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Dr James Timmons

James

Reader, Translational Bioinformatics

Centre: Clinical Pharmacology and Precision Medicine

Email: j.timmons@qmul.ac.uk

Profile

ORCID iD: 0000-0002-2255-1220

James graduated from the Universities of Glasgow and Nottingham (Physiology and Pharmacology) and then spent 7yrs as a team-leader in the pharmaceutical industry (responsible for in vivo and in vitro models). He ran a team working on lead identification and leading optimisation for metabolic disease, thrombosis and atherosclerosis. He set up one of the first human clinical studies (1998) to use global transcriptomics to stratify human responses to exercise therapy and led the pharmacology for an anti-thrombotic drug nomination (2002). 

He moved to the Karolinska Institute in 2003 to re-train in RNA biology, particularly noncoding RNA. During this time his group discovered, with the Cannon lab, the developmental link between ‘brown’ adipocytes and muscle. He was appointed to Chair in Exercise Physiology (2006), first at Heriot-Watt and later at Loughborough University (2013) and a 5yr visiting Professorship at University of Stockholm (2007). In Edinburgh, his group discovered that very brief (<5min) intermittent high intensity exercise (‘HIT’) was sufficient to improve insulin action, challenging 50 years of exercise advice (work that featured in a BBC Horizon documentary). In 2011, he led a FP7 consortium that validated the principal of HIT in randomised clinical trials, and in 2019 WHO exercise guidelines were altered to reflect the work from several independent groups. As Director of Research, he led the School of Biological Sciences RAE2008 return.  

James has also held Professor posts (Research) at the Royal Veterinary College and King’s College London – running molecular physiology studies - funded by the MRC, BBSRC, NIH and Industry – while managing his EU FP7 multi-centred HIT trial. His group have used machine learning to build the first molecular classifier for cardiorespiratory adaptability in humans (2010), and the first transcriptomic multi-tissue classifier of human age (2015). In 2017, after two decades of ‘wet-lab’ activities, he decided to focus full time on bioinformatics - joining WHRI in 2021, as a Senior Fellow (Reader in Data Science). From 1998 to 2022 James has trained >20 graduate and post-doctoral scientists in industry and academia. He has an H-index of 49 (from 90, mostly first or senior authored, articles). He is a visiting Professor at the University of Miami, and a member of the Royal Society of Medicine and the Biochemical Society.

Research

I am interested in RNA biology and study the role of RNA in human aging, common chronic diseases (cardiovascular, metabolic and dementia) and exercise (as a treatment paradigm). The efficacy of exercise therapy in humans is variable, so much so that <20% of individuals demonstrate all the main health benefits. I am part of an international team, that has developed a large human exercise intervention biobank – incorporating global molecular profiling and deep physiological phenotyping. We use this to identify molecular transducers of the physiological responses to exercise. I also work on NIH funded biomarker projects, developing diagnostics and prognostics of cardio-metabolic disease and dementia. We are particularly interested in the following methodologies: 

  • The use of network strategies to study the biology of long noncoding RNAs  
  • Development of RNA pre-processing and gene-splicing methodologies 
  • Application of spatial transcriptomics to study single cell-type treatment responses 
  • Development of transcriptomic models as drug-repurposing tools 
  • Machine learning strategies to stratify human responses to exercise therapy

Publications

  • Mcleod JC, Lim C, Stokes T et al. (publicationYear). Network-based modelling reveals cell-type enriched patterns of non-coding RNA regulation during human skeletal muscle remodelling. nameOfConference


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  • Ma S, Morris M, Hubal M et al. (publicationYear). Sex-Specific Skeletal Muscle Gene Expression Responses to Exercise Reveal Novel Direct Mediators of Insulin Sensitivity Change. nameOfConference


  • Timmons JA, Brenner C (2024). The information theory of aging has not been tested. nameOfConference


  • Stokes T, Cen HH, Kapranov P et al. (2023). Transcriptomics for Clinical and Experimental Biology Research: Hang on a Seq. nameOfConference


  • Timmons J (2022). Variable selection and risk prediction using a penalised modelling framework for high-dimensional data in a nested matched case-control design. RSS International Conference 2022

