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I have a Licenciatura (2002) and MsC (2006) in Informatics Engineering from Instituto Superior Tecnico, and PhD in Bioinformatics (Aix-Marseille University, 2009), supervised by Patrick Lemaire, on the analysis of gene expression and transcriptional regulation in development, resulting in 2 first author publications (111 citations according to Web of Science in November 2023). I did postdoctoral work at the European Bioinformatics Institute, under supervision of Ian Dunham, designing and implementing pipelines to analyze hundreds of human and mouse epigenomic datasets from large projects such as ENCODE. I contributed to 2 major publications (with a combined total of 12004 citations), resulting in the revelation that around 80% of the genome has a potential regulatory function. I helped integrate these results in ENSEMBL, a widely used resource in the life sciences (4 publications, 2114 citations). In 2012 I became a postdoc at Instituto Gulbenkian de Ciência (IGC), and in 2014-2019 head of the Bioinformatics Facility, leading a team of 4-6 persons providing bioinformatics support. I collaborated in several projects at IGC (13 publications, with 269 citations). In 2019 I moved to UCIBIO FCT-NOVA in 2019 to develop my scientific independence and focus on projects related to cancer biology. I contributed to writing the successful application Onco-HIT (250.000¿), where I worked to uncover possible molecular origins of intratumor heterogeneity. I nurtured collaborations producing several results, regarding tumor immune evasion (Fior et al. 2021, 32 citations); the role of glycosylation in human health (Sobral et. al, 2022, publication as first author) and disease tolerance (Singh et al. 2021a, 2021b, 17 citations) and the interplay between genetic and microenvironment heterogeneity in CRC progression (Sobral et al. 2022, publication as first author). In 2022 I moved to INSA Ricardo Jorge in Lisbon, under the supervision of João Paulo Gomes, within the bioinformatics group of the Department of Infectious Diseases, to contribute to viral and microbial pathogen surveillance. I contributed to the effort facing the beginning of the Monkeypox outbreak in Portugal, originating 2 high impact publications (Isidro et al., 2022, 309 citations; Borges et al., 2023). During my scientific career in Biology and Bioinformatics I contributed to 29 publications (13500 citations, 16 h-index), one receiving PLOS Genetics Research Prize 2015, and participated in 9 national and international projects. I lectured 13 courses at MsC and PhD level. I was responsible for the Research in Bioinformatics course of the MsC in Bioinformatics (FCUL). I contributed to the conception of a new Bioinformatics Masters at FCT-NOVA. I organized and taught 10 practical courses in bioinformatics within the GTPB programme at IGC,. I wrote and won grants to organize 2 EMBO practical courses. I supervised and mentored 9 MSc students, 1 PhD student, and examined 2 PhD and 6 MSc thesis. I was a member of the Elixir european bioinformatics infrastructure, and contributed to the genesis of BioData.pt, the portuguese node of Elixir. I was also the MC substitute from Portugal in the COST action CA15205.
Identification

Personal identification

Full name
Daniel Vieira Noro e Silva Sobral

Citation names

  • Sobral, Daniel

Author identifiers

Ciência ID
5C13-14D8-F5A4
ORCID iD
0000-0003-3955-0117
Google Scholar ID
ihHfSkUAAAAJ

Email addresses

  • daniel.sobral@insa.min-saude.pt (Professional)

Addresses

  • Avenida Padre Cruz, 1649-016, Lisboa, Lisboa, Portugal (Professional)

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Natural sciences - Biological Sciences

Languages

Language Speaking Reading Writing Listening Peer-review
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
French Intermediate (B1) Advanced (C1) Intermediate (B1) Upper intermediate (B2)
Education
Degree Classification
2009
Concluded
Doctorat en Biologie - Spécialité Génomique et Bioinformatique (Doutoramento)
Aix-Marseille Université Ecole Doctorale des Sciences de la Vie et de la Santé, France
"Biological Data Integration: Towards a Global Understanding of Ascidian Development" (THESIS/DISSERTATION)
Mention Trés Honorable
2006
Concluded
Mestrado em Engenharia Informática e de Computadores (Mestrado)
Universidade de Lisboa Instituto Superior Técnico, Portugal
"Multi-Level Control For Interactive Narratives - A Proposal for a Narrative Authoring Framework" (THESIS/DISSERTATION)
Aprovado
2002
Concluded
Engenharia Informática e de Computadores (Licenciatura)
Universidade de Lisboa Instituto Superior Técnico, Portugal
16
Affiliation

Science

Category
Host institution
Employer
2022/04/04 - Current Invited Auxiliary Researcher (Research) Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
2019/04/01 - 2022/04/01 Postdoc (Research) UCIBIO - FCT NOVA, Portugal
2015 - 2019/03/31 Principal Investigator (Research) Instituto Gulbenkian de Ciência, Portugal
2011/12/31 - 2015 Postdoc (Research) Instituto Gulbenkian de Ciência, Portugal
2009/12/01 - 2011/12/30 Contracted Researcher (Research) European Bioinformatics Institute, United Kingdom

Teaching in Higher Education

Category
Host institution
Employer
2002/10/01 - 2004/08/31 Tutor (University Teacher) Universidade de Lisboa Instituto Superior Técnico, Portugal

Others

Category
Host institution
Employer
2005/01/01 - 2009/09/30 Gulbenkian PhD Fellow Instituto Gulbenkian de Ciência, Portugal
Projects

