Publications

Publications

2018

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Single-cell transcriptomics identifies CD44 as a new marker and regulator of haematopoietic stem cells development
Oatley M, Vargel Bolukbasi O, Svensson V, Shvartsman M, Ganter K, Zirngibl K, Pavlovich PV, Milchevskaya V, Foteva V, Natarajan KN, Baying B, Benes V, Patil KR, Teichmann SA, Lancrin C. Preprint DOI: 10.1101/338178
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A rapid and robust method for single cell chromatin accessibility profiling
Chen X, Natarajan KN, Teichmann SA. Preprint DOI: 10.1101/309831
Single-cell RNA-sequencing resolves self-antigen expression during mTEC development.
Miragaia RJ, Zhang X, Gomes T, Svensson V, Ilicic T, Henriksson J, Kar G, Lönnberg T. Scientific reports Volume 8 (2018) p.685 DOI: 10.1038/s41598-017-19100-4

2017

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The IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation
Pramanik J, Chen X, Kar G, Gomes T, Henriksson J, Miao Z, Natarajan K, McKenzie ANJ, Mahata B, Teichmann SA. Preprint DOI: 10.1101/235010
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Unbiased classification of mosquito blood cells by single-cell genomics and high-content imaging
Severo MS, Landry JJ, Lindquist RL, Goosmann C, Brinkmann V, Collier P, Hauser AE, Benes V, Henriksson J, Teichmann SA, Levashina EA. Preprint DOI: 10.1101/234492
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Assessment of batch-correction methods for scRNA-seq data with a new test metric
Buttner M, Miao Z, Wolf A, Teichmann SA, Theis FJ. Preprint DOI: 10.1101/200345
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BraCeR: Reconstruction of B-cell receptor sequences and clonality inference from single-cell RNA-sequencing
Lindeman I, Emerton G, Sollid LM, Teichmann S, Stubbington MJT. Preprint DOI: 10.1101/185504
Single cell transcriptomics of pluripotent stem cells: reprogramming and differentiation.
Natarajan KN, Teichmann SA, Kolodziejczyk AA. Current opinion in genetics & development Volume 46 (2017) p.66-76 DOI: 10.1016/j.gde.2017.06.003
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression.
Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Torlai Triglia E, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Nature communications Volume 8 (2017) p.36 DOI: 10.1038/s41467-017-00052-2
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SpatialDE - Identification of spatially variable genes
Svensson V, Teichmann SA, Stegle O. Preprint DOI: 10.1101/143321
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Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression
Kar G, Kim JK, Kolodziejczyk AA, Natarajan KN, Triglia ET, Mifsud B, Elderkin S, Marioni JC, Pombo A, Teichmann SA. Preprint DOI: 10.1101/117267
Power analysis of single-cell RNA-sequencing experiments.
Svensson V, Natarajan KN, Ly LH, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA. Nature methods Volume 14 (2017) p.381-387 DOI: 10.1038/nmeth.4220
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, Montandon R, Soon MS, Fogg LG, Nair AS, Liligeto U, Stubbington MJ, Ly LH, Bagger FO, Zwiessele M, Lawrence ND, Souza-Fonseca-Guimaraes F, Bunn PT, Engwerda CR, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA. Science immunology Volume 2 (2017) DOI: 10.1126/sciimmunol.aal2192
Aging increases cell-to-cell transcriptional variability upon immune stimulation.
Martinez-Jimenez CP, Eling N, Chen HC, Vallejos CA, Kolodziejczyk AA, Connor F, Stojic L, Rayner TF, Stubbington MJT, Teichmann SA, de la Roche M, Marioni JC, Odom DT. Science (New York, N.Y.) Volume 355 (2017) p.1433-1436 DOI: 10.1126/science.aah4115
Nuclear RNA Decay Pathways Aid Rapid Remodeling of Gene Expression in Yeast.
Bresson S, Tuck A, Staneva D, Tollervey D. Molecular cell Volume 65 (2017) p.787-800.e5 DOI: 10.1016/j.molcel.2017.01.005
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Cell biology: tracking a cell's cycle.
Marx V. Nature methods Volume 14 (2017) p.233-236 DOI: 10.1038/nmeth.4186
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Postdocs, What Would You Tell Your Younger Self?
Cell Volume 168 (2017) p.745-748 DOI: 10.1016/j.cell.2017.02.016
Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.
Carmona SJ, Teichmann SA, Ferreira L, Macaulay IC, Stubbington MJ, Cvejic A, Gfeller D. Genome research Volume 27 (2017) p.451-461 DOI: 10.1101/gr.207704.116

