Dissemination

Peer-reviewed publications                                              

Radchuk O, Kerbe W, Schmidt M. (2016) Homo politicus meets Homo ludens: Public participation in serious life science games. Public Understanding of Science

Dudnik A, et al., “BacHberry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits”, Phytochemistry Reviews, submitted

Menezes R, Foito A, Jardim C, Costa I, Garcia G, Rosado-Ramos R, Poejo J, Matias A, Duarte C, Freitag S, Alexander C, Santos CN. Rubus genus as a source of bioactive compounds for neurodegenerative diseases. Nature Chemical Biology, submitted

Feng C, Wang W, Ye J, Li Sh, Wu Q, Yin D, Li B, Xu Y and Wang L. (2017) Polyphenol profile and antioxidant activity of the fruit and leaf of Vaccinium glaucoalbum from the Tibetan Himalayas. Food Chemistry, 219: 490-495

Feng Ch, Su Sh, Wang L, Wu J, Tang Zh, Xu Y, Shu Q and Wang L. (2016) Antioxidant capacities and anthocyanin characteristics of the black-red wild berries obtained in Northeast China. Food Chemistry, 204: 150-158

Su Sh, Wang L, Feng Ch, Liu Y, Li Ch, Du H, Tang Zh, Xu Y and Wang L. (2016) Fingerprints of anthocyanins and flavonols of Vaccinium uliginosum berries from different geographical origins in the Greater Khingan Mountains and their antioxidant capacities. Food Control, 64: 218-225

Su Sh, Wang L, Wu J, Li B, Wang W and Wang L, (2016) Review: chemical compositions and functions of Vaccinium uliginosum (in Chinese). Chinese Bulletin of Botany, 51(5), 691-704

Oliveira AV, Vilaça R, Santos CN, Costa V, Menezes R. Exploring the power of yeast to model aging and age-related neurodegenerative disorders. Biogerontology, in press

Figueira I, Menezes R, Macedo D, Costa I, Santos CN. Polyphenols beyond barriers: a glimpse into the brain. Curr Neuropharm, in press

Menezes R, Tenreiro S, Macedo D, Santos CN, Outeiro TF. (2016) From the baker to the bedside: yeast models of Parkinson's disease. Microbial Cell, 2(8): 262-279.

Macedo D, Tavares L, McDougall GJ, Vicente Miranda H, Stewart D, Ferreira RB, Tenreiro S, Outeiro TF, Santos CN. (2015) (Poly)phenols protect from α-synuclein toxicity by reducing oxidative stress and promoting autophagy. Hum Mol Genet., 24(6): 1717-32.

Garcia G, Nanni S, Figueira I, Ivanov I, McDougall GJ, Stewart D, Ferreira RB, Pinto P, Silva RFM, Brites D, Santos CN. (2017) Bioaccessible (poly)phenol metabolites from raspberry protect neural cells from oxidative stress and attenuate microglia activation. Food Chemistry, 215: 274-83

Eichenberger M, Lehka BJ, Folly C, Fischer D, Martens S, Simón E, Naesby M. Metabolic engineering of Saccharomyces cerevisiae for de novo production of dihydrochalcones with known antioxidant, antidiabetic, and sweet tasting properties. Metabolic Engineering, in press

Jendresen CB, Stahlhut SG, Li M, Gaspar P, Siedler S, Förster J, Maury J, Borodina I and Nielsen AT. (2015) Novel highly active and specific tyrosine ammonia-lyases from diverse origins enable enhanced production of aromatic compounds in bacteria and yeast. Applied and Environmental Microbiology 81(13): 4458–4476.

Kallscheuer N, Vogt M, Kappelmann J, Krumbach K, Noack S, Bott M and Marienhagen J. (2016) Identification of the phd gene cluster responsible for phenylpropanoid utilization in Corynebacterium glutamicum. Applied Microbiology and Biotechnology 100: 1871-1881.

Kallscheuer N, Vogt M, Stenzel A, Gätgens J, Bott M and Marienhagen J. (2016) Construction of a Corynebacterium glutamicum platform strain for the production of stilbenes and (2S)-flavanones. Metabolic Engineering 38: 47-55.

