2016
- Felipe A Vieira Braga, Sarah A Teichmann, Xi Chen. (2016) Genetics and immunity in the era of single cell genomics. Human Molecular Genetics
- Valentina Proserpio, Andrea Piccolo, Liora Haim-Vilmovsky, Gozde Kar, Tapio Lönnberg, Valentine Svensson, Jhuma Pramanik, Kedar Nath Natarajan, Weichao Zhai, Xiuwei Zhang, Giacomo Donati, Melis Kayikci, Jurij Kotar, Andrew N. J. McKenzie, Ruddy Montandon, Oliver Billker, Steven Woodhouse, Pietro Cicuta, Mario NicodemiEmail author and Sarah A. Teichmann. (2016) Single-cell analysis of CD4+ T-cell differentiation reveals three major cell states and progressive acceleration of proliferation Genome Biology
- Proserpio, V. and Mahata, B. (2016), Single-cell technologies to study the immune system. Immunology, 147 133–140
- Michael JT Stubbington, Tapio Lönnberg, Valentina Proserpio, Simon Clare, Anneliese O Speak, Gordon Dougan, Sarah A Teichmann. (2016) T cell fate and clonality inference from single-cell transcriptomes. Nature Methods, 13 329-332
- Sousa, F.L., Parente, D.J., Shis, D.L., Hessman, J.A., Chazelle, A., Bennett, M.R., Teichmann, S.A., Swint-Kruse, L. (2016) AlloRep: A Repository of Sequence, Structural and Mutagenesis Data for the LacI/GalR Transcription Regulators. Journal of Molecular Biology, 428 (4) 671-678
- Ilicic, T., Kim, J.K., Kolodziejczyk, A.A., Bagger, F.O., McCarthy, D.J., Marioni, J.C., Teichmann, S.A. (2016) Classification of low quality cells from single-cell RNA-seq data. Genome Biology, 17 (1)
2015
- Valentina Properpio and Tapio Lonnberg. (2015) Single-cell technologies are revolutionizing the approach to rare cells. Immunology & Cell Biology, 94 225-229
- Ahnert, S.E., Marsh, J.A., Hernández, H., Robinson, C.V., Teichmann, S.A. (2015) Principles of assembly reveal a periodic table of protein complexes. Science, 350 (6266)
- Buettner, F., Natarajan, K.N., Casale, F.P., Proserpio, V., Scialdone, A. (2015) Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nature Biotechnology, 33 (2) 155-160
- Stubbington, M.J.T., Mahata, B., Svensson, V., Deonarine, A., Nissen, J.K. (2015) An atlas of mouse CD4+ T cell transcriptomes. Biology Direct, 10 (1)
- Kolodziejczyk, A.A., Kim, J.K., Tsang, J.C.H., Ilicic, T., Henriksson, J. (2015) Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation. Cell Stem Cell, 17 (4) 471-485
- Xie, X., Stubbington, M.J.T., Nissen, J.K., Andersen, K.G., Hebenstreit, D. (2015) The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding. PLoS Genetics, 11 (6)
- Marsh, J.A., Rees, H.A., Ahnert, S.E., Teichmann, S.A. (2015) Structural and evolutionary versatility in protein complexes with uneven stoichiometry. Nature communications, 6 6394
- Kim, J.K., Kolodziejczyk, A.A., Illicic, T., Teichmann, S.A., Marioni, J.C. (2015) Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression. Nature Communications, 6
2014
- Mahata, B., Zhang, X., Kolodziejczyk, A.A., Proserpio, V., Haim-Vilmovsky, L. (2014) Single-cell RNA sequencing reveals T helper cells synthesizing steroids De Novo to contribute to immune homeostasis. Cell Reports, 7 (4) 1130-1142
- Perica, T., Kondo, Y., Tiwari, S.P., McLaughlin, S.H., Kemplen, K.R. (2014) Evolution of oligomeric state through allosteric pathways that mimic ligand binding. Science, 346 (6216)
- Marsh, J.A., Teichmann, S.A. (2014) Protein Flexibility Facilitates Quaternary Structure Assembly and Evolution. PLoS Biology, 12 (5)
- Marsh, J.A., Teichmann, S.A. (2014) Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure. BioEssays, 36 (2) 209-218
2013
- Marsh, J.A., Hernández, H., Hall, Z., Ahnert, S.E., Perica, T. (2013) Protein complexes are under evolutionary selection to assemble via ordered pathways. Cell, 153 (2) 461-470
