Dr Bridget Holmes

Dr Bridget Holmes
Dr Bridget Holmes

Institution: Danone Research

Tasks in the project:

WP1: methods to measure and analyse the impact of dietary patterns on the association between gut microbiome and host CMD risk features.

WP3: identify relevant methods/tools (e.g. questionnaires) to obtain detailed information about health and lifestyle behaviour of study participants.

WP5: identify methods to visualize dependence of both dietary and environmental patterns with both bacterial and serum metabolic profiles to determine CMD stages.

Read more: biography and main publications

Biography

Bridget completed her undergraduate degree in Nutrition at Cardiff University and went on to do a PhD in Nutrition at King’s College, London. Her thesis involved a dietary validation survey in low income individuals in the UK, the results of which were used to inform government on the dietary assessment method best suited for a national survey of low income individuals (The Low Income Diet and Nutrition Survey). Bridget went on to manage this survey and several other dietary surveys during her time at King’s. In 2010, Bridget relocated to France to work at Danone Research. Her current role involves managing clinical and epidemiological surveys that involve dietary data collection in different countries and population sub-groups. Bridget is managing the dietary assessment and dietary analysis for the Metacardis study.

Main Publications

  1. Bates CJ, Bogin B, Holmes BA, Nutritional Assessment Methods. 2011. In: Human Nutrition. 12th edn. Chapter 31, 607-632. Churchill Livingstone. ISBN:9780702031182 and 9780702044632
  2. Kong LC, Holmes BA, Cotillard A, Habi-Rachedi F, Brazeilles R, et al. (2014) Dietary patterns differently associate with inflammation and gut microbiota in overweight and obese subjects. PLoS ONE 9(10): e109434. doi:10.1371/journal.pone.0109434.
  3. Verger EO, Holmes BA, Huneau JF, Mariotti F. (2014) Simple changes within dietary subgroups can rapidly improve the nutrient adequacy of the diet of French adults. J Nutr 144(6):929-36. doi:10.3945/jn.113.188284
  4. Holmes BA, Kaffa N, Campbell K, Sanders TAB (2012). The contribution of breakfast cereals to the nutritional intake of the materially deprived UK population. Eur J Clin Nutr. 66(1): 10-17. doi:10.1038/ejcn.2011.143
  5. Holmes BA, Roberts CL (2011). Diet quality and the influence of social and physical factors on food consumption and nutrient intake in materially deprived older people. Eur J Clin Nutr 65(4): 538-45. doi:10.1038/ejcn.2010.293
  6. Holmes B, Dick K, Nelson M (2008). A comparison of four dietary assessment methods in materially deprived households in England. Public Health Nutrition. 11: 444-456. doi:10.1017/S1368980007000559

Institute Number: 10

Dr Kristoffer Forslund

Dr Kristoffer Forslund
Dr Kristoffer Forslund

Institution: EMBL

Tasks in the project:

Coordination of efforts on behalf of P5: EMBL, including development and maintenance of the data hub as well as coordination of the data integration efforts. Once original data become available, I hope to apply data mining and modelling techniques to it, then to cooperate with the clinical teams in interpreting these results.

Read more: biography and main publications

Biography

My first brushes with bioinformatics were by developing phylogenetics tools as a summer project back at Uppsala University. For my PhD at Stockholm University I wanted to move closer to clinical applications by work on how protein structure and function evolves and how it can be predicted, aiding in development of resources such as Pfam and InParanoid. For my post-doctoral project at EMBL Heidelberg, funded by the Alexander von Humboldt foundation, I wanted still closer to clinical relevance by analyzing evolution, composition, interaction and functional capacities of human-associated microbes. MetaCardis then realizes this intention, allowing me to apply a variety of computational tools, including sequence analysis, machine learning and evolutionary analysis, to attempting to solve an actual problem of human health.

Main Publications

  1. Forslund K, Sunagawa S, Coelho LP, Bork P. (2014) Metagenomic insights into the human gut resistome and the forces that shape it. BioEssays 36(3):316-29. doi:10.1002/bies.201300143
  2. Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, et al. (2013) Country-specific antibiotic use practices impact the human gut resistome. Genome Res. 23(7):1163-9. doi:10.1101/gr.155465.113
  3. Forslund K, Pekkari I, Sonnhammer EL. (2011) Domain architecture conservation in orthologs. BMC Bioinformatics 12:326. doi:10.1186/1471-2105-12-326
  4. Forslund K, Schreiber F, Thanintorn N, Sonnhammer EL. (2011) OrthoDisease: tracking disease gene orthologs across 100 species. Brief Bioinform. 12(5):463-73. doi:10.1093/bib/bbr024
  5. Forslund K, Sonnhammer EL. (2009) Benchmarking homology detection procedures with low complexity filters. Bioinformatics. 25(19):2500—2505. doi:10.1093/bioinformatics/btp446
  6. Forslund K, Sonnhammer EL. (2008) Predicting protein function from domain content. Bioinformatics. 24(15):1681—1687. doi:10.1093/bioinformatics/btn312
  7. Forslund K, Henricson A, Hollich V, Sonnhammer EL (2008). Domain tree-based analysis of protein architecture evolution. Mol Biol Evol. 25(2):254—264. doi:10.1093/molbev/msm254
  8. Forslund K, Huson DH, Moulton V. VisRD – visual recombination detection. Bioinformatics. 20(18):3654—3655. doi:10.1093/bioinformatics/bth400

Institute Number: 4

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