Kallscheuer N, Vogt M and Marienhagen J. A novel synthetic pathway enables microbial production of polyphenols independent from the endogenous aromatic amino acid metabolism, ACS Syn. Biol., accepted

Sevillano DM, van der Wielen LAM, Hooshyar N, Ottens M. (2014) MPP-UNIFAC, A Predictive Activity Coefficient Model for Polyphenols, Fluid Phase Equilibria, 384: 82–88

Caldas J, Vinga S. (2014) Global Meta-Analysis of Transcriptomics Studies. Plos One, 9(2)
Costa RS, Verissimo A, Vinga S. (2014). KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. BMC Systems Biology, 8: 85

Hartmann A, JM Lemos, S Vinga (2015) Modeling multiple experiments using regularized optimization: a case study on bacterial glucose utilization dynamics. Comput Biol Med. 63:301-309

Hartmann A, Lemos JM, Costa RS, Xavier J and Vinga S. (2015) Identification of switched ARX models via convex optimization and expectation maximization, J. Process Control, 28: 9–16.

Milreu PV, Klein CC, Cottret L, Acuña V, Birmelé E, Borassi M, Junot C, Marchetti-Spaccamela A, Marino A, Stougie L, Jourdan F, Crescenzi P, Lacroix V, Sagot MF. (2014) Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. Bioinformatics. 30(1): 61-70

Fernandes A, and Vinga S. (2016) Improving Protein Expression Prediction Using Extra Features and Ensemble Averaging, Plos One, 11(3): 15.

Julien-Laferrière A, Bulteau L, Parrot D, Marchetti-Spaccamela A, Stougie L, Vinga S, Mary A and Sagot M-F. (2016) A Combinatorial Algorithm for Microbial Consortia Synthetic Design. Scientific Reports, 6, 12.

Costa RS, Hartmann A and Vinga S. (2016) Kinetic modeling of cell metabolism for microbial production. Journal of Biotechnology, 219, 126-141

Hartmann A, Neves AR, Lemos JM and Vinga S. (2016) Identification and automatic segmentation of multiphasic cell growth using a linear hybrid model. Mathematical Biosciences, 279, 83-89

Andrade R, Wannagat M, Cecilia CK, Acuña V, Marchetti-Spaccamela R, Milreu PM, Stougie L and Sagot M-F. (2016) Enumeration of minimal stoichiometric precursor sets in metabolic networks. Algorithms for Molecular Biology, 11:25.

Book chapters

Pei L and Schmidt M. (2016) Sustainable Assessment on Using Bacterial Platform to Produce High-Added-Value Products from Berries through Metabolic Engineering. In. Systems Biology Application in Synthetic Biology. S. Singh (ed), Springer: 71-78

Garcia G, Santos CN, Menezes R. (2016) High-throughput cell (yeast)-based reporter assay to identify compounds with anti-inflammatory potential. Methods Mol Biol., 1449:441-52.

Santos CN, Costa IS, Ferreira RB, Figueira I, Macedo D, Menezes R, Pinto P, Tavares L. (2014) Metabolitos de pequenos frutos para um E-book in the ambit of III International Congress of Studies of Human Aging (English and Portuguese).


Abstracts in Proceedings of Scientific Meetings

Jardim C, Menezes R, Foito A, Stewart D, Ferreira RB, Santos CN. (2014) Yeast SMART platforms: screening of berry bioactive phenolics with protective function towards human degenerative diseases, J. Nutrigenet. Nutrigenomics, 7:75-93

Foito A, Menezes R, Freitag S, Costa I, Jardim C, Garcia G, Ramos R, Santos C, Stewart D. (2016) Bioprospection of novel therapeutic (poly)phenols from a large soft-fruit germplasm collection, The 1st International Conference of Food Bioactives and Health – Programme and Abstracts

Foito A, Menezes R, Freitag S, Santos CN, Stewart D. (2016) Diversidade química em diversas espécies de pequenos frutos, Livro de Resumos – V Colóquio Nacional da Produção de pequenos Frutos

Costa RS, Nguyen S, Hartmann A, Vinga S. (2014) Exploring the cellular objective in flux balance constraint-based models, Lecture Notes in Computer Science, LNBI 8859, 211-224, Springer International Publishing Switzerland

Fernandes A, Vinga S. (2015) Improving Protein Expression Prediction Using Machine Learning and Committee Machines. 17th Portuguese Conference on Artificial Intelligence (EPIA-2015).

