news
Young researcher / PhD position available (29. 5. 2019)
The position of a young researcher / PhD student under the supervision of Prof. Dr. Miha Mraz is available in our group. See more at https://www.uni-lj.si/mma/mraz/2019052813330671/.Tanja Cvitanović Tomaš successfully defended her PhD thesis (3. 12. 2018)
Today, Tanja has successfully defended her PhD thesis entitled Analysis of System Disorders in Liver Metabolism with the SteatoNet Model. The thesis abstract is available here. Congratulations!
Hands-on tutorial at the 2nd Conference of the European Association of Systems Medicine (Utrecht, from 7. to 9. 11. 2018)
We presented our hands-on tutorial on object-oriented modelling of large-scale metabolic models at the 2nd Conference of the European Association of Systems Medicine, which was held in Utrecht (Holland) from 7. to 9. 11. 2018. We also participated at the conference with four poster presentations, describing Grohar, ViDis, iSymbiol and LiverSex computational model. The proceedings of the conference will be puslished in the Journal of Systems Medicine.
Initial state perturbations as a validation method for data-driven fuzzy models of cellular networks (21. 9. 2018)
The paper describing a methodology for the validation of data-driven fuzzy models has been published in BMC Bioinformatics. The paper is available here.Žiga Pušnik successfully defends his MSc thesis and joins our group (14. 9. 2018)
Žiga Pušnik has successfully defended his MSc thesis entitled Computational analysis of viable parameter spaces in high-dimensional dynamical models of biological systems (abstract) and will be joining our group as full time teaching assistant and PhD student. Congratulations!Invited lecture and posters presented at CFGBC scientific symposium (21. 6. 2018)
We presented our results at 13th CFGBC Scientific Symposium, which was held at the Medical faculty on June 20-21 (link). Our work was presented with an invited lecture about Grohar and automated visualisation of genome-scale metabolic models (abstract), and with two scientific posters, the first one describing liver metabolic models (abstract) and the second one describing models of sexual dimorphism of circadian clocks in mammals (abstract).
Computational modelling of liver metabolism and its applications in research and the clinics (20. 6. 2018)
The paper describing different experimental and computational models and their applications in hepatology was published as the first Feature Article in Acta Chimica Slovenica (ACSi). The paper was also featured on the cover of the latest ACSi issue. The paper is available here.
Semi-quantitative modeling of gene regulatory processes with unknown parameter values using fuzzy logic and Petri nets (27. 4. 2018)
The paper describing the computational modelling methodology that combines deterministic modelling with fuzzy logic and Petri nets was published in a special issue Advances in Biological processes and Petri nets (BioPPN) of the journal Fundamenta Informaticae (link).Mattia Petroni successfully defended his PhD thesis (23. 4. 2018)
Today, Mattia Petroni has successfully defended his PhD thesis entitled Computational methodology for enhanced sensitivity analysis of gene regulatory networks. The thesis is available here. Congratulations!
LiverSex accepted for publication (23. 3. 2018)
The paper describing the first large-scale liver metabolic model, which allows a detailed insight into the sex-dependent complex liver pathologies, has been accepted for publication in Frontiers of Physiology.
Grohar published (20. 2. 2018)
The paper describing the software for automated visualisation of genome-scale metabolic models was published today in the Journal of Computational Biology. You can read the draft of the paper here. The software is available at the BitBucket repository of Miha Moškon.
Lidija Magdevska awarded with Prešeren prize (5. 12. 2017)
Lidija Magdevska was awarded with Prešeren prize by the dean of the Faculty of Computer and Information science for her diploma thesis on the fuzzy logic modelling of MAPK signalling pathways (abstract). An interview with Lidija is available here (in Slovene).
Recognition as one of the best 10 research achievements of the University of Ljubljana in 2017 (4. 12. 2017)
The work Large-scale computational models of liver metabolism: how far from the clinics (link) was recognized as one of the best ten research achievements of the University of Ljubljana in 2017 (link). The work was prepared in the collaboration with the Faculty of Medicine, University of Ljubljana (prof. dr. Damjana Rozman and Tanja Cvitanović) and with the Saarland University Medical Center (prof. dr. Frank Lammert and dr. Matthias C. Reichert).
