CompLifeSci 4th Annual Meeting, 2019

NOVEMBER 29th, 2019
9 am–6 pm
Arken, Åbo Akademi University, Tehtaankatu 2, Turku

PROGRAMME

9:00–9:15 Welcoming words & overview of the programme

Host: Manu Tamminen

9:15–10:15 SESSION I: GENOMICS & METAGENOMICS

Chair: Manu Tamminen

Dr. Shane Hogle, University of Turku: Inferring ecological adaptation from genomes of surface ocean bacterial population

Tommi Mäklin, University of Helsinki: Bacterial lineage identification from plate sweep sequencing data

Dr. Johannes Cairns, Sanger Institute: Drug order and bacteriophage determine drug resistance evolution in sequential therapy

10:15–11 Coffee & printed poster viewing

Meet the poster authors:

Group A 10:15-10.35

Group B 10:35-10:55

11–12:30 SESSION II: CRYO-EM & STRUCTURAL BIOLOGY

Chair: Anton Zavialov

Prof. Juha Huiskonen, University of Helsinki/Oxford University: Advances of cryo-EM in understanding macromolecular structure and function

Gaurav Sharma, Thermo Fisher Scientific: Cryo-EM Workflow – The role of 200kV tool

Dr. Serhii Vakal, Åbo Akademi University: Structure-based discovery of nature-derived agrochemical leads via academic collaboration

12:30–13:30 Lunch

13:30–15 SESSION III: ORAL POSTER PRESENTATIONS

Chair: Mia Åstrand

Janne Mäkinen: The mechanism of discrimination against 2’dNTPs by the multisubunit RNA polymerase

Akseli Reunamo: Identifying thermophilic adaptation in Prokaryotes with machine learning and deep learning

Moein Khalighi: Identification and characterization of memory effects in human microbiome time series

Mahlet Tamirat: Structural characterization of Δ⁷⁴⁶ELREA⁷⁵⁰ EGFR deletion mutation – a molecular dynamics simulation study

Ville Laitinen: Leading indicators of state shifts in microbiome time series

Mikko Konki: Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer’s disease

Parthiban Marimuthu: Predicting hotspot residues and allosteric signal transmission mechanism in mouse pro-apoptotic peptide—Mcl1 complexes

Henri Malmi: Uncovering the binding mechanism of FanC, the adhesive main subunit of K99 fimbriae

15–15:30 Coffee & posters; voting for best oral & printed poster

15:30–16:45 SESSION IV: MACHINE LEARNING

Chair: Sampo Pyysalo

Dr. Petri Törönen, University of Helsinki: PANNZER2: Predicting functions for whole genomes

Assoc. prof. Tapio Pahikkala, University of Turku: Machine Learning for Life Sciences under a Structured Feature Value Acquisition Budgets

Poster prizes & certificates

16:45 Refreshments & mingling (until 18:00)

Organising committee 2019: Mia Åstrand, Sampo Pyysalo, Manu Tamminen, Anton Zavialov

– – –

CompLifeSci 3rd Annual Meeting, 2018

DECEMBER 5th, 2018
9 am–6 pm
Vanhalinnan kartanoravintola, Vanha Härkätie 111, 21410 Vanhalinna, Lieto

PROGRAMME

9:00–9:15 Welcoming words & overview of the programme, host: Mark Johnson

9:15–10:15 SESSION I, chair: Ulla Pentikäinen

Dr. Vesa Hytönen, University of Tampere: Mechanical unfolding of talin examined using steered molecular dynamics and single-molecule AFM

MSc. Inka Saarinen, Blueprint Genetics: Understanding our Genomes

10:15–10:45 Coffee & posters

10:45–12:15 SESSION II, chair: Eugen Czeizler

Dr. Esa Kuusela, Varian Medical Systems: Machine Learning approach in Radiotherapy Treatment Planning