- Nishi, H., Fong, J.H., Chang, C., Teichmann, S.A., Panchenko, A.R. (2013) Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: Analysis of human protein complexes. Molecular BioSystems, 9 (7) 1620-1626
- Levy, E.D., Teichmann, S. (2013) Structural, evolutionary, and assembly principles of protein oligomerization. Progress in Molecular Biology and Translational Science, 117 25-51
- Feig, C., Jones, J.O., Kraman, M., Wells, R.J.B., Deonarine, A. (2013) Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic cancer. Proceedings of the National Academy of Sciences of the United States of America, 110 (50) 20212-20217
- Roberts, E.W., Deonarine, A., Jones, J.O., Denton, A.E., Feig, C. (2013) Depletion of stromal cells expressing fibroblast activation protein-α from skeletal muscle and bone marrow results in cachexia and anemia. Journal of Experimental Medicine, 210 (6) 1137-1151
- Hall, Z., Hernández, H., Marsh, J.A., Teichmann, S.A., Robinson, C.V. (2013) The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes. Structure, 21 (8) 1325-1337
- Brennecke, P., Anders, S., Kim, J.K., Kołodziejczyk, A.A., Zhang, X. (2013) Accounting for technical noise in single-cell RNA-seq experiments. Nature Methods, 10 (11) 1093-1098
2012
- Schumann, D., Kiselev, D., Teichmann, S., Synal, H.-A., Kubik, P. (2012) Radiochemical analysis of concrete samples from accelerator waste. Radiochimica Acta, 100 (11) 851-856
- Charoensawan, V., Janga, S.C., Bulyk, M.L., Babu, M.M., Teichmann, S.A. (2012) DNA Sequence Preferences of Transcriptional Activators Correlate More Strongly than Repressors with Nucleosomes. Molecular Cell, 47 (2) 183-192
- Perica, T., Chothia, C., Teichmann, S.A. (2012) Evolution of oligomeric state through geometric coupling of protein interfaces. Proceedings of the National Academy of Sciences of the United States of America, 109 (21) 8127-8132
- Vaquerizas, J.M., Teichmann, S.A., Luscombe, N.M. (2012) How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome. Methods in Molecular Biology, 786 3-19
- Schlosser, M., Kruse, J., Gierl, C., Teichmann, S., Tichelmann, S. (2012) Fast transport, atom sample splitting and single-atom qubit supply in two-dimensional arrays of optical microtraps. New Journal of Physics, 14
- Levy, E.D., De, S., Teichmann, S.A. (2012) Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proceedings of the National Academy of Sciences of the United States of America, 109 (50) 20461-20466
- Brookes, E., De Santiago, I., Hebenstreit, D., Morris, K.J., Carroll, T. (2012) Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. Cell Stem Cell, 10 (2) 157-170
2011
- Hebenstreit, D., Gu, M., Haider, S., Turner, D.J., Lió, P. (2011) EpiChIP: Gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Research, 39 (5)
- Hebenstreit, D., Teichmann, S.A. (2011) Analysis and simulation of gene expression profiles in pure and mixed cell populations. Physical Biology, 8 (3)
- Marsh, J.A., Teichmann, S.A. (2011) Relative solvent accessible surface area predicts protein conformational changes upon binding. Structure, 19 (6) 859-867
- Hebenstreit, D., Fang, M., Gu, M., Charoensawan, V., Van Oudenaarden, A. (2011) RNA sequencing reveals two major classes of gene expression levels in metazoan cells. Molecular Systems Biology, 7
2010
- Charoensawan, V., Adryan, B., Martin, S., Söllner, C., Thisse, B. (2010) The impact of gene expression regulation on evolution of extracellular signaling pathways. Molecular and Cellular Proteomics, 9 (12) 2666-2677
- Su, J., Teichmann, S.A., Down, T.A. (2010) Assessing computational methods of cis-regulatory module prediction. PLoS Computational Biology, 6 (12)
- Martin, S., Söllner, C., Charoensawan, V., Adryan, B., Thisse, B. (2010) Construction of a large extracellular protein interaction network and its resolution by spatiotemporal expression profiling. Molecular and Cellular Proteomics, 9 (12) 2654-2665