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  • Nath M, Romaine SPR, Koekemoer A et al. (2022). Whole blood transcriptomic profiling identifies molecular pathways related to cardiovascular mortality in heart failure. nameOfConference


  • Timmons JA, Anighoro A, Brogan RJ et al. (publicationYear). A human-based multi-gene signature enables quantitative drug repurposing for metabolic disease. nameOfConference


  • Dennison JL, Volmar C-H, Modarresi F et al. (2022). JOTROL, a Novel Formulation of Resveratrol, Shows Beneficial Effects in the 3xTg-AD Mouse Model.. nameOfConference


  • Cen HH, Hussein B, Botezelli JD et al. (2022). Human and mouse muscle transcriptomic analyses identify insulin receptor mRNA downregulation in hyperinsulinemia‐associated insulin resistance. nameOfConference


  • Stokes T, Timmons JA, Crossland H et al. (2020). Molecular Transducers of Human Skeletal Muscle Remodeling under Different Loading States. nameOfConference


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  • Cao H, Salazar-García L, Gao F et al. (publicationYear). Novel approach reveals genomic landscapes of single-strand DNA breaks with nucleotide resolution in human cells. nameOfConference


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  • Timmons JA, Gallagher IJ, Sood S et al. (2019). A statistical and biological response to an informatics appraisal of healthy aging gene signatures. nameOfConference


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  • Timmons JA, Volmar C, Crossland H et al. (2019). Longevity‐related molecular pathways are subject to midlife “switch” in humans. nameOfConference


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  • Timmons JA, Atherton PJ, Larsson O et al. (2018). A coding and non-coding transcriptomic perspective on the genomics of human metabolic disease. nameOfConference


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  • Phillips BE, Kelly BM, Lilja M et al. (publicationYear). A Practical and Time-Efficient High-Intensity Interval Training Program Modifies Cardio-Metabolic Risk Factors in Adults with Risk Factors for Type II Diabetes. nameOfConference


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  • Crossland H, Timmons JA, Atherton PJ (2017). A dynamic ribosomal biogenesis response is not required for IGF‐1–mediated hypertrophy of human primary myotubes. nameOfConference


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  • Dinas PC, Lahart IM, Timmons JA et al. (publicationYear). Effects of physical activity on the link between PGC-1a and FNDC5 in muscle, circulating Ιrisin and UCP1 of white adipocytes in humans: A systematic review. nameOfConference


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  • Pollard AS, Charlton BG, Hutchinson JR et al. (publicationYear). Limb proportions show developmental plasticity in response to embryo movement. nameOfConference


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  • Timmons JA (2017). Molecular Diagnostics of Ageing and Tackling Age-related Disease. nameOfConference


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  • Crossland H, Atherton PJ, Strömberg A et al. (2017). A reverse genetics cell‐based evaluation of genes linked to healthy human tissue age. nameOfConference


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  • Nakhuda A, Josse AR, Gburcik V et al. (2016). Biomarkers of browning of white adipose tissue and their regulation during exercise- and diet-induced weight loss 1 , 2. nameOfConference


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  • Timmons JA, Gallagher IJ (publicationYear). Molecular studies of exercise, skeletal muscle, and ageing. nameOfConference


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  • Sood S, Szkop KJ, Nakhuda A et al. (2016). iGEMS: an integrated model for identification of alternative exon usage events. nameOfConference


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  • Hangelbroek RWJ, Fazelzadeh P, Tieland M et al. (2016). Expression of protocadherin gamma in skeletal muscle tissue is associated with age and muscle weakness. nameOfConference


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  • Sood S, Gallagher IJ, Lunnon K et al. (2015). A novel multi-tissue RNA diagnostic of healthy ageing relates to cognitive health status. nameOfConference


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  • Timmons JA, Szkop KJ, Gallagher IJ (2015). Multiple sources of bias confound functional enrichment analysis of global -omics data. nameOfConference


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  • Timmons JA (2015). Single-Gene Genotyping and Personalized Preventive Care. nameOfConference


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  • Ghosh S, Vivar JC, Sarzynski MA et al. (2013). Integrative pathway analysis of a genome-wide association study of V̇o2max response to exercise training. nameOfConference


