pinheiro, M.; Wells, L.; Bryant, J. M.; McHugh, T. D.; et al. "Genomic Investigations Unmask Mycoplasma amphoriforme, a New Respiratory Pathogen". Clinical Infectious Diseases 60 3 (2014): 381-388. http://dx.doi.org/10.1093/cid/ciu820.
    10.1093/cid/ciu820
  15. Ahmed, Atique M.; Pinheiro, Miguel M.; Divis, Paul C.; Siner, Angela; Zainudin, Ramlah; Wong, Ing Tien; Lu, Chan Woon; et al. "Disease Progression in Plasmodium knowlesi Malaria Is Linked to Variation in Invasion Gene Family Members". PLoS Neglected Tropical Diseases 8 8 (2014): e3086. http://dx.doi.org/10.1371/journal.pntd.0003086.
    10.1371/journal.pntd.0003086
  16. Bettencourt, Raul; Rodrigues, Mónica; Barros, Inês; Cerqueira, Teresa; Freitas, Cátia; Costa, Valentina; Pinheiro, Miguel; Egas, Conceição; Santos, Ricardo Serrão. "Site-related differences in gene expression and bacterial densities in the mussel Bathymodiolus azoricus from the Menez Gwen and Lucky Strike deep-sea hydrothermal vent sites". Fish & Shellfish Immunology 39 2 (2014): 343-353. http://dx.doi.org/10.1016/j.fsi.2014.05.024.
    10.1016/j.fsi.2014.05.024
  17. Borges, V.; Pinheiro, M.; Vieira, L.; Sampaio, D. A.; Nunes, A.; Borrego, M. J.; Gomes, J. P.. "Complete Genome Sequence of Chlamydia trachomatis Ocular Serovar C Strain TW-3". Genome Announcements 2 1 (2014): http://dx.doi.org/10.1128/genomea.01204-13.
    10.1128/genomea.01204-13
  18. Pinto, Cátia; Pinho, Diogo; Sousa, Susana; Pinheiro, Miguel; Egas, Conceição; C. Gomes, Ana. "Unravelling the Diversity of Grapevine Microbiome". PLoS ONE 9 1 (2014): e85622. http://dx.doi.org/10.1371/journal.pone.0085622.
    10.1371/journal.pone.0085622
  19. Pereira-Leal, José B; Abreu, Isabel A; Alabaça, Cláudia S; Almeida, Maria; Almeida, Paulo; Almeida, Tânia; Amorim, Maria; et al. "A comprehensive assessment of the transcriptome of cork oak (Quercus suber) through EST sequencing". BMC Genomics 15 1 (2014): 371. http://dx.doi.org/10.1186/1471-2164-15-371.
    10.1186/1471-2164-15-371
  20. Stefanni, Sergio; Bettencourt, Raul; Pinheiro, Miguel; Moro, Gianluca De; Bongiorni, Lucia; Pallavicini, Alberto. "Transcriptome of the Deep-Sea Black Scabbardfish,Aphanopus carbo(Perciformes: Trichiuridae): Tissue-Specific Expression Patterns and Candidate Genes Associated to Depth Adaptation". International Journal of Genomics 2014 (2014): 1-21. http://dx.doi.org/10.1155/2014/267482.
    10.1155/2014/267482
  21. Figueiredo, Joana; Simões, Maria José; Gomes, Paula; Barroso, Cristina; Pinho, Diogo; Conceição, Luci; Fonseca, Luís; et al. "Assessment of the Geographic Origins of Pinewood Nematode Isolates via Single Nucleotide Polymorphism in Effector Genes". PLoS ONE 8 12 (2013): e83542. http://dx.doi.org/10.1371/journal.pone.0083542.
    10.1371/journal.pone.0083542
  22. Abbasi, M.; Paquete, L.; Liefooghe, A.; Pinheiro, M.; Matias, P.. "Improvements on bicriteria pairwise sequence alignment: algorithms and applications". Bioinformatics 29 8 (2013): 996-1003. http://dx.doi.org/10.1093/bioinformatics/btt098.
    10.1093/bioinformatics/btt098
  23. Egas, Conceição; Pinheiro, Miguel; Gomes, Paula; Barroso, Cristina; Bettencourt, Raul. "The Transcriptome of Bathymodiolus azoricus Gill Reveals Expression of Genes from Endosymbionts and Free-Living Deep-Sea Bacteria". Marine Drugs 10 12 (2012): 1765-1783. http://dx.doi.org/10.3390/md10081765.
