Teichmann Group | Gene expression genomics

Teichmann Group | Gene expression genomics

Teichmann Group

Sarah Teichmann's research group - Gene expression genomics - Wellcome Sanger InstituteWellcome Sanger Institute, Genome Research Limited
Sarah Teichmann's research group - Gene expression genomics - Wellcome Sanger Institute

Our Research and Approach

The teams are using single-cell approaches, so called “cell atlas” technologies to combined with human genetics at the cellular level. We combine cutting-edge techniques in wet and dry lab and are applying these methodologies for further understanding of human health, development and disease.

Sarah Teichmann is co-founder and principal leader of the Human Cell Atlas (HCA) international consortium. The International Human Cell Atlas initiative aims to create comprehensive reference maps of all human cells to further understand health and disease.

The team's research focuses on four complementary study areas:

  • Transcriptional regulation and gene expression
  • Single-cell genomics
  • Immunology
  • Protein complexes

To find out more indepth information please click on the read more button.

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Dr Sarah Teichmann, FMedSci
Group Leader

Sarah’s research combines expertise in computational and systems biology with single-cell biology, genomics, structural biology and immunology.  She is co-founder of the global Human Cell Atlas Consortium.

Aldridge, Sarah

Dr Sarah Aldridge
Head of Science Strategy & Planning for Cellular Genetics Programme

Andrew, Tracey

Andrew, Tracey
Tracey Andrew
Executive Administrator Human Cell Atlas
Show Alumni


Chen, Xi

Chen, Xi
Xi Chen
Senior Staff Scientist

Key Projects, Collaborations, Tools & Data

Programmes, Associate Research Programmes and Facilities

Partners and Funders

Internal Partners


  • Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation.

    Henriksson J, Chen X, Gomes T, Ullah U, Meyer KB et al.

    Cell 2019;176;4;882-896.e18

  • Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.

    Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J et al.

    Cell stem cell 2015;17;4;471-85

  • Evolution of oligomeric state through allosteric pathways that mimic ligand binding.

    Perica T, Kondo Y, Tiwari SP, McLaughlin SH, Kemplen KR et al.

    Science (New York, N.Y.) 2014;346;6216;1254346

  • Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.

    Mahata B, Zhang X, Kolodziejczyk AA, Proserpio V, Haim-Vilmovsky L et al.

    Cell reports 2014;7;4;1130-42

  • DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.

    Charoensawan V, Janga SC, Bulyk ML, Babu MM and Teichmann SA

    Molecular cell 2012;47;2;183-92

  • EpiChIP: gene-by-gene quantification of epigenetic modification levels.

    Hebenstreit D, Gu M, Haider S, Turner DJ, Liò P and Teichmann SA

    Nucleic acids research 2011;39;5;e27

  • RNA sequencing reveals two major classes of gene expression levels in metazoan cells.

    Hebenstreit D, Fang M, Gu M, Charoensawan V, van Oudenaarden A and Teichmann SA

    Molecular systems biology 2011;7;497

  • The impact of gene expression regulation on evolution of extracellular signaling pathways.

    Charoensawan V, Adryan B, Martin S, Söllner C, Thisse B et al.

    Molecular & cellular proteomics : MCP 2010;9;12;2666-77

  • Assembly reflects evolution of protein complexes.

    Levy ED, Boeri Erba E, Robinson CV and Teichmann SA

    Nature 2008;453;7199;1262-5

  • DBD--taxonomically broad transcription factor predictions: new content and functionality.

    Wilson D, Charoensawan V, Kummerfeld SK and Teichmann SA

    Nucleic acids research 2008;36;Database issue;D88-92

  • Gene regulatory network growth by duplication.

    Teichmann SA and Babu MM

    Nature genetics 2004;36;5;492-6

  • Domain combinations in archaeal, eubacterial and eukaryotic proteomes.

    Apic G, Gough J and Teichmann SA

    Journal of molecular biology 2001;310;2;311-25

  • Advances in structural genomics.

    Teichmann SA, Chothia C and Gerstein M

    Current opinion in structural biology 1999;9;3;390-9

  • Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements.

    Teichmann SA, Park J and Chothia C

    Proceedings of the National Academy of Sciences of the United States of America 1998;95;25;14658-63

  • Distinct microbial and immune niches of the human colon.

    James KR, Gomes T, Elmentaite R, Kumar N, Gulliver EL et al.

    Nature immunology 2020;21;3;343-353

  • CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes.

    Efremova M, Vento-Tormo M, Teichmann SA and Vento-Tormo R

    Nature protocols 2020

  • A cell atlas of human thymic development defines T cell repertoire formation.

    Park JE, Botting RA, Domínguez Conde C, Popescu DM, Lavaert M et al.