Oliveira JA, Braga A, Rocha I and Faria N, (2015) The effect of hydrodynamic conditions in Corynebacterium glutamicum growth”, Abstract published in the proceedings of MicroBiotec 2015, University of Évora, Portugal

Oral Presentations:

Lei Pei presented a talk titled “Applications of Synthetic Biology Technologies for Toxicological Sciences” on “Systems Toxicology Workshop Beijing” (14 October 2014, Beijing, China)

Lei Pei presented a lecture titled “Novel Approaches for Biocontainment” at the scientific meeting of the FP7 project CyanoFactory (10 December 2014, Ljubljana, Slovenia).

Lei Pei participated in the EC workshop on “EU ABS Regulation Training Workshops” (20 November 2015, Berlin)

Foito A, “Diversidade quimica em diversas especies de pequenos frutos“, 5th Coloquio Nacional de Pequenos Frutos, Oeiras, Portugal, 14.10.2016

Foito A, “Bioprospection of novel therapeutic (poly)phenols from a large soft fruit germplasm collection“, Food Bioactives and Health Conference 2016, Norwich, UK, 14.09.2016

Foito A, “BachBerry – Bacterial Hosts for the production of berry phenolics“, Synthetic Biology Workshop, Invergowrie, UK, 23.03.2016

Foito A, “Phytochemical mining in Berry species“, Soft fruit and perennial crops workshop, Invergowrie, UK, 30.11.2015

Stewart D, “Bioactive and Functional natural products from sustainable plant and crop sources”, Natural Product Biotechnology, Inverness, UK, 19.11.2015

Stewart D, “Phytochemical mining of berry germplasm”, The 28th International Conference on Polyphenols”, Satellite Workshop “Bacterial Hosts for Production of Bioactive Phenolics from Berry Fruits”, Vienna, Austria, 11.07.2016

Menezes R, Costa I, Jardim C, Garcia G, Ramos R, Foito A, Stewart D, Santos CN. “Novel therapeutic (poly)phenols revealed after berry germplasm bioprospection”, ICP 2016, Vienna, Austria

Foito A, Menezes R, Freitag S, Costa I, Jardim C, Garcia G, Ramos R, Santos CN, Stewart D. “Diversidade química em diversas espécies de pequenos frutos. V Colóquio nacional da produção de pequenos frutos”, Portugal, 2016

Rosado-Ramos R, Garcia G, Menezes R, Costa I, Jardim C, Foito A, Stewart D, Sevillano D, Ottens M, Santos CN. “A framboesa como fonte de novos compostos anti-Huntington. V Colóquio nacional da produção de pequenos frutos”, 2016, Portugal

Santos CN, “Berries Metabolites for a Healthy Ageing of the Brain”, III International Congress of Studies of Human Aging, Brazil, 2014

Santos CN, “Bioprospecting and biodiscovery of novel berry high value phenolics”, The 28th International Conference on Polyphenols”, Satellite Workshop “Bacterial Hosts for Production of Bioactive Phenolics from Berry Fruits”, Vienna, Austria, 11.07.2016

Menezes R, “Novas abordagens para o estudo de bioatividades de pequenos frutos (Novel approaches for the study of berry bioactivities)”, EU-Berry Final Meeting, Lisbon, Portugal, 2015

Menezes R, “Recapitulating molecular aspects of human diseases in yeast models of aggregation, cancer and inflammation: bioprospection of potential therapeutic compounds”, COST Action BM1307 First Proteostasis Meeting, Spain, 2014

Menezes R, "Yeast SMART platform for screening of bioactives in human pathologies”, Summer School on Nutrigenomics, Italy, 2014

Figueira I, Pimpão RC, Garcia G, Tavares L, Ventura MR, Terrasso AP, Silva AC, Brito AC, Alves PM, Williamson G, McDougall G, Stewart D, Ferreira RB, Brites D, Brito MA, Santos CN, “Crossing the blood-brain barrier: unraveling beneficial effects of human bioavailable (poly)phenol metabolites”, 9th World Congress on Polyphenols Applications, Malta, 2015

