General Manager

Magnus Fontes

Oncology & Immunology

“Contributing to advancing fundamental human knowledge through open collaborative research, and through multidisciplinary efforts directly bring value to patients.”

Your role at Institut Roche and brief presentation of your professional background:

I have a PhD in Mathematics and I worked as professor and head of department at the Centre for Mathematical Sciences at Lund University until 2014 when I joined Institut Pasteur in Paris as Director of Bioinformatics for the International Network of Pasteur. In 2018, I joined Genentech as Principal Scientist and head of Systems Immunology within Cancer Immunology and finally in 2020 I joined Institut Roche as General Manager.

My Focus at Institut Roche:

Contributing to a local ecosystem and culture where people have both the freedom and the resources to reach their full potential with the common goal to co-construct and manage high value research projects that have a potential to transform healthcare and clinical practice.

  1. Immune checkpoint inhibitors increase T cell immunity during SARS-CoV-2 infection. Science advances vol. 7, 34 eabg4081. 18 Aug. 2021, doi:10.1126/sciadv.abg4081
  2. Autoantibodies neutralizing type I IFNs are present in ~4% of uninfected individuals over 70 years old and account for ~20% of COVID-19 deaths PaulBastard et al. SCIENCE IMMUNOLOGY, Vol 6, Issue 62, 2021
  3. Genetic risk for skin autoimmunity impacts the safety and efficacy of immune checkpoint blockade in urothelial carcinoma, Zia Khan, Flavia Di Nucci, Antonia Kwan, Christian Hammer, Sanjeev Mariathasan, Vincent Rouilly, Jonathan Carroll, Magnus Fontes, Sergio Ley Acosta, Ellie Guardino, Haiyin Chen-Harris, Tushar Bhangale, Jonathan Rosenberg, Thomas Powles, Julie Hunkapiller, Scott Chandler, Matthew L Albert CLINICAL CANCER RESEARCH 26 (15), 19-20, 2020Polygenic risk for skin autoimmunity impacts immune checkpoint blockade in bladder cancer, Zia Khan, Flavia Di Nucci, Antonia Kwan, Christian Hammer, Sanjeev Mariathasan, Vincent Rouilly, Jonathan Carroll, Magnus Fontes, Sergio Ley Acosta, Ellie Guardino, Haiyin Chen-Harris, Tushar Bhangale, Ira Mellman, Jonathan Rosenberg, Thomas Powles, Julie Hunkapiller, G Scott Chandler, Matthew L Albert Proceedings of the National Academy of Sciences 117 (22), 12288-12294, 2020
  4. Principal Moment Analysis, M Fontes, R Henningsson, ArXiv preprint arXiv:2003.04208
  5. Genetic risk for skin autoimmunity impacts the safety and efficacy of immune checkpoint blockade in urothelial carcinoma. Z Khan et al CLINICAL CANCER RESEARCH, 2020 Volume 26, Issue 15, pp 19-20
  6. Machine learning can identify newly diagnosed patients with CLL at high risk of infection, Rudi Agius, Christian Brieghel, Michael A Andersen, Alexander T Pearson, Bruno Ledergerber, Alessandro Cozzi-Lepri, Yoram Louzoun, Christen L Andersen, Jacob Bergstedt, Jakob H von Stemann, Mette Jørgensen, Man-Hung Eric Tang, Magnus Fontes, Jasmin Bahlo, Carmen D Herling, Michael Hallek, Jens Lundgren, Cameron Ross MacPherson, Jan Larsen, Carsten U Niemann, Nature Communications 11 (1), 1-17, 2020
  7. Sex differences in IL-17 contribute to chronicity in male versus female urinary tract infection, Publication date: 2019/5/30, Journal: JCI insight, Publisher: American Society for Clinical Investigation, Anna Zychlinsky Scharff, Matthieu Rousseau, Livia Lacerda Mariano, Tracy Canton, Camila Rosat Consiglio, Matthew L Albert, Magnus Fontes, Darragh Duffy, Molly A Ingersoll
  8. DISSEQT—DIStribution-based modeling of SEQuence space Time dynamics, R Henningsson, G Moratorio, AV Borderia, M Vignuzzi, M Fontes, Virus Evolution 5 (2), 2019
  9. Sex differences in IL-17 contribute to chronicity in male versus female urinary tract infection Anna Zychlinsky Scharff, Matthieu Rousseau, Livia Lacerda Mariano, Tracy Canton, Camila Rosat Consiglio, Matthew L Albert, Magnus Fontes, Darragh Duffy, Molly A Ingersoll JCI insight Volume 4, Issue 13, 2019