    Science (New York, N.Y.) 2020;367;6480

  • Immunology in the Era of Single-Cell Technologies.

    Efremova M, Vento-Tormo R, Park JE, Teichmann SA and James KR

    Annual review of immunology 2020

  • Deciphering immunity at high plexity and resolution.

    Domínguez Conde C and Teichmann SA

    Nature reviews. Immunology 2020;20;2;77-78

  • Single-cell transcriptomics identifies CD44 as a marker and regulator of endothelial to haematopoietic transition.

    Oatley M, Bölükbası ÖV, Svensson V, Shvartsman M, Ganter K et al.

    Nature communications 2020;11;1;586

  • Nasal DNA methylation profiling of asthma and rhinitis.

    Qi C, Jiang Y, Yang IV, Forno E, Wang T et al.

    The Journal of allergy and clinical immunology 2020

  • Expression Atlas update: from tissues to single cells.

    Papatheodorou I, Moreno P, Manning J, Fuentes AM, George N et al.

    Nucleic acids research 2020;48;D1;D77-D83

  • Computational methods for single-cell omics across modalities.

    Efremova M and Teichmann SA

    Nature methods 2020;17;1;14-17

  • Re-evaluation of human BDCA-2+ DC during acute sterile skin inflammation

    Chen, Yi-Ling, Gomes, Tomas, Hardman et al.

    Journal of Experimental Medicine 2020;217;3

  • scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation.

    Madissoon E, Wilbrey-Clark A, Miragaia RJ, Saeb-Parsy K, Mahbubani KT et al.

    Genome biology 2019;21;1;1

  • Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis.

    Dobie R, Wilson-Kanamori JR, Henderson BEP, Smith JR, Matchett KP et al.

    Cell reports 2019;29;7;1832-1847.e8

  • Immunology Driven by Large-Scale Single-Cell Sequencing.

    Gomes T, Teichmann SA and Talavera-López C

    Trends in immunology 2019;40;11;1011-1021

  • Resolving the fibrotic niche of human liver cirrhosis at single-cell level.

    Ramachandran P, Dobie R, Wilson-Kanamori JR, Dora EF, Henderson BEP et al.

    Nature 2019;575;7783;512-518

  • The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.

    HuBMAP Consortium

    Nature 2019;574;7777;187-192

  • Decoding human fetal liver haematopoiesis.

    Popescu DM, Botting RA, Stephenson E, Green K, Webb S et al.

    Nature 2019;574;7778;365-371

  • Spatiotemporal immune zonation of the human kidney.

    Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW et al.

    Science (New York, N.Y.) 2019;365;6460;1461-1466

  • BBKNN: Fast Batch Alignment of Single Cell Transcriptomes.

    Polański K, Park JE, Young MD, Miao Z, Meyer KB and Teichmann SA

    Bioinformatics (Oxford, England) 2019

  • Single cell analysis of human foetal liver captures the transcriptional profile of hepatobiliary hybrid progenitors.

    Segal JM, Kent D, Wesche DJ, Ng SS, Serra M et al.

    Nature communications 2019;10;1;3350

  • Polychromic Reporter Mice Reveal Unappreciated Innate Lymphoid Cell Progenitor Heterogeneity and Elusive ILC3 Progenitors in Bone Marrow.

    Walker JA, Clark PA, Crisp A, Barlow JL, Szeto A et al.

    Immunity 2019;51;1;104-118.e7

  • 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 et al.

    Nature medicine 2019;25;7;1153-1163

  • The Human Lung Cell Atlas: A High-Resolution Reference Map of the Human Lung in Health and Disease.

    Schiller HB, Montoro DT, Simon LM, Rawlins EL, Meyer KB et al.

    American journal of respiratory cell and molecular biology 2019;61;1;31-41

  • Establishment of porcine and human expanded potential stem cells.

    Gao X, Nowak-Imialek M, Chen X, Chen D, Herrmann D et al.

    Nature cell biology 2019;21;6;687-699

  • Comparative analysis of sequencing technologies for single-cell transcriptomics.

    Natarajan KN, Miao Z, Jiang M, Huang X, Zhou H et al.

    Genome biology 2019;20;1;70

  • The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.

    Taylor DM, Aronow BJ, Tan K, Bernt K, Salomonis N et al.

    Developmental cell 2019;49;1;10-29

  • In conversation with Sarah Teichmann.

    Dhillon P and Teichmann SA

    The FEBS journal 2019;286;8;1445-1450

  • Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation.

    Miragaia RJ, Gomes T, Chomka A, Jardine L, Riedel A et al.

    Immunity 2019;50;2;493-504.e7

  • Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation.

    Henriksson J, Chen X, Gomes T, Ullah U, Meyer KB et al.

