Seminars


Thu, March 5th, 2020

13:00-14:00 Säätiö Auditorium, Medisiina D, Kiinamyllynkatu 10

Dr. Alex Bunker, Faculty of Pharmacy, University of Helsinki: Including the role played by relevant biomembranes in computational drug design through large scale moleculary dynamics simulation

Host: Tiina Salminen

Coffee at 12:45

About the Speaker:

Dr. Alex Bunker co-leads the Pharmaceutical biophysics research group at the Faculty of Pharmacy of the University of Helsinki. The research group combines the expertise of two group leaders, Alex Bunker in computational modelling and Dr. Tapani Viitala in a wide range of experimental analytic tools, mostly focused on tethered membrane and liposome based models. The goal is to develop a synergy in the combined application of experimental and computational tools to develop the mechanistic insight provided by the paradigm of biophysics that can be applied to a broad range of pharmaceutical applications. Alex Bunker graduated with his PhD in Physics in 1998 at the University of Georgia and completed a Post doctoral Fellowship in the Theory group of the Max Planck Institute for Polymer research in 2000, then worked for 5 years in industry before starting work as a group leader in the Faculty of Pharmacy of the University of Helsinki in 2005.

Seminar Abstract:

The dominant “lock and key” paradigm of drug design involves finding active sites on proteins and targeting drugs to fit them while balancing with desired solubility characteristics. Drug action, however, occurs in a broader biophysical context; many important factors are left out by this oversimplified paradigm. This has led to diminishing returns; as the resources spent on drug research increase exponentially the number of new approved drugs per year remains constant. At the same time the computational tools available to consider the broader biophysical context within which drug action occurs have been increasing exponentially. A key element that is left out is the role played by biomembranes. The majority of drug targets are membrane associated proteins, thus interactions with the relevant biomembrane, of both proposed drug molecule structures and the target proteins, will play a role in substrate selection, thus optimum drug molecule structure. Additionally, the mode of action of several drugs does not involve protein targeting at all, but rather involves the direct manipulation of the relevant biomembranes, for example antimicrobial agents that disrupt the structure of bacterial membranes. While a considerable amount of work has been undertaken concerning the role of the membrane in drug design for the case of integral membrane proteins, this has not been the case for the more weakly membrane associated bitopic (single pass) and peripheral membrane proteins; study of the effect of the lipid membrane on their substrate selection has been limited due to the inherent difficulty in their study. I will discuss work I have been involved in, using computational modelling of lipid membranes to, in collaboration with complementary experimental work carried out by collaborators, develop a mechanistic understanding of the role of lipid membranes in drug action for a variety of systems, including drugs that target bitopic and peripheral membrane proteins, antimicrobial agents and other aspects of drug interactions with lipid membranes.

Selected publications:

Aniket Magarkar, Petteri Parkkila, Tapani Viitala, Tatu Lajunen, Edouard Mobarak, Giuseppe Licari, Oana Cramariuc, Eric Vauthey, Tomasz Róg and Alex Bunker. Membrane bound COMT isoform is an interfacial enzyme: general mechanism and new drug design paradigm. Chem. Comm. 54 (28) pp. 3440 – 3443 (2018)

Artturi Koivuniemi, Adyary Fallarero, Alex Bunker. Insight into the antimicrobial mechanism of action of β2,2-amino acid derivatives from molecular dynamics simulation: Dancing the can-can at the membrane surface. BBA – Biomembranes 1876 (11) #182028, (2019)

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Thu, March 19th, 2020

13:00-14:00 Säätiö Auditorium, Medisiina D, Kiinamyllynkatu 10

Dr. David Šafránek, Department of Machine Learning and Data Processing, Faculty of Informatics, Masaryk University, Brno, Czech Republic: Computer-Aided Formal Analysis of Biological Systems

Host: Ion Petre

Coffee at 12:45

About the Speaker:

David Šafránek is working a sa researcher at Masaryk University since 2009. He has become an associate professor of computer science at Masaryk University in 2020. The main research interest of David Šafránek in the last ten years is development of scalable computational methods for advanced analysis of complex dynamical systems with special focus to applications in systems biology. His contribution to the field started with development of a unique methodology for analysis of qualitative and quantitative dynamical models of biological systems under parameter uncertainty. The methodology combines state-of-the-art techniques from the fields of formal verification and systems control. In the most recent work, he focuses on extending the methodology to parameter identification with respect to general temporal constraints on systems dynamics and non-linear constraints on parameters. Key theoretical results have been published in top-ranked conferences in computer science (CAV, ATVA, FM). Several case studies have been published in impacted journals (Microorganisms, BriefBioinf, IEEE/ACM Trans Comput Biol Bioinform, Plos One).

Seminar Abstract:

Model checking together with other computer science formal methods and techniques have been recently adapted for applications to biological and biomedical systems. In contrast to traditional simulation-based approaches, model checking opens an entirely novel way of viewing and analysing dynamics of such systems. In particular, it can help in system identification and parameter synthesis, in comparison of models with respect to a priori given desired properties, in robustness analysis of systems, in relating models to experimental data, or to globally analyse bifurcations of systems behaviour with respect to changes in parameters. In this talk, we would like to briefly describe the state-of-the-art methods and techniques employing model checking to the analysis of biological systems. In particular, we present a brief account of methods based on model checking, followed by a demonstration of their application in advanced analysis of biological systems. Finally, we discuss several case studies that show how fruitfully the methods can be utilised within the computational systems biology and biomedicine domain.

Selected publications:

1. DEMKO, Martin, Lukáš CHRÁST, Pavel DVORÁK, Jirí DAMBORSKÝ and David ŠAFRÁNEK. Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway (2019). Microorganisms,7(11):553.

2. BENEŠ Nikola, Luboš BRIM, Martin DEMKO, Samuel PASTVA and David ŠAFRÁNEK. Pithya: A Parallel Tool for Parameter Synthesis of Piecewise Multi-Affine Dynamical Systems. In Computer Aided Verification (CAV2017). LNCS 10426, Springer, 2017. p. 591-598, 7 pp.