Lidija Magdevska attends SSBSS 2017 (17.7. - 21.7.2017)
Lidija Magdevska attended the 4th International Synthetic & Systems Biology Summer School (SSBSS 2017), which was held at the Robinson College, University of Cambridge (UK) from July 17 to July 21. She presented her work in a talk entitled Application of fuzzy temporal logic to biological systems modelling.
Jure Bordon successfully defended his PhD thesis (16. 2. 2017)
On February 16, 2017, Jure Bordon successfully defended his PhD thesis with the title Modelling simple biological switching systems using fuzzy logic and extended Petri nets. Congratulations!
Slovenian iGEM team winned the Best Foundational advance award at the iGEM jamboree (31. 10. 2016)
Slovenian iGEM team winned the Best Foundational advance award with the project Sonicell, which focused on the cellular mechanosensing and fast signalling. Computational modelling and computational support of the project were the main tasks of our student members, Lidija Magdevska and Žiga Pušnik. Miha Mraz and Miha Moškon also participated in the team as their advisors. You can read more about the project at the wiki of the Slovenian iGEM team 2016 (link). You can also find a brief description of the project here (in Slovenian language).
Hands-on tutorial at the 2nd SysBioMed Tutorial and the 1st Conference of the European Association of Systems Medicine (from 26. to 28. 10. 2016)
We participated at the 2nd SysBioMed Tutorial: Modelling and bioinformatics for personalised medicine with our hands-on tutorial Tackling liver disease: an object oriented modelling approach. The tutorials were organized as satellite events of the 1st Conference of the European Association of Systems Medicine (EASyM) which took place in Berlin from 26. to 28. 10. 2016. We also participated at the conference with the oral presentation SteatoNet model to investigate the gender component of liver related pathologies and the poster presentation Computational framework for the analysis of biological oscillators and its application to p53-Mdm2 interaction. You can read more about the conference in its proceedings (password: EASyMBerlin2016).
Invited workshop at the IBD4HEALTH summer school (4. 7. 2016)
We participated in the IBD4HEALTH summer school with the workshop Simulating dynamical responses of metabolic pathways with Object Oriented Modelling where we spoke about modelling of metabolic networks with Modelica and SysBio library.Participation in the iGEM 2016 Competition (17. 3. 2016)
It is now confirmed that two of our members, Lidija Magdevska and Žiga Pušnik, will participate in iGEM 2016 competition as members of Slovenian team, that will be led by prof. dr. Roman Jerala from the National Institute of Chemistry.
Visiting PhD student - Christiane Rennert (1.3.2016)
PhD student Christiane Rennert from the Institut für Biochemie, Medizinische Fakultät, Universität Leipzig, will be visiting our group at UL-FRI and Damjana Rozman's group at CFGBC from 1.3. to 1.6. 2016 with the support of CASyM Research Exchange Grant.Apply for a position in our group (1.2.2016)
If you are interested in working with us you can apply for a Marie Skłodowska-Curie Individual Fellowship with our group. More information about the position are available here and here. General information about the fellowships are available at here.Our member Manca Bizjak attends SSBSS 2015 (5.7. - 9.7.2015)
The second edition of the international Systems and Synthetic Biology Summer School was held in Taormina, Sicily (Italy), where several renown scientists and industrial leaders of the field presented their work. The event was attended by more than 250 students and researchers from 50 different countries. In a poster Computational approaches for quantitative modeling of gene regulatory networks with multiple transcription factor DNA binding site repeats Manca presented some of our group's present research.
Apply for a position in our group (20.05.2015)
If you are interested in working with us you can apply for a Marie Skłodowska-Curie Individual Fellowship with our group. More information available at http://ec.europa.eu/euraxess/index.cfm/jobs/jobDetails/34013324 and http://ec.europa.eu/euraxess/index.cfm/jobs/jobDetails/34013325.Discover our research topics (19.09.2014)
After changing the location the Computational Biology Group is again fully active in the fields of systems and synthetic biology. Discover our research topics!
New Computational Biology Group Headquarter! (01.08.2014)
Our new faculty location looks stunning. Can't wait to meet you in our new laboratories!
We are moving to a new location (11.06.2014)
The opening ceremony of the faculty's new premises took place last week (link). Moving to our new location is in progress...
