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Department: Any ÅAU / Department of Information Technologies UTU / Department of Information Technology UTU / Department of Mathematics and Statistics UTU / Turku School of Economics, Institute of Information Systems Sciences

Research Unit: Any Algorithmics and Computational Intelligence Group (ACI) Biomathematics Research Unit (BIOMATH) Communication Systems (ComSys) Computational Biomodeling Laboratory (Combio Lab) Data Mining and Knowledge Management Laboratory Distributed Systems Laboratory (DS Lab) Embedded Computer and Electronic Systems (ECES) Embedded Systems Laboratory (ESLAB) FUNDIM, Fundamentals of Computing and Discrete Mathematics Institute for Advanced Management Systems Research (IAMSR) Learning and Reasoning Lab Software Construction Laboratorium Software Development Laboratory (SwDev) Software Engineering Laboratory (SE Lab) Turku BioNLP Group Turku Optimization Group (TOpGroup) UTU Information Systems Science (ISS)

Publication type: Any Monographs Edited books Edited special issues of journals Edited proceedings Articles in journals Articles in proceedings Chapters in edited books Ph.D. thesis Lic. thesis Technical reports

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Articles in journals (19):

• Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre, NetContrl4BioMed: A pipeline for biomedical data acquisition and analysis of network controllability. BMC Bioinformatics 19(7), 3–12, 2018.
• Vladimir Rogojin, Ion Petre, Large-Scale Executable Biology Using Rapid Integration of Computational Models. Computer Science Journal of Moldova 24(1 (70)), 118 – 135, 2016.
• Heidi Marjonen, Alejandra Sierra, Anna Nyman, Vladimir Rogojin, Olli Grohn, Anni-Maija Linden, Sampsa Hautaniemi, Nina Kaminen-Ahola, Early Maternal Alcohol Consumption Alters Hippocampal DNA Methylation, Gene Expression and Volume in a Mouse Model. Plos One 10(5), e0124931, 2015.
• Vladimir Rogojin, Ion Petre, The Structure of Elementary Strategies for Gene Assembly in Ciliates. Fundamenta Informaticae 137, 1–14, 2015.
• Ion Petre, Vladimir Rogojin, Dependency Relations Between Elementary Intramolecular Operations in Gene Assembly in Ciliates. Journal of Automata, Languages and Combinatorics 19(1-4), 265–277, 2014.
• Vladimir Rogojin, On Combinatorial Properties of Elementary Intramolecular Operations. Computer Science Journal of Moldova 22(3), 386–404, 2014.
• Riku Louhimo, Marko Laakso, Tuomas Heikkinen, Susanna Laitinen, Pekka Manninen, Vladimir Rogojin, Minna Miettinen, Carl Blomqvist, Jianjun Liu, Heli Nevanlinna, Sampsa Hautaniemi, Identification of Genetic Markers with Synergistic Survival Effect in Cancer. BMC Systems Biology 7(1), S2, 2013.
• Eugen Czeizler, Vladimir Rogojin, Ion Petre, The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 9(5), 1326–1337, 2012.
• Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre, Vladimir Rogojin, Directed Overlap-Inclusion Graphs as Representations of Ciliate Genes. Fundamenta Informaticae 110(1-4), 29–44, 2011.
• Miika Langille, Ion Petre, Vladimir Rogojin, Three Models for Gene Assembly in Ciliates: A Comparison. Computer Science Journal of Moldova 18(1), 1-26, 2010.
• Victor Mitrana, Ion Petre, Vladimir Rogojin, Accepting Splicing Systems. Theoretical Computer Science 411, 2414–2422, 2010.
• Artiom Alhazov, Ion Petre, Vladimir Rogojin, The Parallel Complexity of Signed Graphs: Decidability and an Improved Algorithm. Theoretical Computer Science , 2009.
• Vladimir Rogojin, Successful Elementary Gene Assembly Strategies. International Journal of Foundations of Computer Science to appear, 2009.
• Artiom Alhazov, Ion Petre, Vladimir Rogojin, Solutions to Computational Problems Through Gene Assembly. Natural computing 7(3), 385–401, 2008.
• Artiom Alhazov, Ion Petre, Vladimir Rogojin, Solutions to Computational Problems through Gene Assembly. Natural Computing 7(3), 385–401, 2008.
• Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg, Patterns of Simple Gene Assembly. Discrete applied mathematics 156(14), 2581–2597, 2008.
• Ion Petre, Vladimir Rogojin, Decision Problems for Shuffled Genes. Information and Computation 206(11), 1346–1352, 2008.
• Tseren-Onolt Ishdorj, Ion Petre, Vladimir Rogojin, Computational Power of Intramolecular Gene Assembly. International Journal of Foundations of Computer Science 18(5), 1123–1136, 2007.
• Tseren-onolt Ishdorj, Ion Petre, Vladimir Rogojin, Computational Power of Intramolecular Gene Assembly. International Journal of Foundations of Computer Science 18(5), 1123–1136, 2007.

