Publications by authors named "Tom C Freeman"

100Publications

The transcriptional signature associated with human motile cilia.

Sci Rep 2020 07 2;10(1):10814. Epub 2020 Jul 2.

The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, EH25 9RG, UK.

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http://dx.doi.org/10.1038/s41598-020-66453-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7331728PMC
July 2020

Two-Dimensional Analysis of Smooth Pursuit Eye Movements Reveals Quantitative Deficits in Precision and Accuracy.

Transl Vis Sci Technol 2019 Sep 11;8(5). Epub 2019 Sep 11.

School of Optometry and Vision Sciences, Cardiff University, Cardiff, UK.

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http://dx.doi.org/10.1167/tvst.8.5.7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6753966PMC
September 2019

Network analysis of canine brain morphometry links tumour risk to oestrogen deficiency and accelerated brain ageing.

Sci Rep 2019 08 29;9(1):12506. Epub 2019 Aug 29.

Royal (Dick) School of Veterinary Studies and Roslin Institute, University of Edinburgh, Easter Bush Campus, Roslin, Midlothian, EH25 9RG, UK.

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http://dx.doi.org/10.1038/s41598-019-48446-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6715702PMC
August 2019

Visualization and analysis of RNA-Seq assembly graphs.

Nucleic Acids Res 2019 08;47(14):7262-7275

Systems Immunology Group, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK.

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http://dx.doi.org/10.1093/nar/gkz599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6698738PMC
August 2019

Oscillatory, Computational, and Behavioral Evidence for Impaired GABAergic Inhibition in Schizophrenia.

Schizophr Bull 2020 02;46(2):345-353

CUBRIC, School of Psychology, College of Biomedical and Life Sciences, Cardiff University, Cardiff, UK.

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http://dx.doi.org/10.1093/schbul/sbz066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7442335PMC
February 2020

A core transcriptional signature of human microglia: Derivation and utility in describing region-dependent alterations associated with Alzheimer's disease.

Glia 2019 07 13;67(7):1240-1253. Epub 2019 Feb 13.

The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, United Kingdom.

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http://dx.doi.org/10.1002/glia.23572DOI Listing
July 2019

Fibroblast polarization over the myocardial infarction time continuum shifts roles from inflammation to angiogenesis.

Basic Res Cardiol 2019 01 11;114(2). Epub 2019 Jan 11.

Department of Physiology and Biophysics, Mississippi Center for Heart Research, University of Mississippi Medical Center, 2500 North State St, Jackson, MS, 39216-4505, USA.

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http://dx.doi.org/10.1007/s00395-019-0715-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6329742PMC
January 2019

Insufficient compensation for self-motion during perception of object speed: The vestibular Aubert-Fleischl phenomenon.

J Vis 2018 12;18(13)

German Center for Vertigo and Balance Disorders (DSGZ), University Hospital of Munich, Ludwig Maximilian University, Munich, Germany.

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http://jov.arvojournals.org/article.aspx?doi=10.1167/18.13.9
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http://dx.doi.org/10.1167/18.13.9DOI Listing
December 2018

Characterisation of the British honey bee metagenome.

Nat Commun 2018 11 26;9(1):4995. Epub 2018 Nov 26.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, EH25 9RG, Edinburgh, UK.

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http://dx.doi.org/10.1038/s41467-018-07426-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6255801PMC
November 2018

Assembly of a parts list of the human mitotic cell cycle machinery.

J Mol Cell Biol 2019 08;11(8):703-718

The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.

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http://dx.doi.org/10.1093/jmcb/mjy063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6788831PMC
August 2019

Network analysis of the social and demographic influences on name choice within the UK (1838-2016).

PLoS One 2018 31;13(10):e0205759. Epub 2018 Oct 31.

The Roslin Institute, University of Edinburgh, Midlothian, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0205759PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6209202PMC
March 2019

Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumors.

Cancer Immunol Res 2018 11 28;6(11):1388-1400. Epub 2018 Sep 28.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.

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http://cancerimmunolres.aacrjournals.org/lookup/doi/10.1158/
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http://dx.doi.org/10.1158/2326-6066.CIR-18-0342DOI Listing
November 2018

A preference for visual speed during smooth pursuit eye movement.

J Exp Psychol Hum Percept Perform 2018 Oct 5;44(10):1629-1636. Epub 2018 Jul 5.

School of Psychology, Cardiff University.

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http://dx.doi.org/10.1037/xhp0000551DOI Listing
October 2018

Mapping macrophage polarization over the myocardial infarction time continuum.

