News
New Publication: Saadat, Nies, Rousset, Ebenhöh
Our new review on "Thermodynamic limits and optimality of microbial growth" is now published! You can find it here
Mathematical modelling during the CEPLAS Friday
Dr. Anna Matuszyńska and Dr. Adélaïde Raguin will give talks after this year's CEPLAS General Assembly. Dr. Matuszyńska will talk about her recently launched DFG project on secondary metabolism of the glandular trichomes, whilst Dr. Raguin will give an overview of several project where she has used stochastic modelling to address biological questions, with the focus on modelling plant cell wall degradation. Talks are open to the public.
- Dr. Anna Matuszyńska, Quantitative and Theoretical Biology, HHU
- Title: "Cell Factories: the origin of high metabolic fluxes in glandular trichomes"
- Dr. Adélaïde Raguin, Quantitative and Theoretical Biology, HHU
- Title: "Plant cell wall degradation: a numerical modelling approach"
Location: HHU, Building 26.11, Lecture Hall 6E, The talks start at about 3pm.
New Publication: Dr Adélaïde Raguin
Mutation in the enzyme tRNA synthetase (aaRS) can lead to severe diseases including neurological disorders. In a new article our postdoc Dr. Adélaïde Raguin investigates with collaborators from University of Aberdeen the aetiology of such diseases by using sophisticated stochastic models combined with experimental data. See the article here!
Congratulations to Dr. Francesco Tacchino
We congratulate Dr. Francesco Tacchino, our former master student, for the successful defense of his PhD thesis at the university of Pavia.
New publication: Dr. Adélaïde Raguin & Prof. Dr. Oliver Ebenhöh
Starch his one of the most important plant-derived carbohydrates for human society. We use it as raw material in several industries and it is crucial for our daily diet. But have you ever wondered how this glucose polymer is synthesized in plants? Research is far from having a full understanding of this process. In a new review Dr. Adélaïde Raguin and Prof. Dr. Ebenhöh worked together with scientists from the ETH Zurich (Switzerland) and the John Innes Centre (UK) to explore as well as reflect possible theoretical and experimental approaches to broaden our knowledge about the synthesis of starch.
Check it out here
We welcome our new postdoc Dr. Rachel Denley-Bowers!
We welcome our new postdoc Dr. Rachel Denley-Bowers. As a scientist and member of the Cluster of Excellence in Plant Sciences (CEPLAS) with theoretical and experimental expertise she will work on diverse interesting topics in the field of plant related biology. We are happy to have her in our group and looking forward to many interesting discussions.
After completing her PhD about "the economic of stomatal development" at the University of Sheffield (PIs: Stuart Casson and Nick Monk), Dr. Rachel Denley-Bowers did her first postdoc position at the John Innes Center (one of the biggest plant science centers in the UK), where she was involved in elucidating the properties of starch and its food biotechnological apllications.
A nice end of the year: Two new preprints from our institute
Whether it is information encoded in the sequences of life or the question if microbes are thermodynamically optimised machines, we are interested in numerous biological topics. In two new reviews (preprints) several members of our group discuss interesting ideas and facts about fundamental principles behind biological systems. A nice end of the year!
Theory Seminar: Rachel Denley Bowers (13.12.19)
This Thursday our future postdoc Rachel Denley Bowers (currently at the John Innes Centre Norwich) is going to present her work on stomatal placements and potential cost in the model plant Arabidopsis thaliana. The title of her talk is: "Modelling plant metabolism and development". We are really looking forward to hear about her past research and are happy to welcome Rachel in our team.
Place and time as usual.
Theroy seminar: Rahmi Lale (19.12.19)
On Thursday the 19th of December Rhami Lale from the Norwegian University of Science and Technology is going to present the talk "Towards Rational Design of Promoters" during the Theory seminar.
New Publications!!!
