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Identificação

Identificação pessoal

Nome completo
Tomás Pires de Carvalho Gomes

Identificadores de autor

Ciência ID
3E11-841C-AE1B
ORCID iD
0000-0003-1333-0191

Endereços de correio eletrónico

  • tomas.gomes@gimm.pt (Profissional)

Domínios de atuação

  • Ciências Exatas - Ciências da Computação e da Informação - Bioinformática
  • Ciências Médicas e da Saúde - Medicina Básica - Imunologia

Idiomas

Idioma Conversação Leitura Escrita Compreensão Peer-review
Português (Idioma materno)
Inglês Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2) Utilizador proficiente (C2)
Alemão Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1) Utilizador elementar (A1)
Formação
Grau Classificação
2016/01/05 - 2020/10/24
Concluído
 Biological Sciences (Doctor of Philosophy)
Wellcome Sanger Institute, Reino Unido

University of Cambridge King's College, Reino Unido
"Tissue-specific adaptation of immune cells" (TESE/DISSERTAÇÃO)
2012/09/15 - 2014/12/15
Concluído
 Bioinformática e Biologia Computacional (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Genome-wide profiling of RNA polymerase II and associated co-transcriptional processes using advanced NET-seq data" (TESE/DISSERTAÇÃO)
 18
2009/09/15 - 2012/07/01
Concluído
 Biologia (Licenciatura)
Especialização em Biologia Molecular e Genética
Universidade de Lisboa Faculdade de Ciências, Portugal
 18
Percurso profissional

Ciência

Categoria Profissional
Instituição de acolhimento 		Empregador
2023/07/01 - Atual Pós-doutorado (Investigação) Gulbenkian Institute for Molecular Medicine, Portugal
Gulbenkian Institute for Molecular Medicine, Portugal
2020/04/15 - 2023/07/01 Pós-doutorado (Investigação) Eidgenössische Technische Hochschule Zürich Department of Biosystems Science and Engineering, Suiça
Eidgenössische Technische Hochschule Zürich Department of Biosystems Science and Engineering, Suiça
Produções

