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Author Details

Tom C Freeman
The Roslin Institute, University of Edinburgh
1990
134
46
PMIDPaper TitleJournal TitlePublished Year
37548242Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis.G3 (Bethesda)2023
35877685Graphia: A platform for the graph-based visualisation and analysis of high dimensional data.PLoS Comput Biol2022
36469788Multiclonal human origin and global expansion of an endemic bacterial pathogen of livestock.Proc Natl Acad Sci U S A2022
36209064A graph-based approach for the visualisation and analysis of bacterial pangenomes.BMC Bioinformatics2022
32313939Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.Brief Bioinform2021
37118005Recruitment of inflammatory monocytes by senescent fibroblasts inhibits antigen-specific tissue immunity during human aging.Nat Aging2021
34939300COVID-19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.Mol Syst Biol2021
34616758A Systems-Level Analysis of Total-Body PET Data Reveals Complex Skeletal Metabolism Networks <i>in vivo</i>.Front Med (Lausanne)2021
34664389COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.Mol Syst Biol2021
32616903The transcriptional signature associated with human motile cilia.Sci Rep2020
36284901Vitamin D<sub>3</sub> replacement enhances antigen-specific immunity in older adults.Immunother Adv2020
33273621Single-cell RNA-seq reveals CD16<sup>-</sup> monocytes as key regulators of human monocyte transcriptional response to Toxoplasma.Sci Rep2020
30635789Fibroblast polarization over the myocardial infarction time continuum shifts roles from inflammation to angiogenesis.Basic Res Cardiol2019
31739805Correction to: The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.Microbiome2019
31467332Network analysis of canine brain morphometry links tumour risk to oestrogen deficiency and accelerated brain ageing.Sci Rep2019
31620455Transcriptomics Analysis of Porcine Caudal Dorsal Root Ganglia in Tail Amputated Pigs Shows Long-Term Effects on Many Pain-Associated Genes.Front Vet Sci2019
31305886Visualization and analysis of RNA-Seq assembly graphs.Nucleic Acids Res2019
30758077A core transcriptional signature of human microglia: Derivation and utility in describing region-dependent alterations associated with Alzheimer's disease.Glia2019
30452682Assembly of a parts list of the human mitotic cell cycle machinery.J Mol Cell Biol2019
28688579Replicable and Coupled Changes in Innate and Adaptive Immune Gene Expression in Two Case-Control Studies of Blood Microarrays in Major Depressive Disorder.Biol Psychiatry2018
29867207High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool.Sci Rep2018
29868933Mapping macrophage polarization over the myocardial infarction time continuum.Basic Res Cardiol2018
30266715Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumors.Cancer Immunol Res2018
30478343Characterisation of the British honey bee metagenome.Nat Commun2018
30379928Network analysis of the social and demographic influences on name choice within the UK (1838-2016).PLoS One2018
29494619Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.PLoS Comput Biol2018
29690918Modelling steroidogenesis: a framework model to support hypothesis generation and testing across endocrine studies.BMC Res Notes2018
29543794A graphical and computational modeling platform for biological pathways.Nat Protoc2018
29377288Effects of anti-inflammatory drugs on the expression of tryptophan-metabolism genes by human macrophages.J Leukoc Biol2018
29375511Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse <i>Bos Taurus</i> Breeds and Basal Diets.Front Microbiol2018
28008606Derivation of marker gene signatures from human skin and their use in the interpretation of the transcriptional changes associated with dermatological disorders.J Pathol2017
28461481Pre/pro-B cells generate macrophage populations during homeostasis and inflammation.Proc Natl Acad Sci U S A2017
28386100Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation.Sci Rep2017
28157210Modulation of macrophage antitumor potential by apoptotic lymphoma cells.Cell Death Differ2017