Grant

Designation Funders
2022/04/04 - Current OneHealth EJP TELE-Vir project
Invited Scientist Fellow
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
European Commission
Ongoing
2023/02/01 - 2027/01/31 DURABLE: Delivering a Unified Research Alliance of Biomedical and public health Laboratories against Epidemics
Researcher
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
European Commission
Ongoing
2024/05/24 - 2026/05/23 Capacity building in genomic epidemiology of viral threats through expansion of INSaFLU and training provision
2023.10492.CPCA.A2
Principal investigator
Instituto Nacional de Saúde Doutor Ricardo Jorge IP Departamento de Doenças Infeciosas, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2021/01/01 - 2022/03/31 Inibição da heterogeneidade intra-tumoral como uma estratégia promissora no tratamento do cancro
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2017/01/01 - 2020/12/31 An OMICS Network to Prevent and Control Infectious Diseases and Antimicrobial Resistance (ONEIDA)
SAICTPAC/0015/2015
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica António Xavier, Portugal
Concluded

Contract

Designation Funders
2023/01/02 - 2024/07/01 A tríade da nutrição, microbiota intestinal e Artrite Reumatóide - Um estudo piloto exploratório
2022.07462.PTDC
Universidade de Lisboa Instituto de Medicina Molecular João Lobo Antunes, Portugal

Associação para a Investigação e Desenvolvimento da Faculdade de Medicina, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2023/02/01 - 2023/12/31 INSaFLU Snakemake
2022.23037.CPCA.A0
Co-Principal Investigator (Co-PI)
Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2019/03/01 - 2021/09/30 Targeting Intra-Tumor Heterogeneity as a promising therapeutic strategy for cancer
PTDC/MED-ONC/28660/2017
Post-doc Fellow
REQUIMTE Unidade de Ciências Biomoleculares Aplicadas, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2017/07/01 - 2019/02/28 BioData.pt - Rede Portuguesa de Dados Biologicos
01/SAICT/2016
Researcher
Instituto Gulbenkian de Ciência, Portugal
Associação para a Inovação e Desenvolvimento da FCT

European Regional Development Fund
Ongoing
2017/01/01 - 2019/02/28 ONEIDA - An Omics Network to Prevent and Control Infectious Diseases and Antimicrobial Resistance
03/SAICT/2015
Researcher
Instituto Gulbenkian de Ciência, Portugal
Associação para a Inovação e Desenvolvimento da FCT

European Regional Development Fund
Concluded
2015/09/01 - 2019/02/28 ELIXIR-EXCELERATE: Fast-track ELIXIR implementation and drive early user exploitation across the life-sciences.
info:eu-repo/grantAgreement/EC/Horizon 2020 Framework Programme/676559/EU
Researcher
Instituto Gulbenkian de Ciência, Portugal
European Commission
Concluded
2009/12/01 - 2012/01/29 CISSTEM - Cis-regulatory logic of the transcriptional control in neural stem cells
FP7 – 223210
Researcher
European Bioinformatics Institute, United Kingdom
Concluded
2005 - 2008 TRANSCODE - Novel tool for high-throughput characterization of genomic elements regulating gene expression in chordates.
511990
Researcher
Institut de Biologie du Développement de Marseille, France
Concluded
2002 - 2003 Victec (Virtual ICT with Empathic Characters)
IST-2001-33310
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Concluded

Other

Designation Funders
2017 - 2020/09/07 Gene Regulation Ensemble Effort for the Knowledge Commons
Researcher
Instituto Gulbenkian de Ciência, Portugal
Concluded
Outputs

