Sarah A Teichmann

Sarah A Teichmann

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Sarah A Teichmann

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Deciphering immunity at high plexity and resolution.

Authors:
Cecilia Domínguez Conde Sarah A Teichmann

Nat Rev Immunol 2019 Dec 4. Epub 2019 Dec 4.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1038/s41577-019-0254-0DOI Listing
December 2019

Immunology Driven by Large-Scale Single-Cell Sequencing.

Authors:
Tomás Gomes Sarah A Teichmann Carlos Talavera-López

Trends Immunol 2019 Nov 20;40(11):1011-1021. Epub 2019 Oct 20.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.

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http://dx.doi.org/10.1016/j.it.2019.09.004DOI Listing
November 2019

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

Authors:
Ross Dobie John R Wilson-Kanamori Beth E P Henderson James R Smith Kylie P Matchett Jordan R Portman Karolina Wallenborg Simone Picelli Anna Zagorska Swetha V Pendem Thomas E Hudson Minnie M Wu Grant R Budas David G Breckenridge Ewen M Harrison Damian J Mole Stephen J Wigmore Prakash Ramachandran Chris P Ponting Sarah A Teichmann John C Marioni Neil C Henderson

Cell Rep 2019 Nov;29(7):1832-1847.e8

Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh EH16 4TJ, UK. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.10.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856722PMC
November 2019

Decoding human fetal liver haematopoiesis.

Authors:
Dorin-Mirel Popescu Rachel A Botting Emily Stephenson Kile Green Simone Webb Laura Jardine Emily F Calderbank Krzysztof Polanski Issac Goh Mirjana Efremova Meghan Acres Daniel Maunder Peter Vegh Yorick Gitton Jong-Eun Park Roser Vento-Tormo Zhichao Miao David Dixon Rachel Rowell David McDonald James Fletcher Elizabeth Poyner Gary Reynolds Michael Mather Corina Moldovan Lira Mamanova Frankie Greig Matthew D Young Kerstin B Meyer Steven Lisgo Jaume Bacardit Andrew Fuller Ben Millar Barbara Innes Susan Lindsay Michael J T Stubbington Monika S Kowalczyk Bo Li Orr Ashenberg Marcin Tabaka Danielle Dionne Timothy L Tickle Michal Slyper Orit Rozenblatt-Rosen Andrew Filby Peter Carey Alexandra-Chloé Villani Anindita Roy Aviv Regev Alain Chédotal Irene Roberts Berthold Göttgens Sam Behjati Elisa Laurenti Sarah A Teichmann Muzlifah Haniffa

Nature 2019 10 9;574(7778):365-371. Epub 2019 Oct 9.

Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK.

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http://dx.doi.org/10.1038/s41586-019-1652-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6861135PMC
October 2019

Spatiotemporal immune zonation of the human kidney.

Authors:
Benjamin J Stewart John R Ferdinand Matthew D Young Thomas J Mitchell Kevin W Loudon Alexandra M Riding Nathan Richoz Gordon L Frazer Joy U L Staniforth Felipe A Vieira Braga Rachel A Botting Dorin-Mirel Popescu Roser Vento-Tormo Emily Stephenson Alex Cagan Sarah J Farndon Krzysztof Polanski Mirjana Efremova Kile Green Martin Del Castillo Velasco-Herrera Charlotte Guzzo Grace Collord Lira Mamanova Tevita Aho James N Armitage Antony C P Riddick Imran Mushtaq Stephen Farrell Dyanne Rampling James Nicholson Andrew Filby Johanna Burge Steven Lisgo Susan Lindsay Marc Bajenoff Anne Y Warren Grant D Stewart Neil Sebire Nicholas Coleman Muzlifah Haniffa Sarah A Teichmann Sam Behjati Menna R Clatworthy

Science 2019 09;365(6460):1461-1466

Molecular Immunity Unit, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.

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http://dx.doi.org/10.1126/science.aat5031DOI Listing
September 2019

BBKNN: Fast Batch Alignment of Single Cell Transcriptomes.

Authors:
Krzysztof Polański Jong-Eun Park Matthew D Young Zhichao Miao Kerstin B Meyer Sarah A Teichmann

Bioinformatics 2019 Aug 10. Epub 2019 Aug 10.

Cellular Genetics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btz625DOI Listing
August 2019

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

Authors:
Herbert B Schiller Daniel T Montoro Lukas M Simon Emma L Rawlins Kerstin B Meyer Maximilian Strunz Felipe A Vieira Braga Wim Timens Gerard H Koppelman G R Scott Budinger Janette K Burgess Avinash Waghray Maarten van den Berge Fabian J Theis Aviv Regev Naftali Kaminski Jayaraj Rajagopal Sarah A Teichmann Alexander V Misharin Martijn C Nawijn

Am J Respir Cell Mol Biol 2019 Jul;61(1):31-41

7 Department of Pathology and Medical Biology.

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https://www.atsjournals.org/doi/10.1165/rcmb.2018-0416TR
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http://dx.doi.org/10.1165/rcmb.2018-0416TRDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6604220PMC
July 2019

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

Authors:
Jennifer A Walker Paula A Clark Alastair Crisp Jillian L Barlow Aydan Szeto Ana C F Ferreira Batika M J Rana Helen E Jolin Noe Rodriguez-Rodriguez Meera Sivasubramaniam Richard Pannell James Cruickshank Maria Daly Liora Haim-Vilmovsky Sarah A Teichmann Andrew N J McKenzie

Immunity 2019 07 22;51(1):104-118.e7. Epub 2019 May 22.

MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2019.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6642165PMC
July 2019

A cellular census of human lungs identifies novel cell states in health and in asthma.