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  • Lessard SJ, Rivas DA, Alves-Wagner AB et al. (2013). Resistance to Aerobic Exercise Training Causes Metabolic Dysfunction and Reveals Novel Exercise-Regulated Signaling Networks. nameOfConference


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  • Crossland H, Kazi AA, Lang CH et al. (2013). Focal adhesion kinase is required for IGF-I-mediated growth of skeletal muscle cells via a TSC2/mTOR/S6K1-associated pathway. nameOfConference


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  • Phillips BE, Williams JP, Gustafsson T et al. (2013). Molecular Networks of Human Muscle Adaptation to Exercise and Age. nameOfConference


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  • Gburcik V, Cleasby ME, Timmons JA (2013). Loss of neuronatin promotes “browning” of primary mouse adipocytes while reducing Glut1-mediated glucose disposal. nameOfConference


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  • Andersen DK, Timmons JA, Cleasby ME (2013). High fat diet induces selective alterations in microRNA expression profile in rat skeletal muscle. nameOfConference

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  • Gburcik V, Cleasby ME, Timmons JA (2013). Loss of neuronatin promotes 'browning' of primary mouse adipocytes. nameOfConference

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  • Poulet B, Ulici V, Stone TC et al. (2012). Time‐series transcriptional profiling yields new perspectives on susceptibility to murine osteoarthritis. nameOfConference


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  • Timmons JA, Baar K, Davidsen PK et al. (2012). Is irisin a human exercise gene?. nameOfConference


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  • Gburcik V, Cawthorn WP, Nedergaard J et al. (2012). An essential role for Tbx15 in the differentiation of brown and “brite” but not white adipocytes. nameOfConference


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  • Gallagher IJ, Stephens NA, MacDonald AJ et al. (2012). Suppression of Skeletal Muscle Turnover in Cancer Cachexia: Evidence from the Transcriptome in Sequential Human Muscle Biopsies. nameOfConference


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  • Poulet B, Veronica U, Stone TC et al. (2012). Gene array profiling of articular chondrocytes in mice with different susceptibility to natural disease reveals specific gene signatures linked to healthy ageing and spontaneous OA. nameOfConference


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  • Timmons JA (2011). Modulation of MicroRNAs During Exercise and Disease in Human Skeletal Muscle. nameOfConference


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  • Timmons JA (2011). What happens if you pose the wrong questions?. nameOfConference


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  • Waldén TB, Hansen IR, Timmons JA et al. (2012). Recruited vs. nonrecruited molecular signatures of brown, “brite,” and white adipose tissues. nameOfConference


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  • Bouchard C, Rankinen T, Timmons JA (2011). Genomics and Genetics in the Biology of Adaptation to Exercise. nameOfConference


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  • Keller P, Gburcik V, Petrovic N et al. (2011). Gene-chip studies of adipogenesis-regulated microRNAs in mouse primary adipocytes and human obesity. nameOfConference


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  • Timmons JA (2011). Genes that AKT to determine physiological heterogeneity in response to exercise. nameOfConference


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  • Timmons JA, Helge JW (2011). A Primer on Systems Biology, as Applied to Exercise Physiology and Metabolism. nameOfConference


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  • Davidsen PK, Gallagher IJ, Hartman JW et al. (2011). High responders to resistance exercise training demonstrate differential regulation of skeletal muscle microRNA expression. nameOfConference


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  • Timmons JA (2011). Variability in training-induced skeletal muscle adaptation. nameOfConference


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  • Keller P, Vollaard NBJ, Gustafsson T et al. (2011). A transcriptional map of the impact of endurance exercise training on skeletal muscle phenotype. nameOfConference


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  • Koch LG, Britton SL, Wisloff U et al. (2010). Development of Rat Models for Low and High Response to Exercise Training. nameOfConference


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  • Shabalina IG, Petrovic N, Walden TB et al. (2010). Thermogenically competent recruitment of uncoupling protein 1 in brown preadipocytes and in a subset of cell precursors from epididymal white adipose tissue by a PPARγ agonist. nameOfConference


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  • Samjoo I, Safdar A, Hamadeh M et al. (2010). Endurance Training‐mediated Differential Regulation of miRNAs in Skeletal Muscle of Lean and Obese Men. nameOfConference


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  • Timmons JA, Knudsen S, Rankinen T et al. (2010). Using molecular classification to predict gains in maximal aerobic capacity following endurance exercise training in humans. nameOfConference


