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Publications

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#.             

bioRxivdoi: https://doi.org/10.1101/2021.02.16.431421

 

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

CellPhoneDB: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes

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

Single-cell sequencing reveals a clonal expansion of pro-inflammatory synovial CD8 T cells expressing tissue homing receptors in psoriatic arthritis

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

 

Nuclear receptor NR2F6 inhibition potentiates responses to PD-L1/PD-1 cancer immune checkpoint blockade

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

Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade

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)