Publications: DR Mirjana Efremova

( 2026 ) . O11 Spatial transcriptomic insights into the early pathogenesis of steatocystoma multiplex . British Journal of Dermatology . vol. 194 ,

de Brito M, Ogden S, Barragan-Vazquez I, Blaydon D, Philpott M, Efremova M, O’Toole E ( 2025 ) . 251 Understanding the early origins of Steatocystoma Multiplex . Journal of Investigative Dermatology . vol. 145 ,

Sánchez-Lanzas R, Jiménez-Pompa A, Smith E, Sumaria N, Kalampalika F, Barclay J, Pennington D, Efremova M et al. ( 2025 ) . 3208 – CELL-TO-CELL INTERACTION RECORDING AND IDENTIFICATION OF CELLULAR INTERACTOMES THAT SUPPORT T CELLS IN THE THYMUS . Experimental Hematology vol. 151 ,

Efremova M ( 2025 ) . Various cell types in tissues cooperate in networks that are disrupted in disease . Nature vol. 643 , ( 8071 ) 344 - 346 .

Ogden S, Metic N, Leylek O, Smith EA, Berner AM, Baker A-M, Uddin I, Buzzetti M et al. ( 2025 ) . Phenotypic heterogeneity and plasticity in colorectal cancer metastasis . Cell Genomics vol. 5 , ( 7 )

Vyas V, Sandhar B, Keane JM, Wood EG, Blythe H, Jones A, Shahaj E, Fanti S et al. ( 2024 ) . Tissue-resident memory T cells in epicardial adipose tissue comprise transcriptionally distinct subsets that are modulated in atrial fibrillation . Nature Cardiovascular Research vol. 3 , ( 9 ) 1067 - 1082 .

Efremova M ( 2023 ) . The role of colorectal cancer plasticity in metastasis and treatment: an interview with Mirjana Efremova . Colorectal Cancer vol. 12 , ( 4 )

Zhang Z, Sun H, Mariappan R, Chen X, Chen X, Jain MS, Efremova M, Teichmann SA et al. ( 2023 ) . scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection . Nature Communications vol. 14 , ( 1 )

Ganuza M, Sanchez-Lanzas R, Jimenez-Pompa A, Efremova M ( 2023 ) . 1009 – GENETIC IDENTIFICATION OF THE CELLULAR INTERACTOME THAT SUPPORTS T-CELL DEVELOPMENT IN THE THYMUS . Experimental Hematology vol. 124 ,

Ganuza M, Sanchez-Lanzas R, Jimenez-Pompa A, Efremova M ( 2023 ) . GENETIC IDENTIFICATION OF THE CELLULAR INTERACTOME THAT SUPPORTS T-CELL DEVELOPMENT IN THE THYMUS . EXPERIMENTAL HEMATOLOGY . vol. 124 , S24 - S24 .

Perrett M, Pickard L, Kumar E, Palladino G, Khan F, Edmondson C, Knight C, Poynton E et al. ( 2022 ) . Longitudinal Single Cell Analyses Reveal the Co-Evolutionary Dynamics of the Tumor and Microenvironment Accompanying Follicular Lymphoma Transformation . Blood . vol. 140 , 748 - 749 .

Caetano AJ, Caetano A, Sharpe P, Volponi AA, Yianni V, Bush M, McKay LK, Wallet S et al. ( 2022 ) . A Roadmap for the Human Oral and Craniofacial Cell Atlas . Journal of Dental Research vol. 101 , ( 11 ) 1274 - 1288 .

Fletcher J, Vegh P, Reynolds G, Botting RA, Huang N, Dixon D, Green K, Stephenson E et al. ( 2022 ) . Spatially resolved poised immunity in human skin . BRITISH JOURNAL OF DERMATOLOGY . Conference: BRITISH JOURNAL OF DERMATOLOGY vol. 187 , E7 - E8 .

Jain MS, Polanski K, Conde CD, Chen X, Park J, Mamanova L, Knights A, Botting RA et al. ( 2021 ) . MultiMAP: dimensionality reduction and integration of multimodal data . Genome Biology vol. 22 , ( 1 )

Jardine L, Webb S, Goh I, Quiroga Londoño M, Reynolds G, Mather M, Olabi B, Stephenson E et al. ( 2021 ) . Blood and immune development in human fetal bone marrow and Down syndrome . Nature vol. 598 , ( 7880 ) 327 - 331 .