Authors:
Felipe A Vieira Braga Gozde Kar Marijn Berg Orestes A Carpaij Krzysztof Polanski Lukas M Simon Sharon Brouwer Tomás Gomes Laura Hesse Jian Jiang Eirini S Fasouli Mirjana Efremova Roser Vento-Tormo Carlos Talavera-López Marnix R Jonker Karen Affleck Subarna Palit Paulina M Strzelecka Helen V Firth Krishnaa T Mahbubani Ana Cvejic Kerstin B Meyer Kourosh Saeb-Parsy Marjan Luinge Corry-Anke Brandsma Wim Timens Ilias Angelidis Maximilian Strunz Gerard H Koppelman Antoon J van Oosterhout Herbert B Schiller Fabian J Theis Maarten van den Berge Martijn C Nawijn Sarah A Teichmann

Nat Med 2019 07 17;25(7):1153-1163. Epub 2019 Jun 17.

Wellcome Sanger Institute, Cambridge, UK.

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http://dx.doi.org/10.1038/s41591-019-0468-5DOI Listing
July 2019

Establishment of porcine and human expanded potential stem cells.

Authors:
Xuefei Gao Monika Nowak-Imialek Xi Chen Dongsheng Chen Doris Herrmann Degong Ruan Andy Chun Hang Chen Melanie A Eckersley-Maslin Shakil Ahmad Yin Lau Lee Toshihiro Kobayashi David Ryan Jixing Zhong Jiacheng Zhu Jian Wu Guocheng Lan Stoyan Petkov Jian Yang Liliana Antunes Lia S Campos Beiyuan Fu Shengpeng Wang Yu Yong Xiaomin Wang Song-Guo Xue Liangpeng Ge Zuohua Liu Yong Huang Tao Nie Peng Li Donghai Wu Duanqing Pei Yi Zhang Liming Lu Fengtang Yang Susan J Kimber Wolf Reik Xiangang Zou Zhouchun Shang Liangxue Lai Azim Surani Patrick P L Tam Asif Ahmed William Shu Biu Yeung Sarah A Teichmann Heiner Niemann Pentao Liu

Nat Cell Biol 2019 06 3;21(6):687-699. Epub 2019 Jun 3.

School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Stem Cell and Regenerative Medicine Consortium, Pokfulam, Hong Kong.

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http://dx.doi.org/10.1038/s41556-019-0333-2DOI Listing
June 2019

Comparative analysis of sequencing technologies for single-cell transcriptomics.

Authors:
Kedar Nath Natarajan Zhichao Miao Miaomiao Jiang Xiaoyun Huang Hongpo Zhou Jiarui Xie Chunqing Wang Shishang Qin Zhikun Zhao Liang Wu Naibo Yang Bo Li Yong Hou Shiping Liu Sarah A Teichmann

Genome Biol 2019 04 9;20(1):70. Epub 2019 Apr 9.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1186/s13059-019-1676-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6454680PMC
April 2019

In conversation with Sarah Teichmann.

Authors:
Paraminder Dhillon Sarah A Teichmann

FEBS J 2019 Apr;286(8):1445-1450

Wellcome Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.1111/febs.14806DOI Listing
April 2019

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

Authors:
Johan Henriksson Xi Chen Tomás Gomes Ubaid Ullah Kerstin B Meyer Ricardo Miragaia Graham Duddy Jhuma Pramanik Kosuke Yusa Riitta Lahesmaa Sarah A Teichmann

Cell 2019 02 10;176(4):882-896.e18. Epub 2019 Jan 10.

Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK; EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK; Theory of Condensed Matter, Cavendish Laboratory, 19 JJ Thomson Ave, Cambridge CB3 0HE, UK. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.11.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6370901PMC
February 2019

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

Authors:
Ricardo J Miragaia Tomás Gomes Agnieszka Chomka Laura Jardine Angela Riedel Ahmed N Hegazy Natasha Whibley Andrea Tucci Xi Chen Ida Lindeman Guy Emerton Thomas Krausgruber Jacqueline Shields Muzlifah Haniffa Fiona Powrie Sarah A Teichmann

Immunity 2019 02 5;50(2):493-504.e7. Epub 2019 Feb 5.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK; Theory of Condensed Matter, Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2019.01.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6382439PMC
February 2019

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

Authors:
Maren Büttner Zhichao Miao F Alexander Wolf Sarah A Teichmann Fabian J Theis

Nat Methods 2019 01 20;16(1):43-49. Epub 2018 Dec 20.

Helmholtz Zentrum München-German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.

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http://www.nature.com/articles/s41592-018-0254-1
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http://dx.doi.org/10.1038/s41592-018-0254-1DOI Listing
January 2019

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

Authors:
Xi Chen Ricardo J Miragaia Kedar Nath Natarajan Sarah A Teichmann

Nat Commun 2018 12 17;9(1):5345. Epub 2018 Dec 17.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://www.nature.com/articles/s41467-018-07771-0
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http://dx.doi.org/10.1038/s41467-018-07771-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6297232PMC
December 2018

Gene expression variability across cells and species shapes innate immunity.

Authors:
Tzachi Hagai Xi Chen Ricardo J Miragaia Raghd Rostom Tomás Gomes Natalia Kunowska Johan Henriksson Jong-Eun Park Valentina Proserpio Giacomo Donati Lara Bossini-Castillo Felipe A Vieira Braga Guy Naamati James Fletcher Emily Stephenson Peter Vegh Gosia Trynka Ivanela Kondova Mike Dennis Muzlifah Haniffa Armita Nourmohammad Michael Lässig Sarah A Teichmann

Nature 2018 11 24;563(7730):197-202. Epub 2018 Oct 24.

Wellcome Sanger Institute, Cambridge, UK.

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http://dx.doi.org/10.1038/s41586-018-0657-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347972PMC
November 2018

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

Authors:
Roser Vento-Tormo Mirjana Efremova Rachel A Botting Margherita Y Turco Miquel Vento-Tormo Kerstin B Meyer Jong-Eun Park Emily Stephenson Krzysztof Polański Angela Goncalves Lucy Gardner Staffan Holmqvist Johan Henriksson Angela Zou Andrew M Sharkey Ben Millar Barbara Innes Laura Wood Anna Wilbrey-Clark Rebecca P Payne Martin A Ivarsson Steve Lisgo Andrew Filby David H Rowitch Judith N Bulmer Gavin J Wright Michael J T Stubbington Muzlifah Haniffa Ashley Moffett Sarah A Teichmann

Nature 2018 11 14;563(7731):347-353. Epub 2018 Nov 14.

