Publications
2023
scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection
Zhang Z, Sun H, Chen X, Mariappan R, Chen X, Jain M, Efremova M, Rajan V, Teichmann SA, Zhang X.
Nature Communications, 14
2021
MultiMAP: Dimensionality Reduction and Integration of Multimodal Data
Jain MS#, Conde CD, Polanski K, Chen X, Park J, Botting RA, Stephenson E, Haniffa M, Lamacraft A, Efremova M#, Teichmann SA#.
Genome Biology, 22
Inference of Ligand-Receptor Pairs from Single-Cell Transcriptomics Data
Efremova M#, Vento-Tormo R#.
Blood and immune development in human fetal bone marrow and Down syndrom
Webb S, Goh I, Quiroga Londoño M, Reynolds G, Mather M, Olabi B, Stephenson E, Botting R, Horsfall D, Engelbert J, Maunder D, Mende N, Murnane C, Dann E, McGrath J, King H, Kucinski I, Queen R, Carey C, Shrubsole C, Poyner E, Acres M, Jones C, Ness T, Coulthard R, Elliott N, O’Byrne S, Haltalli M, Lawrence J, Lisgo S, Balogh P, Meyer K, Prigmore E, Ambridge K, Jain M, Efremova M, Pickard K, Creasey T, Bacardit J, Henderson D, Coxhead J, Filby A, Hussain R, Dixon D, McDonald D, Popescu D, Kowalczyk M, Li B, Ashenberg O, Tabaka M, Dionne D, Tickle T, Slyper M, Rozenblatt-Rosen O, Regev A, Behjati S, Laurenti E, Wilson N, Roy A, Göttgens B, Roberts I, Teichmann S, Haniffa M.
Nature 598
Developmental cell programs are co-opted in inflammatory skin disease
Reynolds G*, Vegh P*, Fletcher J, Poyner EFM, Stephenson E, Goh I, Botting RA, Huang N, Olabi B, Dubois A, Dixon D, Green K, Maunder D, Engelbert J, Efremova M, Polański K, Jardine L, Jones C, Ness T, Horsfall D, McGrath J, Carey C, Popescu DM, Webb S, Wang X, Sayer B, Park J, Negri VA, Belokhvostova D, Lynch MD, McDonald D, Filby A, Hagai T, Meyer KB, Husain A, Coxhead J, 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#.
Science, 371
Skin dendritic cells in melanoma are key for successful checkpoint blockade therapy
Prokopi A, Tripp C, Tummers B, Hornsteiner F, Spoeck S, Crawford JC, Clements DR, Efremova M, Hutter K, Bellmann L, Cappellano G, Cadilha LB, Kobold S, Boon L, Ortner D, Trajanoski Z, Chen S, Gruijl TD, Idoyaga J, Green DR, Stoitzner P.
Journal for ImmunoTherapy of Cancer 9
2020
Efremova M, Vento-Tormo M, Teichmann SA, Vento-Tormo R.
Nature Protocols 15, 1484-1506
Immunology in the era of single-cell technologies
Efremova M*, Vento-Tormo R*, Park JE*, Teichmann SA, James KR.
Annual Review of Immunology 38, 727-757
Single-cell RNA sequencing reveals a dynamic stromal niche that supports tumor growth
Davidson S*, Efremova M*, Riedel A, Mahata B, Pramanik J, Huuhtanen J, Kar G, Vento-Tormo R, Hagai T, Chen X, Haniffa M, Shields JD#, Teichmann SA#.
Cell Reports 31, 107628
Computational methods for single-cell omics across modalities
Efremova M, Teichmann SA.
Nature Methods 17, 14-17
Mosquito cellular immunity at single-cell resolution
Raddi G*, Barletta ABF*, Efremova M, Ramirez JL, Cantera R, Teichmann SA, Barillas-Mury C, Billker O.
Science 369, 1128-1132
Penkava F, Velasco-Herrera MDC, Young MD, Yager N, Nwosu LN, Pratt AG, Lara AL, Guzzo G, Maroof A, Mamanova L, Cole S, Efremova M, Simone D, Filler A, Brown CC, Croxford AL, Issacs JD, Teichmann SA, Bowness P, Behjati S*, Al-Mossawi MS*.
Nature Communications, 11, 4767
2019
Resolving the fibrotic niche of human liver cirrhosis at single cell level
Ramachandran P, Dobie R, Wilson-Kanamori JR, Dora E, Henderson BEP, Luu NT, Portman J, Matchett KP, Brice M, Marwick JA, Taylor RS, Efremova M, Vento-Tormo R, Carragher NO, Kendall TJ, Fallowfield JA, Harrison EM, Mole DJ, Wigmore SJ, Newsome PN, Weston CJ, Iredale JP, Tacke F, Pollard JW, Ponting CP, Marioni JC, Teichmann SA, Henderson NC.