    Cell 2019;176;4;882-896.e18

  • A test metric for assessing single-cell RNA-seq batch correction.

    Büttner M, Miao Z, Wolf FA, Teichmann SA and Theis FJ

    Nature methods 2019;16;1;43-49

  • A rapid and robust method for single cell chromatin accessibility profiling.

    Chen X, Miragaia RJ, Natarajan KN and Teichmann SA

    Nature communications 2018;9;1;5345

  • Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement.

    Jia G, Preussner J, Chen X, Guenther S, Yuan X et al.

    Nature communications 2018;9;1;4877

  • Single-cell reconstruction of the early maternal-fetal interface in humans.

    Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M et al.

    Nature 2018;563;7731;347-353

  • Gene expression variability across cells and species shapes innate immunity.

    Hagai T, Chen X, Miragaia RJ, Rostom R, Gomes T et al.

    Nature 2018;563;7730;197-202

  • Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation.

    Pramanik J, Chen X, Kar G, Henriksson J, Gomes T et al.

    Genome medicine 2018;10;1;76

  • Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors.

    Young MD, Mitchell TJ, Vieira Braga FA, Tran MGB, Stewart BJ et al.

    Science (New York, N.Y.) 2018;361;6402;594-599

  • Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging.

    Severo MS, Landry JJM, Lindquist RL, Goosmann C, Brinkmann V et al.

    Proceedings of the National Academy of Sciences of the United States of America 2018;115;32;E7568-E7577

  • BraCeR: B-cell-receptor reconstruction and clonality inference from single-cell RNA-seq.

    Lindeman I, Emerton G, Mamanova L, Snir O, Polanski K et al.

    Nature methods 2018;15;8;563-565

  • Tissue-Restricted Adaptive Type 2 Immunity Is Orchestrated by Expression of the Costimulatory Molecule OX40L on Group 2 Innate Lymphoid Cells.

    Halim TYF, Rana BMJ, Walker JA, Kerscher B, Knolle MD et al.

    Immunity 2018;48;6;1195-1207.e6

  • Editorial overview: Sequences and topology: Dynamic sequences and topologies of proteins.

    Marsh JA and Teichmann SA

    Current opinion in structural biology 2018;50;vii-viii

  • SpatialDE: identification of spatially variable genes.

    Svensson V, Teichmann SA and Stegle O

    Nature methods 2018;15;5;343-346

  • Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins.

    Natan E, Endoh T, Haim-Vilmovsky L, Flock T, Chalancon G et al.

    Nature structural & molecular biology 2018;25;3;279-288

  • Exponential scaling of single-cell RNA-seq in the past decade.

    Svensson V, Vento-Tormo R and Teichmann SA

    Nature protocols 2018;13;4;599-604

  • Mapping human development at single-cell resolution.

    Behjati S, Lindsay S, Teichmann SA and Haniffa M

    Development (Cambridge, England) 2018;145;3

  • Single Cell Gene Expression to Understand the Dynamic Architecture of the Heart.

    Massaia A, Chaves P, Samari S, Miragaia RJ, Meyer K et al.

    Frontiers in cardiovascular medicine 2018;5;167

  • Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation.

    Hegazy AN, West NR, Stubbington MJT, Wendt E, Suijker KIM et al.

    Gastroenterology 2017;153;5;1320-1337.e16

  • Establishment of mouse expanded potential stem cells.

    Yang J, Ryan DJ, Wang W, Tsang JC, Lan G et al.

    Nature 2017;550;7676;393-397

  • The Human Cell Atlas: from vision to reality.

    Rozenblatt-Rosen O, Stubbington MJT, Regev A and Teichmann SA

    Nature 2017;550;7677;451-453

  • Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation.

    Natarajan KN, Teichmann SA and Kolodziejczyk AA

    Current opinion in genetics & development 2017;46;66-76

  • A practical guide to single-cell RNA-sequencing for biomedical research and clinical applications.

    Haque A, Engel J, Teichmann SA and Lönnberg T

    Genome medicine 2017;9;1;75

  • Computational approaches for interpreting scRNA-seq data.

    Rostom R, Svensson V, Teichmann SA and Kar G

    FEBS letters 2017;591;15;2213-2225

  • Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.

    Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E et al.

    Nature communications 2017;8;1;36

  • Wounding induces dedifferentiation of epidermal Gata6+ cells and acquisition of stem cell properties.

    Donati G, Rognoni E, Hiratsuka T, Liakath-Ali K, Hoste E et al.

    Nature cell biology 2017;19;6;603-613

  • Aging increases cell-to-cell transcriptional variability upon immune stimulation.

    Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA et al.

    Science (New York, N.Y.) 2017;355;6332;1433-1436

  • Are cells from a snowman realistic? Cryopreserved tissues as a source for single-cell RNA-sequencing experiments.