Publications

Book chapter
  1. Pinto, Rui; Sobral, Daniel; Grosso, Ana Rita. "Comprehensive Detection of Pseudogenes Transcribed by Readthrough". In Methods in Molecular Biology, 85-102. Springer US, 2021.
    10.1007/978-1-0716-1503-4_6
  2. Nitta, Kazuhiro R.; Vincentelli, Renaud; Jacox, Edwin; Cimino, Agnès; Ohtsuka, Yukio; Sobral, Daniel; Satou, Yutaka; Cambillau, Christian; Lemaire, Patrick. "High-Throughput Protein Production Combined with High- Throughput SELEX Identifies an Extensive Atlas of Ciona robusta Transcription Factor DNA-Binding Specificities". In High-Throughput Protein Production and Purification, 487-517. Springer New York, 2019.
    10.1007/978-1-4939-9624-7_23
  3. Siwek, Wojciech; Gómez-Rodríguez, Mariluz; Sobral, Daniel; Corrêa, Ivan R.; Jansen, Lars E. T.. "time-ChIP: A Method to Determine Long-Term Locus-Specific Nucleosome Inheritance". In Methods in Molecular Biology, 131-158. Springer New York, 2018.
    10.1007/978-1-4939-8663-7_7
Conference abstract
  1. Ferreira, Rita; Coelho, Luís; Sobral, Daniel; Dourado, João; Isidro, Joana; Mixão, Verónica; Pinto, Miguel; et al. "Performance of metagenomics NGS probe-based pathogen detection in clinical samples - work published on Conference Abstracts Book of the 3rd Symposium of the National Research Infrastructure for Genome Sequencing and Analysis - GenomePT Symposium 2023, Lisbon, Portugal, 17th November". 2023.
    Published
  2. Coelho, Luís; Ferreira, Rita; Sobral, Daniel; Dourado, Joao; Isidro, Joana; Mixão, Verónica; Pinto, Miguel; et al. "Probe-based Metagenomics: an added value for clinical decision? - work published on Conference Abstracts Book of Congress of Microbiology and Biotechnology 2023 (MICRO-BIOTEC'23), Covilhã, Portugal, 7th-9th December". 2023.
    Published
  3. Ferreira, Rita; Coelho, Luís; Sobral, Daniel; Dourado, João; Isidro, Joana; Pinto, Miguel; Mixão, Verónica; et al. "Performance of metagenomics NGS probe-based pathogen detection in clinical samples - work published on Conference Abstracts Book of the 25º European Society for Clinical Virology (ESCV 2023), Milano, Italy, 30 August - 2 September". 2023.
    Published
  4. Guilgur, Leonardo Gaston; Prudencio, Pedro; Sobral, Daniel; Lisekova, D; Martinho, R.G. "Fast and furious: developmental constraint to pre-mRNA splicing during early embryonic development in Drosophila". Paper presented in Eukaryotic mRNA processing, Cold Spring Harbor, 2013.
Conference poster
  1. Ana Balau; Sobral, Daniel; Márcia M. Medeiros; Antunes, Sandra; Carvalho, Maria; Inês Navalho Morais; Filomena Aréde de Carvalho; et al. "Turning a vulnerability into a strength - deciphering the protective mechanisms of pyruvate kinase deficiency against malaria". Paper presented in EMBL Conference: BioMalPar XX: biology and pathology of the malaria parasite, Heidelberg, Germany, 2024.
  2. Coelho, Luis; Ferreira, Rita; Sobral, Daniel; Dourado, João; Isidro, Joana; Mixão, Verónica; Pinto, Miguel; et al. "Probe-based Metagenomics: an added value for clinical decision?". Paper presented in MicroBiotec 2023, 2023.
  3. Balau, Ana; Sobral, Daniel; Abrantes, Patrícia; Carvalho, Maria; Morais, Inês; Mixão, Verónica; Medeiros, Márcia Melo; et al. "Unveiling the Protective Mechanisms of Pyruvate Kinase Deficiency against Malaria: Transforming Vulnerability into Resilience". Paper presented in MicroBiotec 2023, 2023.
  4. Caldas, Paulo; Grosso, Ana Rita; Luz, Mariana; Sobral, Daniel. Corresponding author: Grosso, Ana Rita. "RNA in Disease - IX PT RNA Meeting". Paper presented in Transcription Readthrough is prevalent in healthy human tissues and determined by inherent genomic features, 2023.
  5. Borges, Vitor; Isidro, Joana; Ferreira, Rita; Duarte, Sílvia; Santos, Daniela; Vieira, Luís; Pinto, Miguel; et al. "Genomic epidemiology of SARS-CoV-2 in Portugal: supporting evidence-informed public health decision-making". Paper presented in 3rd INSA's Young Researcher Day, Lisbon, Portugal, 8 November, 2022.
  6. Inácio, Daniel; Amado, Tiago; Sobral, Daniel; Enguita, Francisco J.; Silva-Santos, Bruno; Gomes, AQ. "Uncovering the role of microRNAs in the control of effector gd T cell differentiation.". Paper presented in EMBL Symposium: The Non-Coding Genome, EMBL, 2019.
  7. Inácio, D.; Amado, Tiago; Sobral, Daniel; Enguita, Francisco J.; Gomes, AQ; SILVA-SANTOS, Bruno. "A key role for microRNAs in regulating IL-17 versus IFN-g production by gd T cells.". Paper presented in The 3rd International Symposium on Frontiers in Molecular Science — RNA Regulatory Networks, 2019.
  8. Amado, T; Schmolka, N.; Sobral, Daniel; Enguita, Francisco J.; Inácio, D.; SILVA-SANTOS, Bruno; Gomes, AQ. "A key role for microRNAs in regulating IL-17 versus IFN-g production by gamma-delta T cells". Paper presented in 5th European Congress of Immunology, 2018.
  9. Prudêncio, Pedro; Guilgur, Leonardo Gaston; Lisekova D.; Sobral, Daniel; Martinho, Rui Gonçalo. "Avoidance of premRNA splicing during Drosophila early embryonic development.". Paper presented in 2nd Meeting Portuguese Society for Development Biology. Lisboa, Portugal, 2013.
  10. Prudêncio, Pedro; Guilgur, Leonardo Gaston; Lisekova D; Sobral, Daniel; Martinho, Rui Gonçalo. "Developmental constraints to pre-mRNA splicing during Drosophila early embryogenesis". Paper presented in EMBO|EMBL Symposium The Complex Life of mRNA. Heidelberg, Germany, 2012.
