Publications

Rosenheim J, Gupta RK, Thakker C, Mann T, Bell LCK, ..., Teichmann SA, ..., Chain BM, Lalvani A, Heyderman RS, Chiu C, Noursadeghi M. (2024) SARS-CoV-2 human challenge reveals biomarkers that discriminate early and late phases of respiratory viral infections. Nat Commun PMID: 39616162

Katsoula G, Lawrence JEG, Arruda AL, Tutino M, Balogh P, ..., Swift D, Behjati S, Teichmann SA, Wilkinson JM, Zeggini E. (2024) Primary cartilage transcriptional signatures reflect cell-type-specific molecular pathways underpinning osteoarthritis. Am J Hum Genet PMID: 39579762

To K, Fei L, Pett JP, Roberts K, Blain R, ..., Barker RA, Bayraktar O, Chédotal A, Buckley CD, Teichmann SA. (2024) A multi-omic atlas of human embryonic skeletal development. Nature PMID: 39567793

Yayon N, Kedlian VR, Boehme L, Suo C, Wachter BT, ..., Germain RN, Radtke AJ, Marioni JC, Taghon T, Teichmann SA. (2024) A spatial human thymus cell atlas mapped to a continuous tissue axis. Nature PMID: 39567784

Oliver AJ, Huang N, Bartolome-Casado R, Li R, Koplev S, ..., Salas A, Haniffa M, Jahnsen FL, Elmentaite R, Teichmann SA. (2024) Single-cell integration reveals metaplasia in inflammatory gut diseases. Nature PMID: 39567783

Amit I, Ardlie K, Arzuaga F, Awandare G, Bader G, ..., Teichmann SA, ..., Villani AC, Wells C, Wold B, Yang H, Zhuang X. (2024) The commitment of the human cell atlas to humanity. Nat Commun PMID: 39567491

Lawrence JEG, Roberts K, Tuck E, Li T, Mamanova L, ..., Flanagan A, Young MD, Teichmann SA, Bayraktar O, Behjati S. (2024) HOX gene expression in the developing human spine. Nat Commun PMID: 39567486

Schuster V, Dann E, Krogh A, Teichmann SA. (2024) multiDGD: A versatile deep generative model for multi-omics data. Nat Commun PMID: 39567490

Barnett SN, Cujba AM, Yang L, Maceiras AR, Li S, ..., Nowakowski TJ, Meyer KB, Randi AM, Noseda M, Teichmann SA. (2024) An organotypic atlas of human vascular cells. Nat Med PMID: 39566559

Li R, Strobl J, Poyner EFM, Balbaa A, Torabi F, ..., Allen JE, Jonak C, Brunner PM, Teichmann SA, Haniffa M. (2024) Cutaneous T cell lymphoma atlas reveals malignant T_H2 cells supported by a B cell-rich tumor microenvironment. Nat Immunol PMID: 39558094

Gopee NH, Winheim E, Olabi B, Admane C, Foster AR, ..., Lee J, Gambardella L, Koehler KR, Teichmann SA, Haniffa M. (2024) A prenatal skin atlas reveals immune regulation of human skin morphogenesis. Nature PMID: 39415002

Koplev S, Teichmann SA. (2024) Universal and tissue-specific fibroblasts in chronic inflammation and cancer. Cancer Cell PMID: 39332397

Pacyna CN, Anandapadamanaban M, Loudon KW, Hay IM, Perisic O, ..., Teichmann SA, Behjati S, Campbell PJ, Williams RL, Mitchell TJ. (2024) Multifocal, multiphenotypic tumours arising from an MTOR mutation acquired in early embryogenesis. Oncogene PMID: 39271965

Polański K, Bartolomé-Casado R, Sarropoulos I, Xu C, England N, Jahnsen FL, Teichmann SA, Yayon N. (2024) Bin2cell reconstructs cells from high resolution Visium HD data. Bioinformatics PMID: 39250728

Megas S, Yayon N, Meyer KB, Teichmann SA. (2024) Molecular connectomics: Placing cells into morphological tissue context. PLoS Biol PMID: 39186794

Dennison TW, Edgar RD, Payne F, Nayak KM, Ross ADB, ..., Teichmann SA, Nys J, Heuschkel R, Perrone F, Zilbauer M. (2024) Patient-derived organoid biobank identifies epigenetic dysregulation of intestinal epithelial MHC-I as a novel mechanism in severe Crohn's Disease. Gut PMID: 38857990

Saar KL, Scrutton RM, Bloznelyte K, Morgunov AS, Good LL, Lee AA, Teichmann SA, Knowles TPJ. (2024) Protein Condensate Atlas from predictive models of heteromolecular condensate composition. Nat Commun PMID: 38987300

Drost F, An Y, Bonafonte-Pardàs I, Dratva LM, Lindeboom RGH, Haniffa M, Teichmann SA, Theis F, Lotfollahi M, Schubert B. (2024) Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data. Nat Commun PMID: 38956082

Netskar H, Pfefferle A, Goodridge JP, Sohlberg E, Dufva O, Teichmann SA, ..., Michaëlsson J, Marquardt N, Clancy T, Horowitz A, Malmberg KJ. (2024) Pan-cancer profiling of tumor-infiltrating natural killer cells through transcriptional reference mapping. Nat Immunol PMID: 38956379

Lindeboom RGH, Worlock KB, Dratva LM, Yoshida M, Scobie D, ..., Mayer A, Meyer KB, Chiu C, Nikolić MZ, Teichmann SA. (2024) Human SARS-CoV-2 challenge uncovers local and systemic response dynamics. Nature PMID: 38898278

Easter QT, Fernandes Matuck B, Beldorati Stark G, Worth CL, Predeus AV, ..., Tyc KM, Liu J, Ko KI, Teichmann SA, Byrd KM. (2024) Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis. Nat Commun PMID: 38876998

Palmer JA, Rosenthal N, Teichmann SA, Litvinukova M. (2024) Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics. Circ Res PMID: 38843288

Zhang Z, Kean IRL, Dratva LM, Clark JA, Syrimi E, ..., Meyer KB, Teichmann SA, Bryant C, Taylor G, Pathan N. (2024) Enhanced CD95 and interleukin 18 signalling accompany T cell receptor Vβ21.3+ activation in multi-inflammatory syndrome in children. Nat Commun PMID: 38762592

Matchett KP, Wilson-Kanamori JR, Portman JR, Kapourani CA, Fercoq F, ..., Marioni JC, Teichmann SA, Bird TG, Carlin LM, Henderson NC. (2024) Multimodal decoding of human liver regeneration. Nature PMID: 38693268

Matchett KP, Paris J, Teichmann SA, Henderson NC. (2024) Spatial genomics: mapping human steatotic liver disease. Nat Rev Gastroenterol Hepatol PMID: 38654090

Kedlian VR, Wang Y, Liu T, Chen X, Bolt L, ..., Xiang AP, Meyer KB, Saeb-Parsy K, Teichmann SA, Zhang H. (2024) Human skeletal muscle aging atlas. Nat Aging PMID: 38622407

Woodall MNJ, Cujba AM, Worlock KB, Case KM, Masonou T, ..., Hynds RE, Teichmann SA, Meyer KB, Nikolić MZ, Smith CM. (2024) Age-specific nasal epithelial responses to SARS-CoV-2 infection. Nat Microbiol PMID: 38622380

Gu Y, Bartolomé-Casado R, Xu C, Bertocchi A, Janney A, Heuberger C, Pearson CF, Teichmann SA, Thornton EE, Powrie F. (2024) Immune microniches shape intestinal T<sub>reg</sub> function. Nature PMID: 38570678

Garmire LX, Li Y, Huang Q, Xu C, Teichmann SA, Kaminski N, Pellegrini M, Nguyen Q, Teschendorff AE. (2024) Challenges and perspectives in computational deconvolution of genomics data. Nat Methods PMID: 38374264

Teichmann SA. (2024) Changing course at the dawn of a genomics revolution. Nat Cell Biol PMID: 38263275

Kildisiute G, Kalyva M, Elmentaite R, van Dongen S, Thevanesan C, ..., Teichmann SA, Straathof K, Cortés-Ciriano I, Behjati S, Young MD. (2024) Transcriptional signals of transformation in human cancer. Genome Med PMID: 38195504

Ganier C, Mazin P, Herrera-Oropeza G, Du-Harpur X, Blakeley M, ..., Shaw T, Teichmann SA, Haniffa M, Watt FM, Lynch MD. (2024) Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma. Proc Natl Acad Sci U S A PMID: 38165934