    Vieira Braga FA, Teichmann SA and Stubbington MJ

    Genome biology 2017;18;1;54

  • Power analysis of single-cell RNA-sequencing experiments.

    Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C et al.

    Nature methods 2017

  • Single-cell RNA-seq and computational analysis using temporal mixture modelling resolves Th1/Tfh fate bifurcation in malaria.

    Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I et al.

    Science immunology 2017;2;9

  • Regulation, evolution and consequences of cotranslational protein complex assembly.

    Natan E, Wells JN, Teichmann SA and Marsh JA

    Current opinion in structural biology 2017;42;90-97

  • Intrinsic transcriptional heterogeneity in B cells controls early class switching to IgE.

    Wu YL, Stubbington MJ, Daly M, Teichmann SA and Rada C

    The Journal of experimental medicine 2017;214;1;183-196

  • Single-cell analysis at the threshold.

    Chen X, Love JC, Navin NE, Pachter L, Stubbington MJ et al.

    Nature biotechnology 2016;34;11;1111-1118

  • Genetics and immunity in the era of single-cell genomics.

    Vieira Braga FA, Teichmann SA and Chen X

    Human molecular genetics 2016;25;R2;R141-R148

  • Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway.

    Yu Y, Tsang JC, Wang C, Clare S, Wang J et al.

    Nature 2016;539;7627;102-106

  • MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs.

    Eckersley-Maslin MA, Svensson V, Krueger C, Stubbs TM, Giehr P et al.

    Cell reports 2016;17;1;179-192

  • Data on publications, structural analyses, and queries used to build and utilize the AlloRep database.

    Sousa FL, Parente DJ, Hessman JA, Chazelle A, Teichmann SA and Swint-Kruse L

    Data in brief 2016;8;948-57

  • Single-cell genomics: coming of age.

    Linnarsson S and Teichmann SA

    Genome biology 2016;17;97

  • T cell fate and clonality inference from single-cell transcriptomes.

    Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO et al.

    Nature methods 2016;13;4;329-332

  • Voices of biotech.

    Amit I, Baker D, Barker R, Berger B, Bertozzi C et al.

    Nature biotechnology 2016;34;3;270-5

  • AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators.

    Sousa FL, Parente DJ, Shis DL, Hessman JA, Chazelle A et al.

    Journal of molecular biology 2016;428;4;671-8

  • Classification of low quality cells from single-cell RNA-seq data.

    Ilicic T, Kim JK, Kolodziejczyk AA, Bagger FO, McCarthy DJ et al.

    Genome biology 2016;17;29

  • Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells.

    Macaulay IC, Svensson V, Labalette C, Ferreira L, Hamey F et al.

    Cell reports 2016;14;4;966-977

  • Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation.

    Proserpio V, Piccolo A, Haim-Vilmovsky L, Kar G, Lönnberg T et al.

    Genome biology 2016;17;103

  • Principles of assembly reveal a periodic table of protein complexes.

    Ahnert SE, Marsh JA, Hernández H, Robinson CV and Teichmann SA

    Science (New York, N.Y.) 2015;350;6266;aaa2245

  • Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.

    Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J et al.

    Cell stem cell 2015;17;4;471-85

  • Single-cell transcriptomic reconstruction reveals cell cycle and multi-lineage differentiation defects in Bcl11a-deficient hematopoietic stem cells.

    Tsang JC, Yu Y, Burke S, Buettner F, Wang C et al.

    Genome biology 2015;16;178

  • Computational assignment of cell-cycle stage from single-cell transcriptome data.

    Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA et al.

    Methods (San Diego, Calif.) 2015;85;54-61

  • Structural and evolutionary versatility in protein complexes with uneven stoichiometry.

    Marsh JA, Rees HA, Ahnert SE and Teichmann SA

    Nature communications 2015;6;6394

  • Computational and analytical challenges in single-cell transcriptomics.

    Stegle O, Teichmann SA and Marioni JC

    Nature reviews. Genetics 2015;16;3;133-45

  • Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells.

    Buettner F, Natarajan KN, Casale FP, Proserpio V, Scialdone A et al.

    Nature biotechnology 2015;33;2;155-60

  • Structure, dynamics, assembly, and evolution of protein complexes.

    Marsh JA and Teichmann SA

    Annual review of biochemistry 2015;84;551-75

  • Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis.

    Mahata B, Zhang X, Kolodziejczyk AA, Proserpio V, Haim-Vilmovsky L et al.

    Cell reports 2014;7;4;1130-42

  • Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.

    Marsh JA and Teichmann SA

    BioEssays : news and reviews in molecular, cellular and developmental biology 2014;36;2;209-18