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COMPROC Computational processes in living cells

  • Computational Biomodelling Laboratory
  • Projects
  • COMPROC
Academy of Finland, 2005 — 2010

Ciliates are an ancient group of organisms (about 2.5 billion years old), often classified as the most complex unicellular organisms on Earth. This family includes the fastest living form on Earth (Strombidium), as well as some unicellular organisms with digestive systems almost as complex as ours (Paramecium). A phenomenon unique to ciliates is the presence of two kinds of functional nuclei in the same cell: a micronucleus and a macronucleus. The macronucleus is the household nucleus that provides the RNA transcripts for producing proteins, while the micronucleus is activated only in the process of sexual reproduction, where at some stage the genome of the micronucleus gets transformed into the genome of the macronucleus in the process called gene assembly - this is the most involved process of DNA manipulation known in Nature !

The process of gene assembly has the attention of the Biocomputing community for several years already. It is by now clear that the process of gene assembly in ciliates is highly computational: it turns out that ciliates "know" one of the basic data structures of Computer Science - the linked list - and use it in a very elegant pattern matching manner in the process of gene assembly! We are investigating a set of three molecular operations that accomplishes the gene assembly through the "fold and recombine" paradigm. We introduced the mathematical model of pointer reduction systems to formalize the micronuclear gene patterns (through permutations, strings and graphs) and the gene assembly process. Our investigation of these systems resulted in a uniform explanation of all known experimental results concerning gene assembly in ciliates.

Project webpage: http://combio.abo.fi/projects/gene_assembly.php

People

Ion Petre Leader
Ion Petre, Professor
ion.petre@abo.fi
+358 (0)2 215 3361
Room: 341G
Sepinoud Azimi PhD student
Sepinoud Azimi
sepinoud.azimi@abo.fi
+358 (0)2 215 3315
Room: 340B

Location of room

Partners

  • Tero Harju (University of Turku)
  • Grzegorz Rozenberg (University of Leiden)

Current projects

  • Finnish Grid and Cloud Infrastructure, stage 2: enabling datascience (FGCI)
    Academy of Finland , 2018 – 2019
  • Efficient Stream Computing by Fitting Computations to Cores (ESC)
    Academy of Finland, 2017 – 2021
  • Development of High-Assured Autonomous Systems (AutoSys)
    Nordplus, 2017 – 2018
  • MegaModelling at Runtime - scalable model-based framework for continuous development and runtime validation of complex systems (MegaM@Rt2)
    ECSEL JU, Tekes, 2017 – 2020
  • Towards a More Advanced Loaning and Reading Culture. A Study, Based on Digital Material, of Contemporary Finnish Loaning and Reading Habits (LibDat)
    Academy of Finland, 2017 – 2021
  • Novel Predictive Analytics Technologies for Future Maintenance Business (OPENS)
    Tekes, 2016 – 2019
  • High-performance geoscientific computing in multi-scale mineral potential studies (Gecco)
    Academy of Finland, 2015 – 2019