Basic Res Cardiol 2018 06 4;113(4):26. Epub 2018 Jun 4.

Department of Physiology and Biophysics, Mississippi Center for Heart Research, University of Mississippi Medical Center, 2500 North State St., Jackson, MS, 39216-4505, USA.

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http://dx.doi.org/10.1007/s00395-018-0686-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5986831PMC
June 2018

Modelling steroidogenesis: a framework model to support hypothesis generation and testing across endocrine studies.

BMC Res Notes 2018 Apr 24;11(1):252. Epub 2018 Apr 24.

MRC Centre for Reproductive Health, The Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK.

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http://dx.doi.org/10.1186/s13104-018-3365-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937803PMC
April 2018

A graphical and computational modeling platform for biological pathways.

Nat Protoc 2018 04 15;13(4):705-722. Epub 2018 Mar 15.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK.

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http://www.nature.com/doifinder/10.1038/nprot.2017.144
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http://dx.doi.org/10.1038/nprot.2017.144DOI Listing
April 2018

Effects of anti-inflammatory drugs on the expression of tryptophan-metabolism genes by human macrophages.

J Leukoc Biol 2018 04 26;103(4):681-692. Epub 2018 Jan 26.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Scotland, UK.

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http://doi.wiley.com/10.1002/JLB.3A0617-261R
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http://dx.doi.org/10.1002/JLB.3A0617-261RDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5918594PMC
April 2018

A high resolution atlas of gene expression in the domestic sheep (Ovis aries).

PLoS Genet 2017 Sep 15;13(9):e1006997. Epub 2017 Sep 15.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1006997DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5626511PMC
September 2017

Replicable and Coupled Changes in Innate and Adaptive Immune Gene Expression in Two Case-Control Studies of Blood Microarrays in Major Depressive Disorder.

Biol Psychiatry 2018 Jan 6;83(1):70-80. Epub 2017 Jul 6.

Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom; Cambridgeshire and Peterborough National Health Service Foundation Trust, Cambridge, United Kingdom; ImmunoPsychiatry, GlaxoSmithKline Research & Development, Stevenage, United Kingdom. Electronic address:

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http://dx.doi.org/10.1016/j.biopsych.2017.01.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5720346PMC
January 2018

Pre/pro-B cells generate macrophage populations during homeostasis and inflammation.

Proc Natl Acad Sci U S A 2017 05 1;114(20):E3954-E3963. Epub 2017 May 1.

Centre for Clinical Pharmacology and Therapeutics, Division of Medicine, University College London, London WC1E 6JJ, United Kingdom;

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http://www.pnas.org/lookup/doi/10.1073/pnas.1616417114
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http://dx.doi.org/10.1073/pnas.1616417114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5441795PMC
May 2017

Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation.

Sci Rep 2017 04 6;7(1):668. Epub 2017 Apr 6.

Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, SO16 6YD, Southampton, UK.

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http://dx.doi.org/10.1038/s41598-017-00651-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5428800PMC
April 2017

Modulation of macrophage antitumor potential by apoptotic lymphoma cells.

Cell Death Differ 2017 06 3;24(6):971-983. Epub 2017 Feb 3.

Medical Research Council (MRC) Center for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK.

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http://dx.doi.org/10.1038/cdd.2016.132DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5442466PMC
June 2017

Meta-analysis reveals conserved cell cycle transcriptional network across multiple human cell types.

BMC Genomics 2017 01 5;18(1):30. Epub 2017 Jan 5.

Systems Immunology Group and Developmental Biology Division, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, EH25 9RG, UK.

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http://dx.doi.org/10.1186/s12864-016-3435-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217208PMC
January 2017

Derivation of marker gene signatures from human skin and their use in the interpretation of the transcriptional changes associated with dermatological disorders.

J Pathol 2017 04 24;241(5):600-613. Epub 2017 Feb 24.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Edinburgh, EH25 9RG, UK.

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http://doi.wiley.com/10.1002/path.4864
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http://dx.doi.org/10.1002/path.4864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5363360PMC
April 2017

Distribution of Misfolded Prion Protein Seeding Activity Alone Does Not Predict Regions of Neurodegeneration.

PLoS Biol 2016 Nov 23;14(11):e1002579. Epub 2016 Nov 23.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.1371/journal.pbio.1002579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120774PMC
November 2016

Auditory compensation for head rotation is incomplete.