Haim-Vilmovsky L, Henriksson J, Walker JA, Miao Z, Natan E, Kar G, Clare S, Barlow JL et al. ( 2021 ) . Mapping Rora expression in resting and activated CD4+ T cells . PLOS ONE vol. 16 , ( 5 )

Reynolds G, Vegh P, Fletcher J, Poyner EFM, Stephenson E, Goh I, Botting RA, Huang N et al. ( 2021 ) . Developmental cell programs are co-opted in inflammatory skin disease . Science vol. 371 , ( 6527 )

Prokopi A, Tripp CH, Tummers B, Hornsteiner F, Spoeck S, Crawford JC, Clements DR, Efremova M et al. ( 2021 ) . Skin dendritic cells in melanoma are key for successful checkpoint blockade therapy . Journal for ImmunoTherapy of Cancer vol. 9 , ( 1 )

Efremova M, Vento-Tormo R ( 2021 ) . Inference of Ligand–Receptor Pairs from Single-Cell Transcriptomics Data . Methods in Molecular Biology vol. 2346 , 1 - 10 .

Prokopi N, Tripp C, Tummers B, Crawford J, Efremova M, Hutter K, Bellmann L, Cappellano G et al. ( 2020 ) . P03.31 Skin dendritic cells in melanoma are key for successful checkpoint blockade therapy . a35.2 - a3a36 .

Penkava F, Velasco-Herrera MDC, Young MD, Yager N, Nwosu LN, Pratt AG, Lara AL, Guzzo C et al. ( 2020 ) . Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis . Nature Communications vol. 11 , ( 1 )

Raddi G, Barletta ABF, Efremova M, Ramirez JL, Cantera R, Teichmann SA, Barillas-Mury C, Billker O ( 2020 ) . Mosquito cellular immunity at single-cell resolution . Science vol. 369 , ( 6507 ) 1128 - 1132 .

Davidson S, Efremova M, Riedel A, Mahata B, Pramanik J, Huuhtanen J, Kar G, Vento-Tormo R et al. ( 2020 ) . Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth . Cell Reports vol. 31 , ( 7 )

Efremova M, Vento-Tormo R, Park JE, Teichmann SA, James KR ( 2020 ) . Immunology in the Era of Single-Cell Technologies . Annual Review of Immunology vol. 38 , 727 - 757 .

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 vol. 15 , ( 4 ) 1484 - 1506 .

Efremova M, Teichmann SA ( 2020 ) . Computational methods for single-cell omics across modalities . Nature Methods vol. 17 , ( 1 ) 14 - 17 .

Popescu D-M, Botting RA, Stephenson E, Green K, Webb S, Jardine L, Calderbank EF, Polanski K et al. ( 2019 ) . Decoding human fetal liver haematopoiesis . Nature vol. 574 , ( 7778 ) 365 - 371 .

Ramachandran P, Dobie R, Wilson-Kanamori JR, Dora EF, Henderson BEP, Luu NT, Portman JR, Matchett KP et al. ( 2019 ) . Resolving the fibrotic niche of human liver cirrhosis at single-cell level . Nature vol. 575 , ( 7783 ) 512 - 518 .

Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL et al. ( 2019 ) . Spatiotemporal immune zonation of the human kidney . Science vol. 365 , ( 6460 ) 1461 - 1466 .

Vieira Braga FA, Kar G, Berg M, Carpaij OA, Polanski K, Simon LM, Brouwer S, Gomes T et al. ( 2019 ) . A cellular census of human lungs identifies novel cell states in health and in asthma . Nature Medicine vol. 25 , ( 7 ) 1153 - 1163 .

Prokopi A, Tripp CH, Tummers B, Komenda K, Hutter K, Cappellano G, Bellmann L, Efremova M et al. ( 2019 ) . Abstract A102: Rescue of lost skin dendritic cells in melanoma is key for the resuscitation of antitumor T-cell responses . Cancer Immunology Research . vol. 7 , a102 - a102 .

Prokopi N, Tripp CH, Tummers B, Komenda K, Hutter K, Cappellano G, Bellmann L, Efremova M et al. ( 2019 ) . Restoration of anti-tumor T cell responses by restoration of skin dendritic cell numbers in a spontaneous melanoma mouse model . EXPERIMENTAL DERMATOLOGY . vol. 28 , E76 - E76 .

Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park J-E, Stephenson E et al. ( 2018 ) . Single-cell reconstruction of the early maternal–fetal interface in humans . Nature vol. 563 , ( 7731 ) 347 - 353 .

Klepsch V, Hermann-Kleiter N, Do-Dinh P, Jakic B, Offermann A, Efremova M, Sopper S, Rieder D et al. ( 2018 ) . Nuclear receptor NR2F6 inhibition potentiates responses to PD-L1/PD-1 cancer immune checkpoint blockade . Nature Communications vol. 9 , ( 1 )

Efremova M, Rieder D, Klepsch V, Charoentong P, Finotello F, Hackl H, Hermann-Kleiter N, Löwer M et al. ( 2018 ) . Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution . Nature Communications vol. 9 , ( 1 )

Efremova M, Finotello F, Rieder D, Trajanoski Z ( 2017 ) . Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy . Frontiers in Immunology vol. 8 ,

Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, Hackl H, Trajanoski Z ( 2017 ) . Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade . Cell Reports vol. 18 , ( 1 ) 248 - 262 .