2016

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Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation
Lönnberg T, Svensson V, James KR, Fernandez-Ruiz D, Sebina I, Montandon R, Soon MSF, Fogg LG, Stubbington MJT, Otzen Bagger F, Zwiessele M, Lawrence N, Souza-Fonseca- Guimaraes F, Heath WR, Billker O, Stegle O, Haque A, Teichmann SA. Preprint DOI: 10.1101/074971
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Power Analysis of Single Cell RNA‐Sequencing Experiments
Svensson V, Natarajan KN, Ly L, Miragaia RJ, Labalette C, Macaulay IC, Cvejic A, Teichmann SA. Preprint DOI: 10.1101/073692
Strand-specific, high-resolution mapping of modified RNA polymerase II.
Milligan L, Huynh-Thu VA, Delan-Forino C, Tuck A, Petfalski E, Lombraña R, Sanguinetti G, Kudla G, Tollervey D. Molecular systems biology Volume 12 (2016) p.874 DOI: 10.15252/msb.20166869
The systems biology format converter.
Rodriguez N, Pettit JB, Dalle Pezze P, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N. BMC bioinformatics Volume 17 (2016) p.154 DOI: 10.1186/s12859-016-1000-2
T cell fate and clonality inference from single-cell transcriptomes.
Stubbington MJT, Lönnberg T, Proserpio V, Clare S, Speak AO, Dougan G, Teichmann SA. Nature methods Volume 13 (2016) p.329-332 DOI: 10.1038/nmeth.3800
Cutting-edge single-cell genomics and modelling in immunology.
Proserpio V, Lönnberg T. Immunology and cell biology Volume 94 (2016) p.224 DOI: 10.1038/icb.2015.117
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SC3 - consensus clustering of single-cell RNA-Seq data
Kiselev VY, Kirschner K, Schaub MT, Andrews T, Yiu A, Chandra T, Natarajan KN, Reik W, Barahona M, Green AR, Hemberg M. Preprint DOI: 10.1101/036558