Garcia G, Pinto P, Pais TF, Menezes R, McDougall G, and Santos CN, “(Poly)phenols from quasi-isogenic raspberries: attenuation of neuroinflammation”, 7th International Conference on Polyphenols, Tours, France, 2015

Figueira I, Pimpão RC, Garcia G, Costa I, Ventura MR, Terrasso AP, Silva C, Brito AC, Alves PM, Williamson G, McDougall G, Stewart D, Ferreira RB, Brites D, Brito MA, Santos CN, “Neuroprotective potential of phenolic sulfates, abundant bioavailable metabolites”, 7th International Conference on Polyphenols, Tours, France, 2015

Bassard JEA, “Biotechnologie des Plantes – BacHBerry”, Prins Henrik skole, Frederiksberg, Denmark, March 2015.

Bassard JEA, "Biosynthetic pathway identification of berry phenolics – RNAseq database mining", The 28th International Conference on Polyphenols”, Satellite Workshop “Bacterial Hosts for Production of Bioactive Phenolics from Berry Fruits”, Vienna, Austria, 11.07.2016

Gaspar P, Neves AR and Förster J, “Engineering Lactococcus lactis for the production of resveratrol, a nutraceutical plant-derived polyphenol”, 11th Symposium on Lactic Acid Bacteria: LAB11, Egmond aan Zee, The Netherlands, 31.08 – 4.09.2014

Gaspar P, Neves AR and Förster J, “Engineering resveratrol production in Lactococcus lactis” The Novo Nordisk Foundation Center for Biosustainability Annual Meeting, Hørsholm, Denmark, 26.-27.08.2014

Förster J, “Polyphenol Production in Lactic Acid Bacteria”, 6th ÖGMBT Annual Meeting, Vienna, Austria, 15.09-18.09.2014

Förster J, “BACterial Hosts for production of Bioactive phenolics from bERRY fruits”, High Value Chemical from Plants Workshop 1: Utilizing Plant Diversity to Identify Bioactives, York, UK, 17.6.-18.6.2014

Förster J, “Bacterial hosts for production of bioactive phenolics from berry fruits”, GM Microbiology Lecture Series at University of Copenhagen, Copenhagen, Denmark, 3.3.2015

Förster J, “BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits”, Bio World Congress, Montreal, Canada, July 2015

Förster J, “Bacterial hosts for production of bioactive phenolics from berry fruits”, CAS Conference Synthetic Biology, Munich, Germany, July 2015

Dudnik A, “BacHBerry: BACterial Hosts for production of Bioactive phenolics from bERRY fruits”, Plant Omics and Biotechnology for Human Health symposium, Ghent, Belgium, 21-24.11.2016

Kallscheuer N, “Construction of a Corynebacterium glutamicum platform strain for the production of high-value plant secondary metabolites”, Annual Conference of the German Association of General and Applied Microbiology (VAAM) 2016 in Jena, Germany, 13.-16.03.2016

Marienhagen J, “Metabolic engineering of Corynebacterium glutamicum for the synthesis of plant polyphenols”, The 28th International Conference on Polyphenols, Satellite Workshop “Bacterial Hosts for Production of Bioactive Phenolics from Berry Fruits”, Vienna, Austria, 11.07.2016

Solopova A, “Production of Berry High Value Phenolics in Lactococcus lactis”, The 28th International Conference on Polyphenols, Satellite Workshop “Bacterial Hosts for Production of Bioactive Phenolics from Berry Fruits”, Vienna, Austria, 11.07.2016

Marienhagen J, “Metabolic engineering of Corynebacterium glutamicum for the synthesis of plant polyphenols”, The 28th International Conference on Polyphenols, Satellite Workshop “Bacterial Hosts for Production of Bioactive Phenolics from Berry Fruits”, Vienna, Austria, 11.07.2016

Dudnik A, “Lactococcus lactis as a platform host for the production of plant polyphenols”, The 28th International Conference on Polyphenols”, Satellite Workshop “Bacterial Hosts for Production of Bioactive Phenolics from Berry Fruits”, Vienna, Austria, 11.07.2016

