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Transcriptomics Analysis of Porcine Caudal Dorsal Root Ganglia in Tail Amputated Pigs Shows Long-Term Effects on Many Pain-Associated Genes.

Sandercock DA, Barnett MW, Coe JE, Downing AC, Nirmal AJ, Di Giminiani P, Edwards SA, Freeman TC.

Front Vet Sci. 2019 Sep 18;6:314. doi: 10.3389/fvets.2019.00314. eCollection 2019.


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

Mcilreavy L, Freeman TCA, Erichsen JT.

Transl Vis Sci Technol. 2019 Sep 11;8(5):7. doi: 10.1167/tvst.8.5.7. eCollection 2019 Sep.


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

Rzechorzek NM, Saunders OM, Hiscox LV, Schwarz T, Marioni-Henry K, Argyle DJ, Schoenebeck JJ, Freeman TC.

Sci Rep. 2019 Aug 29;9(1):12506. doi: 10.1038/s41598-019-48446-0.


Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle.

Lima J, Auffret MD, Stewart RD, Dewhurst RJ, Duthie CA, Snelling TJ, Walker AW, Freeman TC, Watson M, Roehe R.

Front Genet. 2019 Aug 8;10:701. doi: 10.3389/fgene.2019.00701. eCollection 2019.


Visualization and analysis of RNA-Seq assembly graphs.

Nazarie FW, Shih B, Angus T, Barnett MW, Chen SH, Summers KM, Klein K, Faulkner GJ, Saini HK, Watson M, Dongen SV, Enright AJ, Freeman TC.

Nucleic Acids Res. 2019 Aug 22;47(14):7262-7275. doi: 10.1093/nar/gkz599.


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

Shaw AD, Knight L, Freeman TCA, Williams GM, Moran RJ, Friston KJ, Walters JTR, Singh KD.

Schizophr Bull. 2019 Jun 20. pii: sbz066. doi: 10.1093/schbul/sbz066. [Epub ahead of print]


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

Patir A, Shih B, McColl BW, Freeman TC.

Glia. 2019 Jul;67(7):1240-1253. doi: 10.1002/glia.23572. Epub 2019 Feb 13.


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

Mouton AJ, Ma Y, Rivera Gonzalez OJ, Daseke MJ 2nd, Flynn ER, Freeman TC, Garrett MR, DeLeon-Pennell KY, Lindsey ML.

Basic Res Cardiol. 2019 Jan 11;114(2):6. doi: 10.1007/s00395-019-0715-4.


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

Garzorz IT, Freeman TCA, Ernst MO, MacNeilage PR.

J Vis. 2018 Dec 3;18(13):9. doi: 10.1167/18.13.9.


Characterisation of the British honey bee metagenome.

Regan T, Barnett MW, Laetsch DR, Bush SJ, Wragg D, Budge GE, Highet F, Dainat B, de Miranda JR, Watson M, Blaxter M, Freeman TC.

Nat Commun. 2018 Nov 26;9(1):4995. doi: 10.1038/s41467-018-07426-0.


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

Giotti B, Chen SH, Barnett MW, Regan T, Ly T, Wiemann S, Hume DA, Freeman TC.

J Mol Cell Biol. 2019 Aug 19;11(8):703-718. doi: 10.1093/jmcb/mjy063.


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

Bush SJ, Powell-Smith A, Freeman TC.

PLoS One. 2018 Oct 31;13(10):e0205759. doi: 10.1371/journal.pone.0205759. eCollection 2018.


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

Nirmal AJ, Regan T, Shih BB, Hume DA, Sims AH, Freeman TC.

Cancer Immunol Res. 2018 Nov;6(11):1388-1400. doi: 10.1158/2326-6066.CIR-18-0342. Epub 2018 Sep 28.


A preference for visual speed during smooth pursuit eye movement.

Freeman TCA, Cucu MO, Smith L.