- Marsh, J.A., Teichmann, S.A. (2010) How do proteins gain new domains?. Genome Biology, 11 (7)
- Ravasi, T., Suzuki, H., Cannistraci, C.V., Katayama, S., Bajic, V.B. (2010) An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man. Cell, 140 (5) 744-752
- Adryan, B., Teichmann, S.A. (2010) The developmental expression dynamics of Drosophila melanogaster transcription factors. Genome Biology, 11 (4)
- Teichmann, S., Chen, B., Dilanian, R.A., Hannaford, P., Van Dao, L. (2010) Experimental aspects of multiharmonic-order coherent diffractive imaging. Journal of Applied Physics, 108 (2)
2009
- Chen, B., Dilanian, R.A., Teichmann, S., Abbey, B., Peele, A.G. (2009) Multiple wavelength diffractive imaging. Physical Review A - Atomic, Molecular, and Optical Physics, 79 (2)
- Teichmann, S., Hannaford, P., Van Dao, L. (2009) Phase-matched emission of few high-harmonic orders from a helium gas cell. Applied Physics Letters, 94 (17)
- Miranda-Saavedra, D., De, S., Trotter, M.W., Teichmann, S.A., Göttgens, B. (2009) BloodExpress: A database of gene expression in mouse haematopoiesis. Nucleic Acids Research, 37 (SUPPL. 1) D873-D879
- Kummerfeld, S.K., Teichmann, S.A. (2009) Protein domain organisation: Adding order. BMC Bioinformatics, 10
- De, S., Teichmann, S.A., Babu, M.M. (2009) The impact of genomic neighborhood on the evolution of human and chimpanzee transcriptome. Genome Research, 19 (5) 785-794
- Suzuki, H., Forrest, A.R.R., Van Nimwegen, E., Daub, C.O., Balwierz, P.J. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, 41 (5) 553-562
- Teichmann, S., Chen, B., Dilanian, R.A., Hannaford, P., Dao, L.V. (2009) Spectral characteristics across the spatial profile of a high-harmonic beam. Journal of Physics D: Applied Physics, 42 (13)
- Pfreundt, U., James, D.P., Tweedie, S., Wilson, D., Teichmann, S.A. (2009) FlyTF: Improved annotation and enhanced functionality of the Drosophila transcription factor database. Nucleic Acids Research, 38 (SUPPL.1) D443-D447
- Watkins, N.A., Gusnanto, A., De Bono, B., De, S., Miranda-Saavedra, D. (2009) A HaemAtlas: Characterizing gene expression in differentiated human blood cells. Blood, 113 (19) e1-e9
- Wilson, N.K., Miranda-Saavedra, D., Kinston, S., Bonadies, N., Foster, S.D. (2009) The transcriptional program controlled by the stem cell leukemia gene Scl /Tal1 during early embryonic hematopoietic development. Blood, 113 (22) 5456-5465
- Dilanian, R.A., Chen, B., Williams, G.J., Quiney, H.M., Nugent, K.A. (2009) Diffractive imaging using a polychromatic high-harmonic generation soft-x-ray source. Journal of Applied Physics, 106 (2)
2008
- Wilson, D., Charoensawan, V., Kummerfeld, S.K., Teichmann, S.A. (2008) DBD - Taxonomically broad transcription factor predictions: New content and functionality. Nucleic Acids Research, 36 (SUPPL. 1) D88-D92
- Loos, R.J.F., Lindgren, C.M., Li, S., Wheeler, E., Zhao, J.H. (2008) Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nature Genetics, 40 (6) 768-775
- Van Dao, L., Teichmann, S., Hannaford, P. (2008) Phase-matching for generation of few high order harmonics in a semi-infinite gas cell. Physics Letters, Section A: General, Atomic and Solid State Physics, 372 (31) 5254-5257
- Lopez-Bigas, N., De, S., Teichmann, S.A. (2008) Functional protein divergence in the evolution of Homo sapiens. Genome Biology, 9 (2)
- Levy, E.D., Erba, E.B., Robinson, C.V., Teichmann, S.A. (2008) Assembly reflects evolution of protein complexes. Nature, 453 (7199) 1262-1265
- Dilanian, R.A., Chen, B., Teichmann, S., Dao, L.V., Quiney, H.M. (2008) High-harmonic-generation spectrum reconstruction from Young's double-slits interference pattern using the maximum entropy method. Optics Letters, 33 (20) 2341-2343