2015

Single-cell technologies to study the immune system.
Proserpio V, Mahata B. Immunology Volume 147 (2016) p.133-140 DOI: 10.1111/imm.12553
Principles of assembly reveal a periodic table of protein complexes.
Ahnert SE, Marsh JA, Hernández H, Robinson CV, Teichmann SA. Science (New York, N.Y.) Volume 350 (2015) p.aaa2245 DOI: 10.1126/science.aaa2245
Single-cell technologies are revolutionizing the approach to rare cells.
Proserpio V, Lönnberg T. Immunology and cell biology Volume 94 (2016) p.225-229 DOI: 10.1038/icb.2015.106
Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.
Kim JK, Kolodziejczyk AA, Ilicic T, Teichmann SA, Marioni JC. Nature communications Volume 6 (2015) p.8687 DOI: 10.1038/ncomms9687
Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation.
Kolodziejczyk AA, Kim JK, Tsang JC, Ilicic T, Henriksson J, Natarajan KN, Tuck AC, Gao X, Bühler M, Liu P, Marioni JC, Teichmann SA. Cell stem cell Volume 17 (2015) p.471-485 DOI: 10.1016/j.stem.2015.09.011
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, Bennett MR, Teichmann SA, Swint-Kruse L. Journal of molecular biology Volume 428 (2016) p.671-678 DOI: 10.1016/j.jmb.2015.09.015
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, Kolodziejczyk AA, Teichmann SA, Lu L, Liu P. Genome biology Volume 16 (2015) p.178 DOI: 10.1186/s13059-015-0739-5
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Simultaneously inferring T cell fate and clonality from single cell transcriptomes
Stubbington MJ, Lönnberg T, Proserpio V, Clare S, Speak AO, Dougan G, Teichmann SA. Preprint DOI: 10.1101/025676
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Biology, wet and dry.
Teichmann S, Pain E. Science (New York, N.Y.) Volume 349 (2015) p.662 DOI: 10.1126/science.349.6248.662
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European Adder bites in dogs in southern Germany. A retrospective study over a 6.5-year period.
Turković V, Teichmann S, Dörfelt R. Tierarztliche Praxis. Ausgabe K, Kleintiere/Heimtiere Volume 43 (2015) p.221-230 DOI: 10.15654/tpk-140364
Computational assignment of cell-cycle stage from single-cell transcriptome data.
Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F. Methods (San Diego, Calif.) Volume 85 (2015) p.54-61 DOI: 10.1016/j.ymeth.2015.06.021
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 genetics Volume 11 (2015) p.e1005251 DOI: 10.1371/journal.pgen.1005251
The technology and biology of single-cell RNA sequencing.
Kolodziejczyk AA, Kim JK, Svensson V, Marioni JC, Teichmann SA. Molecular cell Volume 58 (2015) p.610-620 DOI: 10.1016/j.molcel.2015.04.005
An atlas of mouse CD4(+) T cell transcriptomes.
Stubbington MJ, Mahata B, Svensson V, Deonarine A, Nissen JK, Betz AG, Teichmann SA. Biology direct Volume 10 (2015) p.14 DOI: 10.1186/s13062-015-0045-x
Structural and evolutionary versatility in protein complexes with uneven stoichiometry.
Marsh JA, Rees HA, Ahnert SE, Teichmann SA. Nature communications Volume 6 (2015) p.6394 DOI: 10.1038/ncomms7394
Computational and analytical challenges in single-cell transcriptomics.
Stegle O, Teichmann SA, Marioni JC. Nature reviews. Genetics Volume 16 (2015) p.133-145 DOI: 10.1038/nrg3833
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, Theis FJ, Teichmann SA, Marioni JC, Stegle O. Nature biotechnology Volume 33 (2015) p.155-160 DOI: 10.1038/nbt.3102

2014

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Structure, dynamics, assembly, and evolution of protein complexes.
Marsh JA, Teichmann SA. Annual review of biochemistry Volume 84 (2015) p.551-575 DOI: 10.1146/annurev-biochem-060614-034142
Evolution of oligomeric state through allosteric pathways that mimic ligand binding.
Perica T, Kondo Y, Tiwari SP, McLaughlin SH, Kemplen KR, Zhang X, Steward A, Reuter N, Clarke J, Teichmann SA. Science (New York, N.Y.) Volume 346 (2014) p.1254346 DOI: 10.1126/science.1254346
BioModels: ten-year anniversary.
Chelliah V, Juty N, Ajmera I, Ali R, Dumousseau M, Glont M, Hucka M, Jalowicki G, Keating S, Knight-Schrijver V, Lloret-Villas A, Natarajan KN, Pettit JB, Rodriguez N, Schubert M, Wimalaratne SM, Zhao Y, Hermjakob H, Le Novère N, Laibe C. Nucleic acids research Volume 43 (2015) p.D542-8 DOI: 10.1093/nar/gku1181
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High-flux table-top soft x-ray source driven by sub-2-cycle, CEP stable, 1.85-μm 1-kHz pulses for carbon K-edge spectroscopy.
Cousin SL, Silva F, Teichmann S, Hemmer M, Buades B, Biegert J. Optics letters Volume 39 (2014) p.5383-5386 DOI: 10.1364/ol.39.005383
Protein flexibility facilitates quaternary structure assembly and evolution.
Marsh JA, Teichmann SA. PLoS biology Volume 12 (2014) p.e1001870 DOI: 10.1371/journal.pbio.1001870
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 reports Volume 7 (2014) p.1130-1142 DOI: 10.1016/j.celrep.2014.04.011

