Publications

2024

Marečková M, Garcia-Alonso L, Moullet M, Lorenzi V, Petryszak R, Sancho-Serra C, Oszlanczi A, Icoresi Mazzeo C, Wong FCK, Kelava I, Hoffman S, Krassowski M, Garbutt K, Gaitskell K, Yancheva S, Woon EV, Male V, Granne I, Hellner K, Mahbubani KT, Saeb-Parsy K, Lotfollahi M, Prigmore E, Southcombe J, Dragovic RA, Becker CM, Zondervan KT, Vento-Tormo R. An integrated single-cell reference atlas of the human endometrium. Nat Genet. 2024 Aug 28. doi: 10.1038/s41588-024-01873-w.

Hoo R, Ruiz-Morales ER, Kelava I, Rawat M, Mazzeo CI, Tuck E, Sancho-Serra C, Chelaghma S, Predeus AV, Murray S, Fernandez-Antoran D, Waller RF, Álvarez-Errico D, Lee MCS, Vento-Tormo R. Acute response to pathogens in the early human placenta at single-cell resolution. Cell Syst. 2024 May 15;15(5):425-444.e9. doi: 10.1016/j.cels.2024.04.002.

Gilbertson RJ, Behjati S, Böttcher AL, Bronner ME, Burridge M, Clausing H, Clifford H, Danaher T, Donovan LK, Drost J, Eggermont AMM, Emerson C, Flores MG, Hamerlik P, Jabado N, Jones A, Kaessmann H, Kleinman CL, Kool M, Kutscher LM, Lindberg G, Linnane E, Marioni JC, Maris JM, Monje M, Macaskill A, Niederer S, Northcott PA, Peeters E, Plieger-van Solkema W, Preußner L, Rios AC, Rippe K, Sandford P, Sgourakis NG, Shlien A, Smith P, Straathof K, Sullivan PJ, Suvà ML, Taylor MD, Thompson E, Vento-Tormo R, Wainwright BJ, Wechsler-Reya RJ, Westermann F, Winslade S, Al-Lazikani B, Pfister SM. The Virtual Child. Cancer Discov. 2024 Apr 4;14(4):663-668.

Li Q, Sharkey A, Sheridan M, Magistrati E, Arutyunyan A, Vento-Tormo R*, Turco MY*, Moffett A*. Human uterine natural killer cells regulate differentiation of extravillous trophoblast early in pregnancy. Cell Stem Cell. 2024 Feb 1;31(2):181-195.e9. *co-corresponding

Barmada A, …, Ballestar E*, Vento-Tormo R*, Rodríguez-Ubreva J*. Single-cell multi-omics analysis of COVID-19 patients with pre-existing autoimmune diseases shows aberrant immune responses to infection. Eur J Immunol. 2024 Jan;54(1):e2350633. *co-corresponding

2023

Vento-Tormo R. Nat Rev Genet. 2023 Aug;24(8):492. Single-cell omics meets organoid cultures.

Theis FJ, Dar D, Vento-Tormo R, Vicković S, Wang L, Kagohara LT, Rendeiro AF, Joyce JA. Cell Syst. 2023 Jun 21;14(6):423-427.  What do you most hope spatial molecular profiling will help us understand? Part 1.

Vento-Tormo R, Vilarrasa-Blasi R. Nature. 2023 Jul;619(7970):467-468.Cell-level reference maps for the human body take shape.

Goh I, Botting RA, Rose A, Webb S, …, Vento-Tormo R, Chédotal A, Bayraktar O, Roberts I, Jardine L, Göttgens B, Teichmann SA, Haniffa M. Science. 2023 Aug 18;381(6659):eadd7564. doi: 10.1126/science.add7564. Yolk sac cell atlas reveals multiorgan functions during human early development.

Irie N, Lee SM, Lorenzi V, Xu H, Chen J, Inoue M, Kobayashi T, Sancho-Serra C, Drousioti E, Dietmann S, Vento-Tormo R, Song CX, Surani MA. Nat Cell Biol. 2023 Sep 14. DMRT1 regulates human germline commitment.