J Exp Psychol Hum Percept Perform 2017 02 14;43(2):371-380. Epub 2016 Nov 14.

Medical Research Council/Chief Scientist Office Institute of Hearing Research-Scottish Section, Glasgow Royal Infirmary.

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http://dx.doi.org/10.1037/xhp0000321DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289217PMC
February 2017

Bayesian Models of Individual Differences.

Psychol Sci 2016 12 23;27(12):1562-1572. Epub 2016 Oct 23.

School of Psychology, Cardiff University.

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http://dx.doi.org/10.1177/0956797616665351DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367641PMC
December 2016

Modelling the Structure and Dynamics of Biological Pathways.

PLoS Biol 2016 08 10;14(8):e1002530. Epub 2016 Aug 10.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, Scotland, United Kingdom.

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http://dx.doi.org/10.1371/journal.pbio.1002530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4980033PMC
August 2016

Transcription Analysis of the Myometrium of Labouring and Non-Labouring Women.

PLoS One 2016 13;11(5):e0155413. Epub 2016 May 13.

Tommy's Centre for Maternal and Fetal Health and Medical Research Council (MRC) Centre for Reproductive Health, University of Edinburgh, Edinburgh, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0155413PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866706PMC
July 2017

Defining the Microglia Response during the Time Course of Chronic Neurodegeneration.

J Virol 2015 Dec 30;90(6):3003-17. Epub 2015 Dec 30.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom

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http://dx.doi.org/10.1128/JVI.02613-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4810622PMC
December 2015

Evidence that smooth pursuit velocity, not eye position, modulates alpha and beta oscillations in human middle temporal cortex.

Hum Brain Mapp 2015 Dec 29;36(12):5220-32. Epub 2015 Sep 29.

School of Psychology, CUBRIC (Cardiff University Brain Research Imaging Centre), Cardiff University, Park Place, Cardiff, United Kingdom.

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http://dx.doi.org/10.1002/hbm.23006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6869037PMC
December 2015

Macrophage gene expression associated with remodeling of the prepartum rat cervix: microarray and pathway analyses.

PLoS One 2015 26;10(3):e0119782. Epub 2015 Mar 26.

Center for Perinatal Biology, Loma Linda University School of Medicine, Loma Linda, CA, 92350, United States of America; Departments of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA, 92350, United States of America; Division of Physiology, Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, 92350, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0119782PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374766PMC
March 2016

Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells.

J Leukoc Biol 2015 May 25;97(5):985-995. Epub 2015 Feb 25.

*The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Scotland, United Kingdom; RIKEN Preventive Medicine and Diagnosis Innovation Program, Tsurumi-ku, Yokohama, Japan; RIKEN Center for Life Science Technologies, Division of Genomic Technologies, Tsurumi-ku, Yokohama, Japan; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden; Department of Dermatology and Allergy, Charité Universitätsmedizin Berlin, Germany; Department of Internal Medicine III, University Hospital, University of Regensburg, Germany; Department of Experimental Immunology, Academic Medical Center, Amsterdam, the Netherlands; and **RIKEN Omics Science Center, Tsurumi-ku, Yokohama, Japan

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http://dx.doi.org/10.1189/jlb.6TA1014-477RRDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398258PMC
May 2015

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Authors:
Erik Arner Carsten O Daub Kristoffer Vitting-Seerup Robin Andersson Berit Lilje Finn Drabløs Andreas Lennartsson Michelle Rönnerblad Olga Hrydziuszko Morana Vitezic Tom C Freeman Ahmad M N Alhendi Peter Arner Richard Axton J Kenneth Baillie Anthony Beckhouse Beatrice Bodega James Briggs Frank Brombacher Margaret Davis Michael Detmar Anna Ehrlund Mitsuhiro Endoh Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley Forrester Daniel Goldowitz Reto Guler Thomas Ha Mitsuko Hara Meenhard Herlyn Tomokatsu Ikawa Chieko Kai Hiroshi Kawamoto Levon M Khachigian S Peter Klinken Soichi Kojima Haruhiko Koseki Sarah Klein Niklas Mejhert Ken Miyaguchi Yosuke Mizuno Mitsuru Morimoto Kelly J Morris Christine Mummery Yutaka Nakachi Soichi Ogishima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Xian-Yang Qin Sugata Roy Hiroki Sato Suzana Savvi Alka Saxena Anita Schwegmann Daisuke Sugiyama Rolf Swoboda Hiroshi Tanaka Andru Tomoiu Louise N Winteringham Ernst Wolvetang Chiyo Yanagi-Mizuochi Misako Yoneda Susan Zabierowski Peter Zhang Imad Abugessaisa Nicolas Bertin Alexander D Diehl Shiro Fukuda Masaaki Furuno Jayson Harshbarger Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Yuri Ishizu Masayoshi Itoh Tsugumi Kawashima Miki Kojima Naoto Kondo Marina Lizio Terrence F Meehan Christopher J Mungall Mitsuyoshi Murata Hiromi Nishiyori-Sueki Serkan Sahin Sayaka Nagao-Sato Jessica Severin Michiel J L de Hoon Jun Kawai Takeya Kasukawa Timo Lassmann Harukazu Suzuki Hideya Kawaji Kim M Summers Christine Wells David A Hume Alistair R R Forrest Albin Sandelin Piero Carninci Yoshihide Hayashizaki