3. BENEŠ Nikola, Luboš BRIM, Martin DEMKO, Samuel PASTVA and David ŠAFRÁNEK. A Model Checking Approach to Discrete Bifurcation Analysis. In Formal Methods (FM 2016). LNCS 9995, Springer, 2016. p. 85-101, 16 pp.

4. CEŠKA, Milan, David ŠAFRÁNEK, Sven DRAŽAN and Luboš BRIM. Robustness Analysis of Stochastic Biochemical Systems. Plos One. 9(4):1-23.

5. BRIM, Luboš, Petr DLUHOŠ, David ŠAFRÁNEK and Tomáš VEJPUSTEK (2014). STL*: Extending signal temporal logic with signal-value freezing operator. Information and computation. 236:52-67.

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Thu, April 16th, 2020

14:00-15:00 Alhopuro Auditorium, Medisiina D, Kiinamyllynkatu 10

Dr. Jenni Lehtimäki, Senior researcher, Finnish Environment Institute (SYKE): Urbanized microbiota associates with mammalian health

Host: Leo Lahti

Coffee at 13:45

About the Speaker:

Dr. Lehtimäki is ecologist and evolutionary biologist who studies interlinkages between living environment, microbiota and health. She defended her thesis about biodiversity hypothesis of allergy in 2017 at Faculty of Biological and Environmental sciences, University of Helsinki. After she investigated the role of skin microbiota in co-occurring allergy in pet dogs and their owners at Faculty of Medicine, University of Helsinki. At clinical research Unit COPSAC in Copenhagen, she studied the role of early-life microbiota in airways, gut and house dust in the development immune system, asthma and atopic diseases in rural and urban children. At the seminar, she will present yet unpublished findings and conclude that urban environments limit health-promoting microbial exposure, which is harmful not just for humans, but also for other mammals.

Selected publications:

Lehtimäki J, Sinkko H, Hielm-Björkman A, Salmela E, Laatikainen T, Mäkeläinen S, Kaukonen M, Uusitalo L, Hanski I, Lohi H, and Ruokolainen L. Skin microbiota and allergic symptoms associate with exposure to environmental microbes. PNAS 2018

Ottman N, Ruokolainen L, Suomalainen A, Karisola P, Lehtimäki, J, Lehto M, Hanski I, Alenius H, and Fyhrquist N. Exposure to soil in the living environment modifies gut microbiota and enforces immune tolerance in a mouse model of asthma. JACI 2018

Lehtimäki J, Karkman A, Laatikainen T, Paalanen L, von Hertzen L, Haahtela T, Hanski I, and Ruokolainen L. Patterns in the skin microbiota differ in children and teenagers between rural and urban environments. Scientific Reports 2017:7

Ruokolainen L, Lehtimäki J, Karkman A, Haahtela T, von Hertzen L, and Fyhrquist N. Holistic view on health: Two protective layers of biodiversity. Annales Zoologi Fennici 2017:54

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Tue, April 28th, 2020

Prof. Bert de Groot, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany: tba

Host: Parthiban Marimuthu

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SEMINAR ARCHIVE

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Fri, February 14th, 2020

14:00-15:00 Alhopuro Auditorium, Medisiina D, Kiinamyllynkatu 10

Dr. Lauri Louhivuori, Dept of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden: Decoding cellular linguistics: A window into the architecture of cell type specific signaling

Host: Michael Courtney

Coffee at 13:45

About the Speaker:

Lauri Louhivuori studied Cell and Molecular Biology at the University of Jyväskylä (Finland), and completed his PhD, in Physiology, from the Faculty of Medicine at the University of Helsinki (Finland) in 2015. He then moved as a postdoc to the Department of Medical Biochemistry and Biophysics at the Karolinska Institute in Sweden, where he is currently residing.

Lauri’s key research interests are driven by a fundamental question: how is it that a relatively small core set of signaling pathways are able to mediate such a diverse array of complex cellular decisions.

ORCID: orcid.org/0000-0001-8649-781X

Selected publications:

Neurotransmitters and Endothelins Acting on Radial Glial G-protein Coupled Receptors Are, via Proteolytic NRG/ErbB4 Activation, Able to Modify the Migratory Behavior of Neocortical Cells and Mediate Bipolar-to-Multipolar Transition. Stem Cells Dev. (2020) doi:10.1089/scd.2019.0133 Louhivuori LM, Turunen PM, Louhivuori V, Rayyes IA, Nordström T, Åkerman KE.

The T-type Ca2+ Channel Cav3.2 Regulates Differentiation of Neural Progenitor Cells during Cortical Development via Caspase-3. Neuroscience. (2019) Mar 15;402:78-89. Rebellato P, Kaczynska D, Kanatani S, Rayyes IA, Zhang S, Villaescusa C, Falk A, Arenas E, Hermanson O, Louhivuori L‡, Uhlén P‡.

Altered interplay between endoplasmic reticulum and mitochondria in Charcot-Marie-Tooth type 2A neuropathy. Proc Natl Acad Sci U S A. (2019) Feb 5;116(6):2328-2337. Bernard-Marissal N, van Hameren G, Juneja M, Pellegrino C, Louhivuori L, Bartesaghi L, Rochat C, El Mansour O, Médard JJ, Croisier M, Maclachlan C, Poirot O, Uhlén P, Timmerman V, Tricaud N, Schneider BL, Chrast R.

Predicting a tumour’s drug uptake. Nature Biomedical Engineering (2018) 2, 717–718 Louhivuori L, Kanatani S, Uhlén P

Whole-tissue biopsy phenotyping of three-dimensional tumours reveals cancer heterogeneity Nature Biomedical Engineering (2017) 1, pages796–806 Tanaka N, Kanatani S, Tomer R, Sahlgren C, Kronqvist P, Kaczynska D, Louhivuori L, Kis L, Lindh C, Stepulak A, Corvigno A, Hartman J, Micke P, Mezheyeuski A, Strell C, Carlson J, Moro C, Dahlstrand H, Östman A, Wiklund P, Oya M, Miyakawa A, Deisseroth K, and Uhlén P.

Mapping genes for calcium signaling and their associated human genetic disorders.Bioinformatics (2017) Aug 15;33(16):2547-2554 Hörtenhuber M, Toledo EM, Smedler E, Arenas E, Malmersjö S, Louhivuori L, Uhlén P.

