Publications

2015

An atlas of mouse CD4(+) T cell transcriptomes.
Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK, Betz AG, Teichmann SA.
Biol Direct Volume 10 (2015) p.14

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding.
Xie X, Stubbington MJ, Nissen JK, Andersen KG, Hebenstreit D, Teichmann SA, Betz AG.
PLoS Genet Volume 11 (2015) p.e1005251

2014

Protein flexibility facilitates quaternary structure assembly and evolution.
Marsh JA, Teichmann SA.
PLoS Biol Volume 12 (2014) p.e1001870

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, Taylor AE, Hebenstreit D, Dingler FA, Moignard V, Göttgens B, Arlt W, McKenzie AN, Teichmann SA.
Cell Rep Volume 7 (2014) p.1130-1142

Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.
Marsh JA, Teichmann SA.
Bioessays Volume 36 (2014) p.209-218

2013

Structural, evolutionary, and assembly principles of protein oligomerization.
Levy ED, Teichmann S.
Prog Mol Biol Transl Sci Volume 117 (2013) p.25-51

Global chromatin state analysis reveals lineage-specific enhancers during the initiation of human T helper 1 and T helper 2 cell polarization.
Hawkins RD, Larjo A, Tripathi SK, Wagner U, Luu Y, Lönnberg T, Raghav SK, Lee LK, Lund R, Ren B, Lähdesmäki H, Lahesmaa R.
Immunity Volume 38 (2013) p.1271-1284

From a gene-centric to whole-proteome view of differentiation of T helper cell subsets.
Lönnberg T, Chen Z, Lahesmaa R.
Brief Funct Genomics Volume 12 (2013) p.471-482

T-cell activation induces selective changes of cellular lipidome.
Lonnberg T, Yetukuri L, Seppanen-Laakso T, Lahesmaa R, Oresic M.
Front Biosci (Elite Ed) Volume 5 (2013) p.558-573

Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets.
Chen Z, Lönnberg T, Lahesmaa R.
Scand J Immunol Volume 78 (2013) p.172-180

Depletion of stromal cells expressing fibroblast activation protein-α from skeletal muscle and bone marrow results in cachexia and anemia.
Roberts EW, Deonarine A, Jones JO, Denton AE, Feig C, Lyons SK, Espeli M, Kraman M, McKenna B, Wells RJ, Zhao Q, Caballero OL, Larder R, Coll AP, O'Rahilly S, Brindle KM, Teichmann SA, Tuveson DA, Fearon DT.
J Exp Med Volume 210 (2013) p.1137-1151

Accounting for technical noise in single-cell RNA-seq experiments.
Brennecke P, Anders S, Kim JK, Kołodziejczyk AA, Zhang X, Proserpio V, Baying B, Benes V, Teichmann SA, Marioni JC, Heisler MG.
Nat Methods Volume 10 (2013) p.1093-1095

The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes.
Hall Z, Hernández H, Marsh JA, Teichmann SA, Robinson CV.
Structure Volume 21 (2013) p.1325-1337

Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic cancer.
Feig C, Jones JO, Kraman M, Wells RJ, Deonarine A, Chan DS, Connell CM, Roberts EW, Zhao Q, Caballero OL, Teichmann SA, Janowitz T, Jodrell DI, Tuveson DA, Fearon DT.
Proc Natl Acad Sci U S A Volume 110 (2013) p.20212-20217

Protein complexes are under evolutionary selection to assemble via ordered pathways.
Marsh JA, Hernández H, Hall Z, Ahnert SE, Perica T, Robinson CV, Teichmann SA.
Cell Volume 153 (2013) p.461-470

Non-coding transcription and large-scale nuclear organisation of immunoglobulin recombination.
Stubbington MJ, Corcoran AE.
Curr Opin Genet Dev Volume 23 (2013) p.81-88

Evolution of protein structures and interactions from the perspective of residue contact networks.
Zhang X, Perica T, Teichmann SA.
Curr Opin Struct Biol Volume 23 (2013) p.954-963

Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes.
Nishi H, Fong JH, Chang C, Teichmann SA, Panchenko AR.
Mol Biosyst Volume 9 (2013) p.1620-1626

Immunology meets genomics.
Teichmann SA.
Brief Funct Genomics Volume 12 (2013) p.469-470

2012

The interface of protein structure, protein biophysics, and molecular evolution.
Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.
Protein Sci Volume 21 (2012) p.769-785

Evolution of oligomeric state through geometric coupling of protein interfaces.
Perica T, Chothia C, Teichmann SA.
Proc Natl Acad Sci U S A Volume 109 (2012) p.8127-8132

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.
Levy ED, De S, Teichmann SA.
Proc Natl Acad Sci U S A Volume 109 (2012) p.20461-20466

Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs.
Brookes E, de Santiago I, Hebenstreit D, Morris KJ, Carroll T, Xie SQ, Stock JK, Heidemann M, Eick D, Nozaki N, Kimura H, Ragoussis J, Teichmann SA, Pombo A.
Cell Stem Cell Volume 10 (2012) p.157-170

Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes.
Teichmann SA, Wigge PA, Charoensawan V.
Cell Cycle Volume 11 (2012) p.4487-4488

Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells.
Hebenstreit D, Deonarine A, Babu MM, Teichmann SA.
Curr Opin Cell Biol Volume 24 (2012) p.350-358

DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.
Charoensawan V, Janga SC, Bulyk ML, Babu MM, Teichmann SA.
Mol Cell Volume 47 (2012) p.183-192

How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome.
Vaquerizas JM, Teichmann SA, Luscombe NM.
Methods Mol Biol Volume 786 (2012) p.3-19

The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture.
Perica T, Marsh JA, Sousa FL, Natan E, Colwell LJ, Ahnert SE, Teichmann SA.
Biochem Soc Trans Volume 40 (2012) p.475-491

Probing the diverse landscape of protein flexibility and binding.
Marsh JA, Teichmann SA, Forman-Kay JD.
Curr Opin Struct Biol Volume 22 (2012) p.643-650