Science 2015 Feb 12;347(6225):1010-4. Epub 2015 Feb 12.

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http://dx.doi.org/10.1126/science.1259418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433PMC
February 2015

Quick phases of infantile nystagmus show the saccadic inhibition effect.

Invest Ophthalmol Vis Sci 2015 Feb 10;56(3):1594-600. Epub 2015 Feb 10.

School of Psychology, Cardiff University, Cardiff, United Kingdom.

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http://dx.doi.org/10.1167/iovs.14-15655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351650PMC
February 2015

Saccadic compensation for reflexive optokinetic nystagmus just as good as compensation for volitional pursuit.

J Vis 2015 Jan 26;15(1):15.1.24. Epub 2015 Jan 26.

School of Psychology, Cardiff University, Cardiff, UK Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology, Cardiff University, Cardiff, UK.

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http://jov.arvojournals.org/Article.aspx?doi=10.1167/15.1.24
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http://dx.doi.org/10.1167/15.1.24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4306346PMC
January 2015

Transcriptomic analysis of mononuclear phagocyte differentiation and activation.

Immunol Rev 2014 Nov;262(1):74-84

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, UK.

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http://doi.wiley.com/10.1111/imr.12211
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http://dx.doi.org/10.1111/imr.12211DOI Listing
November 2014

Saccade-like behavior in the fast-phases of optokinetic nystagmus: an illustration of the emergence of volitional actions from automatic reflexes.

J Exp Psychol Gen 2014 Oct 26;143(5):1923-38. Epub 2014 May 26.

Cardiff University Brain Research Imaging Centre, Cardiff University.

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http://dx.doi.org/10.1037/a0037021DOI Listing
October 2014

Analysis of the transcriptional networks underpinning the activation of murine macrophages by inflammatory mediators.

J Leukoc Biol 2014 Aug 10;96(2):167-83. Epub 2014 Apr 10.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Scotland, United Kingdom; and

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http://dx.doi.org/10.1189/jlb.6HI0313-169RDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378362PMC
August 2014

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

Visualisation of BioPAX Networks using BioLayout Express (3D).

F1000Res 2014 20;3:246. Epub 2014 Oct 20.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, Scotland, EH25 9RG, UK.

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http://dx.doi.org/10.12688/f1000research.5499.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406191PMC
May 2015

An expression atlas of human primary cells: inference of gene function from coexpression networks.

BMC Genomics 2013 Sep 20;14:632. Epub 2013 Sep 20.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Edinburgh EH25 9RG, UK.

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http://dx.doi.org/10.1186/1471-2164-14-632DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3849585PMC
September 2013

Distinct molecular signature of human skin Langerhans cells denotes critical differences in cutaneous dendritic cell immune regulation.

J Invest Dermatol 2014 Mar 4;134(3):695-703. Epub 2013 Sep 4.

Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton General Hospital, Southampton, UK.

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http://dx.doi.org/10.1038/jid.2013.375DOI Listing
March 2014

The impact of breed and tissue compartment on the response of pig macrophages to lipopolysaccharide.

BMC Genomics 2013 Aug 28;14:581. Epub 2013 Aug 28.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, Edinburgh EH25 9RG, United Kingdom.

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http://dx.doi.org/10.1186/1471-2164-14-581DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3766131PMC
August 2013

Coexpression analysis of large cancer datasets provides insight into the cellular phenotypes of the tumour microenvironment.

BMC Genomics 2013 Jul 11;14:469. Epub 2013 Jul 11.

Centre for Inflammation Research, University of Edinburgh, The Queen’s Medical Research Institute, Edinburgh, UK.