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Fri, November 29th, 2019: ANNUAL MEETING

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Fri, November 15th, 2019

14:00-15:00 Alhopuro Auditorium, Medisiina D, Kiinamyllynkatu 10

Prof. Hasse Karlsson, Department of Clinical Medicine, University of Turku: The FinnBrain Birth Cohort Study: rationale and design

Dr. Linnea Karlsson, Department of Clinical Medicine, University of Turku: Gut-brain axis studies in the FinnBrain Birth Cohort

Coffee at 13:45

About the speakers:

Linnea Karlsson, MD, PhD, Adj. Prof, is a specialist in child and adolescent psychiatry and is an experienced clinician in these fields. Currently, her main position is as a senior investigator at the University of Turku where she co-leads a pregnancy cohort, FinnBrain Birth Cohort study (www.finnbrain.fi) and the recently established Centre for Population Health Research. Linnea Karlsson did her PhD on the epidemiology of adolescent mood disorders at the National Public Health Institute. Currently, her main line of research is to investigate the influence of prenatal and early life stress exposures to later child brain and behavioral development. She holds an Academy of Finland project grant for gut-brain axis research with special emphasis on early childhood brain and behavioural phenotypes. Her research is inherently multidisciplinary and takes place in international collaborative networks. Linnea Karlsson was also acting as the president of Mannerheim Child Welfare League 2015–2017.

Selected publications:

Aatsinki A, Lahti L, Uusitupa H, Munukka E, Keskitalo A, Nolvi S, O’Mahony S, Pietilä S, Elo L, Eerola E, Karlsson H, Karlsson L. Gut microbiota composition is associated with temperament traits in infants. Brain, Behavior, and Immunity 2019 May 24. pii: S0889-1591(19)30077-7. doi:10.1016/j.bbi.2019.05. 035.

Mustonen P, Karlsson L, Kataja E-L, Scheinin NM, Kortesluoma S, Coimbra B, Rodrigues AJ, Nuno S, Karlsson H. Maternal prenatal hair cortisol is associated with prenatal depressive symptom trajectories. Psychoneuroendocrinol 2019;109:104383. doi: 10.1016/j.psyneuen.2019.104383. [Epub ahead of print]

Karlsson L, Tolvanen M, Scheinin NM, Uusitupa H-M, Korja R, Kataja E-L, Ekholm E, Pajulo M, Huotilainen M, Paunio T, Karlsson H, and the FinnBrain Birth Cohort Study Group. Cohort Profile: the FinnBrain Birth Cohort Study (FinnBrain). Int J Epidemiol 2018;47:15-16j. doi: 10.1093/ije/dyx173.

Davis EP, Korja R, Karlsson L, Glynn L, Sandman CA, Vegetabile B, Katja EL, Nolvi S, Sinervä E, Pelto J, Karlsson H, Stern HS, Baram TZ. Across continents and demographics, unpredictable maternal signals are associated with children’s cognitive function. EBioMed 2019 Jul 27. pii: S2352-3964(19)30460-8. doi: 10.1016/j.ebiom.2019.07.025. [Epub ahead of print].

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Wed, October 9th, 2019

10:00-11:00 Alhopuro Auditorium, Medisiina D, Kiinamyllynkatu 10

Dr. Ana João Rodrigues, ICVS, University of Minho, Portugal: Impact of prenatal stress in the reward circuit: from rodents to humans and back

Host: Linnea Karlsson

Coffee at 9:45

Ana João Rodrigues (AJR, 37 years old) is currently a Researcher at ICVS, University of Minho, Portugal. AJR graduated in Applied Biology in 2003, with the research trainee at LUMC, Holland. In 2008, AJR obtained her PhD in Health Sciences, University of Minho, Portugal (Patricia Maciel’s Lab), at the Neurogenetics Department in UCLA, USA (Daniel Geschwind’s Lab), and at Turku Centre for Biotechnology, Finland (Garry Corthals’ lab). From 2009-2013, AJR performed a post-doctoral fellowship at ICVS (Nuno Sousa’s Lab). Since 2013, AJR is a junior PI at ICVS, and her research is focused in understanding what drives reward and motivated behaviors, and how prenatal stress/glucocorticoid exposure can imprint long-lasting marks in the brain, leading to maladaptive behavior later in life. Her research goes from molecular studies (omics) to animal models (behavioral, electrophysiology, and optogenetic tools) to human studies (neuropsychological evaluation, fMRI). AJR has published 50 peer-reviewed articles and is part of the editorial board at Frontiers in Cellular Neuroscience and Brain Research.

ORCID: orcid.org/0000-0003-1968-7968; Scopus: 12139015600; ResearcherID: D-3782-2012

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Fri, September 20th, 2019

14:00-15:00 Arje Scheinin Auditorium, Dentalia, Lemminkäisenkatu 2

Dr. Jing Tang, Faculty of Medicine, University of Helsinki: Network pharmacology approaches for functional precision medicine

Dr. Vilja Siitonen, Department of Biochemistry, Faculty of Science and Engineering,University of Turku: Unravelling the biosynthesis of antibiotics – Nogalamycin as an example

Coffee at 13:45

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Fri, August 30th, 2019

14:00-15:00 Alhopuro Auditorium, Medisiina D, Kiinamyllynkatu 10

Dr. Noora Kotaja, Institute of Biomedicine, University of Turku: RNA regulation in male germ cells: implications for male fertility and epigenetic inheritance

Prof. Daniel Abankwa, Cancer Cell Biology and Drug Discovery, Life Sciences Research Unit, University of Luxembourg: Ras isoform selective drug development approaches

Coffee at 13:45

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Noora Kotaja is an Associate Professor of Molecular Medicine at the Institute of Biomedicine, University of Turku, Finland. She obtained PhD in Biomedicine at the University of Helsinki under supervision of Profs. Olli Jänne and Jorma Palvimo. She did her postdoctoral training at the Institut de Génétique et de Biologie Moléculaire et Cellulaire, Strasbourg, France, in the research group of Dr. Paolo Sassone-Corsi on germ cell-specific regulation of gene expression. In 2006, she returned back in Finland to establish her own research group at the University of Turku, where she received first an Academy Research Fellow post from the Academy of Finland, followed by a tenure track Professor position in 2012. Her scientific achievements have been recognized by L’Oreal Finland for Women in Science award in 2006, Unto Uotila award form the Finnish Endrocrine Society in 2008 and Young Researcher award from the International Netwolrk of Young Researchers in Male Fertiliy in 2011 and Young Andrologist award from the International Society of Andrology in 2013.