Suo C, Polanski K, Dann E, Lindeboom RGH, Vilarrasa-Blasi R, Vento-Tormo R, Haniffa M, Meyer KB, Dratva LM, Tuong ZK, Clatworthy MR, Teichmann SA. Nat Biotechnol. 2023 Apr 13. Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins.

Arutyunyan A, Roberts K, Troulé K, Wong FCK, Sheridan MA, …, Bayraktar OA, Moffett A, Stegle O, Turco MY, Vento-Tormo R. Nature. 2023 Apr;616(7955):143-151. Spatial multiomics map of trophoblast development in early pregnancy.

García-Alonso L, Zondervan KT, Vento-Tormo R. Nat Rev Endocrinol. 2023 May;19(5):256-257. A novel resource to study endometriosis at the single-cell level.

Vento-Tormo R. Science. 2023 Feb 17;379(6633):655. Decoding foreign antigen tolerance.

2022

Godoy-Tena G, Barmada A, …, Vento-Tormo R, Ballestar E.Genome Med. 2022. Genome Med. 2022 Nov 29;14(1):134. Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines.

Lorenzi V, Vento-Tormo R*, Garcia-Alonso L. Clin Transl Med. 2022 Dec;12(12):e1123. Human gonadal development, cell by cell. * corresponding

Shilts J, Severin Y, Galaway F, Müller-Sienerth N, Chong ZS, Pritchard S, Teichmann S, Vento-Tormo R, Snijder B, Wright GJ. Nature. 2022 Aug;608(7922):397-404. A physical wiring diagram for the human immune system.

Garcia-Alonso L, Lorenzi V, Mazzeo CI, …, Vento-Tormo R. Nature. 2022 Jul;607(7919):540-547. Single-cell roadmap of human gonadal development.

Williams CG, Lee HJ, Asatsuma T, Vento-Tormo R, Haque A. Genome Med. 2022 Jun 27;14(1):68. An introduction to spatial transcriptomics for biomedical research.

Alsinet C, Primo MN, Lorenzi V, …, Gaffney DJ, Alvarez-Errico D, Vento-Tormo R. Nat Commun. 2022 May 24;13(1):2885. Robust temporal map of human in vitro myelopoiesis using single cell genomics.

Marečková M, Massalha H, Lorenzi V, Vento-Tormo R. Annu Rev Genomics Hum Genet. 2022 May 13. Mapping Human Reproduction with Single-Cell Genomics.

Lorenzi V, Vento-Tormo R. Taylor and Francis group https://doi.org/10.1201/9781003024941 Chapter 2: Genetics at the Cell Level. Handbook of Genetic Diagnostic Technologies in Reproductive Medicine.

Rodríguez-Ubreva J, Arutyunyan A, …, Vento-Tormo R*, Ballestar E*. Nat Commun. 2022 Apr 1;13(1):1779. Single-cell Atlas of common variable immunodeficiency shows germinal center-associated epigenetic dysregulation in B-cell responses. * co-corresponding

McGlacken-Byrne SM, Del Valle I, Quesne Stabej PL, Bellutti L, Garcia-Alonso L, …, Vento-Tormo R, Lagos CF, Livera G, Conway GS, Achermann JC. JCI Insight. 2022 Mar 8;7(5):e154671. Pathogenic variants in the human m6A reader YTHDC2 are associated with primary ovarian insufficiency.

Kleshchevnikov V, Shmatko A, …, Arutyunyan A, Vento-Tormo R, Gerstung M, James L, Stegle O, Bayraktar OA. Nat Biotechnol. 2022 May;40(5):661-671. Cell2location maps fine-grained cell types in spatial transcriptomics.

2021

Garcia-Alonso L, Handfield LF, Roberts K, Nikolakopoulou K, …., Bayraktar OA, Teichmann SA, Turco MY, Vento-Tormo R. Nat Genet. 2021 Dec;53(12):1698-1711. doi: 10.1038/s41588-021-00972-2. Epub 2021 Dec 2. Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro.

Ordovás-Montañés J, Gerlach C, Moraes-Vieira P, Vento-Tormo R, Zhang C, Jurado KA. Navigating COVID-19: Starting a lab during the pandemic. Immunity. 2021 Oct 12;54(10):2169-2171. doi: 10.1016/j.immuni.2021.09.020.