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http://dx.doi.org/10.1186/1471-2164-14-469DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3721986PMC
July 2013

Horizontal fixation point oscillation and simulated viewpoint oscillation both increase vection in depth.

J Vis 2012 Nov 26;12(12):15. Epub 2012 Nov 26.

School of Psychology, University of Wollongong, Wollongong, Australia.

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http://dx.doi.org/10.1167/12.12.15DOI Listing
November 2012

Extending signaling pathways with protein-interaction networks. Application to apoptosis.

OMICS 2012 May 2;16(5):245-56. Epub 2012 Mar 2.

Structural Bioinformatics Group, GRIB, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain.

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http://dx.doi.org/10.1089/omi.2011.0130DOI Listing
May 2012

Reprogramming pig fetal fibroblasts reveals a functional LIF signaling pathway.

Cell Reprogram 2012 Apr 17;14(2):112-22. Epub 2012 Feb 17.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, United Kingdom.

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http://dx.doi.org/10.1089/cell.2011.0078DOI Listing
April 2012

Cortical oscillatory changes in human middle temporal cortex underlying smooth pursuit eye movements.

Hum Brain Mapp 2013 Apr 23;34(4):837-51. Epub 2011 Nov 23.

Cardiff University Brain Research Imaging Centre, School of Psychology, Cardiff University, Park Place, Cardiff, United Kingdom.

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http://dx.doi.org/10.1002/hbm.21478DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6869956PMC
April 2013

Macrophages.com: an on-line community resource for innate immunity research.

Immunobiology 2011 Nov 23;216(11):1203-11. Epub 2011 Jul 23.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom.

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http://dx.doi.org/10.1016/j.imbio.2011.07.025DOI Listing
November 2011

Simultaneous adaptation to non-collinear retinal motion and smooth pursuit eye movement.

Vision Res 2011 Jul 14;51(14):1637-47. Epub 2011 May 14.

School of Psychology, Tower Building, Park Place, Cardiff University, CF10 3AT, UK.

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http://dx.doi.org/10.1016/j.visres.2011.05.004DOI Listing
July 2011

Large-scale cell-based microarrays and their use with HEK293T cells and downstream apoptotic assays.

Methods Mol Biol 2011 ;706:27-40

Clinical Sciences Centre, Hammersmith Hospital, London, UK.

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http://dx.doi.org/10.1007/978-1-61737-970-3_3DOI Listing
March 2011

Discrimination contours for the perception of head-centered velocity.

J Vis 2010 Jun 1;10(6):14. Epub 2010 Jun 1.

School of Psychology, Cardiff University, Cardiff, UK.

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http://dx.doi.org/10.1167/10.6.14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672835PMC
June 2010

Humans do not have direct access to retinal flow during walking.

J Vis 2010 Sep 22;10(11):14. Epub 2010 Sep 22.

Multisensory Perception and Action Group, Max Planck Institute for Biological Cybernetics, Tübingen, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3672841PMC
September 2010

Human conjunctival transcriptome analysis reveals the prominence of innate defense in Chlamydia trachomatis infection.

Infect Immun 2010 Nov 7;78(11):4895-911. Epub 2010 Sep 7.

Department of Clinical Research, London School of Hygiene and Tropical Medicine, University of London, London, United Kingdom.

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http://dx.doi.org/10.1128/IAI.00844-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2976339PMC
November 2010

Age, eye movement and motion discrimination.

Vision Res 2010 Nov 21;50(23):2588-99. Epub 2010 Aug 21.

School of Psychology, Cardiff University, Tower Building, Park Place, Cardiff CF10 3YT, UK.

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http://dx.doi.org/10.1016/j.visres.2010.08.015DOI Listing
November 2010

Meta-analysis of lineage-specific gene expression signatures in mouse leukocyte populations.

Immunobiology 2010 Sep-Oct;215(9-10):724-36. Epub 2010 Jun 4.

The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Roslin Biocentre, Roslin, Midlothian, UK.

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http://dx.doi.org/10.1016/j.imbio.2010.05.012DOI Listing
March 2011

The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways.

BMC Syst Biol 2010 May 17;4:65. Epub 2010 May 17.

Division of Pathway Medicine, University of Edinburgh Medical School, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh, UK.

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http://dx.doi.org/10.1186/1752-0509-4-65DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2878301PMC
May 2010

Construction of a large scale integrated map of macrophage pathogen recognition and effector systems.

BMC Syst Biol 2010 May 14;4:63. Epub 2010 May 14.