    10.3390/md10081765
  24. Santos, Carla S; Pinheiro, Miguel; Silva, Ana I; Egas, Conceição; Vasconcelos, Marta W. "Searching for resistance genes to Bursaphelenchus xylophilus using high throughput screening". BMC Genomics 13 1 (2012): 599. http://dx.doi.org/10.1186/1471-2164-13-599.
    10.1186/1471-2164-13-599
  25. Moura, Gabriela R.; Pinheiro, Miguel; Freitas, Adelaide; Oliveira, José L.; Frommlet, Jörg C.; Carreto, Laura; Soares, Ana R.; Bezerra, Ana R.; Santos, Manuel A. S.. "Species-Specific Codon Context Rules Unveil Non-Neutrality Effects of Synonymous Mutations". PLoS ONE 6 10 (2011): e26817. http://dx.doi.org/10.1371/journal.pone.0026817.
    10.1371/journal.pone.0026817
  26. Freitas, A.; Afreixo, V.; Pinheiro, M.; Oliveira, J. L.; Moura, G.; Santos, M.. "Improving the performance of the iterative signature algorithm for the identification of relevant patterns". Statistical Analysis and Data Mining 4 1 (2011): 71-83. http://dx.doi.org/10.1002/sam.10104.
    10.1002/sam.10104
  27. Bettencourt, Raul; Pinheiro, Miguel; Egas, Conceição; Gomes, Paula; Afonso, Mafalda; Shank, Timothy; Santos, Ricardo Serrão. "High-throughput sequencing and analysis of the gill tissue transcriptome from the deep-sea hydrothermal vent mussel Bathymodiolus azoricus". BMC Genomics 11 1 (2010): http://dx.doi.org/10.1186/1471-2164-11-559.
    10.1186/1471-2164-11-559
  28. Moura, Gabriela; Pinheiro, Miguel; Arrais, Joel; Gomes, Ana Cristina; Carreto, Laura; Freitas, Adelaide; Oliveira, José L.; Santos, Manuel A. S.. "Large Scale Comparative Codon-Pair Context Analysis Unveils General Rules that Fine-Tune Evolution of mRNA Primary Structure". PLoS ONE 2 9 (2007): e847. http://dx.doi.org/10.1371/journal.pone.0000847.
    10.1371/journal.pone.0000847
  29. Moura, Gabriela R; Lousado, José P; Pinheiro, Miguel; Carreto, Laura; Silva, Raquel M; Oliveira, José L; Santos, Manuel AS. "Codon-triplet context unveils unique features of the Candida albicans protein coding genome". BMC Genomics 8 1 (2007): 444. http://dx.doi.org/10.1186/1471-2164-8-444.
    10.1186/1471-2164-8-444
  30. Pinheiro, M.; Afreixo, V.; Moura, G.; Freitas, A.; Santos, M. A. S.; Oliveira, J. L.. "Statistical, Computational and Visualization Methodologies to Unveil Gene Primary Structure Features". Methods of Information in Medicine 45 02 (2006): 163-168. http://dx.doi.org/10.1055/s-0038-1634061.
    10.1055/s-0038-1634061
  31. Moura, Gabriela; Pinheiro, Miguel; Silva, Raquel; Miranda, Isabel; Afreixo, Vera; Dias, Gaspar; Freitas, Adelaide; Oliveira, José L; Santos, Manuel AS. "Comparative context analysis of codon pairs on an ORFeome scale". Genome Biology 6 3 (2005): R28. http://dx.doi.org/10.1186/gb-2005-6-3-r28.
    10.1186/gb-2005-6-3-r28
Activities

Jury of academic degree

Topic
Role
Candidate name (Type of degree)
Institution / Organization
2019/11/21 Embryo selection through time-lapse image analysis: a Deep Learning approach
(Thesis) Main arguer
Oldair Euclides Barbosa Mendes (Master)
Universidade de Aveiro, Portugal
Distinctions

Other distinction

2003 2º place awarded by Microsoft 2003