Overview of Fellows Partners Positions Recruitment Research - PowerPoint PPT Presentation

Overview of Fellows Partners Positions Recruitment Research months Problems, consequences, End date By 20 April 2017 solutions ESR 4 Luis de la Higuera Romero (Spain) 36 September 2016 UNILEEDS ESR 5 Marco Ferrarini (Italy) 36 January 2017 Imperial ESR 1 Pedro Costa del Amo (Spain) 36 January 2017 UU ER 3 Aridaman Pandit (India) 24 July 2015 Sara Ciprut (Israel) 6.5 Left 15 June 2014 UMCU ESR 2 Mariona Baliu Pique (Spain) 29.75 Started November 2014 April 2017 NKI ESR 7 Ali Can Sahillioglu (Turkey) 36 September 2016 DKFZ ESR 10 Melania Barile (Italy) 36 October 2016 Charite ESR 11 Domonkos Varga (Hungary) 36 January 2017 IP ER 1 Sary El Daker (Italy) 24 June 2015 INSERM ER 2 Pedro Goncalves (Portugal) 24 July 2015 Evgeniy Vodopyanov (Russia) 5.75 Left August 2014 NUI Amirreza Ghattaei Forooshani (Iran) 0 Turned down the offer Maynooth ESR 8 Giulio Prevedello (Italy) 31 Started September 2014 April 2017 ESR 9 Harry Tideswell (UK) 29 Started October 2014 March 2017 NUI Galway ESR 6 Yaxuan Yu (China) 36 - December 2016 ESR 3 Julio Lahoz Beneytez (Spain) 36 - November 2016 BAYER ER 4 Saikrishna Gadhamsetty (India) 15.75 Started January 2016 April 2017

Review of future training events Main training events and WP Hosts / Date conferences Number Organisers Inaugural Meeting Maynooth 10 NUI Maynooth 29-30 August 2013 Summer School 1 7 NUI Galway 23-24 June 2014 Complementary Skills Workshop 12 Leeds 22-26 September 2014 Summer School 2 8 DKFZ 14-15 January 2015 Complementary Skills Workshop 13 Microsoft Research 3 June 2015 Bayer Technology Industrial Workshop 1 15 19-20 October 2015 Services Complementary Skills Workshop 14 Unilever 16 March 2016 Summer School 3 9 Unilever 17-18 March 2016 Industrial Workshop 2 16 AstraZeneca 21-22 September 2016 Closing Conference 11 Leeds 19-21 April 2017

Milestones (due by month 48)

Deliverables

Dissemination – Publications • “Fundamental properties of unperturbed haematopoiesis from stem cells in vivo”, K Busch, K Klapproth, M Barile, M Flossdorf, T Holland-Letz, SM Schlenner, M Reth, T Höfer & H-R Rodewald, Nature 518, 542 – 546 (February 2015) • “A pharma perspective on the systems medicine and pharmacology of inflammation”, Lahoz-Beneytez, J., Schnizler, K., & Eissing, T. Mathematical Biosciences , 260, 2-5 (February 2015) • “Estimating T - cell repertoire diversity: limitations of classical estimators and a new approach”, DJ Laydon, CRM Bangham, & B Asquith, Philosophical Transactions B , 370 (1675), 2014.0291 (August 2015) • “Reconciling Estimates of Cell Proliferation from Stable Isotope Labeling Experiments”, R Ahmed, L Westera, J Drylewicz, M Elemans, Y Zhang, E Kelly, R Reljic, K Tesselaar, RJ de Boer, DC Macallan, JAM Borghans, & B Asquith, PLoS Computational Biology , 12 (3): e1004796, 2016 • “HIV -1 CCR5 gene therapy will fail unless it is combined with a suicide gene”, Aridaman Pandit and Rob J. de Boer, Scientific Reports , 5: 18088, 2015. • “ LymAnalyzer : a tool for comprehensive analysis of next generation sequencing data of T cell receptors and immunoglobulins”, Y Yu, R Ceredig, and C Seoighe, Nucleic Acids Research, 44 (4): e31, 29 February 2016. • “The memory of a killer T cell: models of CD8$^+$ T cell differentiation”, Bram Gerritsen and Aridaman Pandit, Immunology and Cell Biology , 94, 236-241, 2016. • “ BIITE : A tool to determine HLA class II epitopes from T cell ELISpot data”, Lies Boelen , Patrick K. O’Neill, Kathryn J. Quigley, Catherine J. Reynolds, Bernard Maillere, John H. Robinson, Ganjana Lertmemongkolchai, Daniel M. Altmann, Rosemary J. Boyton, Becca Asquith, PLoS Computational Biology , 12 (3): e1004796, 2016. • “Stem -cell dynamics and lineage topology from in vivo fate mapping in the hematopoietic system”, Thomas Höfer, Melania Barile, Michael Flossdorf, Current Opinion in Biotechnology, 39: 150-156, June 2016.