Henriques da Silva, M, van der Wielen LAM, Ottens M, “Chromatography for the recovery and purification of fermentation-based polyphenols”, PhD Seminar, Biotechnology, Delft University of Technology, Schipluiden, Netherlands, 23.09.2016

Henriques da Silva, M, van der Wielen LAM, Ottens M, “Recovering Polyphenols From A Fermentation Stream: DSP Evaluation Using An Hybrid Approach”, ECAB conference, Nice, France, 27.09-01.102015

Henriques da Silva M, “Downstream Process Development for Fermentation Based Production of Polyphenols”, 11th PhD Chromatography Seminar, Sorpesee, Germany, 15.-17.02.2015

Méndez Sevillano D, “Thermodynamic approach for the prediction of properties of tea polyphenols”, 11th PhD Chromatography Seminar, Sorpesee, Germany, 15.-17.02.2015

Méndez Sevillano D, van de Wielen LAM, Hooshyar N, Ottens M, “Thermodynamic approach for the prediction of properties of tea polyphenols”, 10th European Symposium on Biochemical Engineering Sciences and 6th International Forum on Industrial Bioprocesses, Lille, France, 07.-10.09.2014

Vinga S, “Dynamic modeling and optimization of metabolic networks”, 3rd Workshop on Bio-optimization, Instituto Superior de Agronomia, Lisbon, Portugal, 29.11.2014

Fernandes A, Costa R, Gaspar P, Neves, AR, Vinga S, “Dynamic flux balance analysis for modeling Lactococcus lactis mannitol Production”, 9th European Conference on Mathematical and Theoretical Biology, Gothenburg, Sweden, 15-19.07.2014

Bulteau L, “Visualisation of metabolic subnetworks of interest” Presentation at the LNCC (Laboratório Nacional de Computação Científica), Rio de Janeiro, Brazil, 2015

Sagot M-F, “Species interactions from a mathematical modelling and algorithmic perspective”, Instituto Superior de Agronomia, Lisbon, Portugal, 25.01.2016.

Sagot M-F, “Exploring and exploiting interspecific interactions:, German Conference on Bioinformatics, 14.09.2016, Berlin, Germany

Bulteau L, “Visualisation of metabolic subnetworks of interest”, Presentation at the LNCC (Laboratório Nacional de Computação Científica), Rio de Janeiro, Brazil, 2016

Parrot D, “Phenylpropanoids pathway: Bioinformatics and modeling approaches to increase metabolites of interest”, AFERP/STOLON, Lyon, France, 15.-18.07.2015.

Faria N, “Optimization of microbial phenolics production by fermentation and bioprocess development”, The 28th International Conference on Polyphenols, Satellite Workshop “Bacterial Hosts for Production of Bioactive Phenolics from Berry Fruits”, Vienna, Austria, 11.07.2016

Date

Audience (size)

Comments

13/03/15

Meeting with the Scottish Government Food, Drink and Rural Communities Policy group

Bachberry formed part of the discussion about JHI fruit research and route to impact on the Scottish populations diet via sustainable sources of nutrition and health beneficial food and drink

20/02/15

Pete Wishart, Member of the Scottish Parliament

Bachberry formed part of the discussion about JHI fruit research and route to impact

27/02/15

Cross Scottish Agri-food research institute engagement event

Bachberry formed part of the discussion about JHI fruit research and route to impact

1-2/12/15

Food Security: Mapping Risks, Building Resilience. Chatham House, London

Senior policy-makers, business leaders and key scientists met to map the risks facing the global food system, analyse the potential impact and identify priorities for action. DS (JHI) input, amongst other things, with regard to delivering sustainable bioactive/functional ingredients in a value added supply chain. Bachberry was used as an example for this

12/12/15

Murdo Fraser, Member of the Scottish Parliament

Bachberry formed part of the discussion about JHI fruit research and route to impact

04/12/15 (am)

Presentation to the Growers group, The Blackcurrant foundation

www.blackcurrantfoundation.co.uk.

DS (JHI) is the scientific advisor for the Blackcurrant Foundation. As part of an update on the JHI blackcurrant research the growers were given an update on BachBerry.