Journal article
  1. Rion Brattig-Correia; Joana M Almeida; Margot Julia Wyrwoll; Irene Julca; Daniel Sobral; Chandra Shekhar Misra; Sara Di Persio; et al. "The conserved genetic program of male germ cells uncovers ancient regulators of human spermatogenesis". eLife (2024): https://doi.org/10.7554/eLife.95774.3.
    10.7554/eLife.95774.3
  2. Rion Brattig-Correia; Joana M Almeida; Margot Julia Wyrwoll; Irene Julca; Daniel Sobral; Chandra Shekhar Misra; Sara Di Persio; et al. "The conserved genetic program of male germ cells uncovers ancient regulators of human spermatogenesis". eLife (2024): https://doi.org/10.7554/eLife.95774.
    10.7554/eLife.95774
  3. Santos, João Dourado; Sobral, Daniel; Pinheiro, Miguel; Isidro, Joana; Bogaardt, Carlijn; Pinto, Miguel; Eusébio, Rodrigo; et al. "INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance". Genome Medicine 16 1 (2024): http://dx.doi.org/10.1186/s13073-024-01334-3.
    10.1186/s13073-024-01334-3
  4. Calado, Rita D.A.; Mendes, Bárbara B.; Conniot, João; Ravasco, João M.J.M.; Sobral, Daniel; Ferreira, Carolina; Ferreira, Rita; et al. "Preclinical assessment of an antibiotic-free cationic surfactant-based cellulose hydrogel for sexually and perinatally transmitted infections". Matter (2024): http://dx.doi.org/10.1016/j.matt.2024.04.002.
    10.1016/j.matt.2024.04.002
  5. Daniel Sobral; Ana Filipa Fernandes; Miguel Bernardes; Patrícia Pinto; Helena Santos; João Lagoas-Gomes; José Tavares-Costa; et al. "Molecular Profiling of Axial Spondyloarthritis Patients Reveals an Association between Innate and Adaptive Cell Populations and Therapeutic Response to Tumor Necrosis Factor Inhibitors". Biomolecules (2024): https://doi.org/10.3390/biom14030382.
    10.3390/biom14030382
  6. Paulo Caldas; Mariana Luz; Simone Baseggio; Rita Andrade; Daniel Sobral; Ana Rita Grosso. "Transcription readthrough is prevalent in healthy human tissues and associated with inherent genomic features". Communications Biology (2024): https://doi.org/10.1038/s42003-024-05779-5.
    10.1038/s42003-024-05779-5
  7. Balau, Ana; Sobral, Daniel; Abrantes, Patrícia; Santos, Inês; Mixão, Verónica; Gomes, João Paulo; Antunes, Sandra; Arez, Ana Paula. "Differential Gene Expression of Malaria Parasite in Response to Red Blood Cell-Specific Glycolytic Intermediate 2,3-Diphosphoglycerate (2,3-DPG)". International Journal of Molecular Sciences 24 23 (2023): 16869. http://dx.doi.org/10.3390/ijms242316869.
    Published • 10.3390/ijms242316869
  8. Vítor Borges; Mariana Perez Duque; João Vieira Martins; Paula Vasconcelos; Rita Ferreira; Daniel Sobral; Ana Pelerito; et al. "Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in Portugal". Nature Medicine (2023): https://doi.org/10.1038/s41591-023-02542-x.
    10.1038/s41591-023-02542-x
  9. Mixão, Verónica; Pinto, Miguel; Sobral, Daniel; Di Pasquale, Adriano; Gomes, João Paulo; Borges, Vítor. "ReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data". Genome Medicine 15 1 (2023): http://dx.doi.org/10.1186/s13073-023-01196-1.
    10.1186/s13073-023-01196-1
  10. Chen, Nicholas F. G.; Chaguza, Chrispin; Gagne, Luc; Doucette, Matthew; Smole, Sandra; Buzby, Erika; Hall, Joshua; et al. "Development of an amplicon-based sequencing approach in response to the global emergence of mpox". PLOS Biology 21 6 (2023): e3002151. http://dx.doi.org/10.1371/journal.pbio.3002151.
    10.1371/journal.pbio.3002151
  11. DANIELA COCHICHO; Alexandra Nunes; Daniel Sobral; João P. Gomes; Susana Esteves; Joana Mendonça; Luis Vieira; et al. "Distribution and clinical significance of HPV16 variants in head and neck squamous cell carcinomas: data from a Portuguese cohort and systematic review". Pathobiology (2023): https://doi.org/10.1159/000529723.
    10.1159/000529723
  12. Kislaya, Irina; Casaca, Pedro; Borges, Vítor; Sousa, Carlos; Ferreira, Bibiana I.; Fonte, Ana; Fernandes, Eugénia; et al. "Comparative Effectiveness of COVID-19 Vaccines in Preventing Infections and Disease Progression from SARS-CoV-2 Omicron BA.5 and BA.2, Portugal". Emerging Infectious Diseases 29 3 (2023): 569-575. http://dx.doi.org/10.3201/eid2903.221367.
    10.3201/eid2903.221367
  13. Peixoto, Carolina; Lopes, Marta B.; Martins, Marta; Casimiro, Sandra; Sobral, Daniel; Grosso, Ana Rita; Abreu, Catarina; et al. "Identification of biomarkers predictive of metastasis development in early-stage colorectal cancer using network-based regularization". BMC Bioinformatics 24 1 (2023): http://dx.doi.org/10.1186/s12859-022-05104-z.
    10.1186/s12859-022-05104-z
  14. Tália Feijão; Bruno Marques; Rui D. Silva; Célia Carvalho; Daniel Sobral; Ricardo Matos; Tian Tan; et al. "Polycomb group (PcG) proteins prevent the assembly of abnormal synaptonemal complex structures during meiosis". Proceedings of the National Academy of Sciences (2022): https://doi.org/10.1073/pnas.2204701119.
    10.1073/pnas.2204701119
  15. Isidro, Joana; Borges, Vítor; Pinto, Miguel; Sobral, Daniel; Santos, João Dourado; Nunes, Alexandra; Mixão, Verónica; et al. "Addendum: Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus". Nature Medicine 28 10 (2022): 2220-2221. http://dx.doi.org/10.1038/s41591-022-02036-2.
    10.1038/s41591-022-02036-2