Publications, continued • “ Human neutrophil kinetics: modeling of stable isotope labeling data supports short blood neutrophil half- lives”, J Lahoz -Beneytez, M Elemans, Y Zhang, R Ahmed, A Salam, M Block, C Niederalt, B Asquith, and D Macallan, Blood, 2016, 127: 3431-3438. • “ RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data”, Bram Gerritsen, Aridaman Pandit, Arno C. Andeweg and Rob J. de Boer, Bioinformatics , 2016, 32 (20): 3098-3106. • “Stochastic descriptors to study the fate and potential of naive T cell clonotypes in the periphery”, J . R. Artalejo; A. Gómez Corral; M. López García; C. Molina París, Journal of Mathematical Biology , February 2017, Volume 74, Issue 3, pp 673 – 708. • “T -cell stimuli independently sum to regulate an inherited clonal division fate”, J . M. Marchingo, G. Prevedello, A. Kan, S. Heinzel, P. D. Hodgkin, and K. R. Duffy, Nature Communications , 2016, 7, 13540. • “A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data”, Yaxuan Yu, Rhodri Ceredig and Cathal Seoighe, Journal of Immunology , March 1, 2017, 198 (5) 2202-2210. • “Human T Cell Memory: A Dynamic View”, Derek C. Macallan, José A. M. Borghans and Becca Asquith, Vaccines 2017, 5(1), 5. • “A new mechanism shapes the naïve CD8+ T cell repertoire: the selection for full diversity”, Pedro Gonçalves, Marco Ferrarini, Carmen Molina-Paris, Grant Lythe, Florence Vasseura, Annik Lima, Benedita Rocha, and Orly Azoguib, Molecular Immunology , Volume 85, May 2017, Pages 66 – 80. • “Physiologically Based Simulations of Deuterated Glucose for Quantifying Cell Turnover in Humans”, Julio Lahoz-Beneytez, Stephan Schaller, Derek Macallan, Thomas Eissing, Christoph Niederalt and Becca Asquith, Frontiers in Immunology , 2017, 8:474, Accepted for publication 5 April 2017. Publications to include: “The research leading to these results has received funding from the European Union Seventh Framework Programme (FP7/2007 -2013) under grant agreement 317040 (QuanTI)”

Completed outreach events • Giulio Prevedello and Harry Tideswell – Science Week in Dublin on 9.11.14 • Yaxuan Yu – Transition Year Friday programme in 2014 • Prof Lohning’s group – Berlin’s “ Lange Nacht der Wissenschaften“ each year • Pedro Costa del Amo – UK Big Bang Fair in March 2015 • Giulio Prevedello and Harry Tideswell – Maths Week Ireland on 17.10.15 • Mariona Baliu Pique – public activities during the Open Day in October 2015 at UMCU • Julio Lahoz Beneytez – supervision of school internship in January 2016 • Luis de la Higuera Romero and Marco Ferrarini – Be Curious Festival in March 2016 • Giulio Prevdello and Harry Tideswell – BT Young Scientists exhibition in January 2017

Actual secondments carried out Name of fellow (host institution) Place of secondment Dates of secondment Mariona Baliu Pique Institut Pasteur - laboratory of Antonio Freitas and 2-15 November 2015 (UMCU) Benedita Rocha Melania Barile (DKFZ) AstraZeneca 11 July - 4 August 2016 Pedro Costa del Amo (Imperial) UMCU 22-24 June 2015 Unilever 8 August - 2 September 2016 Bayer Life Sciences, Cologne August 2015 Luis de la Higuera Romero (Leeds) Institut Pasteur July-August 2014 (one week), December 2014 (one week) Institute of Mathematical Science, Chennai 10 March - 10 April 2015 Unilever 8 August - 2 September 2016 Marco Ferrarini (Leeds) NUI Galway 16-26 June 2014 Institut Pasteur 23-28 April 2015 Microsoft Research 18-22 April 2016 Unilever 8 August - 2 September 2016 Julio Lahoz Beneytez (Bayer AG) Imperial 3 months in total in 2014-2015, with a plan in 2016 to spend 2 more months there Aridaman Pandit (Universiteit Utrecht) NKI Regular discussions and interactions with Leila Perie NUI Maynooth Giulio Prevedello (NUI Maynooth) WEHI 18 April - 4 May 2015 MIT October 2015 - April 2016 Harry Tideswell (NUI Maynooth) MIT October 2015 - April 2016 Domonkos Varga (Charite) Unilever 8 August - 2 September 2016 Yaxuan Yu (NUI Galway) Leeds 19-26 September 2014 INSERM 17-24 April 2015