Noora Kotaja’s research focuses on the mechanisms of spermatogenesis and germline-mediated epigenetic inheritance. In particular, her research group is interested in the epigenetic and posttranscriptional regulation of gene expression in meiotic and post-meiotic male germ cells, and the role of large germ cell-specific ribonucleoprotein granules (germ granules) in the control of germ cell’s transcriptome. The research in the Kotaja group combines experimental animal studies with human cohort studies to elucidate key epigenetic processes required for the production of fertile spermatozoa and correct transgenerational transmission of epigenetic information. The research may provide important novel insights into the development of diagnosis, treatment and prevention strategies for male infertility. Importantly, the research will also clarify the mechanisms of epigenetic inheritance, which could help us to understand and potentially prevent the transmission of acquired diseases such as metabolic disorders.

Selected publications:

Pandey RR, Homolka D, Olotu O, Sachidanandam R, Kotaja N, Pillai RS. Exonuclease Domain-Containing 1 Enhances MIWI2 piRNA Biogenesis via Its Interaction with TDRD12. Cell Rep. 2018 24:3423-3432.e4.

Lehtiniemi T, Kotaja N. Germ granule-mediated RNA regulation in male germ cells. Reproduction. 2018 Feb;155(2):R77-R91.

Matteo Da Ros, Tiina Lehtiniemi, Opeyemi Olotu, Daniel Fischer, Fu-Ping Zhang, Helena Vihinen, Eija Jokitalo, Anu Sironen, Jorma Toppari, Noora Kotaja. FYCO1 and autophagy control the integrity of the haploid male germ cell-specific RNP granules. Autophagy. 2017 Feb;13(2):302-321.

Korhonen HM, Yadav RP, Da Ros M, Chalmel F, Zimmermann C, Toppari J, Nef S, Kotaja N. DICER Regulates the Formation and Maintenance of Cell-Cell Junctions in the Mouse Seminiferous Epithelium. Biol Reprod. 2015 Dec;93(6):139.

Goh WS, Falciatori I, Tam OH, Burgess R, Meikar O, Kotaja N, Hammell M, Hannon GJ. piRNA-directed cleavage of meiotic transcripts regulates spermatogenesis. Genes Dev. 2015 May 15;29(10):1032-44.

Da Ros M, Hirvonen N, Olotu O, Toppari J, Kotaja N. Retromer vesicles interact with RNA granules in haploid male germ cells. Mol Cell Endocrinol. 2015 Feb 5;401:73-83.

Meikar O, Vagin VV, Chalmel F, Sõstar K, Lardenois A, Hammell M, Jin Y, Da Ros M, Wasik KA, Toppari J, Hannon GJ, Kotaja N. An atlas of chromatoid body components. RNA. 2014 Apr;20(4):483-95.

Kotaja N, Sassone-Corsi P. The chromatoid body: a germ-cell-specific RNA-processing centre. Nat Rev Mol Cell Biol 8(1):85-90, 2007.

Kotaja N, Kimmins S, Brancorsini S, Hentsch D, Vonesch JL, Davidson I, Parvinen M, Sassone-Corsi P. Preparation, isolation and characterization of stage-specific spermatogenic cells for cellular and molecular analysis. Nat Methods 1(3):249-54, 2004.

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Daniel Abankwa studied chemistry in Göttingen (Germany), and completed his PhD in molecular neurobiology in Düsseldorf (Germany). In 2002, he moved as a postdoc to the EPFL in Switzerland, before he started working on the oncogene RAS with Prof. John Hancock at the Institute for Molecular Bioscience of the University of Queensland (Australia) in 2006. He then became junior group leader with Prof. Kirill Alexandrov at the same institute. In 2010, Daniel moved as adjunct professor to the Turku Centre for Biotechnology (Finland), where he established a prolific research group, with publications e.g. in eLife and Oncogene. Since 2017 he is full professor at the University of Luxembourg.

Daniel Abankwa’s group aims at understanding RAS isoform specificity, drug discovery in particular against cancer stem cells, as well as assay development. They utilize an array of methods, ranging from classical molecular cell biology, computational modelling, quantitative fluorescence microscopy (FRAP, FRET), to superresolution STED-nanoscopy.

Selected recent publications

Buehler U, Schulenburg K, Yurugi H, Šolman M, Abankwa D, Ulges A, Tenzer S, Bopp T, Thiede B, Zipp F, Rajalingam K. Targeting prohibitins at the cell surface prevents Th17-mediated autoimmunity. EMBO J. 2018 Aug 15;37(16). pii: e99429.

I MD Posada, Lectez B, Sharma M, Oetken-Lindholm C, Yetukuri L, Zhou Y, Aittokallio T, Abankwa D Rapalogs can promote cancer cell stemness in vitro in a Galectin-1 and H-ras-dependent manner Sci Rep. 2017 Aug 21;7(1):8944.

Posada IMD, Lectez B, Sharma M, Oetken-Lindholm C, Yetukuri L, Zhou Y, Aittokallio T, Abankwa D. Rapalogs can promote cancer cell stemness in vitro in a Galectin-1 and H-ras-dependent manner. Oncotarget. 2017;8(27):44550-44566.

Najumudeen AK, Jaiswal A, Lectez B, Oetken-Lindholm C, Guzmán C, Siljamäki E, Posada IM, Lacey E, Aittokallio T, Abankwa D. Cancer stem cell drugs target K-ras signaling in a stemness context. Oncogene. 2016 Oct 6;35(40):5248-5262.

Šolman M, Ligabue A, Blaževitš O, Jaiswal A, Zhou Y, Liang H, Lectez B, Kopra K, Guzmán C, Härmä H, Hancock JF, Aittokallio T, Abankwa D. Specific cancer-associated mutations in the switch III region of Ras increase tumorigenicity by nanocluster augmentation. Elife. 2015;4:e08905.