Articles in proceedings (6):

• Vladimir Rogojin, Keivan Kazemi, Krishna Kanhaiya, Eugen Czeizler, Ion Petre, Automatic Discovery of Combined Drug Therapy. In: Andrea Bracciali, David Gilbert, Gilbert MacKenzie (Eds.), Thirteenth International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, University of Stirling, UK, 2016.
• Eugen Czeizler, Vladimir Rogojin, Ion Petre, The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response. In: F. Fages (Ed.), Proceedings of the 9th International Conference on Computational Methods in Systems Biology, 9-24, ACM, 2011.
• Miika Langille, Ion Petre, Vladimir Rogojin, Three Models for Gene Assembly in Ciliates: A Comparison. In: Proceedings of BIONETICS 2008, to appear, 2009.
• Artiom Alhazov, Ion Petre, Vladimir Rogojin, Solutions to Computational Problems Through Gene Assembly. In: Hao Yan Max Garzon (Ed.), DNA Computing, 13th International Meeting on DNA Computing, Lecture Notes in Computer Science 4848, 36–45, Springer Berlin, 2008.
• Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg, Simple Operations for Gene Assembly. In: Proceedings of the 11th International Meeting on DNA-based computers, Lecture Notes in Computer Science 3892, 96–111, Springer, 2006.
• Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg, Simple Operations for Gene Assembly. In: Alessandra Carbone, Niles A. Pierce (Eds.), Proceedings of 11th International Meeting on DNA Computing, DNA11, Lecture Notes in Computer Science, 96–111, Springer, 2005.

Chapters in edited books (2):

• Sergiu Ivanov, Vladimir Rogojin, Sepinoud Azimi, Ion Petre, WEBRSIM: A Web-Based Reaction Systems Simulator. In: Carmen Graciani, Agustín Riscos-Núñez, Gheorghe Păun, Grzegorz Rozenberg, Arto Salomaa (Eds.), Enjoying Natural Computing, 170–181, Springer, 2018.
• Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana Gratie, Bogdan Iancu, Nebiat Ibssa, Ion Petre, Vladimir Rogojin, Tolou Shadbahr, Fatemeh Shokri, An Excursion Through Quantitative Model Refinement. In: Grzegorz Rozenberg, Arto Salomaa, José M. Sempere, Claudio Zandron (Eds.), Membrane Computing, Lecture Notes in Computer Science 9504, 25–47, Springer, 2015.

Ph.D. thesis (1):

• Vladimir Rogojin, Gene Assembly in Stichotrichous Ciliates: Elementary Operations, Parallelism and Computation. TUCS Dissertations 117. Turku Centre for Computer Science, 2009.

Technical reports (10):

• Sergiu Ivanov, Vladimir Rogojin, Sepinoud Azimi, Ion Petre, WEBRSIM: A Web-Based Reaction Systems Simulator. TUCS Technical Reports 1195, TUCS, 2018.
• Charmi Panchal, Vladimir Rogojin, Generating the Logicome from Microarray Data. TUCS Technical Reports 1175, TUCS, 2017.
• Krishna Kanhaiya, Vladimir Rogojin, Keivan Kazemi, Eugen Czeizler, Ion Petre, NetControl4BioMed: A Pipeline for Biomedical Data Acquisition and Analysis of Network Controllability. TUCS Technical Reports 1163, TUCS, 2016.
• Vladimir Rogojin, Keivan Kazemi, Krishna Kanhaiya, Eugen Czeizler, Ion Petre, NetControl4BioMed – Automatic Discovery of Combined Drug Therapy. TUCS Technical Reports 1162, TUCS, 2016.
• Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana Gratie, Bogdan Iancu, Nebiat Ibssa, Ion Petre, Vladimir Rogojin, Tolou Shadbahr, Fatemeh Shokri, An Excursion Through Quantitative Model Refinement. TUCS Technical Reports 1150, Turku Centre for Computer Science (TUCS), 2015.
• Eugen Czeizler, Vladimir Rogojin, Ion Petre, The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response. TUCS Technical Reports 1041, Turku Centre for Computer Science, 2012.
• Sepinoud Azimi, Tero Harju, Miika Langille, Ion Petre, Vladimir Rogojin, Directed Overlap-Inclusion Graphs as Representations of Ciliate Genes. TUCS Technical Reports 1001, Turku Centre for Computer Science, 2011.
• Miika Langille, Ion Petre, Vladimir Rogojin, Three Models for Gene Assembly in Ciliates: a Comparison. TUCS Technical Reports 878, Turku Centre for Computer Science, 2008.
• Tseren-Onolt Ishdorj, Vladimir Rogojin, Ion Petre, Computational Power of Intramolecular Gene Assembly. TUCS Technical Reports 815, Turku Centre for Computer Science, 2007.
• Tero Harju, Ion Petre, Vladimir Rogojin, Grzegorz Rozenberg, Simple Operations for Gene Assembly. TUCS Technical Reports 757, Turku Centre for Computer Science, 2006.