Publicações

Artigo em revista
  1. Lust K; Maynard A; Gomes T; Fleck JS; Camp JG; Tanaka EM; Treutlein B. "Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration.". Science (New York, N.Y.) (2022): http://europepmc.org/abstract/med/36048956.
    10.1101/2022.03.21.485045
  2. Cecilia Domínguez Conde; Chuan Xu; Lorna Jarvis; Daniel Rainbow; Steven B. Wells; Tomás Gomes; Sarah Howlett; et al. "Cross-tissue immune cell analysis reveals tissue-specific features in humans". Science 376 6594 (2022): http://dx.doi.org/10.1126/science.abl5197.
    10.1126/science.abl5197
  3. Kumar S; Fonseca VR; Ribeiro F; Basto AP; Água-Doce A; Monteiro M; Elessa D; et al. "Developmental bifurcation of human T follicular regulatory cells.". Science immunology (2021): http://europepmc.org/abstract/med/34049865.
    10.1126/sciimmunol.abd8411
  4. Elmentaite R; Ross ADB; Roberts K; James KR; Ortmann D; Gomes T; Nayak K; et al. "Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease.". Developmental cell (2020): http://europepmc.org/abstract/med/33290721.
    10.1016/j.devcel.2020.11.010
  5. Gomes T; Teichmann SA. "An antiviral response beyond immune cells.". Nature (2020): http://europepmc.org/abstract/med/32623443.
    10.1038/d41586-020-01916-2
  6. Chen YL; Gomes T; Hardman CS; Vieira Braga FA; Gutowska-Owsiak D; Salimi M; Gray N; et al. "Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation.". The Journal of experimental medicine (2020): http://europepmc.org/abstract/med/31845972.
    10.1084/jem.20190811
  7. Lubrano di Ricco M; Ronin E; Collares D; Divoux J; Grégoire S; Wajant H; Gomes T; et al. "Tumor necrosis factor receptor family costimulation increases regulatory T-cell activation and function via NF-¿B.". European journal of immunology (2020): http://europepmc.org/abstract/med/32012260.
    10.1002/eji.201948393
  8. James KR; Gomes T; Elmentaite R; Kumar N; Gulliver EL; King HW; Stares MD; et al. "Distinct microbial and immune niches of the human colon.". Nature immunology (2020): http://europepmc.org/abstract/med/32066951.
    10.1038/s41590-020-0602-z
  9. Aaron T. L. Lun; participants in the 1st Human Cell Atlas Jamboree; Samantha Riesenfeld; Tallulah Andrews; The Phuong Dao; Tomas Gomes; John Marioni. "EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data". Genome Biology 20 1 (2019): http://dx.doi.org/10.1186/s13059-019-1662-y.
    10.1186/s13059-019-1662-y
  10. Gomes T; Teichmann SA; Talavera-López C. "Immunology Driven by Large-Scale Single-Cell Sequencing.". Trends in immunology (2019): http://europepmc.org/abstract/med/31645299.
    10.1016/j.it.2019.09.004
  11. Felipe Augusto Vieira Braga; Gozde Kar; Marijn Berg; Orestes A. Carpaij; Krzysztof Polanski; Lukas Simon; Sharon Brouwer; et al. "A cellular census of human lungs identifies novel cell states in health and in asthma". Nature Medicine 25 7 (2019): 1153-1163. http://dx.doi.org/10.1038/s41591-019-0468-5.
    10.1038/s41591-019-0468-5
  12. Miragaia RJ; Gomes T; Chomka A; Jardine L; Riedel A; Hegazy AN; Whibley N; et al. "Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation.". Immunity (2019): http://europepmc.org/abstract/med/30737144.
    10.1101/217489
  13. Henriksson J; Chen X; Gomes T; Ullah U; Meyer KB; Miragaia R; Duddy G; et al. "Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation.". Cell (2019): http://europepmc.org/abstract/med/30639098.
    10.1101/196022
  14. Tzachi Hagai; Xi Chen; Ricardo J. Miragaia; Raghd Rostom; Tomás Gomes; Natalia Kunowska; Johan Henriksson; et al. "Gene expression variability across cells and species shapes innate immunity". Nature 563 7730 (2018): 197-202. http://dx.doi.org/10.1038/s41586-018-0657-2.
    10.1038/s41586-018-0657-2
  15. Pramanik J; Chen X; Kar G; Henriksson J; Gomes T; Park JE; Natarajan K; et al. "Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation.". Genome medicine (2018): http://europepmc.org/abstract/med/30355343.
    10.1186/s13073-018-0589-3
  16. Nojima T; Rebelo K; Gomes T; Grosso AR; Proudfoot NJ; Carmo-Fonseca M. "RNA Polymerase II Phosphorylated on CTD Serine 5 Interacts with the Spliceosome during Co-transcriptional Splicing.". Molecular cell (2018): http://europepmc.org/abstract/med/30340024.
    10.1016/j.molcel.2018.09.004
  17. Kunz DJ; Gomes T; James KR. "Immune Cell Dynamics Unfolded by Single-Cell Technologies.". Frontiers in immunology (2018): http://europepmc.org/abstract/med/29997618.
    10.3389/fimmu.2018.01435
  18. Miragaia RJ; Zhang X; Gomes T; Svensson V; Ilicic T; Henriksson J; Kar G; Lönnberg T. "Single-cell RNA-sequencing resolves self-antigen expression during mTEC development.". Scientific reports (2018): http://europepmc.org/abstract/med/29330484.
    10.1038/s41598-017-19100-4
  19. "Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs.". Molecular cell (2017): http://europepmc.org/abstract/med/28017589.
    10.1016/j.molcel.2016.11.029
  20. "Mammalian NET-seq analysis defines nascent RNA profiles and associated RNA processing genome-wide.". Nature protocols (2016): http://europepmc.org/abstract/med/26844429.
    10.1038/nprot.2016.012
  21. "Mammalian NET-Seq Reveals Genome-wide Nascent Transcription Coupled to RNA Processing.". Cell (2015): http://europepmc.org/abstract/med/25910207.
    10.1016/j.cell.2015.03.027
Pré-impressão
  1. Brazovskaja A; Gomes T; Körner C; He Z; Schaffer T; Eckel JC; Hänsel R; et al. "Cell atlas of the regenerating human liver after portal vein embolization". 2021. http://europepmc.org/abstract/PPR/PPR351725.
    10.1101/2021.06.03.444016