Completed projects

  • Network Pharmacology: drug re-purposing and discovery of multi-drug therapies by analytical approaches (NetPharma)
    TEKES, 2016 – 2016
  • Modular Interoperability for Healthcare Cyber-Physical Systems (INTERSYS)
    Academy of Finland, 2016 – 2017
  • Efficient Distributed Media Transcoding Platforms (EASYTRANS)
    Tekes - New knowledge and business from research ideas, 2015 – 2016
  • N4S (N4S)
    Tekes, DIGILE, 2014 – 2016
  • Adaptive Integrated Formal Design of Safety-Critical Systems (ADVICeS)
    Academy of Finland, 2013 – 2017
  • Synthetic controllability of biological networks through understanding and engineering their control elements (NetControl)
    Academy of Finland / Synthetic Biology Programme (FinSynBio), 2013 – 2017
  • Quantitative model refinement (QuantRef)
    Academy of Finland, 2013 – 2017
  • Parallel Acceleration (ParallaX)
    2013 – 2016
  • High-quality Measurement Infrastructure for Future Resilient Control Systems (FResCo)
    Academy of Finland, 2013 – 2015
  • Joint curriculum development for doctoral studies in eBusiness (KURRI)
    CIMO, 2012 – 2014
  • Practical Applications of Model-based technologies to continuous integration & testing methodologies (PAM)
    TEKES, 2012 – 2015
  • Agent Based Management of Embedded Data Reserve (AMEBA)
    2012 – 2014
  • DIGILE Digital Services - SME Services (Digital Services )
    Tekes, 2012 – 2014
  • Collaborative Research into Exascale Systemware, Tools and Applications (CRESTA)
    European Community, 2011 – 2014
  • Dataflow ORiented Automated Design tOolchain (DORADO)
    2011 – 2015
  • E-Math (E-Math)
    2011 – 2013
  • Energy Efficient Digital Hydraulic Hybrid Machines (eDiHy)
    Academy of Finland, 2011 – 2014
  • Regenerative hydraulic hybrid with digi-valve and multi chamber cylinder technology (EFFIMA-Digihybrid)
    2011 – 2014
  • IMPEd (IMPEd)
    2011 – 2014
  • Autonomic software-intensive systems: foundations of safety and resilience (ASSURE)
    Academy of Finland, 2010 – 2013
  • FCEP (CLEEN)
    2010 – 2014
  • Cloud Software Program (Cloud)
    2010 – 2013
  • DISCO (DISCO)
    2010 – 2013
  • Enabling Next GeneratIon NEtworks for broadcast Services (ENGINES)
    TEKES, 2010 – 2012
  • Work and Leadership in a Liminal Space: Projects and Innovations (LIMINARI)
    TEKES, 2010 – 2013
  • Reduced Certification Costs Using Trusted Multi-core Platforms (Recomp)
    Tekes and ARTEMIS-JU, 2010 – 2013
  • SimlTER (SimlTER)
    Academy of Finland, 2010 – 2013
  • TeachEd (TeachEd)
    Finnish National Board of Education, 2010 – 2014
  • Digital Microhydraulics (EFFIMA-DiHy)
    2009 – 2014
  • Validation of Many Models in Many Languages (VAMOLA)
    2009 – 2011
  • Industrial deployment of system engineering methods providing high dependability and productivity (DEPLOY)
    2008 – 2012
  • Device and Interoperability and Ecosystems (DIEM)
    2008 – 2013
  • Distributed Jointly Operating Networks (DIJON)
    Academy of Finland, 2008 – 2011
  • EU Fusion fOR Iter Applications (EUFORIA)
    European Union (FP7), 2008 – 2009
  • Computational modeling of the eukaryotic heat shock response (HeatShock)
    Academy of Finland, 2008 – 2010
  • Titan (Titan)
    2008 – 2011
  • LightweIght formal Methods for distributed component-based Embedded systems (LIME)
    Tekes, 2007 – 2009
  • Deployment of Model-Based Technologies to Industrial Testing (D-Mint)
    ITEA2, Tekes, 2007 – 2010
  • Broadcasting for the 21st Century (B21C)
    2007 – 2009
  • VIBRA (VIBRA)
    2007 – 2009
  • Power and Energy Consumption Testing for NoTA Devices (PECOS)
    Subcontracted from Nokia Research Center, 2006 – 2008
  • Efficient Feature Combination (EFCO)
    2006 – 2008
  • Computational processes in living cells (COMPROC)
    Academy of Finland, 2005 – 2010
  • Improving Transient Control and Energy Efficiency by digital hydraulics (ITCEE)
    TEKES, KITARA-programme, 2005 – 2008
  • Louhi (Louhi)
    Tekes, 2005 – 2008
  • MDA In Co-design ArchitectureS (MICAS)
    Subcontracted by Nokia Research Center, Helsinki, 2004 – 2005
  • Rigorous Open Development Environment for Complex Systems (RODIN)
    EC IST FP6 framework, 2004 – 2007
  • Architecture-driven software engineering for embedded systems (ADSEES)
    TEKES (The National Technology Agency), 2001 – 2003
  • Asynchronous Circuit Design Working Group (ACID-WG)
    EU, 2000 – 2004
  • Asynchronous design of DSP architectures (Asynkron)
    The Academy of Finland, 2000 – 2002
  • Methodologies and Technologies for Industrial Strength Systems Engineering (MATISSE)
    EU FP5-project, 2000 – 2003

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Contact

Phone: +358 (0)2 215 4475
Fax: +358 (0)2 251 5557

Visiting address

Åbo Akademi, Agora
Informationsteknologi
Vattenborgsvägen 3
20500 Åbo

Postal address

Åbo Akademi
Informationsteknologi
Agora
Domkyrkotorget 3
20500 Åbo

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