Zhang B, He P, Lawrence JEG, Wang S, Tuck E, ..., Barker RA, Storer MA, Wold BJ, Zhang H, Teichmann SA. (2024) A human embryonic limb cell atlas resolved in space and time. Nature PMID: 38057666

De Rop FV, Hulselmans G, Flerin C, Soler-Vila P, Rafels A, ..., Teichmann SA, ..., Greenleaf WJ, Buenrostro JD, Regev A, Aerts S, Heyn H. (2024) Systematic benchmarking of single-cell ATAC-sequencing protocols. Nat Biotechnol PMID: 37537502

Suo C, Polanski K, Dann E, Lindeboom RGH, Vilarrasa-Blasi R, ..., Meyer KB, Dratva LM, Tuong ZK, Clatworthy MR, Teichmann SA. (2024) Dandelion uses the single-cell adaptive immune receptor repertoire to explore lymphocyte developmental origins. Nat Biotechnol PMID: 37055623

Barnes JL, Yoshida M, He P, Worlock KB, Lindeboom RGH, ..., Reading JL, Janes SM, Teichmann SA, Meyer KB, Nikolić MZ. (2023) Early human lung immune cell development and its role in epithelial cell fate. Sci Immunol PMID: 38100545

Xu C, Prete M, Webb S, Jardine L, Stewart BJ, Hoo R, He P, Meyer KB, Teichmann SA. (2023) Automatic cell-type harmonization and integration across Human Cell Atlas datasets. Cell PMID: 38134877

Haniffa M, Maartens A, Teichmann SA. (2023) How developmental cell atlases inform stem cell embryo models. Nat Methods PMID: 38057509

Khamwachirapithak P, Guillaume-Schoepfer D, Chansongkrow P, Teichmann SA, Wigge PA, Charoensawan V. (2023) Characterizing Different Modes of Interplay Between Rap1 and H3 Using Inducible H3-depletion Yeast. J Mol Biol PMID: 37935256

Roy S, Roy S, Mahata B, Pramanik J, Hennrich ML, Gavin AC, Teichmann SA. (2023) CLICK-chemoproteomics and molecular dynamics simulation reveals pregnenolone targets and their binding conformations in Th2 cells. Front Immunol PMID: 38022565

Dann E, Cujba AM, Oliver AJ, Meyer KB, Teichmann SA, Marioni JC. (2023) Precise identification of cell states altered in disease using healthy single-cell references. Nat Genet PMID: 37828140

Marsh JA, Teichmann SA. (2023) Predicting pathogenic protein variants. Science PMID: 37725046

Bradke F, Maartens A, Teichmann SA. (2023) Key attributes of successful research institutes. PLoS Biol PMID: 37669250

Goh I, Botting RA, Rose A, Webb S, Engelbert J, ..., Roberts I, Jardine L, Göttgens B, Teichmann SA, Haniffa M. (2023) Yolk sac cell atlas reveals multiorgan functions during human early development. Science PMID: 37590359

Ferreira IATM, Lee CYC, Foster WS, Abdullahi A, Dratva LM, ..., Teichmann SA, ..., Doffinger R, Wills MR, Linterman MA, Clatworthy MR, Gupta RK. (2023) Atypical B cells and impaired SARS-CoV-2 neutralization following heterologous vaccination in the elderly. Cell Rep PMID: 37590132

De Jonghe J, Kaminski TS, Morse DB, Tabaka M, Ellermann AL, ..., Handford CE, Findlay GM, Zernicka-Goetz M, Teichmann SA, Hollfelder F. (2023) spinDrop: a droplet microfluidic platform to maximise single-cell sequencing information content. Nat Commun PMID: 37553326

Kanemaru K, Cranley J, Muraro D, Miranda AMA, Ho SY, ..., Clatworthy MR, Hübner N, Chowdhury RA, Noseda M, Teichmann SA. (2023) Spatially resolved multiomics of human cardiac niches. Nature PMID: 37438528

Arora JK, Opasawatchai A, Teichmann SA, Matangkasombut P, Charoensawan V. (2023) Computational workflow for investigating highly variable genes in single-cell RNA-seq across multiple time points and cell types. STAR Protoc PMID: 37379219

Kumasaka N, Rostom R, Huang N, Polanski K, Meyer KB, ..., Haniffa M, Marioni JC, Stegle O, Hagai T, Teichmann SA. (2023) Mapping interindividual dynamics of innate immune response at single-cell resolution. Nat Genet PMID: 37308670

Sikkema L, Ramírez-Suástegui C, Strobl DC, Gillett TE, Zappia L, ..., Teichmann SA, Misharin AV, Nawijn MC, Luecken MD, Theis FJ. (2023) An integrated cell atlas of the lung in health and disease. Nat Med PMID: 37291214

Zilbauer M, James KR, Kaur M, Pott S, Li Z, ..., Teichmann SA, ..., Simmons A, Snyder MP, Wilson KT, Gut Cell Atlas Consortium, Human Cell Atlas Gut Biological Network Consortium. (2023) A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol PMID: 37258747

Virshup I, Bredikhin D, Heumos L, Palla G, Sturm G, ..., Teichmann SA, Finotello F, Wolf FA, Yosef N, Stegle O, Theis FJ. (2023) The scverse project provides a computational ecosystem for single-cell omics data analysis. Nat Biotechnol PMID: 37037904

Arutyunyan A, Roberts K, Troulé K, Wong FCK, Sheridan MA, ..., Teichmann SA, Bayraktar OA, Moffett A, Stegle O, Turco MY, Vento-Tormo R. (2023) Spatial multiomics map of trophoblast development in early pregnancy. Nature PMID: 36991123

Neikes HK, Kliza KW, Gräwe C, Wester RA, Jansen PWTC, ..., van Heeringen SJ, Logie C, Teichmann SA, Lindeboom RGH, Vermeulen M. (2023) Quantification of absolute transcription factor binding affinities in the native chromatin context using BANC-seq. Nat Biotechnol PMID: 36973556

Guo SA, Bowyer GS, Ferdinand JR, Maes M, Tuong ZK, ..., Dougan G, Navapurkar V, Teichmann SA, Conway Morris A, Clatworthy MR. (2023) Obesity Is Associated with Attenuated Tissue Immunity in COVID-19. Am J Respir Crit Care Med PMID: 36095143

Zhang Z, Sun H, Mariappan R, Chen X, Chen X, Jain MS, Efremova M, Teichmann SA, Rajan V, Zhang X. (2023) scMoMaT jointly performs single cell mosaic integration and multi-modal bio-marker detection. Nat Commun PMID: 36693837

Madissoon E, Oliver AJ, Kleshchevnikov V, Wilbrey-Clark A, Polanski K, ..., Clatworthy MR, Stegle O, Kumasaka N, Teichmann SA, Meyer KB. (2023) A spatially resolved atlas of the human lung characterizes a gland-associated immune niche. Nat Genet PMID: 36543915

Miranda AMA, Janbandhu V, Maatz H, Kanemaru K, Cranley J, Teichmann SA, Hübner N, Schneider MD, Harvey RP, Noseda M. (2023) Single-cell transcriptomics for the assessment of cardiac disease. Nat Rev Cardiol PMID: 36539452

Lim K, Donovan APA, Tang W, Sun D, He P, ..., Teichmann SA, Marioni JC, Meyer KB, Brand AH, Rawlins EL. (2023) Organoid modeling of human fetal lung alveolar development reveals mechanisms of cell fate patterning and neonatal respiratory disease. Cell Stem Cell PMID: 36493780

Knight-Schrijver, V. R., Davaapil, H., Bayraktar, S., Ross, A. D., Kanemaru, K., Cranley, J., Dabrowska, M., Patel, M., Polanski, K., He, X., Vallier, L., Teichmann, S., Gambardella, L., and Sinha, S. (2022) A single-cell comparison of adult and fetal human epicardium defines the age-associated changes in epicardial activity. Nat. Cardiovasc. Res. PMID: 36938497

Li, R., Ferdinand, J. R., Loudon, K. W., Bowyer, G. S., ..., Behjati, S., Clatworthy, M. R., Campbell, P. J., Teichmann, S. A., & Mitchell, T. J. (2022) Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer. Cancer Cell. PMID: 36423636

Rood, J. E., Maartens, A., Hupalowska, A., Teichmann, S. A., & Regev, A. (2022) Impact of the Human Cell Atlas on medicine. Nat. Med. PMID: 36482102

He, P., Lim, K., Sun, D., Pett, J. P., ..., Barker, R. A., Teichmann, S. A., Marioni, J. C., Meyer, K. B., Rawlins, E. L. (2022) A human fetal lung cell atlas uncovers proximal-distal gradients of differentiation and key regulators of epithelial fates. Cell. PMID: 36493756

Wei, J.-R., Hao, Z.-Z., Xu, C., Huang, M., Tang, L., Xu, N., Liu, R., Shen, Y., Teichmann, S. A., Miao, Z., Liu, S. (2022) Identification of visual cortex cell types and species differences using single-cell RNA sequencing. Nat. Commun. PMID: 36371428

Sun, D., Llora Batlle, Ameele, J., Thomas, J. C., [...], Teichmann, S. A., Marioni, J. C., Jackson, S. P., Brand, A. H., and Rawlins, E. L. (2022) SOX9 maintains human foetal lung tip progenitor state by enhancing WNT and RTK signalling. EMBO J. PMID:36121125.