Division of Pathway Medicine, University of Edinburgh, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh EH16 4SB, UK.

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http://dx.doi.org/10.1186/1752-0509-4-63DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2892459PMC
May 2010

A Bayesian model of perceived head-centered velocity during smooth pursuit eye movement.

Curr Biol 2010 Apr 15;20(8):757-62. Epub 2010 Apr 15.

School of Psychology, Cardiff University, Park Place, Cardiff CF10 3AT, UK.

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http://dx.doi.org/10.1016/j.cub.2010.02.059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2861164PMC
April 2010

Precision and accuracy of ocular following: influence of age and type of eye movement.

Exp Brain Res 2010 Mar 15;201(2):271-82. Epub 2009 Oct 15.

School of Psychology, Cardiff University, Tower Building, Park Place, Cardiff, CF10 3AT, UK.

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http://link.springer.com/10.1007/s00221-009-2036-6
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March 2010

Network visualization and analysis of gene expression data using BioLayout Express(3D).

Nat Protoc 2009 1;4(10):1535-50. Epub 2009 Oct 1.

The Roslin Institute, R(D)SVS, University of Edinburgh, Roslin BioCentre, Midlothian, Scotland, UK.

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http://dx.doi.org/10.1038/nprot.2009.177DOI Listing
December 2009

Do we have direct access to retinal image motion during smooth pursuit eye movements?

J Vis 2009 Jan 23;9(1):33.1-11. Epub 2009 Jan 23.

School of Psychology, Cardiff University, UK.

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http://dx.doi.org/10.1167/9.1.33DOI Listing
January 2009

Motion perception during sinusoidal smooth pursuit eye movements: signal latencies and non-linearities.

J Vis 2008 Oct 23;8(14):10.1-14. Epub 2008 Oct 23.

Max Planck Institute for Biological Cybernetics, Tübingen, Germany.

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October 2008

Improved grading and survival prediction of human astrocytic brain tumors by artificial neural network analysis of gene expression microarray data.

Mol Cancer Ther 2008 May 29;7(5):1013-24. Epub 2008 Apr 29.

Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.

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http://dx.doi.org/10.1158/1535-7163.MCT-07-0177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819720PMC
May 2008

A logic-based diagram of signalling pathways central to macrophage activation.

BMC Syst Biol 2008 Apr 23;2:36. Epub 2008 Apr 23.

Division of Pathway Medicine, University of Edinburgh, The Chancellor's Building, College of Medicine, 49 Little France Crescent, Edinburgh, EH16 4SB, UK.

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http://dx.doi.org/10.1186/1752-0509-2-36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2383880PMC
April 2008

Simultaneous adaptation of retinal and extra-retinal motion signals.

Authors:
Tom C A Freeman

Vision Res 2007 Dec 19;47(27):3373-84. Epub 2007 Nov 19.

School of Psychology, Cardiff University, Tower Building, Park Place, Cardiff, Wales CF10 3AT, UK.

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http://dx.doi.org/10.1016/j.visres.2007.10.002DOI Listing
December 2007

From filters to features: scale-space analysis of edge and blur coding in human vision.

J Vis 2007 Oct 19;7(13):7.1-21. Epub 2007 Oct 19.

School of Life & Health Sciences, Aston University, Birmingham, UK.

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http://dx.doi.org/10.1167/7.13.7DOI Listing
October 2007

Extra-retinal vision: firing at will.

Authors:
Tom C A Freeman

Curr Biol 2007 Feb;17(3):R99-101

School of Psychology, Cardiff University, Tower Building, Park Place, Cardiff CF10 3AT, UK.

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http://dx.doi.org/10.1016/j.cub.2007.01.020DOI Listing
February 2007

Identification and characterisation of human apoptosis inducing proteins using cell-based transfection microarrays and expression analysis.

BMC Genomics 2006 Jun 12;7:145. Epub 2006 Jun 12.

MRC Rosalind Franklin Centre for Genomics Research (RFCGR), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK.

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http://dx.doi.org/10.1186/1471-2164-7-145DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1525185PMC
June 2006

Cells expressing murine RAD52 splice variants favor sister chromatid repair.

Mol Cell Biol 2006 May;26(10):3752-63

Department of Genetics and Development, Columbia University Medical Center, HHSC 1608, 701 West 168th St., New York, New York 10032, USA.

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http://dx.doi.org/10.1128/MCB.26.10.3752-3763.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1488992PMC
May 2006