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  • Gallagher IJ, Scheele C, Keller P et al. (publicationYear). Integration of microRNA changes in vivo identifies novel molecular features of muscle insulin resistance in type 2 diabetes. nameOfConference


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  • Stephens NA, Gallagher IJ, Rooyackers O et al. (publicationYear). Using transcriptomics to identify and validate novel biomarkers of human skeletal muscle cancer cachexia. nameOfConference


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  • Petrovic N, Walden TB, Shabalina IG et al. (2010). Chronic Peroxisome Proliferator-activated Receptor γ (PPARγ) Activation of Epididymally Derived White Adipocyte Cultures Reveals a Population of Thermogenically Competent, UCP1-containing Adipocytes Molecularly Distinct from Classic Brown Adipocytes*. nameOfConference


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  • Roos A-K, Eriksson F, Timmons JA et al. (publicationYear). Skin Electroporation: Effects on Transgene Expression, DNA Persistence and Local Tissue Environment. nameOfConference


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  • Timmons JA, Pedersen BK (2009). The Importance of Brown Adipose Tissue. nameOfConference


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  • Vollaard NBJ, Constantin-Teodosiu D, Fredriksson K et al. (2009). Systematic analysis of adaptations in aerobic capacity and submaximal energy metabolism provides a unique insight into determinants of human aerobic performance. nameOfConference


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  • Babraj JA, Vollaard NB, Keast C et al. (2009). Extremely short duration high intensity interval training substantially improves insulin action in young healthy males. nameOfConference


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  • Scheele C, Larsson O, Timmons JA (2009). Chapter 12 Using Functional Genomics to Study PINK1 and Metabolic Physiology. nameOfConference


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  • Fredriksson K, Tjäder I, Keller P et al. (2008). Dysregulation of Mitochondrial Dynamics and the Muscle Transcriptome in ICU Patients Suffering from Sepsis Induced Multiple Organ Failure. nameOfConference


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  • Walden TB, Timmons JA, Keller P et al. (2009). Distinct expression of muscle‐specific MicroRNAs (myomirs) in brown adipocytes. nameOfConference


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  • Franks PW, Scheele C, Loos RJF et al. (2008). Genomic variants at the PINK1 locus are associated with transcript abundance and plasma nonesterified fatty acid concentrations in European whites. nameOfConference


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  • Petrovic N, Shabalina IG, Timmons JA et al. (2008). Thermogenically competent nonadrenergic recruitment in brown preadipocytes by a PPARγ agonist. nameOfConference


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  • Timmons JA (2008). Commentary on Viewpoint: Perspective on the future use of genomics in exercise prescription. nameOfConference


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  • Timmons JA, Sundberg CJ (2006). Oligonucleotide microarray expression profiling: Human skeletal muscle phenotype and aerobic exercise training. nameOfConference


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  • Keller P, Vollaard N, Babraj J et al. (2007). Using systems biology to define the essential biological networks responsible for adaptation to endurance exercise training. nameOfConference


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  • Timmons J, Scheele C, Wahlestedt C (2007). Do mitochondria provide a common link between diabetes and Parkinson's disease?. nameOfConference


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  • Scheele C, Nielsen AR, Walden TB et al. (2007). Altered regulation of the PINK1 locus: a link between type 2 diabetes and neurodegeneration?. nameOfConference


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  • Scheele C, Petrovic N, Faghihi MA et al. (2007). The human PINK1 locus is regulated in vivo by a non-coding natural antisense RNA during modulation of mitochondrial function. nameOfConference


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  • Timmons JA, Wennmalm K, Larsson O et al. (2007). Myogenic gene expression signature establishes that brown and white adipocytes originate from distinct cell lineages. nameOfConference


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  • Unnithan V, Timmons J, Paton J et al. (1995). Physiologic Correlates to Running Performance in Pre-Pubertal Distance Runners. nameOfConference


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  • Nedergaard J, Petrovic N, Timmons JA et al. (2007). Food constituents and quantity as determinants of differentiation of adipose progenitor cells. nameOfConference

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  • Franks PW, Scheele C, Loos RJF et al. (2007). Gene expression and genetic association studies suggest a role for the Parkinson's gene PINK1 in the pathogenesis of type 2 diabetes. nameOfConference