Prof. Pekka Orponen, Aalto University: Algorithmic design of RNA nanostructures

Oral posters:
– Henri Malmi: Pseudoatomic structure of Csu fimbriae from Acinetobacter baumannii
– Mia Åstrand: Structural basis for the ligand-binding properties of Borrelia burgdorferi s.s. BmpA, BmpB, BmpC and BmpD revealed by computational methods
– Chandan Thapa: Cancerous Protein Phosphatase 2A inhibitor proteins – novel perspective for cancer therapy
– Sami Kurkinen: Novel rescoring method to identify active small molecules for drug discovery
– Li-Li Li: A novel mechanism for converting temporally-distinct receptor inputs into contrasting cell signalling outcomes

12:15–13:15 Lunch

13:15–14:45 SESSION III, chair: Michael Courtney

Dr. Tommi Nyrönen, CSC: ELIXIR update and European Open Science Cloud project, focusing on Life Science

Dr. André Juffer, University of Oulu: Computer simulation of biological systems

Oral posters:
– Aaro Salosensaari: FINRISK 2002 human gut microbiome population cohort study
– Anna Aatsinki: Gut Microbiota Composition in infants is associated with early behavioral patterns
– Amirbehzad Akhgari: Synthetic biology for the generation of novel antibiotics
– Joonatan Palmu: Eicosanoid Variation is Strongly Related to Blood Pressure in the General Population
– Victor Popescu: The Network Controllability Application Pipeline

14:45–15:15 Coffee & posters

15:15–16:15 SESSION IV, chair: Leo Lahti

Dr. Elin Org, University of Tartu: The impact of host-gut microbiota interactions on metabolic traits

Dr. Umer Ijaz, University of Glasgow: Understanding microbial communities through in situ omics synthesis

16:15 Get-together, refreshments & prizes (until 18:00), host: Mark Johnson

Organising committee 2018: Michael Courtney, Eugen Czeizler, Mark Johnson, Leo Lahti, Ulla Pentikäinen

– – –

CompLifeSci 2nd Annual Meeting, 2017

DECEMBER 8th, 2017
9 am – 6 pm
ICT house, Aud. Gamma, Joukahaisenkatu 3-5, 20500 Turku, Finland

PROGRAMME

9-10.30 SESSION I, chair Tapio Pahikkala

Antti Airola, PhD (University of Turku): “Machine learning methods for biomedical network prediction”

Anna Cichonska, PhD candidate (FIMM/Aalto University): “Speeding up multiple pairwise kernel learning for drug bioactivity
prediction”

Clare J. Strachan, Prof., PhD (University of Helsinki): “Drugs and dosage forms under the Raman microscope”

10.30-10.45 Coffee break

10.45-12.15 SESSION II, chair Outi Salo-Ahen

Konstantin Denessiouk, PhD (Åbo Akademi University): “Structural Bioinformatics: Building kits for ligand recognition in proteins”

Georgi Belogurov, PhD (University of Turku): “Molecular mechanisms in transcription”

Olli Pentikäinen, Prof., PhD (University of Turku): “Computer-dependent drug discovery wish-box: Single targets, tool compounds or control of signaling pathway?“

12.15-13.30 Lunch (included)

13.30-15 SESSION III, chair Mikko Metsä-Ketelä

Tilmann Weber, PhD (DTU Biosustain, Denmark): “In silico and experimental approaches to understand and engineer the biosynthesis of antibiotics”

David Fewer, PhD (University of Helsinki, Finland): “Genomic and transcriptomic insights into the secondary metabolites of a toxic bloom-forming cyanobacterium”

Sandra Castillo, PhD (VTT Technical Research Centre of Finland Ltd): “CoReCo: a platform for genome-scale metabolic model reconstruction”

15-15.15 Coffee break

15.15-16.45 SESSION IV, chair Pedro Puigbo

Satu Pekkala, PhD (Faculty of Sport and Health Sciences, University of Jyväskylä): “Gut microbes in metabolic disorders – from associations to underlying mechanisms”

Albert Pallejà, PhD (Clinical Microbiomics, University of Copenhagen): “Gut microbiome resilience and resistome analysis after a broad-spectrum antibiotic treatment”