Project proposal invitation for potential ERASynBio partners (08.04.2014)
We would like to invite all potential partners to join us at submitting a project proposal for ERASynBio research project call. ERASynBio 2nd joint call is available on this link and is a part of seventh framework program, aimed at development and coordination of Synthetic Biology in the European research area. We are looking for any partner or consortia interested in our research work as a Computational Biology group. Potential partners or consortia with complementary expertise to our research work (see Research and Publications tab) interested in joining us at submitting the proposal should contact prof. Miha Mraz.
Invitation for foreign students (19.3.2014)
We invite foreign students to enroll in the MSc or the PhD program at the University of Ljubljana, Faculty of Computer and Information Science. You will have a possibility to obtain MSc or PhD title from Computer and Information Science and expert knowledge on the topics presented here under the mentorship of members of our group. Potential candidates can get more information via e-mail miha.mraz@fri.uni-lj.si or on the following link for PhD program or the following link for MSc program.By joining our group, potential foreign students have the opportunity to apply for postgraduate study scholarship.
For more information about PhD study presentation click here. Call for enrolment into Doctoral Study Programmes at the University of Ljubljana is published here.
Annual ski trip to Golté (7.3.2014)
Our day off at the slopes of Golté.
Martin Stražar has been awarded with the prestigious University of Ljubljana Award Prešeren's prize (05.12.2013)
Martin Stražar has been awarded by the University of Ljubljana with the prestigious award Prešeren's prize for his notable work Parallel Evolutionary Algorithm for Knowledge Discovery Model of a Gene Regulatory Network, under the supervision of Miha Moškon and Miha Mraz.
Project proposal invitation for potential ERASynBio partners (03.07.2013)
We would like to invite all potential partners to join us at submitting a project proposal for ERASynBio research project call, which is a part of ERA-NET from seventh framework program and is aimed at development and coordination of Synthetic Biology in the European research area. We are looking for any partner or consortia interested in our research work as a Computational Biology group, described in this document. Potential partners or consortia with complementary expertise to our research work interested in joining us at submitting the proposal should use the contact provided in the linked document.
iGEM 2012 Slovenia team visited the Erasmus Intensive Programme (17.6.2013)
Members of the University of Ljubljana iGEM team 2012 Urban Bezeljak, Maja Somrak, Martin Stražar, Uroš Zupančič, Lucija Kadunc, Anja Golob are taking part in an Erasmus Intensive Programme "Modelling in Systems and Synthetic Biology" in Jelgava, Latvia from 9th to 22th June. The programme consists of a series of lectures and practicals, covering modelling approaches, techniques and available software. Courses are held in cooperation with system and synthetic biology groups from Latvia, Great Britain, Germany and Slovenia. The presentation regarding our team's iGEM project entitled "Synthetic gene Switches and networks. Installing synthetic networks in cells.", held by Mojca Benčina (National Institute of Chemistry of Slovenia) and Martin Stražar (University of Ljubljana) is scheduled on Thursday, 20th June.
Dr. Miha Moškon has been awarded by COBRA Exhange Programme (15.4.2013)
Dr. Miha Moškon will be able to make another visit to Synth-Bio group at the iSSB Evry, due to the awarded funding from COBRA Exchange Programme.
Annual ski trip to Velika Planina (22.3.2013)
Our day off at the slopes of Velika Planina.
Research visit at iSSB Evry, France (from 4.1.2013 to 10.4.2013)
Dr. Miha Moškon has been on a research visit at the University of Evry 
at the institute of Systems and Synthetic Biology (iSSB) from 4.1.2013 to 10.4.2013. Miha was a visiting researcher at Synth-Bio group which is lead by prof. Alfonso Jaramillo.
Invitation for foreign students (2.1.2013)
We invite foreign students to enroll in the MSc or the PhD program at the University of Ljubljana, Faculty of Computer and Information Science. You will have a possibility to obtain MSc or PhD title from Computer and Information Science and expert knowledge on the topics presented here under the mentorship of members of our group. Potential candidates can get more information via e-mail miha.mraz@fri.uni-lj.si or on the following link for PhD program or the following link for MSc program.By joining our group, potential foreign students have the opportunity to apply for postgraduate study scholarship.