  16. Daniel Sobral; Marta Martins; Shannon Kaplan; Mahdi Golkaram; Michael Salmans; Nafeesa Khan; Raakhee Vijayaraghavan; et al. "Genetic and microenvironmental intra-tumor heterogeneity impacts colorectal cancer evolution and metastatic development". Communications Biology (2022): https://doi.org/10.1038/s42003-022-03884-x.
    10.1038/s42003-022-03884-x
  17. Daniel Sobral; Rita Francisco; Laura Duro; Paula Alexandra Videira; Ana Rita Grosso. "Concerted Regulation of Glycosylation Factors Sustains Tissue Identity and Function". Biomedicines (2022): https://doi.org/10.3390/biomedicines10081805.
    10.3390/biomedicines10081805
  18. Joana Isidro; Vítor Borges; Miguel Pinto; Daniel Sobral; João Dourado Santos; Alexandra Nunes; Verónica Mixão; et al. "Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus". Nature Medicine (2022): https://doi.org/10.1038/s41591-022-01907-y.
    10.1038/s41591-022-01907-y
  19. "Predictive and Therapeutic Implications of a Novel PLC¿1/SHP2-Driven Mechanism of Cetuximab Resistance in Metastatic Colorectal Cancer". Clinical Cancer Research 28 6 (2022): 1203-1216. http://dx.doi.org/10.1158/1078-0432.ccr-21-1992.
    10.1158/1078-0432.ccr-21-1992
  20. "The gene regulation knowledge commons: the action area of GREEKC". Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1865 1 (2022): 194768-194768. http://dx.doi.org/10.1016/j.bbagrm.2021.194768.
    10.1016/j.bbagrm.2021.194768
  21. Duarte, Raquel; Rebelo de Almeida, Cátia; Negrão, Magda; Fernandes, Afonso; Borralho, Paula; Sobral, Daniel; Gallego-Paez, Lina Marcela; et al. "Predictive value of a novel PLCgamma1-dependent mechanism of cetuximab resistance in RAS WT metastatic colorectal cancer". Nature Communications (2021):
    Submitted
  22. Sumnima Singh; Patricia Bastos-Amador; Jessica Ann Thompson; Mauro Truglio; Bahtiyar Yilmaz; Silvia Cardoso; Daniel Sobral; Miguel P Soares. "Glycan-based shaping of the microbiota during primate evolution". eLife (2021): https://doi.org/10.7554/eLife.67450.
    10.7554/eLife.67450
  23. Póvoa, Vanda; Rebelo de Almeida, Cátia; Maia-Gil, Mariana; Sobral, Daniel; Domingues, Micaela; Martinez-Lopez, Mayra; de Almeida Fuzeta, Miguel; et al. "Innate immune evasion revealed in a colorectal zebrafish xenograft model". Nature Communications 12 1 (2021): http://dx.doi.org/10.1038/s41467-021-21421-y.
    10.1038/s41467-021-21421-y
  24. Singh, Sumnima; Thompson, Jessica A.; Yilmaz, Bahtiyar; Li, Hai; Weis, Sebastian; Sobral, Daniel; Truglio, Mauro; et al. "Loss of a-gal during primate evolution enhanced antibody-effector function and resistance to bacterial sepsis". Cell Host & Microbe (2021): http://dx.doi.org/10.1016/j.chom.2020.12.017.
    10.1016/j.chom.2020.12.017
  25. André Dias; Anastasiia Lozovska; Filip J Wymeersch; Ana Nóvoa; Anahi Binagui-Casas; Daniel Sobral; Gabriel G Martins; Valerie Wilson; Moises Mallo. "A Tgfbr1/Snai1-dependent developmental module at the core of vertebrate axial elongation". eLife (2020): https://doi.org/10.7554/eLife.56615.
    10.7554/eLife.56615
  26. Robert Pjeta; Herbert Lindner; Leopold Kremser; Willi Salvenmoser; Daniel Sobral; Peter Ladurner; Romana Santos. "Integrative Transcriptome and Proteome Analysis of the Tube Foot and Adhesive Secretions of the Sea Urchin Paracentrotus lividus". International Journal of Molecular Sciences (2020): https://doi.org/10.3390/ijms21030946.
    10.3390/ijms21030946
  27. Arias-Baldrich, Cirenia; Silva, Marta Contreiras; Bergeretti, Filippo; Chaves, Inês; Miguel, Célia; Saibo, Nelson J M; Sobral, Daniel; Faria, Daniel; Barros, Pedro M. "CorkOakDB—The Cork Oak Genome Database Portal". Database 2020 (2020): http://dx.doi.org/10.1093/database/baaa114.
    10.1093/database/baaa114
  28. Lopes, Susana T; Sobral, Daniel; Costa, Bruno; Perdiguero, Pedro; Chaves, Inês; Costa, Augusta; Miguel, Célia M. "Phellem versus xylem: genome-wide transcriptomic analysis reveals novel regulators of cork formation in cork oak". Tree Physiology 40 2 (2019): 129-141. http://dx.doi.org/10.1093/treephys/tpz118.
    10.1093/treephys/tpz118
  29. Pjeta, Robert; Wunderer, Julia; Bertemes, Philip; Hofer, Teresa; Salvenmoser, Willi; Lengerer, Birgit; Coassin, Stefan; et al. "Temporary adhesion of the proseriate flatworm Minona ileanae". Philosophical Transactions of the Royal Society B: Biological Sciences 374 1784 (2019): 20190194. http://dx.doi.org/10.1098/rstb.2019.0194.
    10.1098/rstb.2019.0194
  30. Bonnet, M.; Sarmento, L.M.; Martins, A.C.; Sobral, D.; Silva, J.; Demengeot, J.. "iRAGu: A novel inducible and reversible mouse model for ubiquitous recombinase activity". Frontiers in Immunology 8 NOV (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85034019352&partnerID=MN8TOARS.
    10.3389/fimmu.2017.01525
  31. Passagem-Santos, D.; Bonnet, M.; Sobral, D.; Trancoso, I.; Silva, J.G.; Barreto, V.M.; Athanasiadis, A.; Demengeot, J.; Pereira-Leal, J.B.. "RAG Recombinase as a Selective Pressure for Genome Evolution". Genome biology and evolution 8 11 (2016): 3364-3376. http://www.scopus.com/inward/record.url?eid=2-s2.0-85030437788&partnerID=MN8TOARS.
  32. Zerbino, D.R.; Johnson, N.; Juetteman, T.; Sheppard, D.; Wilder, S.P.; Lavidas, I.; Nuhn, M.; et al. "Ensembl regulation resources". Database 2016 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84969940511&partnerID=MN8TOARS.