- Gsponer, J., Futschik, M.E., Teichmann, S.A., Babu, M.M. (2008) Tight regulation of unstructured proteins: From transcript synthesis to protein degradation. Science, 322 (5906) 1365-1368
- De, S., Lopez-Bigas, N., Teichmann, S.A. (2008) Patterns of evolutionary constraints on genes in humans. BMC Evolutionary Biology, 8 (1)
- Van Dao, L., Teichmann, S., Davis, J., Hannaford, P. (2008) Generation of high flux, highly coherent extreme ultraviolet radiation in a gas cell. Journal of Applied Physics, 104 (2)
2007
- Nir-El, Y., Haquin, G., Yungreiss, Z., Hass, M., Goldring, G. (2007) Precision measurement of the decay rate of Be7 in host materials. Physical Review C - Nuclear Physics, 75 (1)
- Adryan, B., Teichmann, S.A. (2007) Computational identification of site-specific transcription factors in Drosophila. Fly, 1 (3) 142-145
- Clark, A.G., Eisen, M.B., Smith, D.R., Bergman, C.M., Oliver, B. (2007) Evolution of genes and genomes on the Drosophila phylogeny. Nature, 450 (7167) 203-218
- Pereira-Leal, J.B., Levy, E.D., Kamp, C., Teichmann, S.A. (2007) Evolution of protein complexes by duplication of homomeric interactions. Genome Biology, 8 (4)
- Talavera, D., Vogel, C., Orozco, M., Teichmann, S.A., De La Cruz, X. (2007) The (In)dependence of alternative splicing and gene duplication. PLoS Computational Biology, 3 (3) 0375-0388
2006
- Nye, T.M.W., Berzuini, C., Gilks, W.R., Babu, M.M., Teichmann, S. (2006) Predicting the strongest domain-domain contact in interacting protein pairs. Statistical Applications in Genetics and Molecular Biology, 5 (1) i-17
- Pereira-Leal, J.B., Levy, E.D., Teichmann, S.A. (2006) The origins and evolution of functional modules: Lessons from protein complexes. Philosophical Transactions of the Royal Society B: Biological Sciences, 361 (1467) 507-517
- Han, J.-H., Kerrison, N., Chothia, C., Teichmann, S.A. (2006) Divergence of Interdomain Geometry in Two-Domain Proteins. Structure, 14 (5) 935-945
- Kummerfeld, S.K., Teichmann, S.A. (2006) DBD: a transcription factor prediction database.. Nucleic acids research., 34 (Database issue) D74-81
- Syassen, N., Volz, T., Teichmann, S., Dürr, S., Rempe, G. (2006) Collisional decay of Rb87 Feshbach molecules at 1005.8 G. Physical Review A - Atomic, Molecular, and Optical Physics, 74 (6)
- Nye, T.M., Berzuini, C., Gilks, W.R., Babu, M.M., Teichmann, S. (2006) Predicting the strongest domain-domain contact in interacting protein pairs.. Statistical applications in genetics and molecular biology [electronic resource]., 5 (1)
- Levy, E.D., Pereira-Leal, J.B., Chothia, C., Teichmann, S.A. (2006) 3D complex: A structural classification of protein complexes. PLoS Computational Biology, 2 (11) 1395-1406
- Madan Babu, M., Teichmann, S.A., Aravind, L. (2006) Evolutionary Dynamics of Prokaryotic Transcriptional Regulatory Networks. Journal of Molecular Biology, 358 (2) 614-633
2005
- Pereira-Leal, J.B., Teichmann, S.A. (2005) Novel specificities emerge by stepwise duplication of functional modules. Genome Research, 15 (4) 552-559
- Carninci, P., Kasukawa, T., Katayama, S., Gough, J., Frith, M.C. (2005) The transcriptional landscape of the mammalian genome.. Science, 309 (5740) 1559-1563
- Vogel, C., Teichmann, S.A., Pereira-Leal, J. (2005) The relationship between domain duplication and recombination. Journal of Molecular Biology, 346 (1) 355-365
- Wright, C.F., Teichmann, S.A., Clarke, J., Dobson, C.M. (2005) The importance of sequence diversity in the aggregation and evolution of proteins. Nature, 438 (7069) 878-881
- Nye, T.M.W., Berzuini, C., Gilks, W.R., Babu, M.M., Teichmann, S.A. (2005) Statistical analysis of domains in interacting protein pairs. Bioinformatics, 21 (7) 993-1001