Wesley, B. T., Ross, A. D. B., Muraro, D., Miao, Z., [...], Haniffa, M., Stevens, K. R., Zilbauer, M., Teichmann, S. A., and Vallier, L. (2022) Single-cell atlas of human liver development reveals pathways directing hepatic cell fates. Nat Cell Biol. PMID:36109670.

Guo, S. A., Bowyer, G. S., Ferdinand, J. R., Maes, M., [...], Dougan, G., Navapurkar, V., Teichmann, S. A., Conway Morris, and Clatworthy, M. R. (2022) Obesity Is Associated with Attenuated Tissue Immunity in COVID-19. Am J Respir Crit Care Med. PMID:36095143.

Hamed, A. A., Kunz, D. J., El-Hamamy, I., Trinh, Q. M., [...], Taylor, M. D., Teichmann, S. A., Stein, L. D., Simons, B. D., and Dirks, P. B. (2022) A brain precursor atlas reveals the acquisition of developmental-like states in adult cerebral tumours. Nat Commun. PMID:35853870.

Teichmann, S. A., Haniffa, M., and Fisher, J. (2022) Community voices: policy proposals to promote inclusion in academia through the lens of women in science. Nat Commun. PMID:35831416.

Hardt, U., Carlberg, K., Af Klint, Sahlström, P., [...], G. B., Catrina, A. I., Teichmann, S. A., Ståhl, P. L., and Malmström, V. (2022) Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis. Sci Rep. PMID:35831338.

Domínguez Conde, Xu, C., Jarvis, L. B., Rainbow, D. B., [...], Sims, P. A., Farber, D. L., Saeb-Parsy, K., Jones, J. L., and Teichmann, S. A. (2022) Cross-tissue immune cell analysis reveals tissue-specific features in humans. Science. PMID:35549406.

Suo, C., Dann, E., Goh, I., Jardine, L., [...], Horsfall, D., Marioni, J. C., Clatworthy, M. R., Haniffa, M., and Teichmann, S. A. (2022) Mapping the developing human immune system across organs. Science. PMID:35549310.

Arora, J. K., Opasawatchai, A., Poonpanichakul, T., Jiravejchakul, N., Sungnak, W., DENFREE Thailand, Matangkasombut, O., Teichmann, S. A., Matangkasombut, P., and Charoensawan, V. (2022) Single-cell temporal analysis of natural dengue infection reveals skin-homing lymphocyte expansion one day before defervescence. iScience. PMID:35345453.

Liu, X., Jin, S., Hu, S., Li, R., [...], Tu, P., Haniffa, M., Teichmann, S. A., Bai, F., and Wang, Y. (2022) Single-cell transcriptomics links malignant T cells to the tumor immune landscape in cutaneous T cell lymphoma. Nat Commun. PMID:35241665.

Elmentaite, R., Domínguez Conde, C., Yang, L., and Teichmann, S. A. (2022) Single-cell atlases: shared and tissue-specific cell types across human organs. Nat Rev Genet. PMID:35217821.

Yoshida, M., Worlock, K. B., Huang, N., Lindeboom, R. G. H., [...], Misharin, A. V., Janes, S. M., Teichmann, S. A., Nikolić, M. Z., and Meyer, K. B. (2022) Local and systemic responses to SARS-CoV-2 infection in children and adults. Nature. PMID:34937051.

James, K. R., Elmentaite, R., Teichmann, S. A., and Hold, G. L. (2022) Redefining intestinal immunity with single-cell transcriptomics. Mucosal Immunol. PMID:34848830.

Dann, E., Henderson, N. C., Teichmann, S. A., Morgan, M. D., and Marioni, J. C. (2022) Differential abundance testing on single-cell data using k-nearest neighbor graphs. Nat Biotechnol. PMID:34594043.

Chen, S. and Teichmann, S. A. (2021) Completing the cancer jigsaw puzzle with single-cell multiomics. Nat Cancer. PMID:35121921.

Jain, M. S., Polanski, K., Conde, C. D., Chen, X., [...], Stephenson, E., Haniffa, M., Lamacraft, A., Efremova, M., and Teichmann, S. A. (2021) MultiMAP: dimensionality reduction and integration of multimodal data. Genome Biol. PMID:34930412.

Garcia-Alonso, L., Handfield, L., Roberts, K., Nikolakopoulou, K., [...], Moore, L., Bayraktar, O. A., Teichmann, S. A., Turco, M. Y., and Vento-Tormo, R. (2021) Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro. Nat Genet. PMID:34857954.

Börner, K., Teichmann, S. A., Quardokus, E. M., Gee, J. C., [...], and Weber, G. (2021) Anatomical structures, cell types and biomarkers of the Human Reference Atlas. Nat Cell Biol. PMID:34750582.

Osumi-Sutherland, D., Xu, C., Keays, M., Levine, A. P., Kharchenko, P. V., Regev, A., Lein, E., and Teichmann, S. A. (2021) Cell type ontologies of the Human Cell Atlas. Nat Cell Biol. PMID:34750578.

Jardine, L., Webb, S., Goh, I., Quiroga Londoño, [...], Roy, A., Göttgens, B., Roberts, I., Teichmann, S. A., and Haniffa, M. (2021) Blood and immune development in human fetal bone marrow and Down syndrome. Nature. PMID:34588693.

Elmentaite, R., Kumasaka, N., Roberts, K., Fleming, A., [...], Zilbauer, M., Clatworthy, M. R., Haniffa, M., James, K. R., and Teichmann, S. A. (2021) Cells of the human intestinal tract mapped across space and time. Nature. PMID:34497389.

Haniffa, M., Taylor, D., Linnarsson, S., Aronow, B. J., [...], Teichmann, S. A., Treutlein, B., Vento-Tormo, R., Webb, S., and Human Cell Atlas Developmental Biological Network (2021) A roadmap for the Human Developmental Cell Atlas. Nature. PMID:34497388.

Nowicki-Osuch, K., Zhuang, L., Jammula, S., Bleaney, C. W., [...], Saeb-Parsy, K., Sharrocks, A. D., Teichmann, S. A., Marioni, J. C., and Fitzgerald, R. C. (2021) Molecular phenotyping reveals the identity of Barrett's esophagus and its malignant transition. Science. PMID:34385390.

Ross, A. D. B., Perrone, F., Elmentaite, R., Teichmann, S. A., and Zilbauer, M. (2021) Obtaining purified human intestinal epithelia for single-cell analysis and organoid culture. STAR Protoc. PMID:34169291.

Kumar, S., Fonseca, V. R., Ribeiro, F., Basto, A. P., [...], Piaggio, E., Segura, E., Gama-Carvalho, M., Teichmann, S. A., and Graca, L. (2021) Developmental bifurcation of human T follicular regulatory cells. Sci Immunol. PMID:34049865.

Roy, S., Sipthorp, J., Mahata, B., Pramanik, J., Hennrich, M. L., Gavin, A.-C., Ley, S. V., and Teichmann, S. A. (2021) CLICK-enabled analogues reveal pregnenolone interactomes in cancer and immune cells. iScience. PMID:34036248.

Haim-Vilmovsky, L., Henriksson, J., Walker, J. A., Miao, Z., [...], Dougan, G., Fisher, J., Marioni, J. C., McKenzie, A. N. J., and Teichmann, S. A. (2021) Mapping Rora expression in resting and activated CD4+ T cells. PLoS One. PMID:34003838.