From quantum mechanics to hidden patterns of natural variation in plants; the institute of Quantitatve and Theoretical Biology was involved in two new exiciting studies:
- Our paper on quantum mechanical models of the Q-cycle in the cytochrome b6f complex is now online: www.nature.com/articles/s41598-019-52842-x
- Our preprint on natural variations in the accumulation of aliphatic glucosinolates in Arabidopsis thaliana is now available on bioRXiv: https://www.biorxiv.org/content/10.1101/838227v1
Both papers were written in collaboration with former memebers of the QTB group. Dr. Antonella Succuro (currently University Bonn, Germany) a former particle physicist now concentrating on the complex laws of life and Dr. Suraj Sharma, a talented former PhD student now postdoc at the University of Tromsø.
QTB Annual Symposium
This last weekend we had our annual QTB symposium. It was a great time with a lot of scientific discussions, presentations and a ton of new ideas for current and future projects. We talked about possible workshops of time series analysis, how to combine modelling approaches of polymer biochemistry and genome-scale models, the ethical responsibilities of scientists to present their research to the public, and ideas for possible master or bachelor projects (If you are interested, write us an e-mail). This year we stayed at the Forsthaus Lahnquelle in Netphen, a hotel in the middle of nowhere with really delicious food and a cosy atmosphere.
Theory Seminar: Janani Ravichandran, Friday (20.09.2019)
This friday at 2pm we are going to have a theory seminar. Janani Ravichandran will talk about her work at the Institute of Mathematical Sciences, Chennai, India. Location: Room 22.07.00.033
Have a look at our research section :)
We updated our 
research area. Have a look and find out what our research is about. Each section includes a short description of the project and suggests scientific articles that could help you to learn more about the topic. If you are interest in one of our projects, please contact the person who is responsible (you will find contact information by clicking on the names ). We are eager to discuss our work an broaden our scientific network. Also students are welcome. If you want to know how we conduct our research, do not hesitate to ask and write us an e-mail.
New PhD student: Chilperic Armel Foko Kuate
We welcome our new PhD student Chilperic Armel Foko Kuate. As part of the PoLiMeR Marie Skłodowska-Curie Innovative Training Network he will investigate the role of lipids in humans by creating and validating sophisticated mathematical models of lipid synthesis and storage in the liver.
Nima Saadat held his first talk at an international conference
Our PhD student Nima Saadat held his first talk at an international conference (Metabolic Pathway Analysis (MPA) in Riga, Latvia), presenting work he and Dr. Ovidiu Popa conducted to elucidate the role of prophages in metabolic networks . The title of his presentation was "Impact of prophage encoded enzymes on the metabolic capacity of the hosts". He did a great job and we are all proud of him.
Do you know....
...that the institute of Quantitative and Theoretical Biology is very interdisciplinary. Our members have a diverse background and combine different field of science to do great research. This results in many interesting project ranging from plant biology (polymer biochemistry, photosynthesis, resource allocation, photoacclimation) over phage genomics and metabolic network reconstruction / modelling (scopes and reconstruction of non-model organism genome scale models) to investigations about mental diseases (collaboration with the Korthlab) and spinal cord injuries (PSINK see). Soon our research section will be updated and you can read all about it in more detail :)
Have a nice week and when you have any questions do not hesitate to ask!
Theory Seminar 18.07.2019: Pia Rose
After a long time we are going to have a theory seminar again. Pia Rose from the Humboldt University Berlin will introduce us to "mathematical models of heart-arrythmias".
It is a very interesting topic, so do not miss it! :)
Place and time as usual (22.07.00.033, this thursday 18.07.2019 at 11am)
Journal Club: Sascha Ollertz
In this Journal Club Sasscha Ollertz, a bachelor student in our group working on modelling amino acid synthesis, is the chair of our weekly journal club. He is going to present us a paper about viruses that could be used for producing electrical energy. You can find the paper here (not open access). The plan for upcoming papers in the journal club can be found here.
Journal Club: Meik Thiele
Due to a lack of time and holidays we had no journal club these last two weeks, but now it's back and Meik Thiele, a bachelor student working on metabolic scopes in genome scale models of cyanobacteria, was the first of the bachelor students who volunteered to present a paper :) He will tell us something about the "energetic cost of building a virus" (paper by Gita Mahmoudabadi, Ron Milo, and Rob Phillips. You can find the paper here).