- Kunin, V., Teichmann, S.A., Huynen, M.A., Ouzounis, C.A. (2005) The properties of protein family space depend on experimental design. Bioinformatics, 21 (11) 2618-2622
2004
- Luscombe, N.M., Babu, M.M., Yu, H., Snyder, M., Teichmann, S.A. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431 (7006) 308-312
- Teichmann, S.A., Babu, M.M. (2004) Gene regulatory network growth by duplication. Nature Genetics, 36 (5) 492-496
2003
- Apic, G., Huber, W., Teichmann, S.A. (2003) Multi-domain protein families and domain pairs: Comparison with known structures and a random model of domain recombination. Journal of Structural and Functional Genomics, 4 (2-3) 67-78
- Vogel, C., Teichmann, S.A., Chothia, C. (2003) The immunoglobulin superfamily in Drosophila melanogaster and Caenorhabditis elegans and the evolution of complexity. Development, 130 (25) 6317-6328
2002
- Teichmann, S.A. (2002) The constraints protein-protein interactions place on sequence divergence. Journal of Molecular Biology, 324 (3) 399-407
- Teichmann, S.A., Babu, M.M. (2002) Conservation of gene co-regulation in prokaryotes and eukaryotes. Trends in Biotechnology, 20 (10) 407-410
- Rison, S.C.G., Teichmann, S.A., Thornton, J.M. (2002) Homology, pathway distance and chromosomal localization of the small molecule metabolism enzymes in Escherichia coli. Journal of Molecular Biology, 318 (3) 911-932
- Jardine, O., Gough, J., Chothia, C., Teichmann, S.A. (2002) Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae. Genome Research, 12 (6) 916-929
2001
- Qian, J., Stenger, B., Wilson, C.A., Lin, J., Jansen, R. (2001) PartsList: A web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information. Nucleic Acids Research, 29 (8) 1750-1764
- Park, J., Lappe, M., Teichmann, S.A. (2001) Mapping protein family interactions: Intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. Journal of Molecular Biology, 307 (3) 929-938
- Apic, G., Gough, J., Teichmann, S.A. (2001) An insight into domain combinations. Bioinformatics, 17 (SUPPL. 1) S83-S89
- Teichmann, S.A., Rison, S.C.G., Thornton, J.M., Riley, M., Gough, J. (2001) The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. Journal of Molecular Biology, 311 (4) 693-708
- Apic, G., Gough, J., Teichmann, S.A. (2001) Domain combinations in archaeal, eubacterial and eukaryotic proteomes. Journal of Molecular Biology, 310 (2) 311-325
2000
- Teichmann, S.A., Chothia, C. (2000) Immunoglobulin superfamily proteins in Caenorhabditis elegans. Journal of Molecular Biology, 296 (5) 1367-1383
- Teichmann, S.A., Chothia, C., Church, G.M., Park, J. (2000) Fast assignment of protein structures to sequences using the Intermediate Sequence Library PDB-ISL. Bioinformatics, 16 (2) 117-124
1999
- Teichmann, Sarah, Park, Jong, Chothia, Cyrus (1999) Genome sequences and protein structures. Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB,
- Teichmann, S.A., Mitchison, G. (1999) Is there a phylogenetic signal in prokaryote proteins?. Journal of Molecular Evolution, 49 (1) 98-107
1998
- Teichmann, S.A., Parkt, J., Chothia, C. (1998) Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proceedings of the National Academy of Sciences of the United States of America, 95 (25) 14658-14663
- Park, J., Teichmann, S.A. (1998) DIVCLUS: An automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins. Bioinformatics, 14 (2) 144-150
- Bateman, A., Murzin, A.G., Teichmann, S.A. (1998) Structure and distribution of pentapeptide repeats in bacteria. Protein Science, 7 (6) 1477-1480
1997
1996
- Smith, B.O., Ito, Y., Raine, A., Teichmann, S., Ben-Tovim, L. (1996) An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types. Journal of Biomolecular NMR, 8 (3) 360-368