Mamanova, L., Miao, Z., Jinat, A., Ellis, P., Shirley, L., and Teichmann, S. A. (2021) High-throughput full-length single-cell RNA-seq automation. Nat Protoc. PMID:33990801.

Stephenson, E., Reynolds, G., Botting, R. A., Calero-Nieto, F. J., [...], Teichmann, S. A., Clatworthy, M. R., Marioni, J. C., Göttgens, B., and Haniffa, M. (2021) Single-cell multi-omics analysis of the immune response in COVID-19. Nat Med. PMID:33879890.

Lindeboom, R. G. H., Regev, A., and Teichmann, S. A. (2021) Towards a Human Cell Atlas: Taking Notes from the Past. Trends Genet. PMID:33879355.

Huang, N., Pérez, P., Kato, T., Mikami, Y., [...], Lee, J., Boucher, R. C., Teichmann, S. A., Warner, B. M., and Byrd, K. M. (2021) SARS-CoV-2 infection of the oral cavity and saliva. Nat Med. PMID:33767405.

Choudry, F. A., Bagger, F. O., Macaulay, I. C., Farrow, S., [...], Mathur, A., Ouwehand, W. H., Laurenti, E., Teichmann, S. A., and Frontini, M. (2021) Transcriptional characterization of human megakaryocyte polyploidization and lineage commitment. J Thromb Haemost. PMID:33587817.

King, H. W., Orban, N., Riches, J. C., Clear, A. J., Warnes, G., Teichmann, S. A., and James, L. K. (2021) Single-cell analysis of human B cell maturation predicts how antibody class switching shapes selection dynamics. Sci Immunol. PMID:33579751.

Wu, Q., Suo, C., Brown, T., Wang, T., Teichmann, S. A., and Bassett, A. R. (2021) INSIGHT: A population-scale COVID-19 testing strategy combining point-of-care diagnosis with centralized high-throughput sequencing. Sci Adv. PMID:33579697.

Reynolds, G., Vegh, P., Fletcher, J., Poyner, E. F. M., [...], Rajan, N., Reynolds, N. J., Teichmann, S. A., Watt, F. M., and Haniffa, M. (2021) Developmental cell programs are co-opted in inflammatory skin disease. Science. PMID:33479125.

Bock, C., Boutros, M., Camp, J. G., Clarke, L., [...], Stunnenberg, H. G., Teichmann, S. A., Treutlein, B., Vries, R. G. J., and Human Cell Atlas ‘Biological Network’ Organoids (2021) The Organoid Cell Atlas. Nat Biotechnol. PMID:33384458.

Elmentaite, R., Ross, A. D. B., Roberts, K., James, K. R., [...], Heuschkel, R., Vallier, L., Teichmann, S. A., and Zilbauer, M. (2020) Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn's Disease. Dev Cell. PMID:33290721.

Soon, M. S. F., Lee, H. J., Engel, J. A., Straube, J., [...], Davenport, M. P., Svensson, V., Teichmann, S. A., and Haque, A. (2020) Transcriptome dynamics of CD4+ T cells during malaria maps gradual transit from effector to memory. Nat Immunol. PMID:33046889.

Litviňuková, M., Talavera-López, C., Maatz, H., Reichart, D., [...], Seidman, C. E., Noseda, M., Hubner, N., and Teichmann, S. A. (2020) Cells of the adult human heart. Nature. PMID:32971526.

Aldridge, S. and Teichmann, S. A. (2020) Single cell transcriptomics comes of age. Nat Commun. PMID:32855414.

Raddi, G., Barletta, A. B. F., Efremova, M., Ramirez, J. L., Cantera, R., Teichmann, S. A., Barillas-Mury, C., and Billker, O. (2020) Mosquito cellular immunity at single-cell resolution. Science. PMID:32855340.

Beumer, J., Puschhof, J., Bauzá-Martinez, J., Martínez-Silgado, A., [...], Zilbauer, M., Teichmann, S. A., Wu, W., and Clevers, H. (2020) High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells. Cell. PMID:32822568.

Mahata, B., Pramanik, J., Weyden, L., Polanski, K., [...], Okkenhaug, K., Adams, D. J., Shields, J. D., and Teichmann, S. A. (2020) Tumors induce de novo steroid biosynthesis in T cells to evade immunity. Nat Commun. PMID:32680985.

Gomes, T. and Teichmann, S. A. (2020) An antiviral response beyond immune cells. Nature. PMID:32623443.

Davidson, S., Efremova, M., Riedel, A., Mahata, B., [...], Chen, X., Haniffa, M. A., Shields, J. D., and Teichmann, S. A. (2020) Single-Cell RNA Sequencing Reveals a Dynamic Stromal Niche That Supports Tumor Growth. Cell Rep. PMID:32433953.

Miao, Z., Moreno, P., Huang, N., Papatheodorou, I., Brazma, A., and Teichmann, S. A. (2020) Putative cell type discovery from single-cell gene expression data. Nat Methods. PMID:32424270.

Beumer, J., Puschhof, J., Bauzá-Martinez, J., Martínez-Silgado, A., [...], Zilbauer, M., Teichmann, S. A., Wu, W., and Clevers, H. (2020) High-Resolution mRNA and Secretome Atlas of Human Enteroendocrine Cells. Cell. PMID:32407674.

Park, J.-E., Jardine, L., Gottgens, B., Teichmann, S. A., and Haniffa, M. (2020) Prenatal development of human immunity. Science. PMID:32381715.

Wilbrey-Clark, A., Roberts, K., and Teichmann, S. A. (2020) Cell Atlas technologies and insights into tissue architecture. Biochem J. PMID:32339226.

Hewitson, J. P., West, K. A., James, K. R., Rani, G. F., Dey, N., Romano, A., Brown, N., Teichmann, S. A., Kaye, P. M., and Lagos, D. (2020) Malat1 Suppresses Immunity to Infection through Promoting Expression of Maf and IL-10 in Th Cells. J Immunol. PMID:32321759.

Lavaert, M., Liang, K. L., Vandamme, N., Park, J., [...], Guilliams, M., Teichmann, S. A., Saeys, Y., and Taghon, T. (2020) Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes. Immunity. PMID:32304633.

McCarthy, D. J., Rostom, R., Huang, Y., Kunz, D. J., [...], Gaffney, D. J., Simons, B. D., Stegle, O., and Teichmann, S. A. (2020) Cardelino: computational integration of somatic clonal substructure and single-cell transcriptomes. Nat Methods. PMID:32203388.

Efremova, M., Vento-Tormo, M., Teichmann, S. A., and Vento-Tormo, R. (2020) CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes. Nat Protoc. PMID:32103204.

Park, J., Botting, R. A., Conde, C., Popescu, D., [...], Clatworthy, M. R., Taghon, T., Haniffa, M., and Teichmann, S. A. (2020) A cell atlas of human thymic development defines T cell repertoire formation. Science. PMID:32079746.

Efremova, M., Vento-Tormo, R., Park, J.-E., Teichmann, S. A., and James, K. R. (2020) Immunology in the Era of Single-Cell Technologies. Annu Rev Immunol. PMID:32075461.

James, K. R., Gomes, T., Elmentaite, R., Kumar, N., [...], Clatworthy, M. R., Saeb-Parsy, K., Lawley, T. D., and Teichmann, S. A. (2020) Distinct microbial and immune niches of the human colon. Nat Immunol. PMID:32066951.

Oatley, M., Svensson, V., Shvartsman, M., Ganter, K., [...], Benes, V., Patil, K. R., Teichmann, S. A., and Lancrin, C. (2020) Single-cell transcriptomics identifies CD44 as a marker and regulator of endothelial to haematopoietic transition. Nat Commun. PMID:31996681.

Efremova, M. and Teichmann, S. A. (2020) Computational methods for single-cell omics across modalities. Nat Methods. PMID:31907463.

Chen, Y., Gomes, T., Hardman, C. S., Braga, F. A., [...], McKenzie, A. N. J., Teichmann, S. A., Haniffa, M., and Ogg, G. (2020) Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation. J Exp Med. PMID:31845972.

Domínguez Conde, C. and Teichmann, S. A. (2020) Deciphering immunity at high plexity and resolution. Nat Rev Immunol. PMID:31797907.

Polański, K., Young, M. D., Miao, Z., Meyer, K. B., Teichmann, S. A., and Park, J.-E. (2020) BBKNN: fast batch alignment of single cell transcriptomes. Bioinformatics. PMID:31400197.