PS: We now have a wiki site where you can find the planned journal club topics. If you are interested, check it out here.
First-time proposal by Dr. Matuszyńska has been funded
We have a great pleasure to inform that Dr. Matuszyńska has been granted three years funding by the Deutsche Forschungsgemeinschaft, to conduct an interdisciplinary project in a collaboration with Prof. Dr. Alain Tissier (IPB Halle). "iPHACTORY: Interdisziplinäre Untersuchung von photosynthetischen glanduläre Trichome als zelluläre Stoffwechselfabriken" proposes a combined multi-omics and modelling approach towards understanding trichome metabolism in tomato. Congratulations to Dr. Matuszyńska. We are looking forward to the first results.
More about the project soon.
Fascination of Plants Day 2019
As several times before the Institute of Quantitative and Theoretical Biology together with the Cluster of Excellence on Plant Sciences (Ceplas) organized the Fascination of Plants Day here at the Heinrich-Heine-University Duesseldorf. We invited students from different elementary schools (Duesseldorf and surrounding) to visit the HHU and learn about plants in several small experimental settings. Do plants breathe? Do they move? Why are they green? Can they shine or swim? All these questions are covered and will be explained.
We hope that this day will be great and that the students have as much fun as we have.
Open Postdoc Positions at the Institute of Qunatitative and Theoretical Biology
We have currently some postdoctoral positions free for applications. If you are interested check out our 
"Offene Stellen/ Open Positions" page
Journal Club: Marvin van Aalst (16.5.2019)
Now its Marvin's turn to present us an exciting paper in the journal club. The title of the paper he presents is: "A temporal shift in resource allocation facilitates flowering before leaf out and spring vessel maturation in precocious species" (by Jessica A. Savage). You can find the paper here
Echt oder Fake Tuesday 14.5.2019 Lecture Hall 5K
Tomorrow a few of our members will be part of "ECHT oder FAKE". It is an event where scientists from different disciplines present their topics in an easy to understand style but not everything they say is true. Therefore, it is the audience's task to figure out what is correct or not.
We are very excited and looking forward to an evening full of fun, interesting talks and science.
Oh.. and the person who can best figure out what is true or fake can win a prize ... fingers crossed :)
Theory Seminar: Wolfram Liebermeister ( Wednesday 08.05.2019, 11am)
Wolfram Liebermeister from the INRA Jouy-en-Josas will give a very interesting theory seminar with the title "Resource allocation in kinetic models of cell metabolism"
Guest: Wolfram Liebermeister
This week we have a guest at our Institute. Wolfram Liebermeister is a well known systems biologist, who focuses on control and optimal metabolic states in cells.
Journal Club: Prof. Dr. Oliver Ebenhöh
This time (Thursday 25-4-2019) our PI Prof. Dr. Oliver Ebenhöh is the chair of our Journal Club. He is going to present us a paper published by Yinan M. Bar-On, Rob Phillips and Ron Milo that attempts to give a census of the biomass on earth. You can find this very interesting paper here.
Counting cells
Journal Club: Dr. Ovidiu Popa
This Thursday Dr. Ovidiu Popa, a postdoc in our institute working on phage genetic elements in prokaryotic cells and the diversification in Arabidopsis thaliana populations, is going to present us a paper about the systematic discovery of antiphage defense systems in microbial pangenomes (here).
New PhD student Yvan Rousset
We welcome our new PhD student Yvan Rousset. He is part of the PoLiMeR network and is going to work on mathematical models of human diseases.
Theory Seminar: Valerii Sukhorukov
This Thursday in our Theory Seminar Valerii Sukhorukov is going to talk about a spatially resolved model of mitochondrial network and physiology.
And again Journal Club: Felix Risse 28.3.2019
This time Felix Risse, a master student focusing on the mathematical modelling of auxin pattern formation in plants, presents us a whole cell model originally proposed by Karr et al.. Please find the paper here.