Haniffa M, Taylor D, Linnarsson S, …, Vento-Tormo R, Webb S; A roadmap for the Human Developmental Cell Atlas. Nature. 2021 Sep;597(7875):196-205. doi: 10.1038/s41586-021-03620-1.

Molè MA, Coorens THH, Shahbazi MN, Weberling A, Weatherbee BAT, …, Behjati S*, Vento-Tormo R*, Zernicka-Goetz M*.  A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre Nat Commun. 2021 Jun 17;12(1):3679. doi: 10.1038/s41467-021-23758-w. *co-corresponding

Coorens THH, Oliver TRW, Sanghvi R, Sovio U, Cook E, Vento-Tormo R, […] Inherent mosaicism and extensive mutation of human placentas. Nature. 2021 Mar 10. doi: 10.1038/s41586-021-03345-1.

Efremova M, Vento-Tormo R. Inference of Ligand-Receptor Pairs from Single-Cell Transcriptomics Data. Methods Mol Biol. 2021 Feb 25. doi: 10.1007/7651_2020_343.

2020

Chan Zuckerberg Initiative Single-Cell COVID-19 Consortia, Ballestar E, Farber DL, Glover S, Horwitz B, Meyer K, Nikolić M, Ordovas-Montanes J, Sims P, Shalek A, Vandamme N, Vandekerckhove L, Vento-Tormo R, Villani A-C. Single cell profiling of COVID-19 patients: an international data resource from multiple tissues. bioRxiv 2020. https://doi.org/10.1101/2020.11.20.20227355

Reynolds G, Vegh P, […], Vento-Tormo R, Behjati S, Lisgo S, Villani AC, Bacardit J, Jones PH, O’Toole EA, Ogg GS, Rajan N, Reynolds NJ, Teichmann SA, Watt FM, Haniffa M. Developmental cell programs are co-opted in inflammatory skin disease. Science. 2021 Jan 22;371(6527):eaba6500. doi: 10.1126/science.aba6500.

Hoo R, Nakimuli A, Vento-Tormo R. Innate immune mechanisms to protect against infection at the human maternal-fetal interface. Front Immunol. 2020 Sep 10;11:2070.

Davidson S, Efremova M, […], Vento-Tormo R, Hagai T, Chen X, Haniffa MA, Shields JD, Teichmann SA. Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth. Cell Rep. 2020 May 19;31(7):107628.

Efremova M, Vento-Tormo M, Teichmann SA, Vento-Tormo R (2020) CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nature Protocols. Apr;15(4):1484-1506.

Park JE, […] Vento-Tormo R, Bayraktar OA, Barker RA, Meyer KB, Saeys Y, Bonfanti P, Behjati S, Clatworthy MR, Taghon T, Haniffa M, Teichmann SA. A cell atlas of human thymic development defines T cell repertoire formation. Science. 2020 Feb 21;367(6480). pii: eaay3224.

Efremova M*, Vento-Tormo R*, Park J.P*, Teichmann SA,and James K. Immunology in the era of single-cell technologies. Annu Rev Immunol. 2020 Feb 19.

2019

Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL, Staniforth JUL, Vieira Braga FA, Botting RA, Popescu DM, Vento-Tormo R, […] (2019) Spatiotemporal immune zonation of the human kidney. Science. 365(6460):1461-1466. 

Popescu DM, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K, Goh I, Efremova M, Acres M, Maunder D, Vegh P, Gitton Y, Park JE, Vento-Tormo R, […] (2019) Decoding human fetal liver haematopoiesis. Nature. 574(7778):365-371. 

Ramachandran P, Dobie R, Wilson-Kanamori JR, Dora EF, Henderson BEP, Luu NT, Portman JR, Matchett KP, Brice M, Marwick JA, Taylor RS, Efremova M, Vento-Tormo R, […] (2019) Resolving the fibrotic niche of human liver cirrhosis at single-cell level. Nature. 575(7783):512-518. 

Vieira Braga FA, Kar G, Berg M, Carpaij OA, Polanski K, Simon LM, Brouwer S, Gomes T, Hesse L, Jiang J, Fasouli ES, Efremova M, Vento-Tormo R, […] (2019) A cellular census of human lungs identifies novel cell states in health and in asthma. Nature Medicine. 25(7):1153-1163.