J Exp Psychol Hum Percept Perform. 2018 Oct;44(10):1629-1636. doi: 10.1037/xhp0000551. Epub 2018 Jul 5.


Mapping macrophage polarization over the myocardial infarction time continuum.

Mouton AJ, DeLeon-Pennell KY, Rivera Gonzalez OJ, Flynn ER, Freeman TC, Saucerman JJ, Garrett MR, Ma Y, Harmancey R, Lindsey ML.

Basic Res Cardiol. 2018 Jun 4;113(4):26. doi: 10.1007/s00395-018-0686-x.


High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool.

Henriques D, Browne KA, Barnett MW, Parejo M, Kryger P, Freeman TC, Muñoz I, Garnery L, Highet F, Jonhston JS, McCormack GP, Pinto MA.

Sci Rep. 2018 Jun 4;8(1):8552. doi: 10.1038/s41598-018-26932-1.


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

O'Hara L, O'Shaughnessy PJ, Freeman TC, Smith LB.

BMC Res Notes. 2018 Apr 24;11(1):252. doi: 10.1186/s13104-018-3365-y.


A graphical and computational modeling platform for biological pathways.

Livigni A, O'Hara L, Polak ME, Angus T, Wright DW, Smith LB, Freeman TC.

Nat Protoc. 2018 Apr;13(4):705-722. doi: 10.1038/nprot.2017.144. Epub 2018 Mar 15.


Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J; IIBDGC Consortium, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA.

PLoS Comput Biol. 2018 Mar 1;14(3):e1005934. doi: 10.1371/journal.pcbi.1005934. eCollection 2018 Mar.


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

Regan T, Gill AC, Clohisey SM, Barnett MW, Pariante CM, Harrison NA; MRC Immunopsychiatry Consortium, Hume DA, Bullmore ET, Freeman TC.

J Leukoc Biol. 2018 Apr;103(4):681-692. doi: 10.1002/JLB.3A0617-261R. Epub 2018 Jan 26.


Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Bos Taurus Breeds and Basal Diets.

Auffret MD, Stewart R, Dewhurst RJ, Duthie CA, Rooke JA, Wallace RJ, Freeman TC, Snelling TJ, Watson M, Roehe R.

Front Microbiol. 2018 Jan 9;8:2642. doi: 10.3389/fmicb.2017.02642. eCollection 2017.


The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.

Auffret MD, Dewhurst RJ, Duthie CA, Rooke JA, John Wallace R, Freeman TC, Stewart R, Watson M, Roehe R.

Microbiome. 2017 Dec 11;5(1):159. doi: 10.1186/s40168-017-0378-z.


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

Clark EL, Bush SJ, McCulloch MEB, Farquhar IL, Young R, Lefevre L, Pridans C, Tsang HG, Wu C, Afrasiabi C, Watson M, Whitelaw CB, Freeman TC, Summers KM, Archibald AL, Hume DA.

PLoS Genet. 2017 Sep 15;13(9):e1006997. doi: 10.1371/journal.pgen.1006997. eCollection 2017 Sep.


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

Leday GGR, Vértes PE, Richardson S, Greene JR, Regan T, Khan S, Henderson R, Freeman TC, Pariante CM, Harrison NA; MRC Immunopsychiatry Consortium, Perry VH, Drevets WC, Wittenberg GM, Bullmore ET.

Biol Psychiatry. 2018 Jan 1;83(1):70-80. doi: 10.1016/j.biopsych.2017.01.021. Epub 2017 Jul 6.


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

Audzevich T, Bashford-Rogers R, Mabbott NA, Frampton D, Freeman TC, Potocnik A, Kellam P, Gilroy DW.

Proc Natl Acad Sci U S A. 2017 May 16;114(20):E3954-E3963. doi: 10.1073/pnas.1616417114. Epub 2017 May 1.


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

Polak ME, Ung CY, Masapust J, Freeman TC, Ardern-Jones MR.