  10. Natural variation in the parameters of innate immune cells is preferentially driven by genetic factors, Etienne Patin, Milena Hasan, Jacob Bergstedt Vincent Rouilly, Valentina Libri, Alejandra Urrutia, Cécile Alanio, Petar Scepanovic, Christian Hammer, Friederike Jönsson, Benoît Beitz, Hélène Quach, Yoong Wearn Lim, Julie Hunkapiller, Magge Zepeda, Cherie Green, Barbara Piasecka, Claire Leloup, Lars Rogge, François Huetz, Isabelle Peguillet, Olivier Lantz, Magnus Fontes, James P Santo, Stéphanie Thomas Jacques Fellay, Darragh Duffy, Lluís Quintana-Murci, Matthew L Albert Nature immunology 19 (3), 302, 2018
  11. Human thymopoiesis is influenced by a common genetic variant within the TCRA-TCRD locus, Emmanuel Clave, Itauá Leston Araujo, Cécile Alanio, Etienne Patin, Jacob Bergstedt, Alejandra Urrutia, Silvia Lopez-Lastra, Yan Li, Bruno Charbit, Cameron Ross MacPherson, Milena Hasan, Breno Luiz Melo-Lima, Corinne Douay, Noémie Saut, Marine Germain, David-Alexandre Trégouët, Pierre-Emmanuel Morange, Magnus Fontes, Darragh Duffy, James P Di Santo, Lluis Quintana-Murci, Matthew L Albert, Antoine Toubert, Milieu Intérieur Consortium, , Science translational medicine 10 (457) 2018
  12. SMSSVD: SubMatrix Selection Singular Value Decomposition, Rasmus Henningsson Magnus Fontes, Bioinformatics, https://doi.org/10.1093/bioinformatics/bty566, July 2018
  13. Standardized whole-blood transcriptional profiling enables the deconvolution of complex induced immune responses Alejandra Urrutia, Darragh Duffy, Vincent Rouilly, Céline Posseme, Raouf Djebali, Gabriel Illanes, Valentina Libri, Benoit Albaud, David Gentien, Barbara Piasecka, Milena Hasan, Magnus Fontes, Lluis Quintana-Murci, Matthew L. Albert* Cell Reports 2016 http://www.cell.com/cell-reports/fulltext/S2211-1247(16)31057-9
  14. Attenuation of RNA viruses by redirecting their evolution in sequence space by Gonzalo Moratorio, Rasmus Henningsson, Cyril Barbezange, Lucia Carrau, Antonio V Bordería, Hervé Blanc, Stephanie Beaucourt, Enzo Z Poirier, Thomas Vallet, Jeremy Boussier, Bryan C Mounce, Magnus Fontes &Marco Vignuzzi, Nature microbiology Volume 2 (2017)
  15. What is a “unimodal” cell population? Using statistical tests as criteria for unimodality in automated gating and quality control, K Johnsson, M Linderoth, M Fontes, Cytometry Part A 91 (9), 908-916 (2017)
  16. Deconvolution of the response to BCG reveals NF-κB–induced cytokines as autocrine mediators of innate immunity A Bisiaux, J Boussier, D Duffy, L Quintana-Murci, M Fontes, M Albert, Frontiers in Immunology 8, 796, (2017)
  17. K Johnsson, J Wallin, M Fontes BayesFlow: latent modeling of flow cytometry cell populations BMC bioinformatics 17 (1), 1 2016
  18. Kenneth A Stapleford, Gonzalo Moratorio, Rasmus Henningsson, Rubing Chen, Séverine Matheus, Antoine Enfissi, Daphna Weissglas-Volkov, Ofer Isakov, Hervé Blanc, Bryan C Mounce, Myrielle Dupont-Rouzeyrol, Noam Shomron, Scott Weaver, Magnus Fontes, Dominique Rousset, Marco Vignuzzi Whole-Genome Sequencing Analysis from the Chikungunya Virus Caribbean Outbreak Reveals Novel Evolutionary Genomic Elements PLoS Negl Trop Dis 10 (1), 2016
  19. Rosmari Rodriguez-Roche, Hervé Blanc, Antonio V Bordería, Gisell Díaz, Rasmus Henningsson, Daniel Gonzalez, Emidalys Santana, Mayling Alvarez, Osvaldo Castro, Magnus Fontes, Marco Vignuzzi, Maria G Guzman Increasing clinical severity during a dengue virus type 3 Cuban epidemic: deep sequencing of evolving viral populations Journal of virology, JVI. 2016
  20. Novel ETV6-RUNX1-like and DUX4-rearranged subtypes in pediatric B-cell precursor acute lymphoblastic leukemia” by Henrik Lilljebjörn, RasmusHenningsson, Axel Hyrenius-Wittsten, Linda Olsson, Christina Orsmark-Pietras, Sofia von Palffy, Maria Askmyr, Marianne Rissler, Martin Schrappe, Gunnar Cario, Anders Castor, Cornelis Pronk, Mikael Behrendtz, Felix Mitelman, Bertil Johansson, Kajsa Paulsson, Anna Andersson, Magnus Fontes,&Thoas Fioretos Nature Communications Vol 7 2016
  21. Charlotte Soneson and Magnus Fontes, Incorporation of gene exchangabilities improves the reproducability of gene set rankings. Computational Statistics and Data Analysis 2014, 71, 588-598.