Wellcome Sanger Institute, Cambridge, UK.

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http://www.nature.com/articles/s41586-018-0698-6
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http://dx.doi.org/10.1038/s41586-018-0698-6DOI Listing
November 2018

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

Authors:
Jhuma Pramanik Xi Chen Gozde Kar Johan Henriksson Tomás Gomes Jong-Eun Park Kedar Natarajan Kerstin B Meyer Zhichao Miao Andrew N J McKenzie Bidesh Mahata Sarah A Teichmann

Genome Med 2018 10 24;10(1):76. Epub 2018 Oct 24.

Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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https://genomemedicine.biomedcentral.com/articles/10.1186/s1
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http://dx.doi.org/10.1186/s13073-018-0589-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6199730PMC
October 2018

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

Authors:
Maiara S Severo Jonathan J M Landry Randall L Lindquist Christian Goosmann Volker Brinkmann Paul Collier Anja E Hauser Vladimir Benes Johan Henriksson Sarah A Teichmann Elena A Levashina

Proc Natl Acad Sci U S A 2018 08 23;115(32):E7568-E7577. Epub 2018 Jul 23.

Vector Biology Unit, Max Planck Institute for Infection Biology, 10117 Berlin, Germany;

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http://dx.doi.org/10.1073/pnas.1803062115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6094101PMC
August 2018

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

Authors:
Ida Lindeman Guy Emerton Lira Mamanova Omri Snir Krzysztof Polanski Shuo-Wang Qiao Ludvig M Sollid Sarah A Teichmann Michael J T Stubbington

Nat Methods 2018 08;15(8):563-565

Wellcome Sanger Institute, Hinxton, UK.

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http://dx.doi.org/10.1038/s41592-018-0082-3DOI Listing
August 2018

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

Authors:
Matthew D Young Thomas J Mitchell Felipe A Vieira Braga Maxine G B Tran Benjamin J Stewart John R Ferdinand Grace Collord Rachel A Botting Dorin-Mirel Popescu Kevin W Loudon Roser Vento-Tormo Emily Stephenson Alex Cagan Sarah J Farndon Martin Del Castillo Velasco-Herrera Charlotte Guzzo Nathan Richoz Lira Mamanova Tevita Aho James N Armitage Antony C P Riddick Imran Mushtaq Stephen Farrell Dyanne Rampling James Nicholson Andrew Filby Johanna Burge Steven Lisgo Patrick H Maxwell Susan Lindsay Anne Y Warren Grant D Stewart Neil Sebire Nicholas Coleman Muzlifah Haniffa Sarah A Teichmann Menna Clatworthy Sam Behjati

Science 2018 08;361(6402):594-599

Wellcome Sanger Institute, Hinxton CB10 1SA, UK.

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http://dx.doi.org/10.1126/science.aat1699DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104812PMC
August 2018

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

Authors:
Timotheus Y F Halim Batika M J Rana Jennifer A Walker Bernhard Kerscher Martin D Knolle Helen E Jolin Eva M Serrao Liora Haim-Vilmovsky Sarah A Teichmann Hans-Reimer Rodewald Marina Botto Timothy J Vyse Padraic G Fallon Zhi Li David R Withers Andrew N J McKenzie

Immunity 2018 06 12;48(6):1195-1207.e6. Epub 2018 Jun 12.

MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2018.05.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6015114PMC
June 2018

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

Authors:
Joseph A Marsh Sarah A Teichmann

Curr Opin Struct Biol 2018 06;50:vii-viii

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2018.07.005DOI Listing
June 2018

SpatialDE: identification of spatially variable genes.

Authors:
Valentine Svensson Sarah A Teichmann Oliver Stegle

Nat Methods 2018 05 19;15(5):343-346. Epub 2018 Mar 19.

European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.

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http://dx.doi.org/10.1038/nmeth.4636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350895PMC
May 2018

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

Authors:
Valentine Svensson Roser Vento-Tormo Sarah A Teichmann

Nat Protoc 2018 04 1;13(4):599-604. Epub 2018 Mar 1.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1038/nprot.2017.149DOI Listing
April 2018

Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins.

Authors:
Eviatar Natan Tamaki Endoh Liora Haim-Vilmovsky Tilman Flock Guilhem Chalancon Jonathan T S Hopper Bálint Kintses Peter Horvath Lejla Daruka Gergely Fekete Csaba Pál Balázs Papp Erika Oszi Zoltán Magyar Joseph A Marsh Adrian H Elcock M Madan Babu Carol V Robinson Naoki Sugimoto Sarah A Teichmann

Nat Struct Mol Biol 2018 03 12;25(3):279-288. Epub 2018 Feb 12.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1038/s41594-018-0029-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5995306PMC
March 2018

Mapping human development at single-cell resolution.

Authors:
Sam Behjati Susan Lindsay Sarah A Teichmann Muzlifah Haniffa

Development 2018 02 8;145(3). Epub 2018 Feb 8.

Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne NE2 4HH, UK

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http://dx.doi.org/10.1242/dev.152561DOI Listing
February 2018

The Human Cell Atlas.

Authors:
Aviv Regev Sarah A Teichmann Eric S Lander Ido Amit Christophe Benoist Ewan Birney Bernd Bodenmiller Peter Campbell Piero Carninci Menna Clatworthy Hans Clevers Bart Deplancke Ian Dunham James Eberwine Roland Eils Wolfgang Enard Andrew Farmer Lars Fugger Berthold Göttgens Nir Hacohen Muzlifah Haniffa Martin Hemberg Seung Kim Paul Klenerman Arnold Kriegstein Ed Lein Sten Linnarsson Emma Lundberg Joakim Lundeberg Partha Majumder John C Marioni Miriam Merad Musa Mhlanga Martijn Nawijn Mihai Netea Garry Nolan Dana Pe'er Anthony Phillipakis Chris P Ponting Stephen Quake Wolf Reik Orit Rozenblatt-Rosen Joshua Sanes Rahul Satija Ton N Schumacher Alex Shalek Ehud Shapiro Padmanee Sharma Jay W Shin Oliver Stegle Michael Stratton Michael J T Stubbington Fabian J Theis Matthias Uhlen Alexander van Oudenaarden Allon Wagner Fiona Watt Jonathan Weissman Barbara Wold Ramnik Xavier Nir Yosef

Elife 2017 12 5;6. Epub 2017 Dec 5.