    10.1093/database/bav119
  33. Gilchrist, M.J.; Sobral, D.; Khoueiry, P.; Daian, F.; Laporte, B.; Patrushev, I.; Matsumoto, J.; et al. "A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis". Developmental Biology 404 2 (2015): 149-163. http://www.scopus.com/inward/record.url?eid=2-s2.0-84937736575&partnerID=MN8TOARS.
    10.1016/j.ydbio.2015.05.014
  34. Guilgur, L.G.; Prudêncio, P.; Sobral, D.; Liszekova, D.; Rosa, A.; Martinho, R.G.. "Requirement for highly efficient pre-mRNA splicing during Drosophila early embryonic development". eLife 2014 3 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-85006411606&partnerID=MN8TOARS.
    10.7554/eLife.02181.001
  35. Barroso-Batista, J.; Sousa, A.; Lourenço, M.; Bergman, M.-L.; Sobral, D.; Demengeot, J.; Xavier, K.B.; Gordo, I.. "The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps". PLoS Genetics 10 3 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84897389131&partnerID=MN8TOARS.
    10.1371/journal.pgen.1004182
  36. Flicek, Paul; Ahmed, Ikhlak; Amode, M. Ridwan; Barrell, Daniel; Beal, Kathryn; Brent, Simon; Carvalho-Silva, Denise; et al. "Ensembl 2013". Nucleic Acids Research 41 D1 (2012): D48-D55. http://dx.doi.org/10.1093/nar/gks1236.
    10.1093/nar/gks1236
  37. Dunham, I.; Kundaje, A.; Aldred, S.F.; Collins, P.J.; Davis, C.A.; Doyle, F.; Epstein, C.B.; et al. "An integrated encyclopedia of DNA elements in the human genome". Nature 489 7414 (2012): 57-74. http://www.scopus.com/inward/record.url?eid=2-s2.0-84865790047&partnerID=MN8TOARS.
    10.1038/nature11247
  38. Flicek, P.; Amode, M. R.; Barrell, D.; Beal, K.; Brent, S.; Carvalho-Silva, D.; Clapham, P.; et al. "Ensembl 2012". Nucleic Acids Research 40 D1 (2011): D84-D90. http://dx.doi.org/10.1093/nar/gkr991.
    10.1093/nar/gkr991
  39. Myers, R.M.; Stamatoyannopoulos, J.; Snyder, M.; Dunham, I.; Hardison, R.C.; Bernstein, B.E.; Gingeras, T.R.; et al. "A user's guide to the Encyclopedia of DNA elements (ENCODE)". PLoS Biology 9 4 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79955550445&partnerID=MN8TOARS.
    10.1371/journal.pbio.1001046
  40. Robin, F.B.; Dauga, D.; Tassy, O.; Sobral, D.; Daian, F.; Lemaire, P.. "Creating 3D digital replicas of ascidian embryos from stacks of confocal images". Cold Spring Harbor Protocols 6 10 (2011): 1251-1261. http://www.scopus.com/inward/record.url?eid=2-s2.0-80053593777&partnerID=MN8TOARS.
    10.1101/pdb.prot065862
  41. Flicek, P.; Amode, M.R.; Barrell, D.; Beal, K.; Brent, S.; Chen, Y.; Clapham, P.; et al. "Ensembl 2011". Nucleic Acids Research 39 SUPPL. 1 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-78651289449&partnerID=MN8TOARS.
    10.1093/nar/gkq1064
  42. Robin, F.B.; Dauga, D.; Tassy, O.; Sobral, D.; Daian, F.; Lemaire, P.. "Imaging of fixed Ciona embryos for creating 3D digital replicas". Cold Spring Harbor Protocols 6 10 (2011): 1247-1250. http://www.scopus.com/inward/record.url?eid=2-s2.0-80053616143&partnerID=MN8TOARS.
    10.1101/pdb.prot065854
  43. Robin, F.B.; Dauga, D.; Tassy, O.; Sobral, D.; Daian, F.; Lemaire, P.. "Time-lapse imaging of live Phallusia embryos for creating 3D digital replicas". Cold Spring Harbor Protocols 6 10 (2011): 1244-1246. http://www.scopus.com/inward/record.url?eid=2-s2.0-80053588205&partnerID=MN8TOARS.
    10.1101/pdb.prot065847
  44. Tassy, O.; Dauga, D.; Daian, F.; Sobral, D.; Robin, F.; Khoueiry, P.; Salgado, D.; et al. "The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program". Genome Research 20 10 (2010): 1459-1468. http://www.scopus.com/inward/record.url?eid=2-s2.0-78649268796&partnerID=MN8TOARS.
    10.1101/gr.108175.110
  45. Sobral, D.; Tassy, O.; Lemaire, P.. "Highly Divergent Gene Expression Programs Can Lead to Similar Chordate Larval Body Plans". Current Biology 19 23 (2009): 2014-2019. http://www.scopus.com/inward/record.url?eid=2-s2.0-71949122066&partnerID=MN8TOARS.
    10.1016/j.cub.2009.10.036
Online resource
  1. Miguel, Célia; Arias-Baldrich Cirenia; Bergeretti, Filippo; Chaves, Inês; Saibo, Nelson; Sobral, Daniel; Faria, Daniel; Barros, Pedro. CorkOakDB. 2020. http://corkoakdb.org.
Preprint
  1. Felipe Espigares; M. Victoria Alvarado; Diana Abad-Tortosa; Susana A. M. Varela; Daniel Sobral; Pedro Faísca; Tiago Paixão; Rui F. Oliveira. "Optimistic and pessimistic cognitive judgement bias modulates the stress response and cancer progression in zebrafish". 2024. https://doi.org/10.1101/2024.05.29.596384.
    10.1101/2024.05.29.596384
  2. Verónica Mixão; Miguel Pinto; Holger Brendebach; Daniel Sobral; João Dourado Santos; Nicolas Radomski; Anne Sophie Majgaard Uldall; et al. "Multi-country and intersectoral assessment of cluster congruence between different bioinformatics pipelines for genomics surveillance of foodborne bacterial pathogens". 2024. https://doi.org/10.1101/2024.07.24.24310933.
    10.1101/2024.07.24.24310933
  3. Isidro, Joana; Borges, Vítor; Pinto, Miguel; Ferreira, Rita; Sobral, Daniel; Nunes, Alexandra; Santos, João D.; et al. "First draft genome sequence of Monkeypox virus associated with the suspected multi-country outbreak, May 2022 (confirmed case in Portugal)". 2022. https://virological.org/t/first-draft-genome-sequence-of-monkeypox-virus-associated-with-the-suspected-multi-country-outbreak-may-2022-confirmed-case-in-portugal/799.