For more information about scholarship for postgraduate study of nationals of Egypt and Tunisia for the year 2013, click here.
Our group member Jure Bordon attends Winter Simulation Conference 2012 in Berlin and visits Brandenburg University of Technology in Cottbus (12.12.2012)
Earlier in November we contacted prof.dr.Monika Heiner, head of Data Structures and Software Dependability group from Brandenburg University of Technology in Cottbus, with a suggestion of adding certain functionalities to their already powerful tool SNOOPY used for Petri Net modeling and simulation. During his stay in Germany, our group member Jure attended Winter Simulation Conference 2012 in Berlin where he met prof. dr. Heiner. On his last day in Germany he also visited the rest of her group in Cottbus where he gave a short talk about his research work and discussed possibilities of working together on SNOOPY.
iGEM 2012 team Slovenia is 1. runner up at iGEM World Championship (5.11.2012).
Held at Massachusetts Institute of Technology (MIT) in Cambridge (MA), our iGEM team reached the finals and the second absolute position among 190 iGEM 2012 teams confirming as well as one of the best team in the world. Slovenian team was also awarded with best Health and Medicine prize, with best Model prize and for the best Wiki page (official results). Congratulations to all team members, especially to Maja, Dušan and Martin!
iGEM 2012 team Slovenia is among three European finalists (7.10.2012)
European iGEM 2012 Jamboree is now officially over. Slovenian team was chosen as one of the three finalists among 54 teams from the whole Europe and was awarded for the best wiki presentation (official results). Congratulations to our team members for their excellent performance.
Slovenian team is lead by professor Roman Jerala and is comprised of the following members: Urban Bezeljak (Biochemistry), Anja Golob (Biotechnology), Miha Jerala (Medicine), Lucija Kadunc (Biotechnology), Zala Lužnik (Medicine), Fedja Pavlovec (Medicine), Boštjan Pirš (Medicine), Maja Somrak (Computer Science), Martin Stražar (Computer Science), Dušan Vučko (Computer Science) and Uroš Zupančič (Biotechnology).
iGEM 2012 team Slovenia wiki is now officially open (27.9.2012)
The wiki presentation of the work that will be presented on the Regional Jamboree in Amsterdam is now officially available on http://2012.igem.org/Team:Slovenia. Congratulations to our team members for their outstanding work. Well done Maja, Dušan and Martin.
Invitation for foreign students (20.6.2012)
We invite foreign students to enroll in the MSc or the PhD program at the University of Ljubljana, Faculty of Computer and Information Science. You will have a possibility to obtain MSc or PhD title from Computer and Information Science and expert knowledge on the topics presented here under the mentorship of members of our group. Potential candidates can get more information via e-mail miha.mraz@fri.uni-lj.si or on the following link for PhD program or the following link for MSc program.By joining our group, potential foreign students have the opportunity to apply for postgraduate study scholarship.
For more information about scholarship for postgraduate study of nationals of Western Balkans in Slovenia for the year 2012, click here. Applications for the award of scholarships to the nationals of the Arab Republic of Egypt and the Tunisian Republic can apply here.
Visit of J. Craig Venter Institute (20.4.2012)
One of our iGEM 2012 team members (Maja Somrak) visited J. Craig Venter Institute in San Diego, where the institute staff presented their work with emphasis on current projects.
iGEM 2012 (10.4.2012)
Our members (Maja Somrak, Martin Stražar and Dušan Vučko as students and Miha Mraz, Nikolaj Zimic and Miha Moškon as mentors) will participate in the synthetic biology competition iGEM 2012 as a part of team Slovenia led by professor Roman Jerala.
Profesor Mraz visits Peking University (20.6.2011)
Professor Mraz visited the Peking University iGEM 2011 team and gave a talk about the work of our group.
iGEM 2010 - winners announced (8.11.2010)
Team Slovenia is the Winner of the BioBrick Trophy.
iGEM 2010 (5.4.2010)
Our members (Jure Bordon, Mattia Petroni, Rok Češnovar and Rok Pustoslemšek as students and Miha Mraz, Nikolaj Zimic and Miha Moškon as mentors) will participate in the synthetic biology competition iGEM 2010 as a part of team Slovenia led by professor Roman Jerala.