04/12/15 (pm)

Discussion with LR Suntory (makers of Ribena)

The move of Ribena to LR Suntory has seen an increased interest in health beneficial polyphenolics and health (and nutrition) enhanced drinks. They appreciated the update and JHI will pursue this along with the new JHI-LR Suntory £650K blackcurrant breeding contract

18-20-/11/15

Presentation at Natural Product Biotechnology, Inverness, Scotland

The invited presentation “Bioactive and functional natural products from sustainable plant and crop sources” was given by DS (JHI).

Articles on EU portals
http://ec.europa.eu/research/infocentre/article_en.cfm?artid=41556 http://cordis.europa.eu/result/rcn/190649_en.html.

Posters Presentations

Kallscheuer N, Vogt M, Bott M and Marienhagen M, “Identification of a phenylpropanoid degradation pathway in Corynebacterium glutamicum”, Annual Conference of the German Association of General and Applied Microbiology (VAAM) in Marburg, Germany, 01.-04.03.2015

Vogt M, Kallscheuer N, Krumbach K and Marienhagen J, “Development of biosensors for the detection of precursors involved in plant polyphenol production with Corynebacterium glutamicum”, Annual Conference of the German Association of General and Applied Microbiology (VAAM) in Jena, Germany, 13.-16.03.2016

Kallscheuer N, Vogt M, Bott M and Marienhagen J, “Construction of a Corynebacterium glutamicum platform strain for the production of high-value plant secondary metabolites”, Metabolic Engineering Conference XI, The Westin Awaji Island, Japan, 26.-30.06.2016

Kallscheuer N, Vogt M, and Marienhagen J, Metabolic engineering of Corynebacterium glutamicum for the synthesis of plant polyphenols, The 28th International Conference on Polyphenols, Vienna, Austria, 11.-15.07.2016

Dudnik A and Forster J, “Development of tools for precise genome engineering of Lactococcus lactis”, Cell Factories & Biosustainability 2015 conference, Hillerod, Denmark, 17.-21.05.2015

Dudnik A and Forster J, “Development of tools for precise genome engineering and biosynthetic pathway construction in lactic acid bacteria”, Genome engineering and synthetic biology: tools and technologies conference, Ghent, Belgium, 28.-29.01.2016

Dudnik A and Forster J, “Development of tools for precise genome engineering and biosynthetic pathway construction in lactic acid bacteria”, Metabolic Engineering Conference XI, The Westin Awaji Island, Japan, 26.-30.06.2016

Gaspar P, Vereira A, Neves AR and Forster J. “Production of the stilbene resveratrol in Lactococcus lactis”, 18th international conference on Gram-positive microorganisms, Montecatini Terme, Italy, 21.-25.06.2015

Gaspar P, Dudnik A, Neves AR and Forster J. “Lactococcus lactis as a platform host for the production of plant polyphenols”, Metabolic Engineering Conference XI, The Westin Awaji Island, Japan, 26.-30.06.2016

Stahlhut S, Siedler S, Malla S, Harrison SJ, Maury J, Neves AR and Forster J. “Production of the plant polyphenol fisetin in Escherichia coli - Elucidation and assembly of a novel biosynthetic pathway”, Cell Factories & Biosustainability 2015 conference, Hillerod, Denmark, 17.-21.05.2015

Stahlhut S, Siedler S, Malla S, Harrison SJ, Maury J, Neves AR and Forster J. Engineering of Escherichia coli for the production of flavonol fisetin”, 2nd Synthetic Biology Congress, London, United Kingdom, 20.-21.10.2015

Ferro R and Norholm M, Developing of a membrane protein production platform in Lactococcus lactis, Synthetic Biology in Action, Heidelberg, Germany, 06.2015

Solopova A, Gaspar P, Förster J, Kuipers OP. “Assembly and grafting of pathways for synthesis of berry high-value phenolics in Lactococcus lactis”, 6th Congress of European Microbiologists (FEMS), Maastricht, The Netherlands, 7.-11.07.2015

Gaspar P, Neves AR and Förster J, “Engineering Lactococcus lactis for the production of resveratrol, a nutraceutical plant-derived polyphenol”, 11th Symposium on Lactic Acid Bacteria: LAB11, Egmond aan Zee, The Netherlands, 31.08 – 4.09.2014 (Selected poster for oral presentation)