Brooks AJ, Dai W, O’Mara ML, Abankwa D, Chhabra Y, Pelekanos RA, Gardon O, Tunny KA, Blucher KM, Morton CJ, Parker MW, Sierecki E, Gambin Y, Gomez GA, Alexandrov K, Wilson IA, Doxastakis M, Mark AE, Waters MJ. Mechanism of activation of protein kinase JAK2 by the growth hormone receptor. Science. 2014 May 16;344(6185):1249783.

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Tue, May 28th, 2019

14:00-15:00 Alhopuro Auditorium, Medisiina D, Kiinamyllynkatu 10

Dr. Sergiu Ivanov, IBISC, Univ Évry, Paris-Saclay University, France: Sequential Reprogramming of Biological Network Fate

Host: Ion Petre

Dr. Sergiu Ivanov is an associate professor (maître de conférences) of computer science at the Department of Computer Science of Université d’Évry, Université Paris-Saclay. He is currently member of the IBISC Laboratory and belongs to team COSMO, who study the fundamental properties of complex systems, and notably biological systems.

Dr. Sergiu Ivanov defended his PhD thesis focused on the computational power of biologically-inspired models of computing at Université Paris-Est in 2015. His principal research interest lies in applying formal models to gain insight into medical and biological problems. He is currently working on employing formal networks to help infer cancer therapies and better understand the molecular and evolutionary causes of this disease (e.g., resilience, atavistic theory of cancer, etc.).

Dr. Sergiu Ivanov’s main research domains are:
• precision medicine,
• theoretical biology,
• complex systems, and
• bio-inspired models of computing.

Sergiu Ivanov’s home page: https://www.ibisc.univ-evry.fr/~sivanov/

Key Publications:

Artiom Alhazov, Rudolf Freund, *Sergiu Ivanov*, Sergey Verlan: Tissue P Systems with Point Mutation Rules. Int. Conf. on Membrane Computing 2018: 33-56

Quoc-Trung Vuong, Roselyne Chauvin, *Sergiu Ivanov*, Nicolas Glade, Laurent Trilling: A Logical Constraint-based Approach to Infer and Explore Diversity and Composition in Thresholded Boolean Automaton Networks. COMPLEX NETWORKS 2017: 567-579

Sepinoud Azimi, Cristian Gratie, *Sergiu Ivanov*, Luca Manzoni, Ion Petre, Antonio E. Porreca: Complexity of model checking for reaction systems. Theor. Comput. Sci. 623: 103-113 (2016)

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Fri, May 3rd, 2019

11:00-12:00 Säätiö Auditorium, Medisiina D, Kiinamyllynkatu 10

Prof. Lars Juhl Jensen, Disease Systems Biology Program, University of Copenhagen: Using text mining in biomedical databases

Host: Sampo Pyysalo

Lars Juhl Jensen started his research career in Søren Brunak’s group at the Technical University of Denmark (DTU), from which he in 2002 received the Ph.D. degree in bioinformatics for his work on non-homology based protein function prediction. During this time, he also developed methods for visualization of microbial genomes, pattern recognition in promoter regions, and microarray analysis. From 2003 to 2008, he was at the European Molecular Biology Laboratory (EMBL) where he worked on literature mining, integration of large-scale experimental datasets, and analysis of biological interaction networks. Since the beginning of 2009, he has continued this line of research as a professor at the Novo Nordisk Foundation Center for Protein Research at the Panum Institute in Copenhagen and as a co-founder and scientific advisor of Intomics A/S.

Selected publications:

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, Simonovic M, Doncheva NT, Morris JH, Bork P*, Jensen LJ* and von Mering C* (2019). STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47:D607-D613.

Oprea TI, Bologa CG, Brunak S, Campbell A, Gan GN, Gaulton A, Gomez SM, Guha R, Hersey A, Holmes J, Jadhav A, Jensen LJ, Johnson GL, Karlson A, Leach AR, Ma’ayan A, Malovannaya A, Mani S, Mathias SL, McManus MT, Meehan TF, von Mering C, Muthas D, Nguyen DT, Overington JP, Papadatos G, Qin J, Reich C, Roth BL, Schürer SC, Simeonov A, Sklar LA, Southall N, Tomita S, Tudose I, Ursu O, Vidovic D, Waller A, Westergaard D, Yang JJ and Zahoránszky-Köhalmi G (2018). Unexplored therapeutic opportunities in the human genome. Nature Reviews Drug Discovery, 17:377.

Westergaard D, Stærfeldt H-H, Tønsberg C, Jensen LJ* and Brunak S* (2018). Text mining of 15 million full-text scientific articles. PLOS Computational Biology, 14:e1005962.

Pafilis E, Buttigieg PL, Ferrell B, Pereira E, Schnetzer J, Arvanitidis C and Jensen LJ (2016). EXTRACT: Interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. Database, 2016:baw005.

Pletscher-Frankild S, Pallejà A, Tsafou K, Binder JX and Jensen LJ (2015). DISEASES: Text mining and data integration of disease–gene associations. Methods, 74:83-89

Fri, April 12th, 2019

14:00-15:00 Agora Auditorium XX, Vesilinnantie 5, 1st floor

Dr. Michael Courtney, Group Leader of the Neuronal Signalling Lab, Turku Bioscience, University of Turku and Section Leader of the Turku Screening Unit: Shining a light on hidden signalling processes and druggability of disease signalling

Dr. Majid Momeny, postdoc research fellow, Prof. Jukka Westermarck’s lab, Turku Centre for Biotechnology, University of Turku: Oncogenic phosphatases: Novel targets to overcome therapy resistance in HER2+ breast cancer

Fri, March 22nd, 2019

14:00-15:00 Alhopuro Auditorium, Medisiina D, Kiinamyllynkatu 10

Prof. Jukka Westermarck, Centre for Biotechnology and Institute of Biomedicine, University of Turku: Phosphoproteome and Functional Landscape of Protein Phosphatase 2A (PP2A) in Cancer Cells

The focus of our laboratory is to understand role and regulation of PP2A in human cancers and especially function of PP2A inhibitor proteins as human oncoproteins. To achieve this, we use a combination of advanced cell and molecular biology approaches combined with genetically modified mouse cancer models. We also have special interest on targeted therapies against PP2A inhibitor proteins. Our recent results suggest that a potential biological outcome of aberrant PP2A signaling in cancer is conferring drug resistance (Cancer Research, 2016, Sci.Transl. Med, 2018). Based both on these results, and on wide-spectrum role of PP2A on cellular signaling, we hypothesize that re-activation of PP2A, via targeting of its endogenous inhibitory proteins, could be used as a general strategy for multi-target inhibition of chemoresistance in common human cancer types. In addition, these results may have importance in patient stratification for monotherapies using the identified small molecule compounds.