Manu Tamminen, PhD (Department of Biology, University of Turku): “Using dropletbased single cell genomics to detect functional and spatial structuring of microbial communities”

16.45 Closing of the meeting

Get together with wine, cheese and biscuits (serving until 18.00)

CompLifeSci 1st Annual Meeting, 2016

DECEMBER 9th, 2016
9 am – 6 pm
Alvarium, Puutarhakatu 8, 20100 Turku, Finland
Registration needed

PROGRAMME
9-10.30 SESSION I, chair Tiina Salminen
Lari Lehtiö (University of Oulu): Structural Biology of ADP-ribosylation and discovery of chemical probes
Tomi Airenne (Åbo Akademi University): Structural studies on avidins: From native oddies to antidins
Mikko Metsä-Ketelä (University of Turku): Structure Based Engineering of Antibiotic Biosynthesis Enzymes

10.30-10.45 Coffee break

10.45-12.15 SESSION II, chair Ion Petre
Laura Elo-Uhlgren (University of Turku): Boosting prediction of disease and treatment risks
Andre S. Ribeiro (Tampere University of Technology): Modelling, Predicting, and Validating the Mechanics of a Gene Regulatory Mechanism
Eugen Czeizler (Åbo Akademi University and National Institute of Research and Development for Biological Sciences, Romania): DNA rendering of polyhedral meshes at the nano-scale

12.15-13.30 Lunch (included)

13.30-15 SESSION III, chair Tero Aittokallio
Juho Rousu (Aalto University): Machine Learning for Small Molecules
Tapio Pahikkala (University of Turku): Estimating AUC of Machine Learning Methods with Small Samples

15-15.15 Coffee break

15.15-16.45 SESSION IV, chair Riikka Lund
Johanna Lagensjö (Uppsala University): Sequencing and method development at the SNP&SEQ Technology Platform (NGI Sweden)
Gioele La Manno (Science for Life Laboratory and Karolinska Institutet): Molecular diversity of midbrain development: from cell type homologies to replacement therapies

16.45 Closing of the meeting

Get together

CompLifeSci Kick-off Meeting

JUNE 3rd, 2016
9 am – 1 pm
ICT Auditorium Beta, Joukahaisenkatu 3-5, Turku
PROGRAMME
Introduction: Ion Petre. 9:00 am

I SESSION: Molecular Methodologies
9:10 am – 9:50 am (5 minutes each group)
Finnish Microarray and Sequencing Centre and Biomedical Epigenomics (Riikka Lund Group)
Mobile DNA and Next-Generation Phylogenomics (Harri Savilahti and Pere Puigbò Groups)
Molecular Mechanisms of Transcription Georgiy Belogurov Group)
Epiproteomics: A top-down approach to gene activity modulation by proteins (Peter James Group)
Structural Studies of Proteins (Tassos Papageorgiou Group)
Structure-Based Drug Design (Anton Zavialov Group)
Antibiotic Biosynthesis Enzymes (Mikko Metsä-Ketelä and Jarmo Niemi Groups)
Tuning PET Imaging Performance of Biomolecules with Chemistry (Xiang-Guo Li Group)

Coffee break + Posters
09:50 am – 10:20 am

II SESSION: Computational Methodologies
10:20 am – 11:00 am (5 minutes each group)
Structural Bioinformatics Laboratory (Mark S. Johnson, Tiina A. Salminen, Outi Salo-Ahen and Jukka Lehtonen Groups)
Evolution and Adaptive Dynamics (Kalle Parvinen Group)
Data Mining and Modeling for Systems Biology and Pharmacology (Tero Aittokallio Group)
COSPHAR: Computational Systems Pharmacology (Jing Tang Group)
Computational Modeling and Simulation (Ion Petre Group)
Algorithms of Data Science (Tapio Pahikkala Group)
Turku BioNLP (Tapio Salakoski and Filip Ginter Groups)
Bioinformatics Software (Vladimir Rogojin Group)

Discussion & Closing remarks
11:00 am – 11:10 am

Lunch, Posters & Networking
11:15 am – 1:00 pm