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”
Dr. Manu Tamminen, Department of Biology, University of Turku: “Understanding antibiotic resistance using next-generation DNA sequencing”
Coffee at 13:45
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
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.
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
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
Coffee at 13:45
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  and international  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) , parasitic (membrane-bound pyrophosphatases)  and bacterial (quorum-sensing inhibitors) diseases, neuropathic pain (opioid receptors and toll-like receptors) , stem-cell inducers for application e.g. in stroke , and in-silico predictive ADME (metabolic proteins, ABC transporters [7,8] and glucoronidation enzymes ). 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.
 Drug discovery and chemical biology – Finnish national consortium http://www.ddcb.fi/
[2 EU Openscreen partner site – http://www.eu-openscreen.eu/
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.
 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
 GLORIA EU-FP7 consortium – http://gloria.helsinki.fi/
 3i-regeneration consortium – http://www.3iregeneration.com/
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.
 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.
 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.
 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.
 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/
 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
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
Coffee at 12:45
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”
Coffee served at 13:45.
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
Coffee served at 13:45.
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
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
Alpha auditorium, ICT-city building (ground floor), Joukahaisenkatu 3-5, Turku
APRIL 13th, 2018
PharmaCity Auditorium, Itäinen Pitkäkatu 4B, Turku
Dr. Eugen Czeizler, Åbo Akademi, Computational Biomodelling Laboratory: “Computational Approaches in DNA Algorithmic Self-Assembly”
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”
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
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
Prof. Outi Salo-Ahen, Åbo Akademi University: “In search of novel antimicrobial agents against multiresistant bacteria – Computer-aided drug design approaches“. Host: 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