Henriques da Silva MD, van der Wielen LAM, Ottens M, “Downstream Process Development for Bio‐Based Production of Phenolics”, 5th NBC Meeting, Ede, The Netherlands, 27.-28.05.2014

Henriques da Silva MD, van der Wielen LAM, Ottens M, “Downstream Process Development for Bio‐Based Production of Phenolics”, 10th European Symposium on Biochemical Engineering Sciences and 6th International Forum on Industrial Bioprocesses, Lille, France, 07.-10.09.2014

Silva, M, van der Wielen LAM, Ottens M, “Chromatography for the recovery and purification of fermentation-based polyphenols”, ESBES conference, Dublin, Ireland, 11.-14.09.2016

Costa RS, Nguyen HS and Vinga S, “Comparison of cellular objectives in flux balance constraint-based models”. ECCB'14 - 13th European Conference on Computational Biology, Strasbourg, France, 7.-10.09.2014

Costa RS, Verissimo A and Vinga S, “KiMOSys: An experimental data repository for Kinetic MOdels of biological Systems”, Whole-cell modelling summer school, Rostock, Germany, 09.-13.03.2015

Costa RS, Fernandes A, Hartmann A, Veríssimo A, Julien-Laferriere A, Wannagat M, Andrade R, Parrot D, Sagot M-F and Vinga S, “Modeling Lactococcus lactis for synthetic biology”, 7th Conference in the Copenhagen Bioscience Conferences series "Cell Factories and Biosustainability – technologies for cell factory construction", Hillerod, Denmark, 17.-21.05.2015

Parrot D, Julien-Laferrière A, Bulteau L, Andrade R, Lacroix V, Hartmann A, Costa R. S, Fernandes A, Verissimo A, Vinga S, Sagot M-F, “Phenylpropanoids pathway: Bioinformatics and modeling approaches to increase metabolites of interest”, International Summer School on Natural Products, Naples, Italy, 6.-10.07.2015 (Natural Product Research Award for the best poster)

Julien-Laferrière A, Bulteau L, Parrot D, Marchetti-Spaccamela A, Stougie L, Vinga S, Sagot M-F, Journées Ouvertes: Biologie, Informatique, Mathématique (Jobim - French Conference on Bioinformatics), Lyon, France, 28.-30.06.2016

Veríssimo A, Oliveira AL, Sagot M-F, Vinga S. “DegreeCox – Network-based regularization method for survival analysis”, ECCB’2016 – European Conference on Computational Biology 2016, The Hague, Netherlands, 3.-7.09.2016.

Oliveira JA, Braga A, Rocha I and Faria N, (2015) The effect of hydrodynamic conditions in Corynebacterium glutamicum growth”, MicroBiotec 2015, University of Évora, Portugal, 12.2015

Conference Proceedings

- Costa R.S., Son Nguyen, Andras Hartmann, Susana Vinga (2014) Exploring the cellular objective in flux balance constraint-based models, Lecture Notes in Computer Science, LNBI 8859, 211-224, (2014). Springer International Publishing Switzerland DOI: 10.1007/978-3-319-12982-2_15.

- Fernandes A., S. Vinga. Improving Protein Expression Prediction Using Machine Learning and Committee Machines. Submitted to the Seventeenth Portuguese Conference on Artificial Intelligence (EPIA-2015).

Workshops/Schools

Two workshops have been organized within the frame of BacHBerry. The first one was a one-day training workshop organized by Bjoern Hamberger (UCPH) in Lyon (France) in November 2015 during the 4th project meeting of BacHBerry. This workshop was targeting PhD student and postdocs, and aimed at assisting their career development. The second workshop was a half-a-day satellite workshop organized by Claudia Santos (iBET) and Alexey Dudnik (DTU) at the “The 28th International Conference on Polyphenols” in Vienna (Austria) on the 11th of July 2016. The workshop was targeting participants of the conference and aimed at dissemination of BacHBerry’s activities and its vision of biotechnology and bio-based economy.