2013

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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. Proceedings of the National Academy of Sciences of the United States of America Volume 110 (2013) p.20212-20217 DOI: 10.1073/pnas.1320318110
Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.
Marsh JA, Teichmann SA. BioEssays : news and reviews in molecular, cellular and developmental biology Volume 36 (2014) p.209-218 DOI: 10.1002/bies.201300134
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Immunology meets genomics.
Teichmann SA. Briefings in functional genomics Volume 12 (2013) p.469-470 DOI: 10.1093/bfgp/elt037
From a gene-centric to whole-proteome view of differentiation of T helper cell subsets.
Lönnberg T, Chen Z, Lahesmaa R. Briefings in functional genomics Volume 12 (2013) p.471-482 DOI: 10.1093/bfgp/elt033
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. Nature methods Volume 10 (2013) p.1093-1095 DOI: 10.1038/nmeth.2645
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Holistic systems biology approaches to molecular mechanisms of human helper T cell differentiation to functionally distinct subsets.
Chen Z, Lönnberg T, Lahesmaa R. Scandinavian journal of immunology Volume 78 (2013) p.172-180 DOI: 10.1111/sji.12071
Evolution of protein structures and interactions from the perspective of residue contact networks.
Zhang X, Perica T, Teichmann SA. Current opinion in structural biology Volume 23 (2013) p.954-963 DOI: 10.1016/j.sbi.2013.07.004
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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 (London, England : 1993) Volume 21 (2013) p.1325-1337 DOI: 10.1016/j.str.2013.06.004
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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 DOI: 10.1016/j.immuni.2013.05.011
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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. The Journal of experimental medicine Volume 210 (2013) p.1137-1151 DOI: 10.1084/jem.20122344
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 DOI: 10.1016/j.cell.2013.02.044
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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. Molecular bioSystems Volume 9 (2013) p.1620-1626 DOI: 10.1039/c3mb25514j
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Structural, evolutionary, and assembly principles of protein oligomerization.
Levy ED, Teichmann S. Progress in molecular biology and translational science Volume 117 (2013) p.25-51 DOI: 10.1016/b978-0-12-386931-9.00002-7
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T-cell activation induces selective changes of cellular lipidome.
Lonnberg T, Yetukuri L, Seppanen-Laakso T, Lahesmaa R, Oresic M. Frontiers in bioscience (Elite edition) Volume 5 (2013) p.558-573 DOI: 10.2741/e638

2012

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Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.
Levy ED, De S, Teichmann SA. Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.20461-20466 DOI: 10.1073/pnas.1209312109
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Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes.
Teichmann SA, Wigge PA, Charoensawan V. Cell cycle (Georgetown, Tex.) Volume 11 (2012) p.4487-4488 DOI: 10.4161/cc.22666
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Probing the diverse landscape of protein flexibility and binding.
Marsh JA, Teichmann SA, Forman-Kay JD. Current opinion in structural biology Volume 22 (2012) p.643-650 DOI: 10.1016/j.sbi.2012.08.008
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DNA sequence preferences of transcriptional activators correlate more strongly than repressors with nucleosomes.
Charoensawan V, Janga SC, Bulyk ML, Babu MM, Teichmann SA. Molecular cell Volume 47 (2012) p.183-192 DOI: 10.1016/j.molcel.2012.06.028
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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. Biochemical Society transactions Volume 40 (2012) p.475-491 DOI: 10.1042/bst20120056
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Evolution of oligomeric state through geometric coupling of protein interfaces.
Perica T, Chothia C, Teichmann SA. Proceedings of the National Academy of Sciences of the United States of America Volume 109 (2012) p.8127-8132 DOI: 10.1073/pnas.1120028109
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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 science : a publication of the Protein Society Volume 21 (2012) p.769-785 DOI: 10.1002/pro.2071
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Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells.
Hebenstreit D, Deonarine A, Babu MM, Teichmann SA. Current opinion in cell biology Volume 24 (2012) p.350-358 DOI: 10.1016/j.ceb.2012.03.007
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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 DOI: 10.1016/j.stem.2011.12.017
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 in molecular biology (Clifton, N.J.) Volume 786 (2012) p.3-19 DOI: 10.1007/978-1-61779-292-2_1