Selected publications:

Kauko O, O´Connor CM, Kulesskiy E, Sangodkar J, Aakula A, Izadhmehr S, Yetukuri L, Yadav B, Padzik A, Laajala TD, Haapaniemi P, Momeny M, Varila T, Ohlmeyer M, Aittokallio T, Wennerberg K, Narla G*, and Westermarck J*; PP2A inhibition is a druggable MEK inhibitor resistance mechanism in KRAS-mutant lung cancer cells. Science Translational Medicine 10(450), doi: 10.1126/scitranslmed.aaq1093, 2018.

Kaur A, Denisova OV, Qiao X, Jumppanen M, Peuhu E, Ahmed SU, Raheem O, Haapasalo H, Eriksson J, Chalmers AJ, Laakkonen P and Westermarck J; PP2A inhibitor PME-1 drives kinase inhibitor resistance in glioma cells. Cancer Research 76(23): 7001-7011, 2016.

Laine A, Sihto H, Come C, Rosenfeldt MT, Zwolinska A, Niemelä M, Khanna A, Chan EK, Kähäri V-M, Kellokumpu-Lehtinen P-L, Sansom OJ, Evan GI, Junttila MR, Ryan KM, Marine J-C, Joensuu H, and Westermarck J; Senescence sensitivity of breast cancer cells is defined by positive feedback loop between CIP2A and E2F1. Cancer Discovery 3(2): 182-197, 2013.

Puustinen P, Junttila MR, Vanhatupa S, Sablina AA, Hector ME, Teittinen K, Raheem O, Ketola K, Lin S, Kast J, Haapasalo H, Hahn WC, and Westermarck J; PME-1 protects ERK pathway activity from protein phosphatase 2A-mediated inactivation in human malignant glioma. Cancer Research 69: 2870-2877, 2009.

Khanna A, Böckelman C, Hemmes A, Junttila MR, Wiksten J-P, Lundin P, Junnila S, Murphy D, Evan GI, Haglund C, Westermarck J*, and Ristimäki A*; MYC-dependent regulation and prognostic role of CIP2A in gastric cancer. Journal of the National Cancer Institute 101: 793-805, 2009.
Junttila, MR, Puustinen P, Niemelä M, Ahola R, Arnold H, Böttzauw T, Ala-aho R, Nielsen C, Ivaska J, Taya Y, Lu SL, Li S, Chan EKL, Wang X-J, Grenman R, Kast J, Kallunki T, Sears R, Kähäri V-M, and Westermarck J; CIP2A inhibits PP2A in human malignancies. Cell 130: 51–62, 2007

Fri, February 22nd, 2019

14:00-15:00 Alhopuro Auditorium, Medisiina D, Kiinamyllynkatu 10

Dr. Leo Lahti, Department of Mathematics and Statistics, University of Turku: “Trends in microbiome data science”

and

Dr. Manu Tamminen, Department of Biology, University of Turku: “Understanding antibiotic resistance using next-generation DNA sequencing”

Leo Lahti is Docent in applied mathematics and Academy Research Fellow at the Department of Mathematics and Statistics where he leads the Computational biosciences group. He obtained PhD in statistical machine learning and bioinformatics in 2010 in Aalto University, followed by a six year postdoctoral period in The Netherlands and Belgium. Lahti is also a founding member of Helsinki Computational History group and Open Knowledge Finland working groups which received Ministry of Education awards on Open Science in 2016 and 2017, respectively. His current research focuses on modern data science methods and applications in human microbiome research. More info: http://www.iki.fi/Leo.Lahti

Key publications:

A hierarchical Ornstein-Uhlenbeck model for stochastic time series analysis. Ville Laitinen and Leo Lahti. In: Advances in Intelligent Data Analysis XVII. Springer, 2018.

Tipping elements in the human intestinal ecosystem. Leo Lahti, Jarkko Salojärvi, Anne Salonen, Marten Scheffer, and Willem M. de Vos. Nature Communications, 5:4344, 2014

Signatures of ecological processes in microbial community time series. Karoline Faust, Franziska Bauchinger, Beatrice Laroche, Sophie de Buyl, Leo Lahti, Alex D Washburne, Didier Gonze, and Stefanie Widder. Microbiome, 6(120) 2018.

Microbial communities as dynamical systems. Didier Gonze, Katharine Z Coyte, Leo Lahti, and Karoline Faust. Current Opinion in Microbiology, 44:41–49, 2018.

Alchemy & algorithms: perspectives on the philosophy and history of open science. Leo Lahti, Filipe da Silva, Markus Petteri Laine, Viivi Lähteenoja, and Mikko Tolonen. RIO Journal, 3:e13593, 2017.

Manu Tamminen is developing and applying single cell genome sequencing techniques to gain improved insights into complex bacterial communities and their role at the emergence of antibiotic resistant bacterial strains. He defended his doctoral thesis at the University of Helsinki and has since carried out his research at MIT and ETH Zürich. He is currently employed as a senior lecturer of genetics at the University of Turku.

Key publications:

Tamminen, M., Betz, A., Thali, M., Matthews, B., Suter, M. and Narwani, A. (2018) Proteome evolution under essential resource limitation. Nature Communications 9: 4650.

Krismer, J., Tamminen, M., Fontana, S., Zenobi, R. and Narwani. A. (2017) Single-cell mass spectrometry reveals the importance of genetic diversity and plasticity for phenotypic variation in nitrogen limited Chlamydomonas. ISME Journal 11: 988-998.