Sci Rep. 2017 Apr 6;7(1):668. doi: 10.1038/s41598-017-00651-5.


Modulation of macrophage antitumor potential by apoptotic lymphoma cells.

Voss JJLP, Ford CA, Petrova S, Melville L, Paterson M, Pound JD, Holland P, Giotti B, Freeman TC, Gregory CD.

Cell Death Differ. 2017 Jun;24(6):971-983. doi: 10.1038/cdd.2016.132. Epub 2017 Feb 3.


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

Giotti B, Joshi A, Freeman TC.

BMC Genomics. 2017 Jan 5;18(1):30. doi: 10.1186/s12864-016-3435-2.


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

Shih BB, Nirmal AJ, Headon DJ, Akbar AN, Mabbott NA, Freeman TC.

J Pathol. 2017 Apr;241(5):600-613. doi: 10.1002/path.4864. Epub 2017 Feb 24.


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

Alibhai J, Blanco RA, Barria MA, Piccardo P, Caughey B, Perry VH, Freeman TC, Manson JC.

PLoS Biol. 2016 Nov 23;14(11):e1002579. doi: 10.1371/journal.pbio.1002579. eCollection 2016 Nov.


Auditory compensation for head rotation is incomplete.

Freeman TC, Culling JF, Akeroyd MA, Brimijoin WO.

J Exp Psychol Hum Percept Perform. 2017 Feb;43(2):371-380. doi: 10.1037/xhp0000321. Epub 2016 Nov 14.


Bayesian Models of Individual Differences.

Powell G, Meredith Z, McMillin R, Freeman TC.

Psychol Sci. 2016 Dec;27(12):1562-1572. doi: 10.1177/0956797616665351. Epub 2016 Oct 23.


Modelling the Structure and Dynamics of Biological Pathways.

O'Hara L, Livigni A, Theo T, Boyer B, Angus T, Wright D, Chen SH, Raza S, Barnett MW, Digard P, Smith LB, Freeman TC.

PLoS Biol. 2016 Aug 10;14(8):e1002530. doi: 10.1371/journal.pbio.1002530. eCollection 2016 Aug.


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

Sharp GC, Hutchinson JL, Hibbert N, Freeman TC, Saunders PT, Norman JE.

PLoS One. 2016 May 13;11(5):e0155413. doi: 10.1371/journal.pone.0155413. eCollection 2016.


CIB1: a small protein with big ambitions.

Leisner TM, Freeman TC, Black JL, Parise LV.

FASEB J. 2016 Aug;30(8):2640-50. doi: 10.1096/fj.201500073R. Epub 2016 Apr 26. Review.


Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance.

Roehe R, Dewhurst RJ, Duthie CA, Rooke JA, McKain N, Ross DW, Hyslop JJ, Waterhouse A, Freeman TC, Watson M, Wallace RJ.

PLoS Genet. 2016 Feb 18;12(2):e1005846. doi: 10.1371/journal.pgen.1005846. eCollection 2016 Feb.


Microglial brain region-dependent diversity and selective regional sensitivities to aging.

Grabert K, Michoel T, Karavolos MH, Clohisey S, Baillie JK, Stevens MP, Freeman TC, Summers KM, McColl BW.

Nat Neurosci. 2016 Mar;19(3):504-16. doi: 10.1038/nn.4222. Epub 2016 Jan 18.


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

Vincenti JE, Murphy L, Grabert K, McColl BW, Cancellotti E, Freeman TC, Manson JC.

J Virol. 2015 Dec 30;90(6):3003-17. doi: 10.1128/JVI.02613-15.


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

Dunkley BT, Freeman TC, Muthukumaraswamy SD, Singh KD.

Hum Brain Mapp. 2015 Dec;36(12):5220-32. doi: 10.1002/hbm.23006. Epub 2015 Sep 29.


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

Dobyns AE, Goyal R, Carpenter LG, Freeman TC, Longo LD, Yellon SM.

