User:AndreaS

Publications

• Andrea Sackmann, Discrete Modeling; Chapter V in: I. Koch, F. Schreiber, W. Reisig (Ed.), Modeling in systems biology: the Petri net approach; to appear in Springer.
• Andrea Sackmann, Dorota Formanowicz, Piotr Formanowicz, Jacek Blazewicz, New insights into the human body iron metabolism analyzed by a Petri net based approach, Biosystems (2009) 96(1): 104-113.
• Jacek Blazewicz, Dorota Formanowicz, Piotr Formanowicz, Andrea Sackmann, Michal Sajkowski, Modeling the process of human body iron homeostasis using a variant of timed Petri nets, Discrete Applied Mathematics (2009) 157(10): 2221-2231.

Conferences

• Mini EURO Conference on Computational Biology, Bioinformatics and Medicine, Rome, Italy, September 15-17, 2008
  A DNA based algorithm for calculating the maxflow in networks, talk.
• First Convention of the Polish Bioinformatics Society 2008, Jadwisin, Poland, October 3-5, 2008
  A DNA computing algorithm for calculating the maxflow in networks, talk.
• Fifth Bioptrain workshop, Florence, Italy, June 10-12, 2009
  A DNA computing algorithm calculating the max flow in networks, talk.

(Pending) Publications

• Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Björn H. Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch, Modularization of biochemical networks based on classification of Petri net t-invariants, BMC Bioinformatics (2008) 9: 90.
• Andrea Sackmann, Kristelle Brown, Piotr Formanowicz, Jonathan M. Garibaldi, Kevin Morgan, Jacek Blazewicz, A DNA algorithm calculating the value of max flow in a network, submitted.

Talks

• DNA-based algorithm for calculating the max-flow in networks
  2007-12-04, research seminar of the Institute of Computing Science (Poznan University of Technology)
• DNA-based algorithm for calculating the max-flow in networks
  2008-08-08, research seminar of the School of Molecular Medical Sciences (University of Nottingham)

Conferences

• COMBI '07: V Computational Biology Workshop, Uniejow, Poland, October 5-6, 2007
  Modeling the human body iron homeostasis using a variant of timed Petri nets, talk.
• RECOMB2008, Singapore, March 30 - April 2, 2008
  A DNA based algorithm for calculating the maxflow in networks, poster.
• Bioinformatics 2008 Conference, Warsaw, Poland, April 24 - 27, 2008
  A DNA based algorithm for calculating the maxflow in networks, poster.
• EurOPT2008: EURO Mini Conference, Neringa, Lithuania, May 20-23, 2008
  A DNA based algorithm for calculating the max-flow in networks, talk.

(Pending) Publications

• Andrea Sackmann, Dorota Formanowicz, Piotr Formanowicz, Ina Koch, Jacek Blazewicz, An analysis of the Petri net based model of the human body iron homeostasis process, Computational Biology and Chemistry (2007) 31(1): 1-10.
• Dorota Formanowicz, Andrea Sackmann, Piotr Formanowicz, Jacek Blazewicz, Petri net based model of the body iron homeostasis, Journal of Biomedical Informatics (2007) 40(5): 476-485.
• Dorota Formanowicz, Andrea Sackmann, Piotr Formanowicz, Jacek Blazewicz, Some aspects of the anemia of chronic disorders modeled and verified by Petri net based approach, submitted.

Conferences

• Workshop on Networks in Computational Biology, Ankara, Turkey, September 10-12, 2006
  Modeling body iron homeostasis using Petri nets, talk.
• 1st Winter School on Systems Biology for Medical Applications, Puerto de la Cruz, Tenerife, Spain, February 27 - March 2, 2007
  Modeling the human body iron homeostasis with Petri nets, poster.
• EURO-CBBM Workshop on OR in Computational Biology, Bioinformatics, and Medicine, Prague, Czech Republic, July 8, 2007
  A DNA Computing algorithm for calculating the max flow in networks, talk.
• EURO XXII, Prague, Czech Republic, July 9 - July 11, 2007.