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  • Timmons JA, Good L (2006). Does everything now make (anti)sense?. nameOfConference


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  • Baker DJ, Constantin-Teodosiu D, Jones SW et al. (2006). Chronic Treatment with the β2-Adrenoceptor Agonist Prodrug BRL-47672 Impairs Rat Skeletal Muscle Function by Inducing a Comprehensive Shift to a Faster Muscle Phenotype. nameOfConference


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  • Baker DJ, Greenhaff PL, MacInnes A et al. (2006). The Experimental Type 2 Diabetes Therapy Glycogen Phosphorylase Inhibition Can Impair Aerobic Muscle Function During Prolonged Contraction. nameOfConference


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  • Baker DJ, Greenhaff PL, Timmons JA (2006). Glycogen phosphorylase inhibition as a therapeutic target: a review of the recent patent literature. nameOfConference


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  • Timmons JA, Sundberg CJ (2006). Oligonucleotide microarray expression profiling: Human skeletal muscle phenotype and aerobic exercise training (vol 58, pg 15, 2006). nameOfConference

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  • Timmons JA, Norrbom J, Schéele C et al. (2006). Expression profiling following local muscle inactivity in humans provides new perspective on diabetes-related genes. nameOfConference


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  • Timmons JA, Jansson E, Fischer H et al. (2005). Modulation of extracellular matrix genes reflects the magnitude of physiological adaptation to aerobic exercise training in humans. nameOfConference


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  • Baker DJ, Timmons JA, Greenhaff PL (2005). Glycogen Phosphorylase Inhibition in Type 2 Diabetes Therapy A Systematic Evaluation of Metabolic and Functional Effects in Rat Skeletal Muscle. nameOfConference


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  • MacInnes A, Timmons JA (2005). Metabolic adaptations to repeated periods of contraction with reduced blood flow in canine skeletal muscle. nameOfConference


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  • Larsson O, Wahlestedt C, Timmons JA (publicationYear). Considerations when using the significance analysis of microarrays (SAM) algorithm. nameOfConference


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  • Timmons JA, Larsson O, Jansson E et al. (2005). Human muscle gene expression responses to endurance training provide a novel perspective on Duchenne muscular dystrophy. nameOfConference


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  • Gustafsson T, Ameln H, Fischer H et al. (2005). VEGF-A splice variants and related receptor expression in human skeletal muscle following submaximal exercise. nameOfConference


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  • Timmons JA (2005). CHASING THE “GHOST” OF THE ACETYL GROUP DEFICIT. nameOfConference


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  • Timmons JA, Constantin‐Teodosiu D, Poucher SM et al. (2004). Acetyl group availability influences phosphocreatine degradation even during intense muscle contraction. nameOfConference


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  • Jones SW, Baker DJ, Gardiner SM et al. (2004). The Effect of the β2-Adrenoceptor Agonist Prodrug BRL-47672 on Cardiovascular Function, Skeletal Muscle Myosin Heavy Chain, and MyoD Expression in the Rat. nameOfConference


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  • Greenhaff PL, Campbell‐O’Sullivan SP, Constantin‐Teodosiu D et al. (2004). Metabolic inertia in contracting skeletal muscle: a novel approach for pharmacological intervention in peripheral vascular disease. nameOfConference


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  • Timmons JA (2002). Can we “switch” the emphasis please?. nameOfConference


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  • Greenhaff PL, Campbell-O'Sullivan SP, Constantin-Teodosiu D et al. (2002). An acetyl group deficit limits mitochondrial ATP production at the onset of exercise. nameOfConference


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  • Greenhaff PL, Campbell S, Constantin-Teodosiu D et al. (2002). The acetyl-group deficit limits mitochondrial ATP production at the onset of exercise. nameOfConference


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  • MacInnes A, Timmons JA (2002). PDE inhibition by UK-114,542 does not alter skeletal muscle function during partial ischaemia in the anaesthetised dog. nameOfConference

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  • Timmons JA, MacInnes A (2002). The effects of the PDE inhibitor UK-114,542 on skeletal muscle glucose uptake in the anaesthetised dog. nameOfConference