Ragon Institute of MGH, MIT and Harvard, Cambridge, United States.

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http://dx.doi.org/10.7554/eLife.27041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5762154PMC
December 2017

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

Authors:
Ahmed N Hegazy Nathaniel R West Michael J T Stubbington Emily Wendt Kim I M Suijker Angeliki Datsi Sebastien This Camille Danne Suzanne Campion Sylvia H Duncan Benjamin M J Owens Holm H Uhlig Andrew McMichael Andreas Bergthaler Sarah A Teichmann Satish Keshav Fiona Powrie

Gastroenterology 2017 11 4;153(5):1320-1337.e16. Epub 2017 Aug 4.

Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, University of Oxford, United Kingdom; Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, United Kingdom. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2017.07.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5687320PMC
November 2017

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

Authors:
Kedar Nath Natarajan Sarah A Teichmann Aleksandra A Kolodziejczyk

Curr Opin Genet Dev 2017 Oct 1;46:66-76. Epub 2017 Jul 1.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, UK; European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.

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http://dx.doi.org/10.1016/j.gde.2017.06.003DOI Listing
October 2017

Single-cell transcriptomics to explore the immune system in health and disease.

Authors:
Michael J T Stubbington Orit Rozenblatt-Rosen Aviv Regev Sarah A Teichmann

Science 2017 10;358(6359):58-63

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1126/science.aan6828DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5654495PMC
October 2017

Establishment of mouse expanded potential stem cells.

Authors:
Jian Yang David J Ryan Wei Wang Jason Cheuk-Ho Tsang Guocheng Lan Hideki Masaki Xuefei Gao Liliana Antunes Yong Yu Zhexin Zhu Juexuan Wang Aleksandra A Kolodziejczyk Lia S Campos Cui Wang Fengtang Yang Zhen Zhong Beiyuan Fu Melanie A Eckersley-Maslin Michael Woods Yosuke Tanaka Xi Chen Adam C Wilkinson James Bussell Jacqui White Ramiro Ramirez-Solis Wolf Reik Berthold Göttgens Sarah A Teichmann Patrick P L Tam Hiromitsu Nakauchi Xiangang Zou Liming Lu Pentao Liu

Nature 2017 10 11;550(7676):393-397. Epub 2017 Oct 11.

Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.

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http://dx.doi.org/10.1038/nature24052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5890884PMC
October 2017

The Human Cell Atlas: from vision to reality.

Authors:
Orit Rozenblatt-Rosen Michael J T Stubbington Aviv Regev Sarah A Teichmann

Nature 2017 10;550(7677):451-453

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http://dx.doi.org/10.1038/550451aDOI Listing
October 2017

Computational approaches for interpreting scRNA-seq data.

Authors:
Raghd Rostom Valentine Svensson Sarah A Teichmann Gozde Kar

FEBS Lett 2017 08 12;591(15):2213-2225. Epub 2017 Jun 12.

The European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.

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http://dx.doi.org/10.1002/1873-3468.12684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5575496PMC
August 2017

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

Authors:
Ashraful Haque Jessica Engel Sarah A Teichmann Tapio Lönnberg

Genome Med 2017 08 18;9(1):75. Epub 2017 Aug 18.

Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland.

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http://dx.doi.org/10.1186/s13073-017-0467-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5561556PMC
August 2017

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

Authors:
Giacomo Donati Emanuel Rognoni Toru Hiratsuka Kifayathullah Liakath-Ali Esther Hoste Gozde Kar Melis Kayikci Roslin Russell Kai Kretzschmar Klaas W Mulder Sarah A Teichmann Fiona M Watt

Nat Cell Biol 2017 Jun 15;19(6):603-613. Epub 2017 May 15.

King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK.

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http://dx.doi.org/10.1038/ncb3532DOI Listing
June 2017

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

Authors:
Gozde Kar Jong Kyoung Kim Aleksandra A Kolodziejczyk Kedar Nath Natarajan Elena Torlai Triglia Borbala Mifsud Sarah Elderkin John C Marioni Ana Pombo Sarah A Teichmann

Nat Commun 2017 06 26;8(1):36. Epub 2017 Jun 26.

European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1038/s41467-017-00052-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5484669PMC
June 2017

Power analysis of single-cell RNA-sequencing experiments.

Authors:
Valentine Svensson Kedar Nath Natarajan Lam-Ha Ly Ricardo J Miragaia Charlotte Labalette Iain C Macaulay Ana Cvejic Sarah A Teichmann

Nat Methods 2017 Apr 6;14(4):381-387. Epub 2017 Mar 6.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1038/nmeth.4220DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376499PMC
April 2017

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types.

Authors:
Santiago J Carmona Sarah A Teichmann Lauren Ferreira Iain C Macaulay Michael J T Stubbington Ana Cvejic David Gfeller

Genome Res 2017 03 13;27(3):451-461. Epub 2017 Jan 13.

Ludwig Center for Cancer Research, University of Lausanne, 1066 Epalinges, Switzerland.