Elmentaite, R., Teichmann, S. A., and Madissoon, E. (2019) Studying immune to non-immune cell cross-talk using single-cell technologies. Curr Opin Syst Biol. PMID:32984660.

Madissoon, E., Wilbrey-Clark, A., Miragaia, R. J., Saeb-Parsy, K., [...], Stubbington, M. J. T., Teichmann, S. A., Stegle, O., and Meyer, K. B. (2019) scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation. Genome Biol. PMID:31892341.

Dobie, R., Wilson-Kanamori, J. R., Henderson, B. E. P., Smith, J. R., [...], Ponting, C. P., Teichmann, S. A., Marioni, J. C., and Henderson, N. C. (2019) Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis. Cell Rep. PMID:31722201.

Gomes, T., Teichmann, S. A., and Talavera-López, C. (2019) Immunology Driven by Large-Scale Single-Cell Sequencing. Trends Immunol. PMID:31645299.

Stewart, B. J., Ferdinand, J. R., Young, M. D., Mitchell, T. J., [...], Haniffa, M., Teichmann, S. A., Behjati, S., and Clatworthy, M. R. (2019) Spatiotemporal immune zonation of the human kidney. Science. PMID:31604275.

HuBMAP Consortium (2019) The human body at cellular resolution: the NIH Human Biomolecular Atlas Program. Nature. PMID:31597973.

Popescu, D., Botting, R. A., Stephenson, E., Green, K., [...], Behjati, S., Laurenti, E., Teichmann, S. A., and Haniffa, M. (2019) Decoding human fetal liver haematopoiesis. Nature. PMID:31597962.

Ramachandran, P., Dobie, R., Wilson-Kanamori, J. R., Dora, E. F., [...], Ponting, C. P., Marioni, J. C., Teichmann, S. A., and Henderson, N. C. (2019) Resolving the fibrotic niche of human liver cirrhosis at single-cell level. Nature. PMID:31597160.

Braga, F. A., Kar, G., Berg, M., Carpaij, O. A., [...], Theis, F. J., Berge, M., Nawijn, M. C., and Teichmann, S. A. (2019) A cellular census of human lungs identifies novel cell states in health and in asthma. Nat Med. PMID:31209336.

Gao, X., Nowak-Imialek, M., Chen, X., Chen, D., [...], Yeung, W. S. B., Teichmann, S. A., Niemann, H., and Liu, P. (2019) Establishment of porcine and human expanded potential stem cells. Nat Cell Biol. PMID:31160711.

Walker, J. A., Clark, P. A., Crisp, A., Barlow, J. L., [...], Daly, M., Haim-Vilmovsky, L., Teichmann, S. A., and McKenzie, A. N. J. (2019) Polychromic Reporter Mice Reveal Unappreciated Innate Lymphoid Cell Progenitor Heterogeneity and Elusive ILC3 Progenitors in Bone Marrow. Immunity. PMID:31128961.

Dhillon, P. and Teichmann, S. A. (2019) In conversation with Sarah Teichmann. FEBS J. PMID:31012289.

Schiller, H. B., Montoro, D. T., Simon, L. M., Rawlins, E. L., [...], Rajagopal, J., Teichmann, S. A., Misharin, A. V., and Nawijn, M. C. (2019) The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease. Am J Respir Cell Mol Biol. PMID:30995076.

Natarajan, K. N., Miao, Z., Jiang, M., Huang, X., [...], Li, B., Hou, Y., Liu, S., and Teichmann, S. A. (2019) Comparative analysis of sequencing technologies for single-cell transcriptomics. Genome Biol. PMID:30961669.

Miragaia, R. J., Gomes, T., Chomka, A., Jardine, L., [...], Shields, J., Haniffa, M., Powrie, F., and Teichmann, S. A. (2019) Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation. Immunity. PMID:30737144.

Henriksson, J., Chen, X., Gomes, T., Ullah, U., [...], Pramanik, J., Yusa, K., Lahesmaa, R., and Teichmann, S. A. (2019) Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation. Cell. PMID:30639098.

Büttner, M., Miao, Z., Wolf, F. A., Teichmann, S. A., and Theis, F. J. (2019) A test metric for assessing single-cell RNA-seq batch correction. Nat Methods. PMID:30573817.

Chen, X., Miragaia, R. J., Natarajan, K. N., and Teichmann, S. A. (2018) A rapid and robust method for single cell chromatin accessibility profiling. Nat Commun. PMID:30559361.

Massaia, A., Chaves, P., Samari, S., Miragaia, R. J., Meyer, K., Teichmann, S. A., and Noseda, M. (2018) Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart. Front Cardiovasc Med. PMID:30525044.

Vento-Tormo, R., Efremova, M., Botting, R. A., Turco, M. Y., [...], Stubbington, M. J. T., Haniffa, M., Moffett, A., and Teichmann, S. A. (2018) Single-cell reconstruction of the early maternal-fetal interface in humans. Nature. PMID:30429548.

Hagai, T., Chen, X., Miragaia, R. J., Rostom, R., [...], Haniffa, M., Nourmohammad, A., Lässig, M., and Teichmann, S. A. (2018) Gene expression variability across cells and species shapes innate immunity. Nature. PMID:30356220.

Pramanik, J., Chen, X., Kar, G., Henriksson, J., [...], Miao, Z., McKenzie, A. N. J., Mahata, B., and Teichmann, S. A. (2018) Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation. Genome Med. PMID:30355343.

Young, M. D., Mitchell, T. J., Braga, F. A., Tran, M. G. B., [...], Haniffa, M., Teichmann, S. A., Clatworthy, M., and Behjati, S. (2018) Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors. Science. PMID:30093597.

Marsh, J. A. and Teichmann, S. A. (2018) Editorial overview: Sequences and topology: Dynamic sequences and topologies of proteins. Curr Opin Struct Biol. PMID:30080482.

Lindeman, I., Emerton, G., Mamanova, L., Snir, O., Polanski, K., Qiao, S.-W., Sollid, L. M., Teichmann, S. A., and Stubbington, M. J. T. (2018) BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq. Nat Methods. PMID:30065371.

Severo, M. S., Landry, J. J. M., Lindquist, R. L., Goosmann, C., [...], Benes, V., Henriksson, J., Teichmann, S. A., and Levashina, E. A. (2018) Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging. Proc Natl Acad Sci U S A. PMID:30038005.

Svensson, V., Teichmann, S. A., and Stegle, O. (2018) SpatialDE: identification of spatially variable genes. Nat Methods. PMID:29553579.

Svensson, V., Vento-Tormo, R., and Teichmann, S. A. (2018) Exponential scaling of single-cell RNA-seq in the past decade. Nat Protoc. PMID:29494575.

Behjati, S., Lindsay, S., Teichmann, S. A., and Haniffa, M. (2018) Mapping human development at single-cell resolution. Development. PMID:29439135.

Natan, E., Endoh, T., Haim-Vilmovsky, L., Flock, T., [...], Babu, M. M., Robinson, C. V., Sugimoto, N., and Teichmann, S. A. (2018) Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins. Nat Struct Mol Biol. PMID:29434345.

Regev, A., Teichmann, S. A., Lander, E. S., Amit, I., [...], and Yosef, N. (2017) The Human Cell Atlas. Elife. PMID:29206104.

Rozenblatt-Rosen, O., Stubbington, M. J. T., Regev, A., and Teichmann, S. A. (2017) The Human Cell Atlas: from vision to reality. Nature. PMID:29072289.

Stubbington, M. J. T., Rozenblatt-Rosen, O., Regev, A., and Teichmann, S. A. (2017) Single-cell transcriptomics to explore the immune system in health and disease. Science. PMID:28983043.

Haque, A., Engel, J., Teichmann, S. A., and Lönnberg, T. (2017) A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications. Genome Med. PMID:28821273.

Hegazy, A. N., West, N. R., Stubbington, M. J. T., Wendt, E., [...], Bergthaler, A., Teichmann, S. A., Keshav, S., and Powrie, F. (2017) Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation. Gastroenterology. PMID:28782508.

Natarajan, K. N., Teichmann, S. A., and Kolodziejczyk, A. A. (2017) Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation. Curr Opin Genet Dev. PMID:28675884.

Kar, G., Kim, J. K., Kolodziejczyk, A. A., Natarajan, K. N., Torlai Triglia, E., Mifsud, B., Elderkin, S., Marioni, J. C., Pombo, A., and Teichmann, S. A. (2017) Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression. Nat Commun. PMID:28652613.