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  • MacInnes A, Hogan MC, Hepple RT et al. (2000). Is there a role for neutrophil plugging in canine skeletal muscle contractile dysfunction during partial ischaemia?. nameOfConference

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  • Timmons JA (1999). A conflicting role for the pyruvate dehydrogenase complex in resting versus contracting skeletal muscle?. nameOfConference

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  • Timmons JA, Poucher SM, Constantin-Teodosiu D et al. (1998). Regulation of skeletal muscle carbohydrate oxidation during steady-state contraction. nameOfConference


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  • Timmons JA, Gustafsson T, Sundberg CJ et al. (1998). Muscle acetyl group availability is a major determinant of oxygen deficit in humans during submaximal exercise. nameOfConference


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  • Greenhaff PL, Timmons JA (1998). 1 Interaction Between Aerobic and Anaerobic Metabolism During Intense Muscle Contraction.. nameOfConference


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  • Timmons JA, Poucher SM, Greenhaff PL (1998). Inhibition of lipolysis and mitochondrial lipid uptake during contraction in ischaemic skeletal muscle. nameOfConference

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  • Greenhaff PL, Timmons JA (1998). Pyruvate Dehydrogenase Complex Activation Status and Acetyl Group Availability as a Site of Interchange between Anaerobic and Oxidative Metabolism during Intense Exercise. nameOfConference


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  • Timmons JA, Gustafsson T, Sundberg CJ et al. (1998). Substrate availability limits human skeletal muscle oxidative ATP regeneration at the onset of ischemic exercise.. nameOfConference


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  • Timmons JA, Greenhaff PL, Poucher SM (1998). The effects of asparagine infusion on ischaemic contractile function in canine skeletal muscle. nameOfConference

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  • Timmons JA, Poucher SM, Constantin-Teodosiu D et al. (1997). Metabolic responses from rest to steady state determine contractile function in ischemic skeletal muscle. nameOfConference


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  • Greenhaff PL, Casey A, ConstantinTeodosiu D et al. (1997). Biochemical aspects of muscle fatigue. nameOfConference

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  • Hultman E, Soderlund K, Timmons JA et al. (1996). Muscle creatine loading in men. nameOfConference


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  • Timmons JA, Poucher SM, Constantin-Teodosiu D et al. (1996). Metabolic responses of canine gracilis muscle during contraction with partial ischemia. nameOfConference


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  • Unnithan VB, Timmons JA, Brogan RT et al. (1996). Submaximal running economy in run-trained pre-pubertal boys.. nameOfConference

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  • Timmons JA, Poucher SM, Constantin-Teodosiu D et al. (1996). Increased acetyl group availability enhances contractile function of canine skeletal muscle during ischemia.. nameOfConference


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  • Timmons JA, Constantin-Teodosiu D, Poucher SM et al. (1995). DICHLOROACETATE ENHANCES SKELETAL MUSCLE PERFORMANCE DURING ISCHAEMIC WORK: 17.. nameOfConference


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  • Unnithan VB, Murray LA, Timmons JA et al. (1995). Reproducibility of cardiorespiratory measurements during submaximal and maximal running in children.. nameOfConference


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  • Unnithan VB, Wilson J, Buchanan D et al. (1994). Validation of the Sensormedics (S2900Z) Metabolic Cart for Pediatric Exercise Testing. nameOfConference


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  • Timmons J, Poucher S, Constantin-Teodosiu D et al. (1994). An in vivo Technique for Modelling the Metabolic Responses of Skeletal Muscle to Ischaemic Work. nameOfConference


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Sponsors

My research has benefited from the following sources of funding:

Collaborators

Internal

External

  • Professor William Kraus (Duke University)
  • Professor Stuart Phillips (McMaster University)
  • Professor Claes Wahlestedt (University of Miami)
  • Professor Nilesh Samani (University of Leicester)
  • Professor Bethan Phillips (University of Nottingham)
  • Professor James Johnson (University of British Columbia)
  • Professor Phillip Atherton (University of Nottingham)
  • Professor Andrew Pitsillides (University of London)
  • Associate Professor Claude Volmar (University of Miami)
  • Associate Professor Iain Gallagher (Napier University Edinburgh)
  • Associate Professor Mintu Nath (University of Aberdeen)
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