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http://dx.doi.org/10.1101/gr.207704.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340972PMC
March 2017

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

Authors:
Felipe A Vieira Braga Sarah A Teichmann Michael J T Stubbington

Genome Biol 2017 03 24;18(1):54. Epub 2017 Mar 24.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1186/s13059-017-1192-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364640PMC
March 2017

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

Authors:
Tapio Lönnberg Valentine Svensson Kylie R James Daniel Fernandez-Ruiz Ismail Sebina Ruddy Montandon Megan S F Soon Lily G Fogg Arya Sheela Nair Urijah Liligeto Michael J T Stubbington Lam-Ha Ly Frederik Otzen Bagger Max Zwiessele Neil D Lawrence Fernando Souza-Fonseca-Guimaraes Patrick T Bunn Christian R Engwerda William R Heath Oliver Billker Oliver Stegle Ashraful Haque Sarah A Teichmann

Sci Immunol 2017 Mar;2(9)

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1126/sciimmunol.aal2192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5365145PMC
March 2017

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

Authors:
Celia Pilar Martinez-Jimenez Nils Eling Hung-Chang Chen Catalina A Vallejos Aleksandra A Kolodziejczyk Frances Connor Lovorka Stojic Timothy F Rayner Michael J T Stubbington Sarah A Teichmann Maike de la Roche John C Marioni Duncan T Odom

Science 2017 03;355(6332):1433-1436

University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK.

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http://dx.doi.org/10.1126/science.aah4115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405862PMC
March 2017

Regulation, evolution and consequences of cotranslational protein complex assembly.

Authors:
Eviatar Natan Jonathan N Wells Sarah A Teichmann Joseph A Marsh

Curr Opin Struct Biol 2017 02 12;42:90-97. Epub 2016 Dec 12.

MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2016.11.023DOI Listing
February 2017

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

Authors:
Yee Ling Wu Michael J T Stubbington Maria Daly Sarah A Teichmann Cristina Rada

J Exp Med 2017 01 19;214(1):183-196. Epub 2016 Dec 19.

Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, England, UK

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http://dx.doi.org/10.1084/jem.20161056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5206502PMC
January 2017

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

Authors:
Yong Yu Jason C H Tsang Cui Wang Simon Clare Juexuan Wang Xi Chen Cordelia Brandt Leanne Kane Lia S Campos Liming Lu Gabrielle T Belz Andrew N J McKenzie Sarah A Teichmann Gordon Dougan Pentao Liu

Nature 2016 11 29;539(7627):102-106. Epub 2016 Sep 29.

Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.

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http://dx.doi.org/10.1038/nature20105DOI Listing
November 2016

Single-cell analysis at the threshold.

Authors:
Xi Chen J Christopher Love Nicholas E Navin Lior Pachter Michael J T Stubbington Valentine Svensson Jonathan V Sweedler Sarah A Teichmann

Nat Biotechnol 2016 11;34(11):1111-1118

Wellcome Trust Sanger Institute, Cambridge, UK.

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http://dx.doi.org/10.1038/nbt.3721DOI Listing
November 2016

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

Authors:
Felipe A Vieira Braga Sarah A Teichmann Xi Chen

Hum Mol Genet 2016 Oct 12;25(R2):R141-R148. Epub 2016 Jul 12.

Wellcome Trust Sanger Institute

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http://dx.doi.org/10.1093/hmg/ddw192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036872PMC
October 2016

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

Authors:
Filipa L Sousa Daniel J Parente Jacob A Hessman Allen Chazelle Sarah A Teichmann Liskin Swint-Kruse

Data Brief 2016 Sep 9;8:948-57. Epub 2016 Jul 9.

The Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS 66160, USA.

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http://dx.doi.org/10.1016/j.dib.2016.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4961497PMC
September 2016

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

Authors:
Mélanie A Eckersley-Maslin Valentine Svensson Christel Krueger Thomas M Stubbs Pascal Giehr Felix Krueger Ricardo J Miragaia Charalampos Kyriakopoulos Rebecca V Berrens Inês Milagre Jörn Walter Sarah A Teichmann Wolf Reik

Cell Rep 2016 09;17(1):179-192

Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055476PMC
http://dx.doi.org/10.1016/j.celrep.2016.08.087DOI Listing
September 2016

Erratum to: Single cell analysis of CD4+ T cell differentiation reveals three major cell states and progressive acceleration of proliferation.

Authors:
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 Kylie R James Daniel Fernandez-Ruiz William R Heath Ashraful Haque Oliver Billker Steven Woodhouse Pietro Cicuta Mario Nicodemi Sarah A Teichmann

Genome Biol 2016 Jun 22;17(1):133. Epub 2016 Jun 22.

EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s13059-016-0998-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4918121PMC
June 2016

Single-cell genomics: coming of age.

Authors:
Sten Linnarsson Sarah A Teichmann

Genome Biol 2016 May 10;17:97. Epub 2016 May 10.

Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s13059-016-0960-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4862185PMC
May 2016

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

Authors:
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 Nicodemi Sarah A Teichmann

Genome Biol 2016 May 12;17:103. Epub 2016 May 12.

EMBL, European Bioinformatics Institute (EBI), Hinxton, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s13059-016-0957-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866375PMC
May 2016

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

Authors:
Michael J T Stubbington Tapio Lönnberg Valentina Proserpio Simon Clare Anneliese O Speak Gordon Dougan Sarah A Teichmann

Nat Methods 2016 Apr 7;13(4):329-332. Epub 2016 Mar 7.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK.

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http://dx.doi.org/10.1038/nmeth.3800DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4835021PMC
April 2016

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

Authors:
Filipa L Sousa Daniel J Parente David L Shis Jacob A Hessman Allen Chazelle Matthew R Bennett Sarah A Teichmann Liskin Swint-Kruse

J Mol Biol 2016 Feb 25;428(4):671-678. Epub 2015 Sep 25.

Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA. Electronic address:

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http://dx.doi.org/10.1016/j.jmb.2015.09.015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4783282PMC
February 2016

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

Authors:
Iain C Macaulay Valentine Svensson Charlotte Labalette Lauren Ferreira Fiona Hamey Thierry Voet Sarah A Teichmann Ana Cvejic

Cell Rep 2016 Feb 21;14(4):966-977. Epub 2016 Jan 21.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge CB2 0PT, UK; Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, Cambridge CB2 1QR, UK. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.12.082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742565PMC
February 2016

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

Authors:
Tomislav Ilicic Jong Kyoung Kim Aleksandra A Kolodziejczyk Frederik Otzen Bagger Davis James McCarthy John C Marioni Sarah A Teichmann

Genome Biol 2016 Feb 17;17:29. Epub 2016 Feb 17.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s13059-016-0888-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4758103PMC
February 2016

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Authors:
Jong Kyoung Kim Aleksandra A Kolodziejczyk Tomislav Ilicic Sarah A Teichmann John C Marioni

Nat Commun 2016 Jan 11;7:10415. Epub 2016 Jan 11.

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http://dx.doi.org/10.1038/ncomms10415DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4729893PMC
January 2016

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

Authors:
Joseph A Marsh Sarah A Teichmann

Annu Rev Biochem 2015 8;84:551-75. Epub 2014 Dec 8.

Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom; email:

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http://dx.doi.org/10.1146/annurev-biochem-060614-034142DOI Listing
December 2015

Principles of assembly reveal a periodic table of protein complexes.

Authors:
Sebastian E Ahnert Joseph A Marsh Helena Hernández Carol V Robinson Sarah A Teichmann

Science 2015 Dec;350(6266):aaa2245

Theory of Condensed Matter Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK. European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1126/science.aaa2245DOI Listing
December 2015

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

Authors:
Aleksandra A Kolodziejczyk Jong Kyoung Kim Jason C H Tsang Tomislav Ilicic Johan Henriksson Kedar N Natarajan Alex C Tuck Xuefei Gao Marc Bühler Pentao Liu John C Marioni Sarah A Teichmann

Cell Stem Cell 2015 Oct;17(4):471-85

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.stem.2015.09.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4595712PMC
October 2015

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression.

Authors:
Jong Kyoung Kim Aleksandra A Kolodziejczyk Tomislav Ilicic Tomislav Illicic Sarah A Teichmann John C Marioni

Nat Commun 2015 Oct 22;6:8687. Epub 2015 Oct 22.

European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1038/ncomms9687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627577PMC
October 2015

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

Authors:
Antonio Scialdone Kedar N Natarajan Luis R Saraiva Valentina Proserpio Sarah A Teichmann Oliver Stegle John C Marioni Florian Buettner

Methods 2015 Sep 2;85:54-61. Epub 2015 Jul 2.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Institute of Computational Biology, Helmholtz Zentrum München, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10462023153000
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http://dx.doi.org/10.1016/j.ymeth.2015.06.021DOI Listing
September 2015

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

Authors:
Jason C H Tsang Yong Yu Shannon Burke Florian Buettner Cui Wang Aleksandra A Kolodziejczyk Sarah A Teichmann Liming Lu Pentao Liu

Genome Biol 2015 Sep 21;16:178. Epub 2015 Sep 21.

Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.

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http://dx.doi.org/10.1186/s13059-015-0739-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576406PMC
September 2015

The Regulatory T Cell Lineage Factor Foxp3 Regulates Gene Expression through Several Distinct Mechanisms Mostly Independent of Direct DNA Binding.

Authors:
Xin Xie Michael J T Stubbington Jesper K Nissen Kristian G Andersen Daniel Hebenstreit Sarah A Teichmann Alexander G Betz

PLoS Genet 2015 Jun 24;11(6):e1005251. Epub 2015 Jun 24.

MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.

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https://dx.plos.org/10.1371/journal.pgen.1005251
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4480970PMC
June 2015

The technology and biology of single-cell RNA sequencing.

Authors:
Aleksandra A Kolodziejczyk Jong Kyoung Kim Valentine Svensson John C Marioni Sarah A Teichmann

Mol Cell 2015 May;58(4):610-20

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2015.04.005DOI Listing
May 2015

An atlas of mouse CD4(+) T cell transcriptomes.

Authors:
Michael Jt Stubbington Bidesh Mahata Valentine Svensson Andrew Deonarine Jesper K Nissen Alexander G Betz Sarah A Teichmann

Biol Direct 2015 Apr 3;10:14. Epub 2015 Apr 3.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK.

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http://dx.doi.org/10.1186/s13062-015-0045-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384382PMC
April 2015

Computational and analytical challenges in single-cell transcriptomics.

Authors:
Oliver Stegle Sarah A Teichmann John C Marioni

Nat Rev Genet 2015 Mar 28;16(3):133-45. Epub 2015 Jan 28.

1] European Molecular Biology Laboratory European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. [2] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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March 2015

Structural and evolutionary versatility in protein complexes with uneven stoichiometry.

Authors:
Joseph A Marsh Holly A Rees Sebastian E Ahnert Sarah A Teichmann

Nat Commun 2015 Mar 16;6:6394. Epub 2015 Mar 16.

1] European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK [2] Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK [3] Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.

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http://dx.doi.org/10.1038/ncomms7394DOI Listing
March 2015

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

Authors:
Florian Buettner Kedar N Natarajan F Paolo Casale Valentina Proserpio Antonio Scialdone Fabian J Theis Sarah A Teichmann John C Marioni Oliver Stegle

Nat Biotechnol 2015 Feb 19;33(2):155-60. Epub 2015 Jan 19.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1038/nbt.3102DOI Listing
February 2015

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

Authors:
Tina Perica Yasushi Kondo Sandhya P Tiwari Stephen H McLaughlin Katherine R Kemplen Xiuwei Zhang Annette Steward Nathalie Reuter Jane Clarke Sarah A Teichmann

Science 2014 Dec;346(6216):1254346

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1126/science.1254346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4337988PMC
December 2014

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

Authors:
Bidesh Mahata Xiuwei Zhang Aleksandra A Kolodziejczyk Valentina Proserpio Liora Haim-Vilmovsky Angela E Taylor Daniel Hebenstreit Felix A Dingler Victoria Moignard Berthold Göttgens Wiebke Arlt Andrew N J McKenzie Sarah A Teichmann

Cell Rep 2014 May 10;7(4):1130-42. Epub 2014 May 10.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.04.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4039991PMC
May 2014

Protein flexibility facilitates quaternary structure assembly and evolution.