Other

Dataset
  1. Mixão, Verónica; Brendebach, Holger; Pinto, Miguel; Sobral, Daniel; Gomes, João Paulo; Deneke, Carlus; Tausch, Simon; Borges, Vítor. Genome assemblies and respective wg/cgMLST profiles of a diverse dataset comprising 3,076 Campylobacter jejuni isolates. https://zenodo.org/record/7230105#.Y-ftJi0qJQI.
    https://doi.org/10.5281/zenodo.7120166
  2. Mixão, Verónica; Brendebach, Holger; Pinto, Miguel; Sobral, Daniel; Gomes, João Paulo; Deneke, Carlus; Tausch, Simon; Borges, Vítor. Genome assemblies and respective wg/cgMLST profiles of a diverse dataset comprising 1,434 Salmonella enterica isolates. https://zenodo.org/record/7230091#.Y-fvrC0qJQI.
    https://doi.org/10.5281/zenodo.7119735
  3. Mixão, Verónica; Brendebach, Holger; Pinto, Miguel; Sobral, Daniel; Gomes, Joao Paulo; Deneke, Carlus; Tausch, Simon; Borges, Vítor. Genome assemblies and respective cgMLST profiles of a diverse dataset comprising 1,874 Listeria monocytogenes isolates. https://zenodo.org/record/7230003#.Y-fvCC0qJQI.
    https://doi.org/10.5281/zenodo.7116878
  4. Mixão, Verónica; Brendebach, Holger; Pinto, Miguel; Sobral, Daniel; Gomes, João Paulo; Deneke, Carlus; Tausch, Simon; Borges, Vítor. Genome assemblies and respective wg/cgMLST profiles of a diverse dataset comprising 1,999 Escherichia coli isolates. https://zenodo.org/record/7230102#.Y-fuTi0qJQI.
    https://doi.org/10.5281/zenodo.7120057
Software
  1. Mixão, Verónica; Pinto, Miguel; Sobral, Daniel; Di Pasquale, Adriano; Gomes, João Paulo; Borges, Vitor. "ReporTree". https://github.com/insapathogenomics/ReporTree. Instituto Nacional de Saúde Doutor Ricardo Jorge. Unix and Windows WSL. Available in Docker. 2023.
Activities

Supervision

Thesis Title
Role
Degree Subject (Type)
Institution / Organization
2022/09/01 - 2023/09/30 Implementation of a Data Analysis Pipeline for the Genetic Characterization of Viral Pathogens in the Context of Laboratory Surveillance of Viral Outbreaks
Supervisor
Biologia Computacional e Bioinformática (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2021/09/01 - 2023/05/30 Finding Biomarkers of Metastatic Potential in Colorectal Cancer
Supervisor
Mestrado em Bioinformática e Biologia Computacional (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021/01/01 - 2022/06/21 Assess the effect of angiogenesis inhibition in Intra-Tumor Heterogeneity
Co-supervisor
Análise e Engenharia de Big Data (Master)
Universidade Nova de Lisboa, Portugal
2019/09 - 2020/09 Supervision of MsC Thesis: Deciphering mechanisms underlying tumour heterogeneity using Multi-Omics approaches
Co-supervisor
Biotecnologia (Engenharia Bioquímica) (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Event organisation