Gallasch R, Efremova M, Charoentong P, Hackl H, Trajanoski Z ( 2013 ) . Mathematical models for translational and clinical oncology . Journal of Clinical Bioinformatics vol. 3 , ( 1 )

Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, Krabichler B, Speicher MR et al. ( 2013 ) . A survey of tools for variant analysis of next-generation genome sequencing data . Briefings in Bioinformatics vol. 15 , ( 2 ) 256 - 278 .

Charoentong P, Angelova M, Efremova M, Gallasch R, Hackl H, Galon J, Trajanoski Z ( 2012 ) . Bioinformatics for cancer immunology and immunotherapy . Cancer Immunology, Immunotherapy vol. 61 , ( 11 ) 1885 - 1903 .

Braga FAV, Kar G, Berg M, Carpaij OA, Polanski K, Simon LM, Brouwer S, Gomes T et al. . A cellular census of healthy lung and asthmatic airway wall identifies novel cell states in health and disease .

Del Castillo Velasco-Herrera M, Young MD, Braga FAV, Rosser EC, Miranda E, Marshall L, Wilkinson MGL, Mamanova L et al. . A novel innate lymphoid cell delineates childhood autoimmune arthritis .

Efremova M, Vento-Tormo M, Teichmann SA, Vento-Tormo R . CellPhoneDB v2.0: Inferring cell-cell communication from combined expression of multi-subunit receptor-ligand complexes .

Popescu D-M, Botting RA, Stephenson E, Green K, Jardine L, Calderbank EF, Efremova M, Acres M et al. . Decoding the development of the blood and immune systems during human fetal liver haematopoiesis .

Jardine L, Webb S, Goh I, Londoño MQ, Reynolds G, Mather M, Olabi B, Stephenson E et al. . Intrinsic and extrinsic regulation of human fetal bone marrow haematopoiesis and perturbations in Down syndrome .

Raddi G, Barletta ABF, Efremova M, Ramirez JL, Cantera R, Teichmann SA, Barillas-Mury C, Billker O . Mosquito cellular immunity at single-cell resolution .

Jain MS, Polanski K, Conde CD, Chen X, Park J, Mamanova L, Knights A, Botting RA et al. . MultiMAP: Dimensionality Reduction and Integration of Multimodal Data .

Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, Hackl H, Trajanoski Z . Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade .

Efremova M, Ogden S, Metic N, Smith E, Berner A, Baker A-M, Uddin I, Chelala C et al. . Phenotypic plasticity mediates colorectal cancer metastasis .

Reynolds G, Vegh P, Fletcher J, Poyner EFM, Stephenson E, Goh I, Botting RA, Huang N et al. . Poised cell circuits in human skin are activated in disease .

Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park J, Stephenson E et al. . Reconstructing the human first trimester fetal–maternal interface using single cell transcriptomics .

Ramachandran P, Dobie R, Wilson-Kanamori, Dora E, Henderson B, Taylor R, Matchett K, Portman et al. . Resolving the fibrotic niche of human liver cirrhosis using single-cell transcriptomics .

Haim-Vilmovsky L, Henriksson J, Walker JA, Miao Z, Natan E, Kar G, Clare S, Barlow JL et al. . Rora regulates activated T helper cells during inflammation .

Davidson S, Efremova M, Riedel A, Mahata B, Pramanik J, Huuhtanen J, Kar G, Vento-Tormo R et al. . Single-cell RNA sequencing reveals a dynamic stromal niche within the evolving tumour microenvironment .

Penkava F, Del Castillo Velasco-Herrera M, Young MD, Yager N, Lara AL, Guzzo C, Maroof A, Mamanova L et al. . Single-cell sequencing reveals a clonal expansion of pro-inflammatory synovial CD8 T cells expressing tissue homing receptors in psoriatic arthritis .

Efremova M, Klepsch V, Charoentong P, Finotello F, Rieder D, Hackl H, Hermann-Kleiter N, Löwer M et al. . Targeting the PD-1/PD-L1 pathway potentiates immunoediting and changes the dynamics of neutral evolution in a mouse model of colorectal cancer .

Longhi P, Vyas V, Sandhar B, Wood E, Blythe H, Jones A, Shahaj E, Fanti S et al. . Tissue-resident memory T cells in Epicardial adipose tissue comprise transcriptionally distinct subsets that are modulated in Atrial Fibrillation .

Zhang Z, Sun H, Mariappan R, Chen X, Chen X, Jain MS, Efremova M, Teichmann SA et al. . scMoMaT: Mosaic integration of single cell multi-omics data using matrix tri-factorization .

Zhang Z, Sun H, Mariappan R, Chen X, Chen X, Jain MS, Efremova M, Teichmann S et al. . scMoMaT: a unified framework for single cell mosaic integration and multi-modal bio-marker detection .