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Identification

Personal identification

Full name
Tomás Pires de Carvalho Gomes

Author identifiers

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

Email addresses

  • tomas.gomes@gimm.pt (Professional)

Knowledge fields

  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Medical and Health Sciences - Basic Medicine - Immunology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
German Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2016/01/05 - 2020/10/24
Concluded
 Biological Sciences (Doctor of Philosophy)
Wellcome Sanger Institute, United Kingdom

University of Cambridge King's College, United Kingdom
"Tissue-specific adaptation of immune cells" (THESIS/DISSERTATION)
2012/09/15 - 2014/12/15
Concluded
 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" (THESIS/DISSERTATION)
 18
2009/09/15 - 2012/07/01
Concluded
 Biologia (Licenciatura)
Major in Biologia Molecular e Genética
Universidade de Lisboa Faculdade de Ciências, Portugal
 18
Affiliation

Science

Category
Host institution 		Employer
2023/07/01 - Current Postdoc (Research) Gulbenkian Institute for Molecular Medicine, Portugal
Gulbenkian Institute for Molecular Medicine, Portugal
2020/04/15 - 2023/07/01 Postdoc (Research) Eidgenössische Technische Hochschule Zürich Department of Biosystems Science and Engineering, Switzerland
Eidgenössische Technische Hochschule Zürich Department of Biosystems Science and Engineering, Switzerland
Outputs

Publications

Journal article
  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
Preprint
  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