PLoS One. 2015 Mar 26;10(3):e0119782. doi: 10.1371/journal.pone.0119782. eCollection 2015.


Gateways to the FANTOM5 promoter level mammalian expression atlas.

Lizio M, Harshbarger J, Shimoji H, Severin J, Kasukawa T, Sahin S, Abugessaisa I, Fukuda S, Hori F, Ishikawa-Kato S, Mungall CJ, Arner E, Baillie JK, Bertin N, Bono H, de Hoon M, Diehl AD, Dimont E, Freeman TC, Fujieda K, Hide W, Kaliyaperumal R, Katayama T, Lassmann T, Meehan TF, Nishikata K, Ono H, Rehli M, Sandelin A, Schultes EA, 't Hoen PA, Tatum Z, Thompson M, Toyoda T, Wright DW, Daub CO, Itoh M, Carninci P, Hayashizaki Y, Forrest AR, Kawaji H; FANTOM consortium.

Genome Biol. 2015 Jan 5;16:22. doi: 10.1186/s13059-014-0560-6.


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

Joshi A, Pooley C, Freeman TC, Lennartsson A, Babina M, Schmidl C, Geijtenbeek T; FANTOM Consortium, Michoel T, Severin J, Itoh M, Lassmann T, Kawaji H, Hayashizaki Y, Carninci P, Forrest AR, Rehli M, Hume DA.

J Leukoc Biol. 2015 May;97(5):985-995. doi: 10.1189/jlb.6TA1014-477RR. Epub 2015 Feb 25.


Oncogenic properties of apoptotic tumor cells in aggressive B cell lymphoma.

Ford CA, Petrova S, Pound JD, Voss JJ, Melville L, Paterson M, Farnworth SL, Gallimore AM, Cuff S, Wheadon H, Dobbin E, Ogden CA, Dumitriu IE, Dunbar DR, Murray PG, Ruckerl D, Allen JE, Hume DA, van Rooijen N, Goodlad JR, Freeman TC, Gregory CD.

Curr Biol. 2015 Mar 2;25(5):577-88. doi: 10.1016/j.cub.2014.12.059. Epub 2015 Feb 19.


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

Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C; FANTOM Consortium, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y.

Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12.


Quick phases of infantile nystagmus show the saccadic inhibition effect.

Harrison JJ, Sumner P, Dunn MJ, Erichsen JT, Freeman TC.

Invest Ophthalmol Vis Sci. 2015 Feb 10;56(3):1594-600. doi: 10.1167/iovs.14-15655.


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

Harrison JJ, Freeman TC, Sumner P.

J Vis. 2015 Jan 26;15(1):15.1.24. doi: 10.1167/15.1.24.


Transcriptomic analysis of mononuclear phagocyte differentiation and activation.

Hume DA, Freeman TC.

Immunol Rev. 2014 Nov;262(1):74-84. doi: 10.1111/imr.12211. Review.


Sertoli cells maintain Leydig cell number and peritubular myoid cell activity in the adult mouse testis.

Rebourcet D, O'Shaughnessy PJ, Monteiro A, Milne L, Cruickshanks L, Jeffrey N, Guillou F, Freeman TC, Mitchell RT, Smith LB.

PLoS One. 2014 Aug 21;9(8):e105687. doi: 10.1371/journal.pone.0105687. eCollection 2014.


Discrimination contours for moving sounds reveal duration and distance cues dominate auditory speed perception.

Freeman TC, Leung J, Wufong E, Orchard-Mills E, Carlile S, Alais D.

PLoS One. 2014 Jul 30;9(7):e102864. doi: 10.1371/journal.pone.0102864. eCollection 2014.


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

Harrison JJ, Freeman TC, Sumner P.

J Exp Psychol Gen. 2014 Oct;143(5):1923-38. doi: 10.1037/a0037021. Epub 2014 May 26.


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