New Paper: Balancing energy supply during photosynthesis – a theoretical perspective
GREAT NEWS! :The paper "Balancing energy supply during photosynthesis - a theoretical perspective" written by our postdoc Dr. Anna Matuszyńska, our phD student Nima Saadat and our head of institute Prof. Dr. Oliver Ebenhöh is now available. You can find the paper in the Journal Physiologia Plantarum - it is open access (Click here)
Journal Club: Nima Saadat
This Thursday Nima Saadat, a phD student in the institute working on genome scale models and the plastic consuming bacterial species Idonella sakaiensis , is going to present us a paper about diet induced changes of our gut microbiome. You can find the paper here.
Journal Club: Dr. Adélaïde Raguin
This Thursday Dr. Adélaïde Raguin, a postdoc in our institute working on stochastic models of starch and lignin formation and degradation, is going to present us a paper dealing with a quantitative description of actin networks and how these influence the lamellipodium motility in cells. You can find the paper here
A new paper from our institute is going to be published
GREAT NEWS! :The paper "Balancing energy supply during photosynthesis - a theoretical perspective" written by our postdoc Dr. Anna Matuszyńska, our phD student Nima Saadat and our head of institute Prof. Dr. Oliver Ebenhöh is going to be published in the Journal Physiologia Plantarum. The link will follow as soon as it is accessible.
Journal Club 7.3.2019
We will have our next Journal Club this Thursday (7.3.2019). Tim Nies a master student from our institute is going to talk about microbial communities and an extended MacArthur-Consumer-Resource-Model proposed by Marsland III et al.
You can find the paper here
First Journal Club
We will have our first Journal Club !!! Thomas Wenske, a master student in our institute working on phage genomics, is going to talk about the paper "Phage Therapy: Going Temperate?" by Rodrigo Monteiro et al., Cell 2018. You can find the paper here
Theory Seminar: Jürgen Schönborn
Jürgen Schönborn (Institute of Systems Biology of Lipid Metabolism at the Heinrich-Heine-University) will talk about Flux Balance Modelling in Drosophila larvae
A new paper on modelling microbial populations is published
Our paper on modelling emergent subpopulations of E.coli has been
published. Click here
Balancing energy supply during photosynthesis - a theoretical perspective
Our theoretical view of photosynthesis as a molecular economy supply-demand system has just been published on the BioRxiv. Hope to read it soon in the Special Issue on Photosynthesis of the Physiologia Plantarum.
First software paper on-line
We have released the first QTB software. The modelbase package is a free expandable Python package for building and analysing dynamic mathematical models of biological systems. Originally it was designed for the simulation of metabolic systems, but it can be used for virtually any deterministic chemical processes. We are proud that it is the first paper with two of our bachelor students as co-authors. Open access
Another Poster Prize goes to our Institute
Dr. Anna Matuszyńska has received the People's Choice Award for her poster presented during the second edition of the Science Polish Perspective Meetup in Berlin. Anna presented her work on the MeProPhot project, supported by the funds from the Strategischer Forschungsfonds (SFF).
Best Poster Prize for our PhD student
Our PhD student Nima Saadat has won the prize for the Best Poster Presentation during this year's International Study Group for Systems Biology (ISGSB) conference in Tromsø, Norway. Congratulations and many more successes on your way!
Plant-Rhizobia symbiosis paper out
Our paper on metabolic modelling of the interaction between plants and nitrogen fixing rhizobia is now published and freely available by open access: https://www.nature.com/articles/s41598-018-30884-x.pdf
Biochemical mechanisms driving rapid fluxes in C 4 photosynthesis
A preprint of our paper on drivers of the high metabolic fluxes in C4 photosynthesis is available on bioRXiv.
Two preprints available from our Lab this month
PoLiMeR: PhD student vacancies & website online
The website of the PoLiMeR project has launched: http://polimer-itn.eu
Find open PhD student positions here: polimer-itn.eu/vacancies/
Strategischer Forschungsfonds for Dr. Matuszyńska
Dr. Matuszyńska has been granted 10.000 € from the Strategic Research Fund, to start her own project MeProPhot: Data mining to investigate high Metabolic Productivity of Photosynthetic glandular trichomes. The project will be running from the 1st of July till the end of the 2018. Two Student Assistants (Wissenschaftliche Hilfskraft) will be employed to support this project, so if you are interested in trichome biology please monitor our News section for more details.