  22. Darragh Duffy, Rasha Mamdouh, Melissa Laird, Charlotte Soneson, Lenaig Le Fouler, Maï El‐Daly, Armanda Casrouge, Jérémie Decalf, Amal Abbas, Noha Sharaf Eldin, Magnus Fontes, Mohamed Abdel‐Hamid, Mostafa K Mohamed, Mona Rafik, Arnaud Fontanet, Matthew L Albert. The ABCs of viral hepatitis that define biomarker signatures of acute viral hepatitis. Hepatology 2014 Vol. 59, Issue 4, pp 1273-1282.
  23. Kerstin Johnsson, Charlotte Soneson and Magnus Fontes. Low Bias Local Intrinsic Dimension Estimation from Expected Simplex Skewness. IEEE Transactions on Pattern Analysis and Machine Intelligence, 2014 Volume: 37, Issue: 1, pp. 196 – 202.
  24. Magnus Fontes and Charlotte Soneson. The projection score-an evaluation criterion for variable subset selection in PCA visualization. BMC Bioinformatics. Volume 12. 2011
  25. Charlotte Soneson and Magnus Fontes. A framework for list representation, enabling list stabilization through incorporation of gene exchangeabilities. Biostatistics. 2011. Volume 13. Issue 1; 129-141
  26. Charlotte Soneson and Magnus Fontes. A method for visual identification of small sample subgroups and potential biomarkers. The Annals of Applied Statistics. 2011. Volume 5. Issue 3. pgs. 2131-2149
  27. Charlotte Soneson, Henrik Lilljebjörn, Thoas Fioretos, Magnus Fontes Integrative analysis of gene expression and copy number alterations using canonical correlation analysis BMC Bioinformatics, 2010, 11, No 191, pp. 1–20
  28. M Fontes Optimal Results for the Nonhomogeneous Initial-Boundary Value Problem for the Two-Dimensional Navier–Stokes Equations, Journal of Mathematical Fluid Mechanics 2010, Vol 12 (3), pp. 412-434
  29. E Alexandersson, JÅH Danielson, J Råde, VK Moparthi, M Fontes et al Transcriptional regulation of aquaporins in accessions of Arabidopsis in response to drought stress The Plant Journal 2010, Vol 61 (4), 650-660
  30. Charlotte Soneson, Magnus Fontes, Yongxia Zhou, Vladimir Denisov, Jane S Paulsen, Deniz Kirik, Åsa Petersén, Huntington Study Group PREDICT-HD investigators Early changes in the hypothalamic region in prodromal Huntington disease revealed by MRI analysis Neurobiology of Disease 2010 Vol 40 (3) 531-543
  31. M Fontes, O Verdier Time-periodic solutions of the Burgers equation Journal of Mathematical Fluid Mechanics 2009, Vol 11 (2), pp. 303-323
  32. M. Fontes Initial-boundary value problems for parabolic equations Annales- academiae scientiarum fennicae mathematica; 2009, Vol 34; pp. 583-605
  33. G Sahin, C Soneson, M Fontes, D Kirik Investigation of the blood-brain barrier transport of L-DOPA in intact and 6-OHDA lesioned rats Movement disorders 2008, Vol 23 (1).
  34. Anna Andersson, Cecilia Ritz, David Lindgren, Patrik Edén, Carin Lassen, Jesper Heldrup, Tor Olofsson, Johan Råde, Magnus Fontes, A Porwit-Macdonald, Mikael Behrendtz, Mattias Höglund, Bertil Johansson, Thoas Fioretos. Microarray based classification of a consecutive series of 121 childhood acute leukemias: prediction of leukemic and genetic subtype as well as of minimal residual disease status Leukemia 2007, Vol 21, Issue 6, pp 1198-1203
  35. Andersson A, Olofsson T, Lindgren D, Nilsson B, Eden P, Lassen C, Råde J, Fontes M, Heldrup J, Behrendtz M, Höglund M, Johansson B, Fioretos T. Molecular signatures in childhood acute leukemia and their correlations to expression pattern in normal hematopoietic subpopulations. Proc Natl Acad Sci USA 2005;102:19069-19074.
  36. Nilsson J, Fioretos T, Höglund M, Fontes M Approximate geodesic distances reveal biologically relevant structures in microarray data. Bioinformatics. 2004 Apr 12;20(6):874-80
  37. M Fontes A Monotone operator method for elliptic—parabolic equations Communications in Partial Differential Equations 2000, Vol 25 (3-4), pp. 681-702
  38. E Fontes, M Fontes, D Simonsson Effects of different design parameters on the performance of MCFC cathodes Electrochimica acta 1996 Vol. 41 (1), pp. 1-13
  39. E Fontes, M Fontes, D Simonsson A heterogeneous model for the MCFC cathode Electrochimica acta 40 (11), 1641-1651
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