Rostom, R., Svensson, V., Teichmann, S. A., and Kar, G. (2017) Computational approaches for interpreting scRNA-seq data. FEBS Lett. PMID:28524227.

Donati, G., Rognoni, E., Hiratsuka, T., Liakath-Ali, K., [...], Kretzschmar, K., Mulder, K. W., Teichmann, S. A., and Watt, F. M. (2017) Wounding induces dedifferentiation of epidermal Gata6+ cells and acquisition of stem cell properties. Nat Cell Biol. PMID:28504705.

Martinez-Jimenez, C. P., Eling, N., Chen, H., Vallejos, C. A., [...], Teichmann, S. A., Roche, M., Marioni, J. C., and Odom, D. T. (2017) Aging increases cell-to-cell transcriptional variability upon immune stimulation. Science. PMID:28360329.

Lönnberg, T., Svensson, V., James, K. R., Fernandez-Ruiz, D., [...], Billker, O., Stegle, O., Haque, A., and Teichmann, S. A. (2017) Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria. Sci Immunol. PMID:28345074.

Vieira Braga, F. A., Teichmann, S. A., and Stubbington, M. J. T. (2017) Are cells from a snowman realistic? Cryopreserved tissues as a source for single-cell RNA-sequencing experiments. Genome Biol. PMID:28340618.

Svensson, V., Natarajan, K. N., Ly, L.-H., Miragaia, R. J., Labalette, C., Macaulay, I. C., Cvejic, A., and Teichmann, S. A. (2017) Power analysis of single-cell RNA-sequencing experiments. Nat Methods. PMID:28263961.

Carmona, S. J., Teichmann, S. A., Ferreira, L., Macaulay, I. C., Stubbington, M. J. T., Cvejic, A., and Gfeller, D. (2017) Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types. Genome Res. PMID:28087841.

Wu, Y. L., Stubbington, M. J. T., Daly, M., Teichmann, S. A., and Rada, C. (2017) Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE. J Exp Med. PMID:27994069.

Natan, E., Wells, J. N., Teichmann, S. A., and Marsh, J. A. (2017) Regulation, evolution and consequences of cotranslational protein complex assembly. Curr Opin Struct Biol. PMID:27969102.

Chen, X., Love, J. C., Navin, N. E., Pachter, L., Stubbington, M. J. T., Svensson, V., Sweedler, J. V., and Teichmann, S. A. (2016) Single-cell analysis at the threshold. Nat Biotechnol. PMID:27824834.

Yu, Y., Tsang, J. C. H., Wang, C., Clare, S., [...], McKenzie, A. N. J., Teichmann, S. A., Dougan, G., and Liu, P. (2016) Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway. Nature. PMID:27749818.

Eckersley-Maslin, M. A., Svensson, V., Krueger, C., Stubbs, T. M., [...], Milagre, I., Walter, J., Teichmann, S. A., and Reik, W. (2016) MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs. Cell Rep. PMID:27681430.

Sousa, F. L., Parente, D. J., Hessman, J. A., Chazelle, A., Teichmann, S. A., and Swint-Kruse, L. (2016) Data on publications, structural analyses, and queries used to build and utilize the AlloRep database. Data Brief. PMID:27508249.

Vieira Braga, F. A., Teichmann, S. A., and Chen, X. (2016) Genetics and immunity in the era of single-cell genomics. Hum Mol Genet. PMID:27412011.

Proserpio, V., Piccolo, A., Haim-Vilmovsky, L., Kar, G., [...], Woodhouse, S., Cicuta, P., Nicodemi, M., and Teichmann, S. A. (2016) Erratum to: Single cell analysis of CD4+ T cell differentiation reveals three major cell states and progressive acceleration of proliferation. Genome Biol. PMID:27333907.

Proserpio, V., Piccolo, A., Haim-Vilmovsky, L., Kar, G., [...], Woodhouse, S., Cicuta, P., Nicodemi, M., and Teichmann, S. A. (2016) Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation. Genome Biol. PMID:27176874.

Linnarsson, S. and Teichmann, S. A. (2016) Single-cell genomics: coming of age. Genome Biol. PMID:27160975.

Stubbington, M. J. T., Lönnberg, T., Proserpio, V., Clare, S., Speak, A. O., Dougan, G., and Teichmann, S. A. (2016) T cell fate and clonality inference from single-cell transcriptomes. Nat Methods. PMID:26950746.

Ilicic, T., Kim, J. K., Kolodziejczyk, A. A., Bagger, F. O., McCarthy, D. J., Marioni, J. C., and Teichmann, S. A. (2016) Classification of low quality cells from single-cell RNA-seq data. Genome Biol. PMID:26887813.

Macaulay, I. C., Svensson, V., Labalette, C., Ferreira, L., Hamey, F., Voet, T., Teichmann, S. A., and Cvejic, A. (2016) Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells. Cell Rep. PMID:26804912.

Kim, J. K., Kolodziejczyk, A. A., Ilicic, T., Teichmann, S. A., and Marioni, J. C. (2016) Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. Nat Commun. PMID:26752026.

Sousa, F. L., Parente, D. J., Shis, D. L., Hessman, J. A., Chazelle, A., Bennett, M. R., Teichmann, S. A., and Swint-Kruse, L. (2016) AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators. J Mol Biol. PMID:26410588.

Ahnert, S. E., Marsh, J. A., Hernández, H., Robinson, C. V., and Teichmann, S. A. (2015) Principles of assembly reveal a periodic table of protein complexes. Science. PMID:26659058.

Kim, J. K., Kolodziejczyk, A. A., Ilicic, T., Illicic, T., Teichmann, S. A., and Marioni, J. C. (2015) Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. Nat Commun. PMID:26489834.

Kolodziejczyk, A. A., Kim, J. K., Tsang, J. C. H., Ilicic, T., [...], Bühler, M., Liu, P., Marioni, J. C., and Teichmann, S. A. (2015) Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation. Cell Stem Cell. PMID:26431182.

Tsang, J. C. H., Yu, Y., Burke, S., Buettner, F., Wang, C., Kolodziejczyk, A. A., Teichmann, S. A., Lu, L., and Liu, P. (2015) Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells. Genome Biol. PMID:26387834.

Scialdone, A., Natarajan, K. N., Saraiva, L. R., Proserpio, V., Teichmann, S. A., Stegle, O., Marioni, J. C., and Buettner, F. (2015) Computational assignment of cell-cycle stage from single-cell transcriptome data. Methods. PMID:26142758.

Xie, X., Stubbington, M. J. T., Nissen, J. K., Andersen, K. G., Hebenstreit, D., Teichmann, S. A., and Betz, A. G. (2015) The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding. PLoS Genet. PMID:26107960.

Kolodziejczyk, A. A., Kim, J. K., Svensson, V., Marioni, J. C., and Teichmann, S. A. (2015) The technology and biology of single-cell RNA sequencing. Mol Cell. PMID:26000846.

Stubbington, M. J., Mahata, B., Svensson, V., Deonarine, A., Nissen, J. K., Betz, A. G., and Teichmann, S. A. (2015) An atlas of mouse CD4(+) T cell transcriptomes. Biol Direct. PMID:25886751.

Marsh, J. A., Rees, H. A., Ahnert, S. E., and Teichmann, S. A. (2015) Structural and evolutionary versatility in protein complexes with uneven stoichiometry. Nat Commun. PMID:25775164.

Stegle, O., Teichmann, S. A., and Marioni, J. C. (2015) Computational and analytical challenges in single-cell transcriptomics. Nat Rev Genet. PMID:25628217.

Buettner, F., Natarajan, K. N., Casale, F. P., Proserpio, V., Scialdone, A., Theis, F. J., Teichmann, S. A., Marioni, J. C., and Stegle, O. (2015) Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nat Biotechnol. PMID:25599176.

Marsh, J. A. and Teichmann, S. A. (2015) Structure, dynamics, assembly, and evolution of protein complexes. Annu Rev Biochem. PMID:25494300.

Perica, T., Kondo, Y., Tiwari, S. P., McLaughlin, S. H., Kemplen, K. R., Zhang, X., Steward, A., Reuter, N., Clarke, J., and Teichmann, S. A. (2014) Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Science. PMID:25525255.

Marsh, J. A. and Teichmann, S. A. (2014) Protein flexibility facilitates quaternary structure assembly and evolution. PLoS Biol. PMID:24866000.