Authors:
Joseph A Marsh Sarah A Teichmann

PLoS Biol 2014 May 27;12(5):e1001870. Epub 2014 May 27.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pbio.1001870DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035275PMC
May 2014

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

Authors:
Joseph A Marsh Sarah A Teichmann

Bioessays 2014 Feb 25;36(2):209-18. Epub 2013 Nov 25.

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1002/bies.201300134DOI Listing
February 2014

Evolution of protein structures and interactions from the perspective of residue contact networks.

Authors:
Xiuwei Zhang Tina Perica Sarah A Teichmann

Curr Opin Struct Biol 2013 Dec 25;23(6):954-63. Epub 2013 Jul 25.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2013.07.004DOI Listing
December 2013

Targeting CXCL12 from FAP-expressing carcinoma-associated fibroblasts synergizes with anti-PD-L1 immunotherapy in pancreatic cancer.

Authors:
Christine Feig James O Jones Matthew Kraman Richard J B Wells Andrew Deonarine Derek S Chan Claire M Connell Edward W Roberts Qi Zhao Otavia L Caballero Sarah A Teichmann Tobias Janowitz Duncan I Jodrell David A Tuveson Douglas T Fearon

Proc Natl Acad Sci U S A 2013 Dec 25;110(50):20212-7. Epub 2013 Nov 25.

Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom.

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http://dx.doi.org/10.1073/pnas.1320318110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3864274PMC
December 2013

Accounting for technical noise in single-cell RNA-seq experiments.

Authors:
Philip Brennecke Simon Anders Jong Kyoung Kim Aleksandra A Kołodziejczyk Xiuwei Zhang Valentina Proserpio Bianka Baying Vladimir Benes Sarah A Teichmann John C Marioni Marcus G Heisler

Nat Methods 2013 Nov 22;10(11):1093-5. Epub 2013 Sep 22.

1] European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. [2].

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http://www.nature.com/doifinder/10.1038/nmeth.2645
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November 2013

Immunology meets genomics.

Authors:
Sarah A Teichmann

Brief Funct Genomics 2013 Nov;12(6):469-70

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http://dx.doi.org/10.1093/bfgp/elt037DOI Listing
November 2013

The role of salt bridges, charge density, and subunit flexibility in determining disassembly routes of protein complexes.

Authors:
Zoe Hall Helena Hernández Joseph A Marsh Sarah A Teichmann Carol V Robinson

Structure 2013 Aug 11;21(8):1325-37. Epub 2013 Jul 11.

Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK.

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http://dx.doi.org/10.1016/j.str.2013.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737473PMC
August 2013

Regulation of protein-protein binding by coupling between phosphorylation and intrinsic disorder: analysis of human protein complexes.

Authors:
Hafumi Nishi Jessica H Fong Christiana Chang Sarah A Teichmann Anna R Panchenko

Mol Biosyst 2013 Jul 30;9(7):1620-6. Epub 2013 Jan 30.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.

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http://dx.doi.org/10.1039/c3mb25514jDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665713PMC
July 2013

Depletion of stromal cells expressing fibroblast activation protein-α from skeletal muscle and bone marrow results in cachexia and anemia.

Authors:
Edward W Roberts Andrew Deonarine James O Jones Alice E Denton Christine Feig Scott K Lyons Marion Espeli Matthew Kraman Brendan McKenna Richard J B Wells Qi Zhao Otavia L Caballero Rachel Larder Anthony P Coll Stephen O'Rahilly Kevin M Brindle Sarah A Teichmann David A Tuveson Douglas T Fearon

J Exp Med 2013 Jun 27;210(6):1137-51. Epub 2013 May 27.

Department of Medicine, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, England, UK.

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http://dx.doi.org/10.1084/jem.20122344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3674708PMC
June 2013

Protein complexes are under evolutionary selection to assemble via ordered pathways.

Authors:
Joseph A Marsh Helena Hernández Zoe Hall Sebastian E Ahnert Tina Perica Carol V Robinson Sarah A Teichmann

Cell 2013 Apr;153(2):461-70

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.cell.2013.02.044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009401PMC
April 2013

Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes.

Authors:
Sarah A Teichmann Philip A Wigge Varodom Charoensawan

Cell Cycle 2012 Dec 19;11(24):4487-8. Epub 2012 Nov 19.

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http://dx.doi.org/10.4161/cc.22666DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3562284PMC
December 2012

Cellular crowding imposes global constraints on the chemistry and evolution of proteomes.

Authors:
Emmanuel D Levy Subhajyoti De Sarah A Teichmann

Proc Natl Acad Sci U S A 2012 Dec 26;109(50):20461-6. Epub 2012 Nov 26.

Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.

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http://dx.doi.org/10.1073/pnas.1209312109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3528536PMC
December 2012

Probing the diverse landscape of protein flexibility and binding.

Authors:
Joseph A Marsh Sarah A Teichmann Julie D Forman-Kay

Curr Opin Struct Biol 2012 Oct 20;22(5):643-50. Epub 2012 Sep 20.

MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom.

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http://dx.doi.org/10.1016/j.sbi.2012.08.008DOI Listing
October 2012

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

Authors:
Varodom Charoensawan Sarath Chandra Janga Martha L Bulyk M Madan Babu Sarah A Teichmann

Mol Cell 2012 Jul;47(2):183-92

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

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http://dx.doi.org/10.1016/j.molcel.2012.06.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566590PMC
July 2012

Duel of the fates: the role of transcriptional circuits and noise in CD4+ cells.

Authors:
Daniel Hebenstreit Andrew Deonarine M Madan Babu Sarah A Teichmann

Curr Opin Cell Biol 2012 Jun 11;24(3):350-8. Epub 2012 Apr 11.

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.

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http://dx.doi.org/10.1016/j.ceb.2012.03.007DOI Listing
June 2012

The interface of protein structure, protein biophysics, and molecular evolution.