Our paper on modelling toggle switch is out
The work conducted in a collaboration with the researchers from the University of Glasgow has been published today in the Journal of The Royal Society Interface. Mathematical modelling has been used to design a robust one-input binary switch, which combines a transcriptional toggle switch with a DNA inversion switch. This combined circuit switches between the two states every time it receives a pulse of a single-input signal. Such genetic switches can be used in synthetic biology to encode memory and control gene expression and therefore the proposed switch is a promising candidate for further use as a basic element of binary counting devices. You can download the paper from the journal site.
BIO.NRW.academy. QTB meets Industry
Dr. Matuszyńska will give a talk during the BIO.NRW.academy, a full-day symposium on Tuesday, May 15 at Forschungszentrum Jülich. For the first time the BIO.NRW.academy invites together leading industry representatives and young scientists to present concrete questions of the industry and to get to know the current research at the junior level in the same field. It is an experiment from which the organisers expect a new dynamic in technology transfer in the life sciences in North Rhine-Westphalia and we are happy to be a part of it.
Our paper on modeling heat shock response in Chlamy is out
The work conducted by our alumni Dr. Magni and Dr. Succurro during their position at the Institute has been published today in the Journal of The Royal Society Interface. They studied the dynamics of heat shock response (HSR) in the photosynthetic model organism Chlamydomonas reinhardtii with a data-driven mathematical model of HSR. With their model, they demonstrate that the HSR of C. reinhardtii efficiently avoids the accumulation of misfolded proteins under conditions most likely to prevail in nature.
You can download the paper from the journal site.
On-line guest lecture at Ferdowsi University of Mashhad
Dr. Matuszyńska has been invited to give two lectures for systems biology PhD students at the F.U.M Agriculture Faculty Ferdowsi University of Mashhad. The first lecture will take place on the 1st of May and will focus on application of mathematical models in photosynthetic research. It is our first, of hopefully many, on-line lecturing experiences.
Our work on modelling phosphorus uptake in microalgae is published
Our paper on modelling phosphorus (P) uptake is finally out! The study of molecular mechanisms underlying P uptake and storage in microalgae has become recently of great interest. There is a critical need to practise P recovery from waste and establish a circular economy applicable to P resources. In our paper, we review phosphate models, which express the growth rate as a function of intra- and extracellular phosphorus content for better understanding of phosphate uptake and dynamics of phosphate pools.
The research was performed in a collaboration with Dr. Nedbal from the Forschungszentrum Jülich.
Date for MPA 2019 confirmed
The next MPA (Metabolic Pathway Analysis) meeting moves from Bozeman (USA) to Latvia! It will take place in Riga, between 12 - 16 Aug 2019, organised by Egils Stalidzans of the University of Latvia. The MPA conference series is one of the preeminent international meetings for the scientific community analysing the topological structure-function relationships of metabolic networks. The QTB Team regularly takes an active part in the meetings and you will definitely see some of us in Riga next year.
Dr. Popa discusses evolution in Venice
Dr. Ovidiu Popa is giving this week a talk at the Stochastic Models in Ecology and Evolutionary Biology (SMEEB 2018) workshop in Venice. His presentation entitled "Evolutionary Footprint in the Genome of Arabidopsis thaliana" will cover his newest results on the Arabidopsis project.
Tutorial lectures during the aSSB 2018
Next week, from 19th to 23rd of March 2018, Prof. Ebenhöh and Dr. Popa will give a tutorial lectures on basic concepts of mathematical modelling with Python, as a part of the programme of the aDvances in Systems and Synthetic Biology (aSSB) thematic research school. The school started in 2002 and it is the 16th edition, taking place in Évry. To read more about the school visit: https://assb.lri.fr/en/index.php
Full Professorship
Today, our Head of the Institute, Dr. Oliver Ebenhöh was appointed Professorship at the Faculty of Mathematics and Natural Sciences. The QTB Team celebrated together this well deserved achievement and wish great success with the new position.