Mahata, B., Zhang, X., Kolodziejczyk, A. A., Proserpio, V., [...], Göttgens, B., Arlt, W., McKenzie, A. N. J., and Teichmann, S. A. (2014) Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis. Cell Rep. PMID:24813893.

Marsh, J. A. and Teichmann, S. A. (2014) Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure. Bioessays. PMID:24272815.

Teichmann, S. A. (2013) Immunology meets genomics. Brief Funct Genomics. PMID:24273194.

Brennecke, P., Anders, S., Kim, J. K., Kołodziejczyk, A. A., [...], Benes, V., Teichmann, S. A., Marioni, J. C., and Heisler, M. G. (2013) Accounting for technical noise in single-cell RNA-seq experiments. Nat Methods. PMID:24056876.

Zhang, X., Perica, T., and Teichmann, S. A. (2013) Evolution of protein structures and interactions from the perspective of residue contact networks. Curr Opin Struct Biol. PMID:23890840.

Hall, Z., Hernández, H., Marsh, J. A., Teichmann, S. A., and Robinson, C. V. (2013) The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes. Structure. PMID:23850452.

Roberts, E. W., Deonarine, A., Jones, J. O., Denton, A. E., [...], Brindle, K. M., Teichmann, S. A., Tuveson, D. A., and Fearon, D. T. (2013) Depletion of stromal cells expressing fibroblast activation protein-α from skeletal muscle and bone marrow results in cachexia and anemia. J Exp Med. PMID:23712428.

Marsh, J. A., Hernández, H., Hall, Z., Ahnert, S. E., Perica, T., Robinson, C. V., and Teichmann, S. A. (2013) Protein complexes are under evolutionary selection to assemble via ordered pathways. Cell. PMID:23582331.

Nishi, H., Fong, J. H., Chang, C., Teichmann, S. A., and Panchenko, A. R. (2013) Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes. Mol Biosyst. PMID:23364837.

Levy, E. D., De, S., and Teichmann, S. A. (2012) Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc Natl Acad Sci U S A. PMID:23184996.

Teichmann, S. A., Wigge, P. A., and Charoensawan, V. (2012) Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes. Cell Cycle. PMID:23165207.

Marsh, J. A., Teichmann, S. A., and Forman-Kay, J. D. (2012) Probing the diverse landscape of protein flexibility and binding. Curr Opin Struct Biol. PMID:22999889.

Charoensawan, V., Janga, S. C., Bulyk, M. L., Babu, M. M., and Teichmann, S. A. (2012) DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes. Mol Cell. PMID:22841002.

Perica, T., Marsh, J. A., Sousa, F. L., Natan, E., Colwell, L. J., Ahnert, S. E., and Teichmann, S. A. (2012) The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture. Biochem Soc Trans. PMID:22616857.

Perica, T., Chothia, C., and Teichmann, S. A. (2012) Evolution of oligomeric state through geometric coupling of protein interfaces. Proc Natl Acad Sci U S A. PMID:22566652.

Liberles, D. A., Teichmann, S. A., Bahar, I., Bastolla, U., [...], and Whelan, S. (2012) The interface of protein structure, protein biophysics, and molecular evolution. Protein Sci. PMID:22528593.

Hebenstreit, D., Deonarine, A., Babu, M. M., and Teichmann, S. A. (2012) Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells. Curr Opin Cell Biol. PMID:22498241.

Brookes, E., Santiago, I., Hebenstreit, D., Morris, K. J., [...], Kimura, H., Ragoussis, J., Teichmann, S. A., and Pombo, A. (2012) Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell. PMID:22305566.

Vaquerizas, J. M., Teichmann, S. A., and Luscombe, N. M. (2012) How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome. Methods Mol Biol. PMID:21938617.

Hebenstreit, D., Fang, M., Gu, M., Charoensawan, V., van Oudenaarden, A., and Teichmann, S. A. (2011) RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Mol Syst Biol. PMID:21654674.

Marsh, J. A. and Teichmann, S. A. (2011) Relative solvent accessible surface area predicts protein conformational changes upon binding. Structure. PMID:21645856.

Hebenstreit, D. and Teichmann, S. A. (2011) Analysis and simulation of gene expression profiles in pure and mixed cell populations. Phys Biol. PMID:21572174.

Hebenstreit, D., Gu, M., Haider, S., Turner, D. J., Liò, P., and Teichmann, S. A. (2011) EpiChIP: gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Res. PMID:21131282.

Su, J., Teichmann, S. A., and Down, T. A. (2010) Assessing computational methods of cis-regulatory module prediction. PLoS Comput Biol. PMID:21152003.

Charoensawan, V., Adryan, B., Martin, S., Söllner, C., Thisse, B., Thisse, C., Wright, G. J., and Teichmann, S. A. (2010) The impact of gene expression regulation on evolution of extracellular signaling pathways. Mol Cell Proteomics. PMID:20935258.

Charoensawan, V., Wilson, D., and Teichmann, S. A. (2010) Genomic repertoires of DNA-binding transcription factors across the tree of life. Nucleic Acids Res. PMID:20675356.

Charoensawan, V., Wilson, D., and Teichmann, S. A. (2010) Lineage-specific expansion of DNA-binding transcription factor families. Trends Genet. PMID:20675012.

Venkatakrishnan, A. J., Levy, E. D., and Teichmann, S. A. (2010) Homomeric protein complexes: evolution and assembly. Biochem Soc Trans. PMID:20658970.

Marsh, J. A. and Teichmann, S. A. (2010) How do proteins gain new domains?. Genome Biol. PMID:20630117.

Levy, E. D. and Teichmann, S. A. (2010) Systemizing the structures and structuring the system. Expert Rev Proteomics. PMID:20536302.

Teichmann, S. A. and Grishin, N. (2010) Sequences and topology: evolution of proteins and evolution of computational approaches. Curr Opin Struct Biol. PMID:20483587.

Adryan, B. and Teichmann, S. A. (2010) The developmental expression dynamics of Drosophila melanogaster transcription factors. Genome Biol. PMID:20384991.

Pfreundt, U., James, D. P., Tweedie, S., Wilson, D., Teichmann, S. A., and Adryan, B. (2010) FlyTF: improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Res. PMID:19884132.

Wilson, N. K., Miranda-Saavedra, D., Kinston, S., Bonadies, N., [...], Sun, X., Teichmann, S. A., Bannister, A. J., and Göttgens, B. (2009) The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development. Blood. PMID:19346495.

Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A., and Luscombe, N. M. (2009) A census of human transcription factors: function, expression and evolution. Nat Rev Genet. PMID:19274049.

De, S., Teichmann, S. A., and Babu, M. M. (2009) The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Res. PMID:19233772.

Kummerfeld, S. K. and Teichmann, S. A. (2009) Protein domain organisation: adding order. BMC Bioinformatics. PMID:19178743.

Miranda-Saavedra, D., De, S., Trotter, M. W., Teichmann, S. A., and Göttgens, B. (2009) BloodExpress: a database of gene expression in mouse haematopoiesis. Nucleic Acids Res. PMID:18987008.

Gsponer, J., Futschik, M. E., Teichmann, S. A., and Babu, M. M. (2008) Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science. PMID:19039133.

Ahnert, S. E. and Teichmann, S. A. (2008) Networks for all. Genome Biol. PMID:18983700.

De, S., Lopez-Bigas, N., and Teichmann, S. A. (2008) Patterns of evolutionary constraints on genes in humans. BMC Evol Biol. PMID:18840274.

Levy, E. D., Boeri Erba, E., Robinson, C. V., and Teichmann, S. A. (2008) Assembly reflects evolution of protein complexes. Nature. PMID:18563089.

Teichmann, S. A. and Grishin, N. V. (2008) Sequences and topology: from genome structure to protein structure. Curr Opin Struct Biol. PMID:18539451.

Lopez-Bigas, N., De, S., and Teichmann, S. A. (2008) Functional protein divergence in the evolution of Homo sapiens. Genome Biol. PMID:18279504.

Wilson, D., Charoensawan, V., Kummerfeld, S. K., and Teichmann, S. A. (2008) DBD--taxonomically broad transcription factor predictions: new content and functionality. Nucleic Acids Res. PMID:18073188.

Adryan, B. and Teichmann, S. A. (2007) Computational identification of site-specific transcription factors in Drosophila. Fly (Austin). PMID:18820428.