Event name
Type of event (Role)
Institution / Organization
2020/07/06 - 2020/07/10 EMBO Practical Course on "Deciphering tumour heterogeneity and evolution by integration of multi-omics data". This course aims to provide practical insights for cancer researchers regarding the potentials and challenges of using high throughput sequencing to estimate intra-tumoral diversity in its multiple facets. This will include the detection of mutational patterns, selection pressures and driver mutations, as well as techniques for the determination of subclonal diversity and clonal evolution. (2020/07/06 - 2020/07/10)
Workshop (Co-organisor)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2019/06/03 - 2019/06/07 GTPB Workshop: Analysis of Differential Expression using RNAseq (2019/06/03 - 2019/06/07)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2019/02/07 - 2019/02/08 GTPB Workshop: Introduction to Bioinformatics (2019/02/04 - 2019/02/08)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2018/10/08 - 2018/10/12 GTPB Workshop: Analysis of Differential Expression using RNAseq (2018/10/08 - 2018/10/12)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2018/05/07 - 2018/05/11 Elixir Excelerate Workshop on Marine Metagenomics (2018/05/07 - 2018/05/11)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2018/05/03 - 2018/05/03 ONEIDA Workshop: Bioinformatics Applications (2018/05/02 - 2018/05/04)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2018/04/09 - 2018/04/13 GTPB Workshop: Analysis of Differential Expression using RNAseq (2018/04/09 - 2018/04/13)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2018/02/22 - 2018/02/23 GTPB Workshop: Introduction to Bioinformatics (2018/02/19 - 2018/02/23)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2017/12/04 - 2017/12/07 GTPB Workshop: Analysis of Differential Expression using RNAseq (2017/12/04 - 2017/12/07)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2017/11/09 - 2017/11/10 GTPB Workshop: Introduction to Bioinformatics (2017/11/06 - 2017/11/10)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2017/10/23 - 2017/10/27 Elixir Excelerate Workshop on Genome Assembly and Annotation (2017/10/23 - 2017/10/27)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2017/09/21 - 2017/09/22 COST Course Molecular Biology meets Bioadhesion Research (2017/09/18 - 2017/09/22)
Workshop (Co-organisor)
Universität Innsbruck, Austria
2017/05/11 - 2017/05/12 GTPB Workshop: Introduction to Bioinformatics (2017/05/08 - 2017/05/11)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2017/04/17 - 2017/04/20 GTPB Workshop: Analysis of Differential Expression using RNA-Seq (2017/04/17 - 2017/04/20)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal
2015/07/27 - 2015/07/31 EMBO Practical Course on Measuring intra-species diversity using high-throughput sequencing. This EMBO Practical Course aimed to show evolutionary biologists and population geneticists potentials and perils of using high throughput sequencing to estimate intra-specific genetic diversity, from individuals to populations. 20 selected participants had the opportunity to interact with experienced researchers that successfully applied the technology in a wide variety of high impact studies, and learn from their successes as well as from their failures. (2015/07/27 - 2015/07/31)
Workshop (Co-organisor)
Instituto Gulbenkian de Ciência, Portugal

Jury of academic degree

Topic
Role
Candidate name (Type of degree)
Institution / Organization
2023/12/15 Vias desreguladas em células dendríticas plasmocitóides envolvidas na doença pulmonar intersticial associada à esclerose sistémica.
(Thesis) Arguer
Raquel dos Anjos Dias Simões (Master)
Universidade de Aveiro, Portugal
2022/07/15 Identification of biotechnological potential on genomic nonfunctionalized orthologs elements
(Thesis) Main arguer
Pedro Miguel Agostinho Escudeiro (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2021/01/15 A transcriptomic approach to the metabolism of porphyrin-like pigments in a marine Polychaeta (Eulalia sp.)
(Thesis) Main arguer
Maria Leonor Veríssimo dos Santos (Master)
Universidade Nova de Lisboa, Portugal
2019/11/26 Jury of MsC Thesis: Optimizing Data Selection for Contact Prediction in Proteins
(Thesis) Main arguer
Guilherme José Gago Fial (Master)
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
2018/04/06 Jury of PhD Thesis: Analyses of the genomic variation to study cork oak evolution and adaptation: from past to future climatic changes
(Thesis) Arguer
Francisco Rente de Pina Martins (PhD)
Universidade de Lisboa Faculdade de Ciências, Portugal
2018/03/22 Jury of MsC Thesis: Bioinformatics analyses and approaches to RNA-Seq Data
(Thesis) Main arguer
Eric Serafim Ramos De Sousa (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016/10/24 Jury of MsC Thesis: Post-transcriptional circadian gene expression regulation in Trypanosoma brucei
(Thesis) Main arguer
Daniel Pinto de Oliveira Gonçalves Neves (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2016/07/21 Jury of MSc Thesis: Transcriptomic analysis of maritime pine response to infection with Bursaphelenchus Xylophilus, the causing agent of pine wilt disease
(Thesis) Main arguer
Daniel Filipe Branco Gaspar (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2013/12/02 Jury of MsC Thesis: Evaluating differential gene expression using RNA-sequencing data: a case study in host-pathogen interaction upon Listeria monocytogenes infection
(Thesis) Main arguer
Joana Rita Gonçalves da Cruz (Master)
Universidade de Lisboa Instituto Superior Técnico, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2018/03/28 - 2018/04/04 Investigação em Bioinformática Mestrado em Bioinformática e Biologia Computacional (Mestrado) Universidade de Lisboa Faculdade de Ciências, Portugal

Instituto Gulbenkian de Ciência, Portugal
2018/03/01 - 2018/03/02 Introduction to Bioinformatics, IGC PhD Program Introduction to Bioinformatics (Curso de doutoramento (conclusão de unidades curriculares)) Instituto Gulbenkian de Ciência, Portugal

Evaluation committee

Activity description
Role
Institution / Organization Funding entity
2017 - Current Member of Evaluation Committee for PhD Thesis of Catarina Isabel Ventura Pereira: Systems-Wide Identification of Cystic Fibrosis Disease Map
Evaluator
Universidade de Lisboa Faculdade de Ciências, Portugal

Mentoring / Tutoring

Topic Student name
2021/05/01 - Current Member of PhD Thesis Committee Ana Marta Fernandes Bica
2018/02 - 2018/09 Mentorship of MsC student in Bioinformatics. Cirenia Baldrich
2017 - 2018 Member of PhD Thesis Committee. Ana Paula Aguiar
2016/09 - 2017/02 Mentorship of MsC student in Bioinformatics. Pedro Perdiguero
2015/09/01 - 2016/09/30 Mentorship of MsC student in Bioinformatics. Samuel Dias Rosa Viana
2015/01 - 2015/06 Mentorship of MsC student in Bioinformatics. David M. F. Francisco
2014/05/01 - 2014/12/28 Mentorship of MsC student in Bioinformatics. Patrícia Alexandra Silva Santos
Distinctions

Award

2015 PLOS Genetics Research Prize 2015
Public Library of Science, United States