29228991The rumen microbiome as a reservoir of antimicrobial resistance and pathogenicity genes is directly affected by diet in beef cattle.Microbiome2017
28915238A high resolution atlas of gene expression in the domestic sheep (Ovis aries).PLoS Genet2017
28056781Meta-analysis reveals conserved cell cycle transcriptional network across multiple human cell types.BMC Genomics2017
26780511Microglial brain region-dependent diversity and selective regional sensitivities to aging.Nat Neurosci2016
27880767Distribution of Misfolded Prion Protein Seeding Activity Alone Does Not Predict Regions of Neurodegeneration.PLoS Biol2016
27509052Modelling the Structure and Dynamics of Biological Pathways.PLoS Biol2016
27176052Transcription Analysis of the Myometrium of Labouring and Non-Labouring Women.PLoS One2016
26891056Bovine 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.PLoS Genet2016
25723102Gateways to the FANTOM5 promoter level mammalian expression atlas.Genome Biol2015
26719249Defining the Microglia Response during the Time Course of Chronic Neurodegeneration.J Virol2015
25843246A transcriptional perspective on human macrophage biology.Semin Immunol2015
25678556Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.Science2015
25702581Oncogenic properties of apoptotic tumor cells in aggressive B cell lymphoma.Curr Biol2015
25717144Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells.J Leukoc Biol2015
25811906Macrophage gene expression associated with remodeling of the prepartum rat cervix: microarray and pathway analyses.PLoS One2015
24005050Distinct molecular signature of human skin Langerhans cells denotes critical differences in cutaneous dendritic cell immune regulation.J Invest Dermatol2014
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Collaborators

David A Hume
Mater Research Institute-UQ, Translational Research Institute
Co-authored papers 25
John Kenneth Baillie
Roslin Institute, University of Edinburgh
Co-authored papers 13
Kim M Summers
Mater Research Institute-University of Queensland, Translational Research Institute
Co-authored papers 9
Peter Ghazal
UK System Immunity Research Institute, Cardiff University
Co-authored papers 6
Piero Carninci
RIKEN Center for Integrative Medical Sciences
Co-authored papers 6
Hideya Kawaji
RIKEN Center for Integrative Medical Sciences
Co-authored papers 6
Alistair R R Forrest
RIKEN Center for Integrative Medical Sciences
Co-authored papers 5
Yoshihide Hayashizaki
Center for Integrative Medical Sciences
Co-authored papers 5
Masayoshi Itoh
RIKEN Center for Integrative Medical Sciences
Co-authored papers 5
Alan L Archibald
The Roslin Institute and R(D)SVS, University of Edinburgh
Co-authored papers 5
Timo Lassmann
Telethon Kids Institute, University of Western Australia
Co-authored papers 5
Geoffrey J Faulkner
Mater Research Institute - University of Queensland
Co-authored papers 5
Carsten O Daub
International Institute of Molecular and Cell Biology in Warsaw
Co-authored papers 4
Michael Rehli
University Hospital Regensburg
Co-authored papers 4
Derek W Wright
Co-authored papers 4
Lynsey Fairbairn
Co-authored papers 4
Jessica Severin
Center for Integrative Medical Sciences
Co-authored papers 4
Laurence Calzone
Institut Curie, Universite PSL
Co-authored papers 4
Albin Sandelin
University of Copenhagen
Co-authored papers 4
Marina Lizio
Cerevance Ltd
Co-authored papers 4
Robin Andersson
University of Copenhagen
Co-authored papers 3
Takeya Kasukawa
RIKEN Center for Integrative Medical Sciences
Co-authored papers 3
Jayson Harshbarger
RIKEN Center for Integrative Medical Sciences
Co-authored papers 3
Augustin Luna
Harvard Medical School
Co-authored papers 3
Alexander D Diehl
Jacobs School of Medicine and Biomedical Sciences, University at Buffalo
Co-authored papers 3
Chris Sander
Broad Institute of MIT and Harvard
Co-authored papers 3
Andreas Lennartsson
Karolinska Institute
Co-authored papers 3
Terrence F Meehan
European Bioinformatics Institute
Co-authored papers 3
Peter Heutink
German Center for Neurodegenerative Diseases (DZNE).
Co-authored papers 3
Naoto Kondo
Nagoya City University Graduate School of Medical Sciences
Co-authored papers 3
Release 1.2