Publication

• Andrea Sackmann, Monika Heiner, Ina Koch, Application of Petri net based analysis techniques to signal transduction pathways, BMC Bioinformatics (2006) 7: 482.

Talks

• Modelling signal transduction pathways using Petri nets
  2005-09-09, research seminar of the Institute of Computing Science (Poznan University of Technology)
• Analysis of Petri net based models
  2005-12-20, research seminar of the Institute of Computing Science (Poznan University of Technology)
• On some aspects of DNA Computing
  2006-06-06, research seminar of the Institute of Computing Science (Poznan University of Technology)

Posts

• Research fellow / training & knowledge transfer officer, University of Nottingham, March 16 - June 15, 2009.
• Research assistant, Leibniz Institute of Plant Genetics and Crop Plant Research, April 1 - August 31, 2009.

Fellowship meetings

• BIOPTRAIN meeting, Innsbruck, Austria, January 12, 2009
• BIOPTRAIN workshop, Florence, Italy, June 10-12, 2009

Teaching activity

• Lecture about DNA Computing for undergraduates, May 18, 2009.

Visits abroad

• University of Nottingham, October 7 - October 23, 2008.

Cooperations

• Linda Fiaschi, University of Nottingham, Nottingham/UK

Courses

• Research seminars of the Laboratory of Theory of Algorithms and Programming Systems, Institute of Computing Science (Poznan University of Technology)

Communication skills

• Polish language course, Adam Mickiewicz University, Poznan

PhD

• Economy exam June 18, 2008.
• Operational Research exam June 23, 2008.
• English exam August 26, 2008.
• Thesis Network algorithms and bioinformatics problems (Algorytmy sieciowe w bioinformatyce)
  defended September 29, 2008. Supervisor: Jacek Błażewicz. Referees: Andrzej Świerniak, Silesian University of Technology, Gliwice/Poland; Marta Kasprzak, Poznan University of Technology.

Teaching activity

• Guiding an undergraduate in writing his Master thesis about DNA Computing (defended October 2008).

Visits abroad

• University of Nottingham, February 14 - March 25, 2008.
• University of Nottingham, April 8 - April 17, 2008.
• University of Nottingham, July 5 - August 9, 2008.

Cooperations

• Kristelle Brown, Kevin Morgan and Jon Garibaldi, University of Nottingham, Nottingham/UK

Courses

• Time management workshop, Tempus, 2007-09-15, Karchow, Germany
• Scheduling for parallel processing, Institute of Computing Science (Poznan University of Technology)
• Development directions of metacheuristic algorithms, Institute of Computing Science (Poznan University of Technology)
• Research seminars of the Laboratory of Theory of Algorithms and Programming Systems, Institute of Computing Science (Poznan University of Technology)

Communication skills

• Polish language course, Adam Mickiewicz University, Poznan

Cooperations

• Eva Grafahrend-Belau, Björn H. Junker and Falk Schreiber, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben/Germany
• Michał Sajkowski, Poznan University of Technology, Poznan/Poland

Courses

• Type Systems for Programming Languages, Institute of Computing Science (Poznan University of Technology)
• Advanced Techniques in Pattern Recognition, Institute of Computing Science (Poznan University of Technology)
• Research seminars of the Laboratory of Theory of Algorithms and Programming Systems, Institute of Computing Science (Poznan University of Technology)

Communication skills

• Polish language course, Poznan University of Technology

Cooperations

• Dorota Formanowicz, Poznan University of Medical Sciences, Poznan/Poland
• Ina Koch, Max Planck Institute for Molecular Genetics, Berlin/Germany
• Monika Heiner, Brandenburg University of Technology, Cottbus/Germany

Courses

• Advanced Informatics Systems, Institute of Computing Science (Poznan University of Technology)
• Preference Modelling and Decision Support, Institute of Computing Science (Poznan University of Technology)
• Scheduling Theory, Institute of Computing Science (Poznan University of Technology)
• Topics in Artificial Intelligence, Institute of Computing Science (Poznan University of Technology)
• Research seminars of the Laboratory of Theory of Algorithms and Programming Systems, Institute of Computing Science (Poznan University of Technology)

Communication skills

• Polish language course, Poznan University of Technology