Pereira-Leal, J. B., Levy, E. D., Kamp, C., and Teichmann, S. A. (2007) Evolution of protein complexes by duplication of homomeric interactions. Genome Biol. PMID:17411433.

Han, J.-H., Batey, S., Nickson, A. A., Teichmann, S. A., and Clarke, J. (2007) The folding and evolution of multidomain proteins. Nat Rev Mol Cell Biol. PMID:17356578.

Talavera, D., Vogel, C., Orozco, M., Teichmann, S. A., and de la Cruz, X. (2007) The (in)dependence of alternative splicing and gene duplication. PLoS Comput Biol. PMID:17335345.

Levy, E. D., Pereira-Leal, J. B., Chothia, C., and Teichmann, S. A. (2006) 3D complex: a structural classification of protein complexes. PLoS Comput Biol. PMID:17112313.

Han, J.-H., Kerrison, N., Chothia, C., and Teichmann, S. A. (2006) Divergence of interdomain geometry in two-domain proteins. Structure. PMID:16698554.

Adryan, B. and Teichmann, S. A. (2006) FlyTF: a systematic review of site-specific transcription factors in the fruit fly Drosophila melanogaster. Bioinformatics. PMID:16613907.

Madan Babu, M., Teichmann, S. A., and Aravind, L. (2006) Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol. PMID:16530225.

Pereira-Leal, J. B., Levy, E. D., and Teichmann, S. A. (2006) The origins and evolution of functional modules: lessons from protein complexes. Philos Trans R Soc Lond B Biol Sci. PMID:16524839.

Kummerfeld, S. K. and Teichmann, S. A. (2006) DBD: a transcription factor prediction database. Nucleic Acids Res. PMID:16381970.

Wright, C. F., Teichmann, S. A., Clarke, J., and Dobson, C. M. (2005) The importance of sequence diversity in the aggregation and evolution of proteins. Nature. PMID:16341018.

Teichmann, S. A., Bornberg-Bauer, E., and Luscombe, N. M. (2005) Transcriptional networking. Genome Biol. PMID:16168097.

Pereira-Leal, J. B. and Teichmann, S. A. (2005) Novel specificities emerge by stepwise duplication of functional modules. Genome Res. PMID:15805495.

Kunin, V., Teichmann, S. A., Huynen, M. A., and Ouzounis, C. A. (2005) The properties of protein family space depend on experimental design. Bioinformatics. PMID:15769834.

Bornberg-Bauer, E., Beaussart, F., Kummerfeld, S. K., Teichmann, S. A., and Weiner, 3rd, J. (2005) The evolution of domain arrangements in proteins and interaction networks. Cell Mol Life Sci. PMID:15719170.

Kummerfeld, S. K. and Teichmann, S. A. (2005) Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet. PMID:15680510.

Vogel, C., Teichmann, S. A., and Pereira-Leal, J. (2005) The relationship between domain duplication and recombination. J Mol Biol. PMID:15663950.

Nye, T. M. W., Berzuini, C., Gilks, W. R., Babu, M. M., and Teichmann, S. A. (2005) Statistical analysis of domains in interacting protein pairs. Bioinformatics. PMID:15509600.

Luscombe, N. M., Babu, M. M., Yu, H., Snyder, M., Teichmann, S. A., and Gerstein, M. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature. PMID:15372033.

Teichmann, S. A. and Veitia, R. A. (2004) Genes encoding subunits of stable complexes are clustered on the yeast chromosomes: an interpretation from a dosage balance perspective. Genetics. PMID:15342545.

Babu, M. M., Luscombe, N. M., Aravind, L., Gerstein, M., and Teichmann, S. A. (2004) Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol. PMID:15193307.

Teichmann, S. A. and Babu, M. M. (2004) Gene regulatory network growth by duplication. Nat Genet. PMID:15107850.

Vogel, C., Berzuini, C., Bashton, M., Gough, J., and Teichmann, S. A. (2004) Supra-domains: evolutionary units larger than single protein domains. J Mol Biol. PMID:15095989.

Vogel, C., Bashton, M., Kerrison, N. D., Chothia, C., and Teichmann, S. A. (2004) Structure, function and evolution of multidomain proteins. Curr Opin Struct Biol. PMID:15093836.

Schwabe, J. W. R. and Teichmann, S. A. (2004) Nuclear receptors: the evolution of diversity. Sci STKE. PMID:14747695.

Apic, G., Huber, W., and Teichmann, S. A. (2003) Multi-domain protein families and domain pairs: comparison with known structures and a random model of domain recombination. J Struct Funct Genomics. PMID:14649290.

Vogel, C., Teichmann, S. A., and Chothia, C. (2003) The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Development. PMID:14623821.

Bankier, A. T., Spriggs, H. F., Fartmann, B., Konfortov, B. A., Madera, M., Vogel, C., Teichmann, S. A., Ivens, A., and Dear, P. H. (2003) Integrated mapping, chromosomal sequencing and sequence analysis of Cryptosporidium parvum. Genome Res. PMID:12869580.

Chothia, C., Gough, J., Vogel, C., and Teichmann, S. A. (2003) Evolution of the protein repertoire. Science. PMID:12805536.

Madan Babu, M. and Teichmann, S. A. (2003) Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res. PMID:12582243.

Madan Babu, M. and Teichmann, S. A. (2003) Functional determinants of transcription factors in Escherichia coli: protein families and binding sites. Trends Genet. PMID:12547514.

Teichmann, S. A. (2002) The constraints protein-protein interactions place on sequence divergence. J Mol Biol. PMID:12445777.

Teichmann, S. A. (2002) Principles of protein-protein interactions. Bioinformatics. PMID:12386009.

Teichmann, S. A. and Babu, M. M. (2002) Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends Biotechnol. PMID:12220896.

Rison, S. C. G., Teichmann, S. A., and Thornton, J. M. (2002) Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. J Mol Biol. PMID:12054833.

Jardine, O., Gough, J., Chothia, C., and Teichmann, S. A. (2002) Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae. Genome Res. PMID:12045145.

Teichmann, S. A., Rison, S. C., Thornton, J. M., Riley, M., Gough, J., and Chothia, C. (2001) Small-molecule metabolism: an enzyme mosaic. Trends Biotechnol. PMID:11711174.

Teichmann, S. A., Rison, S. C., Thornton, J. M., Riley, M., Gough, J., and Chothia, C. (2001) The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J Mol Biol. PMID:11518524.

Apic, G., Gough, J., and Teichmann, S. A. (2001) An insight into domain combinations. Bioinformatics. PMID:11472996.

Apic, G., Gough, J., and Teichmann, S. A. (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol. PMID:11428892.

Teichmann, S. A., Murzin, A. G., and Chothia, C. (2001) Determination of protein function, evolution and interactions by structural genomics. Curr Opin Struct Biol. PMID:11406387.

Park, J., Lappe, M., and Teichmann, S. A. (2001) Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol. PMID:11273711.

Teichmann, S. A., Chothia, C., Church, G. M., and Park, J. (2000) Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL. Bioinformatics. PMID:10842732.

Teichmann, S. A. and Chothia, C. (2000) Immunoglobulin superfamily proteins in Caenorhabditis elegans. J Mol Biol. PMID:10698639.

Teichmann, S. A. and Mitchison, G. (2000) Computing protein function. Nat Biotechnol. PMID:10625385.

Teichmann, S. A. and Mitchison, G. (1999) Is there a phylogenetic signal in prokaryote proteins?. J Mol Evol. PMID:10368438.

Teichmann, S. A., Chothia, C., and Gerstein, M. (1999) Advances in structural genomics. Curr Opin Struct Biol. PMID:10361097.

O'Reilly, M., Teichmann, S. A., and Rhodes, D. (1999) Telomerases. Curr Opin Struct Biol. PMID:10047586.

Teichmann, S. A. and Mitchison, G. (1999) Making family trees from gene families. Nat Genet. PMID:9916790.

Teichmann, S. A., Park, J., and Chothia, C. (1998) Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc Natl Acad Sci U S A. PMID:9843945.

Bateman, A., Murzin, A. G., and Teichmann, S. A. (1998) Structure and distribution of pentapeptide repeats in bacteria. Protein Sci. PMID:9655353.

Park, J. and Teichmann, S. A. (1998) DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics. PMID:9545446.

Park, J., Teichmann, S. A., Hubbard, T., and Chothia, C. (1997) Intermediate sequences increase the detection of homology between sequences. J Mol Biol. PMID:9367767.