Brito, I. L., Yilmaz, S., Huang, K., Xu, L., Jupiter, S.D., Jenkins, A.P., Naisilisili, W. Tamminen, M., Smillie, C.S., Wortman, J.R., Birren, B.W., Xavier, R.J., Blainey, P.C., Singh, A.K., Gevers, D., Alm, E.J. (2016) Mobile genes in the human microbiome are structured from global to individual scales. Nature 535: 435-439

Spencer, S.*, Tamminen, M.*, Preheim, S., Guo, M., Briggs, A., Brito, I., Weitz, D., Pitkänen, L., Vigneault, F., Virta, M., Alm, E. (2016) Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers. ISME Journal 10: 427-436. *Equal contribution.

Tamminen, M., Virta, M., Fani, R. & Fondi, M. (2012) Analysis of plasmid relationships through gene sharing networks. Molecular Biology and Evolution 29: 1225-1240

Wed, DECEMBER 5th, 2018: Annual Meeting

09:00-18:00 Vanhalinnan kartanoravintola, Lieto

Fri, NOVEMBER 23rd, 2018

14:00-15:00 PharmaCity Auditorium, Itäinen Pitkäkatu 4B, Turku

Dr. Henri Xhaard, Division of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki: “10-year retrospective of the Computational Drug Discovery group at the Faculty of Pharmacy, University of Helsinki”

Host: Tiina Salminen

Dr. Xhaard obtained his  PhD from the university Åbo Akademi in 2006 under the supervision of Prof. Mark S. Johnson. In 2008 he was selected as principal investigator by the Faculty of Pharmacy, University of Helsinki, where he founded the computational drug discovery group. The group has since developed and is to date composed of 6-8 researchers, and is well integrated in national [1] and international [2] infrastructure around chemical biology.

The group uses computational drug discovery methods, both chemoinformatics and molecular modeling, applied to different therapeutic areas as part of local or international research networks/consortia: sleep disorders (orexin receptors) [3], parasitic (membrane-bound pyrophosphatases) [4] and bacterial (quorum-sensing inhibitors) diseases, neuropathic pain (opioid receptors and toll-like receptors) [5], stem-cell inducers for application e.g. in stroke [6], and in-silico predictive ADME (metabolic proteins, ABC transporters [7,8] and glucoronidation enzymes [9]). These projects include many interdisciplinary components and collaboration for example with pharmacology, molecular biology, medicinal chemistry, and X-ray crystallography.

The group is also working to benchmark and develop existing computational methods [see e.g. 10]. We have a strong expertise with data mining [11,12]. The presentation will include current unpublished research in structural bioinformatics, where we develop novel ways to represent the interaction environment around selected atoms, with broad applications to e.g. score molecular complexes or predict the location of elements (hydrogen atoms, water molecules, metal ions, molecular fragments.. ) absent from crystallographic structures or structural models.

[1] Drug discovery and chemical biology – Finnish national consortium http://www.ddcb.fi/

[2 EU Openscreen partner site – http://www.eu-openscreen.eu/

[3]Pharmacophore Model To Discover OX1 and OX2 Orexin Receptor Ligands. Turku A, Borrel A, Leino TO, Karhu L, Kukkonen JP, Xhaard H. J Med Chem. 2016 59:8263-75.

[4] Integral membrane pyrophosphatases: a novel drug target for human pathogens? Shah NR, Vidilaseris K, Xhaard H, Goldman A. AIMS biophysics 2016, 3: 171-194. doi: 10.3934/biophy.2016.1.171

[5] GLORIA EU-FP7 consortium – http://gloria.helsinki.fi/

[6] 3i-regeneration consortium – http://www.3iregeneration.com/

[7]A structure-activity relationship study of ABCC2 inhibitors. Wissel G, Deng F, Kudryavtsev P, Ghemtio L, Wipf P, Xhaard H, Kidron H. Eur J Pharm Sci. 2017, 103:60-69.

[8] Exploring the structure-activity relationships of ABCC2 modulators using a screening approach. Wissel G, Kudryavtsev P, Ghemtio L, Tammela P, Wipf P, Yliperttula M, Finel M, Urtti A, Kidron H, Xhaard H. Bioorg Med Chem. 2015 23:3513-25.

[9] SVM classification and CoMSIA modeling of UGT1A6 interacting molecules. Ghemtio L, Soikkeli A, Yliperttula M, Hirvonen J, Finel M, Xhaard H.

J Chem Inf Model. 2014, 54:1011-26.

[10] Visually interpretable models of kinase selectivity related features derived from field-based proteochemometrics. Subramanian V, Prusis P, Pietilä LO, Xhaard H, Wohlfahrt G. J Chem Inf Model. 2013, 53:3021-30.

[11] IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data. Legehar A, Xhaard H, Ghemtio L. J Cheminform. 2016; 8:33. http://idaapm.helsinki.fi/

[12]  Structural Isosteres of Phosphate Groups in the Protein Data Bank. Zhang Y, Borrel A, Ghemtio L, Regad L, Boije Af Gennäs G, Camproux AC, Yli-Kauhaluoma J, Xhaard H. J Chem Inf Model. 2017 57:499-516.

Fri, 26th OCTOBER, 2018

Ensembl browser workshop

09:00-17:00 University of Turku, Natura building, IT class 420

Dr Astrid Gall, Ensembl Outreach Officer, European Molecular Biology Laboratory – European Bioinformatics Institute (EMBL-EBI)

Seating is limited to 30 pre-registered participants. Link to registration

Mon, OCTOBER 1st, 2018

13:00-15:00 Alhopuro Auditorium, Medisiina D, Kiinamyllynkatu 10

Pak Yang Chum, Illumina: “BaseSpace Sequence Hub Workshop: An Introduction and Workflow Walkthrough”
BaseSpace Sequence Hub is a genomics cloud computing platform designed to bring simplified data management and analytical sequencing tools directly to investigators in a user-friendly format.