Nature, 575, 512–518
Spatiotemporal immune zonation of the human kidney
Stewart BJ*, Ferdinand JP*, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz R, Frazer GL, Staniforth JUL, Vieira Braga FA, Botting RA5, Popescu DM, Vento-Tormo R, Stephenson E, Cagan A, Farndon SJ, Polanski K, Efremova M, Green K, Velasco-Herrera MDC, Guzzo C, Collord G, Mamanova L, Aho T, Armitage JN, Riddick ACP, Mushtaq I, Farrell S, Rampling D, Nicholson J, Filby A, Burge J, Lisgo S, Lindsay S, Bajenoff M, Warren AY, Stewart GD, Sebire N, Coleman N, Haniffa M#, Teichmann SA#, Behjati S#, Clatworthy MR#.
Science 365, 1461-1466
Decoding human fetal liver haematopoiesis
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 J, Vento-Tormo T, Miao M, Rowell R, McDonald D, Fletcher J, Dixon D, Poyner E, Reynolds G, Mather M, Moldovan C, Mamanova L, Greig F, Young M, Meyer K, Lisgo S, Bacardit J, Fuller A, Millar B, Innes B, Lindsay S, Stubbington MJT, Kowalczyk MS, Li B, Ashenbrg O, Tabaka M, Dionne D, Tickle TL, Slyper M, Rozenblatt-Rosen O, Filby A, Carey P, Villani AC, Roy A, Regev A, Chedotal A, Roberts I, Göttgens B, Laurenti E#, Behjati S#, Teichmann SA#, Haniffa M#.
Nature, 574, 365-371
A cellular census of human lungs identifies novel cell states in health and in asthma
Vieira Braga FA*, Kar G*, Berg M*, Carpaij OA*, Polanski K*, Simon L., Brouwer S, Gomes T, Hesse L, Jiang J, Fasouli ES, Efremova M, Vento-Tormo R, Talavera-López C, Jonker MR, Affleck K, Palit S, Strzelecka P, Firth H.V, Mahbubani KTA, Cvejic A, Meyer K, Saeb-Parsy K, Luinge M, Brandsma C.-A, Timens W, Angelidis I, Strunz M, Koppelman GH, van Oosterhout AJ, Schiller HB, Theis FJ, van den Berge M, Nawijn MC#, Teichmann SA#.
Nature Medicine 25, 1153-1163
2018
Single-cell reconstruction of the early maternal-fetal interface in humans
Vento-Tormo R*, Efremova M*, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park JE, Stephenson E, Polański K, Goncalves A, Gardner L, Holmqvist S, Henriksson J, Zou A, Sharkey AM, Millar B, Innes B, Wood L, Wilbrey-Clark A, Payne RP, Ivarsson MA, Lisgo S, Filby A, Rowitch DH, Bulmer JN, Wright GJ, Stubbington MJT, Haniffa M#, Moffett A#, Teichmann SA#.
Nature 563, 347-353
Klepsch V, Hermann-Kleiter N, Do-Dinh P, Jakic B, Offermann A, Efremova M, Sopper S, Rieder D, Krogsdam A, Gamerith G, Perner S, Tzankov A, Trajanoski Z, Wolf D, Baier G.
Nature Communications 9, 1538
Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolutio
Efremova M, Rieder D, Klepsch V, Charoentong P, Finotello F, Hackl H, Hermann-Kleiter N, Löwer M, Baier G, Krogsdam AM#, Trajanoski Z#.
Nature Communications 9, 32
2017
Neoantigens generated by individual mutations and their role in cancer immunity and immunotherapy
Efremova M, Finotello F, Rieder D, Trajanoski Z.
Frontiers in Immunology 8, 1679
Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, Hackl H, Trajanoski Z.
Cell Reports 18, 248-262
Older
A survey of tools for variant analysis of next-generation genome sequencing data
Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR, Zschocke J, Trajanoski Z.
Briefings in Bioinformatics 15, 256-278
Mathematical models for translational and clinical oncology
Gallasch R, Efremova M, Charoentong P, Hackl H, Trajanoski Z.
J Clin Bioinformatics 3, 23
Bioinformatics for Cancer Immunology and Immunotherapy
Charoentong P, Angelova M, Efremova M, Gallasch R, Hackl H, Galon J, Trajanoski Z.
Cancer Immunology, Immunotherapy 61, 1885-903 (2012)