Authors:
David A Liberles Sarah A Teichmann Ivet Bahar Ugo Bastolla Jesse Bloom Erich Bornberg-Bauer Lucy J Colwell A P Jason de Koning Nikolay V Dokholyan Julian Echave Arne Elofsson Dietlind L Gerloff Richard A Goldstein Johan A Grahnen Mark T Holder Clemens Lakner Nicholas Lartillot Simon C Lovell Gavin Naylor Tina Perica David D Pollock Tal Pupko Lynne Regan Andrew Roger Nimrod Rubinstein Eugene Shakhnovich Kimmen Sjölander Shamil Sunyaev Ashley I Teufel Jeffrey L Thorne Joseph W Thornton Daniel M Weinreich Simon Whelan

Protein Sci 2012 Jun 23;21(6):769-85. Epub 2012 Apr 23.

Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA.

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http://www.tau.ac.il/~talp/publications/proteinStructureAndE
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http://doi.wiley.com/10.1002/pro.2071
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http://dx.doi.org/10.1002/pro.2071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3403413PMC
June 2012

The emergence of protein complexes: quaternary structure, dynamics and allostery. Colworth Medal Lecture.

Authors:
Tina Perica Joseph A Marsh Filipa L Sousa Eviatar Natan Lucy J Colwell Sebastian E Ahnert Sarah A Teichmann

Biochem Soc Trans 2012 Jun;40(3):475-91

MRC Laboratory of Molecular Biology, Hills Road, Cambridge, U.K.

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http://dx.doi.org/10.1042/BST20120056DOI Listing
June 2012

Evolution of oligomeric state through geometric coupling of protein interfaces.

Authors:
Tina Perica Cyrus Chothia Sarah A Teichmann

Proc Natl Acad Sci U S A 2012 May 7;109(21):8127-32. Epub 2012 May 7.

Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 OQH, United Kingdom.

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http://dx.doi.org/10.1073/pnas.1120028109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3361393PMC
May 2012

How do you find transcription factors? Computational approaches to compile and annotate repertoires of regulators for any genome.

Authors:
Juan M Vaquerizas Sarah A Teichmann Nicholas M Luscombe

Methods Mol Biol 2012 ;786:3-19

EMBL-European Bioinformatics Institute, Cambridge, UK.

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http://dx.doi.org/10.1007/978-1-61779-292-2_1DOI Listing
February 2012

Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs.

Authors:
Emily Brookes Inês de Santiago Daniel Hebenstreit Kelly J Morris Tom Carroll Sheila Q Xie Julie K Stock Martin Heidemann Dirk Eick Naohito Nozaki Hiroshi Kimura Jiannis Ragoussis Sarah A Teichmann Ana Pombo

Cell Stem Cell 2012 Feb;10(2):157-70

Genome Function Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK.

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http://dx.doi.org/10.1016/j.stem.2011.12.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682187PMC
February 2012

Analysis and simulation of gene expression profiles in pure and mixed cell populations.

Authors:
Daniel Hebenstreit Sarah A Teichmann

Phys Biol 2011 Jun 13;8(3):035013. Epub 2011 May 13.

MRC Laboratory of Molecular Biology, Hills Rd, Cambridge CB2 0QH, UK.

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http://dx.doi.org/10.1088/1478-3975/8/3/035013DOI Listing
June 2011

Relative solvent accessible surface area predicts protein conformational changes upon binding.

Authors:
Joseph A Marsh Sarah A Teichmann

Structure 2011 Jun;19(6):859-67

MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB20QH, UK.

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http://dx.doi.org/10.1016/j.str.2011.03.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145976PMC
June 2011

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

Authors:
Daniel Hebenstreit Miaoqing Fang Muxin Gu Varodom Charoensawan Alexander van Oudenaarden Sarah A Teichmann

Mol Syst Biol 2011 Jun 7;7:497. Epub 2011 Jun 7.

Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK.

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http://dx.doi.org/10.1038/msb.2011.28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159973PMC
June 2011

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

Authors:
Daniel Hebenstreit Muxin Gu Syed Haider Daniel J Turner Pietro Liò Sarah A Teichmann

Nucleic Acids Res 2011 Mar 3;39(5):e27. Epub 2010 Dec 3.

MRC Laboratory of Molecular Biology, Hills Rd, CB2 0QH Cambridge, UK.

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http://dx.doi.org/10.1093/nar/gkq1226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3061070PMC
March 2011

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

Authors:
Varodom Charoensawan Boris Adryan Stephen Martin Christian Söllner Bernard Thisse Christine Thisse Gavin J Wright Sarah A Teichmann

Mol Cell Proteomics 2010 Dec 8;9(12):2666-77. Epub 2010 Oct 8.

Medical Research Council Laboratory of Molecular Biology, Cambridge CB20QH, United Kingdom.

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http://dx.doi.org/10.1074/mcp.M110.003020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3101855PMC
December 2010

Assessing computational methods of cis-regulatory module prediction.

Authors:
Jing Su Sarah A Teichmann Thomas A Down

PLoS Comput Biol 2010 Dec 2;6(12):e1001020. Epub 2010 Dec 2.

MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.

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http://dx.doi.org/10.1371/journal.pcbi.1001020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2996316PMC
December 2010

Genomic repertoires of DNA-binding transcription factors across the tree of life.

Authors:
Varodom Charoensawan Derek Wilson Sarah A Teichmann

Nucleic Acids Res 2010 Nov 30;38(21):7364-77. Epub 2010 Jul 30.

MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.

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http://dx.doi.org/10.1093/nar/gkq617DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995046PMC
November 2010

Lineage-specific expansion of DNA-binding transcription factor families.

Authors:
Varodom Charoensawan Derek Wilson Sarah A Teichmann

Trends Genet 2010 Sep 31;26(9):388-93. Epub 2010 Jul 31.

MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.

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https://linkinghub.elsevier.com/retrieve/pii/S01689525100012
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http://dx.doi.org/10.1016/j.tig.2010.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2937223PMC
September 2010