IDMEC and INRIA have organized a summer school “ADDICTION (ADdressing DIfficult problems in a Computationally Tractable fashION)” that took place November 16-21, 2014, in Lisbon, Portugal. The goal of the summer school was to focus on smart data structures, algorithm engineering and experimental algorithms, probabilistic algorithms, and (M)ILP approaches simple and enumerative for dealing with exponential problems with a particular focus on computational biology. The school was targeting young international researchers at the PhD student or postdoc level, but also to any other interested listeners.

BacHBerry was also involved in preparation of a team for the iGEM (international Genetically Engineered Machine) competition in 2015. The team has been coached by Bjoern Hamberger (UCPH), and worked on engineering of the moss Physcomitrella patens for production of a polyphenol resveratrol. Activities, results, and funders of the team could be found under the following link: http://2015.igem.org/Team:UNIK_Copenhagen. The BacHBerry-supported team was awarded a gold medal and additionally received the following nominations: “Best Composite Part” (only 5 nominees out of 259 teams) and “Best Environmental Project” (only 4 nominees out of 33). Their work has been featured in “The Scientist” and “Times of India”, as well as by the Danish news agency Ritzau, where it became the most printed article since the launch of the agency. One of the articles could be found under https://www.newscientist.com/article/mg22830414-900-moss-on-mars-plant-species-being-cultivated-for-astronaut-drugs/

See the first press release in UCPH University post:
http://universitypost.dk/article/life-mars-attempt-grow-moss-space


- J.E.A. Bassard  (2015) “Biotechnologie des Plantes – BacHBerry”.
Prins Henrik skole, Frederiksberg, Denmark, March 2015.

Public dissemination activities:

Nov. 11, 2014

Vienna (students)

Dec. 20, 2014

Beijing

Feb. 5, 2015

Copenhagen

Mar. 6, 2015

Vienna

Cross-consortia dissemination

An EU FP7 Cross consortia meeting was organized on 16.12.2013 at the Royal Holloway University of London (United Kingdom). The meeting was attended by DISCO project’s leader PPaul Fraser, BacHBerry coordinator Jochen Forster, and BacHBerry participants Bjoern Hamberger and Markus Schmidt; as well as TriForC project members Soren Bak and Anne Osbourn.

Jochen Forster, Soren Bak and Paul Fraser met during the “High Value Chemical from Plants Workshop 1: Utilizing Plant Diversity to Identify Bioactives” in York, UK on 17.06.–18.06.2014 and had a production discussion about the progress and perspectives of the three projects.
Between November 9th and 13th 2014, the DISCO consortium came together for its 1st Progress Meeting in Valparaiso and Santiago de Chile to discuss the project’s scientific progress and further collaboration. As part of the internal meeting, the consortium met with Pilar Bañados from the Pontificia Universidad Católica de Chile, a member of the BacHBerry project, which is funded under the same EC call as DISCO. This meeting gave added value to the cross-cluster exchange and offered the opportunity to discuss future collaboration between both EU projects.

Lastly, coordinators of the FP7 projects funded under the theme KBBE.2013.3.1-01: “Plant High Value Products - from discovery to final product” came together at the “Plant Omics and Biotechnology for Human Health” Symposium in Ghent, Belgium on November 21.11.-24.11.2016. The coordinators Alexey Dudnik (BacHBerry), Soren Bak (TriForC) and Paul Fraser (DISCO) presented the key outcomes of the project in front of the members of the Phytochemical Society of Europe (PSE).

Online Science game “Berry Maker”
http://berrymaker.modalog.at

Documentary movie on BacHBerry
https://vimeo.com/193467652

Software

KiMoSys (http://www.kimosys.org/),
OrfFinder (http://github.com/averissimo/orf_finder),
MassBlast (http://github.com/averissimo/mass-blast/),
GeneExtractor (https://github.com/averissimo/gene-extractor),
SON-EM (http://www.mathworks.com/matlabcentral/fileexchange/49967-son-em),
Dinghy (http://dinghy.gforge.inria.fr/),
OptPipe (https://github.com/AndrasHartmann/OptPipe),
Sasita (http://sasita.gforge.inria.fr),
Totoro and Kotoura (http://hyperstories.gforge.inria.fr/),
MultiPus (http://multipus.gforge.inria.fr/),
MultiOpt (http://web.ist.utl.pt/~susanavinga/MultiOpt/).     

http://www.bachberry.eu/dissemination
21 AUGUST 2017