Host: Riikka Lund

Fri, SEPTEMBER 21st, 2018

14:00-15:00 Agora Auditorium XX, Vesilinnantie 5, 1st floor

Dr. Jarmo Niemi, Department of Biochemistry, University of Turku: “Genome mining for the unknown – identifying biosynthetic genes for C-nucleosides”

Dr. Georgi Belogurov, Department of Biochemistry, University of Turku: “Unraveling the mechanism of RNA polymerase translocation along the DNA”

Thu, SEPTEMBER 13th, 2018

14:00-15:00 Auditorium Biokemi, 3rd floor, Biocity, Tykistökatu 6

Prof. Ramanathan Sowdhamini, National Centre for Biological Sciences, Tata Institute of Fundamental Research: “Toll-Interleukin receptor (TIR) domains – from modeling and molecular dynamics perspective”

Host: Mark Johnson

MAY 31st, 2018

14:00-15:00 Agora Auditorium XXI, Vesilinnantie 5, 1st floor

Dr. Laurent Guyon, CEA-Grenoble, Biosciences and Biotechnology Institute of Grenoble, France: Gene selection and interpretation in large scale datasets: network based approaches, high content screening, mRNAs and microRNAs”

MAY 18th, 2018

10:00-11:00

Lambda auditorium, ICT-city building (ground floor), Joukahaisenkatu 3-5, Turku (coffee at 09:45)

Adj. Prof. Kalle Parvinen, University of Turku, Department of Mathematics and Statistics: Adaptive dynamics – understanding evolution by natural selection using mathematical modelling.

Assoc. Prof. Anton Zavialov, University of Turku, Joint Biotechnology Laboratory (JBL), Department of Chemistry: Structural basis for Acinetobacter baumannii biofilm formation.

APRIL 20th, 2018
9:00-16:00
Alpha auditorium, ICT-city building (ground floor), Joukahaisenkatu 3-5, Turku

Single Cell Omics Symposium

APRIL 13th, 2018

14:00-15:00
PharmaCity Auditorium, Itäinen Pitkäkatu 4B, Turku

Dr. Eugen Czeizler, Åbo Akademi, Computational Biomodelling Laboratory: “Computational Approaches in DNA Algorithmic Self-Assembly”

and

Dr. Jukka Lehtonen, Åbo Akademi, Structural Bioinformatics Laboratory: “Where is your file? Thoughts on data management”

FEBRUARY 16th, 2018

14:00-15:00 Pharmacity Auditorium

Dr. Xiang-Guo Li, University of Turku, Turku PET Centre, Radiopharmaceutical Chemistry Laboratory: “Making your drug candidates and drug targets brighter with positron emission tomography (PET) techniques”

and

Dr. Ulla Pentikäinen, University of Turku, Institute of Biomedicine, Pharmacology, Drug Development and Therapeutics: “What goes wrong in diseases: Towards understanding of the molecular mechanism of mitral valve prolapse”

JANUARY 19th, 2018

11:00-12:00 Pharmacity Auditorium,
Dr. Adam S. Wilkins, Institute of Theoretical Biology, Humboldt Universität, Germany: “The unusual face of Homo sapiens and its evolutionary origins”

Hosts: Harri Savilahti and Petter Portin

DECEMBER 8th, 2017
Annual Meeting

OCTOBER 12th, 2017

10.00-11:00 Pharmacity Auditorium
Robert Lyle, Oslo University Hospital and University of Oslo, Norway: “Long-term prenatal exposure to paracetamol is associated with DNA methylation differences in children diagnosed with ADHD”
Host: Riikka Lund

OCTOBER 5th, 2017
FOS Seminar: Prof. Antti Poso, University of Kuopio & Distinguished Visiting Professor at the University of Tübingen in Germany: “From drug design to target selection: developing new anti-cancer and CNS-targeting compounds”. Host: Outi Salo

JUNE 2nd, 2017
10.00-11:00 Pharmacity Auditorium

Prof. Peter James, Turku Centre for Biotechnology: “Modern technologies and their application to the diagnosis, prognosis and treatment of breast cancer”.

&

Ass.Prof. Tapio Pahikkala, Department of Information Technology, University of Turku: “Small data AUC estimation of machine learning methods: Pitfalls and remedies”.

Coffee served at 9:45

MAY 23rd, 2017
11-12 Pharmacity Auditorium.
Docent Miina Ollikainen, University of Helsinki & FIMM: “Unraveling epigenetics and traits of complex diseases using twin approaches”. Host: Riikka Lund.
Coffee served at 11.00

MAY 5th, 2017
12.00-13.00, Pharmacity Auditorium.

Ass. Prof. Filip Ginter, Department of Information Technology, University of Turku: “Turku Natural Language Group: Text Mining of Biomedical Literature… and beyond”.
&
Ass. Prof. Hongbo Zhang, Drug Development and diagnostics, Åbo Akademi University: “Biological Analysis in Droplets, the Power of Mirofluidics”.

DECEMBER 9th, 2016
CompLifeSci The 1st Annual Meeting 

NOVEMBER 18th, 2016
12.00-13.00, Agora
Prof. Outi Salo-Ahen, Åbo Akademi University“In search of novel antimicrobial agents against multiresistant bacteria – Computer-aided drug design approachesHost: Tiina Salminen
Coffee served at 11.45

OCTOBER 21st, 2016
11.00-12.00, Pharmacity Auditorium

Tapio Lönnberg, PhD, Postdoctoral Fellow at EMBL-EBI & Visiting Scientist at Wellcome Trust Sanger Institute, UK, 09/2016- Senior Scientist at Turku Centre for Biotechnology, University of Turku: “Single Cell RNA-sequencing and T cell fate decisions“. Host: Riikka Lund
Coffee served at 10.45

SEPTEMBER 29th, 2016
14.00-15.00, ICT beta lecture room

Jing Tang, PhD, TCSM Group Leader, Department of Mathematics and Statistics, University of Turku: Network-based drug combination discovery for personalized medicine – data integration, model prediction and mechanistic understanding“. Host: Tero Aittokallio
Coffee served at 13.45

AUGUST 25th, 2016
14.00-15.00, Biocity 5th floor BTK seminar room
Prof. Savvas Savvides, VIB Inflammation Research Center & Ghent University, Belgium: Structure, Mechanisms and Antagonism of pro-inflammatory cytokine-receptor complexes”. Host: Tassos Papageorgiou
Coffee served at 13.45