Genome-scale brain metabolic networks as scaffolds for mapping disease-related alterations


Our recent webinar on June 11st was given by Assoc. Prof. Tunahan Cakir from Gebze Technical University. In this session with high attendance, systems-wide analysis of cell metabolism and modeling networks at genome-scale were major topics. Focuses through the presentation were on 1) metabolism and interactions between neuron-astrocyte, two essential cell types in the brain, 2) mapping transcriptome data for neurodegenerative diseases using a graph-based approach termed reporter pathways, 3) constraint-based modelling of brain metabolic networks and flux balance analysis (FBA) for the metabolic evaluation of brain tumors.

If you missed the live session or you may want to watch it again, it is on the Youtube:  https://youtu.be/z8MV-eu65zI

We appreciate this enlightening webinar and thank Dr.Cakir on behalf of our community!!



Evolutionary genomics for conservation and biodiversity – Ismail Saglam


We had our last webinar on April 16th, given by Dr. Ismail Saglam from Hacettepe University. In this interesting session, we get to know more about evolutionary genomics, and how computational approaches can help us to study conservation and biodiversity. Ismail summarised common methods and questions in the area in general, and he also gave an insight into his research, done in collaboration with different labs in Turkey and US. In particular, he explained how genomics can help 1) to test different evolutionary models and understand the forces shaping the diversity, 2) to discover the evolutionary history of species to set conservation strategies, and 3) to understand the evolutionary basis of adaptation.

One of the most interesting comments for me was towards to the end, when he referred evolutionary genomics as an applied field. Most of us tend to consider evolutionary thinking as more of a philosophical way of approaching a biological phenomenon but no – he mentioned how most of the global problems like chronic complex diseases can be explained by the mismatch between phenotype and environment, and could be re-formulated as a question for evolutionary genomics. Although it was just a comment he shared at the end of presentation, I think it was an important one which made me rethink the importance of evolutionary biology education and the current funding schemes..

If you missed the live session, don’t worry – you can still watch it on youtube: https://youtu.be/PzRpvKu8GMk

We appreciate this enlightening webinar and thank Ismail on behalf of our community!!

An easy way to understand a study: Student Presentations

Turkce icin tiklayin!


First student webinar of this year, which held on March 12th has presented by Melike Donertas. Ageing as one of the inevitable biological process was focus of the presentation named “Gene Expression-Based Drug Repurposing to Target Ageing “. During almost two hours, Melike presented not only the methodology of the study for drug repurposing, but also a general overview of ageing studies, until now. Simultaneously, all applicants contributed the presentation by questions and suggestions.

Brief explanation of the study by herself as follows: “Ageing is the largest risk factor for a variety of non-communicable diseases. Previous studies on model organisms suggest life- and health-span can be modulated through genetic and chemical perturbations. In this study, instead of a target-centric approach, we adopt a systems level drug repurposing methodology to discover drugs that can combat human ageing. Using multiple publicly available gene expression datasets, we first identify the expression changes that can characterize ageing in human brain. We then compare these changes in gene expression with the drug induced expression changes to find drugs that are likely to modulate ageing. The drugs that we identified included significant number of already identified pro-longevity drugs, indicating that the method can discover de novo drugs that meliorate ageing. The approach has the advantages that, by using data from human brain ageing data it focuses on processes relevant in human ageing and that it is unbiased, making it possible to discover new targets for ageing studies.”

If you feel curious about this study, you may find the link here.

The First Webinar of 2018- Integrative Modeling of Biomolecular Complexes

Turkce icin tiklayin!

We are very excited to revive our webinar series again! The first webinar of this year was given by Assoc. Prof. Ezgi Karaca from Izmir Biomedicine and Genome Center on January 31st. She mentioned about the main techniques in structural biology, data types and how integrate the experimental structural biology data into biomolecular simulations. In particular, she raised our curiosity in computational structural biology by mentioning about “docking” program HADDOCK, and her latest work on “integrative modeling” which was published on Nature Methods. Around 100 people registered our webinar. Our aim is to increase this number and reach more people in soon!

We would like to thank Dr. Ezgi Karaca for this extensive informative seminar and supporting our webinar series! If you also interested in computational structural biology, you can follow this link: https://www.bigmarker.com/bioinfonet/EzgiKaraca

We are looking forward our next webinar!

Call for contributions

Thanks to our community members and colleagues from ISCB RSG Turkey, BioInfoNet Project is growing day by day. We now have 172 members signed up to our Biomarker community and we have proudly organised 3 important webinars! It is good to know that there will be more ahead!

At this stage, we felt that we are ready to make calls for presentations for both professionals and students.

We are proud to have the set up to invite you to organise your dream webinar with us. If you like the idea, please fill the appropriate form at presentation calls page.

We are looking forward to your contributions. Thank you!

W#2 Computational Metagenomics on the Species Level

After Dr. Can’s (METU, Ankara – Turkey) talk, our next guest was from Robert Koch Institute, Berlin, Germany. Dr. Bernhard Y Renard heads the bioinformatics research group at Robert Koch Institute, the German national institute for infectious disease in Berlin, Germany and is an adjunct senior lecturer (Privatdozent) at the department of mathematics and computer science at Freie Universität Berlin.

Dr. Renard’s talk was on computational metagenomics on the species level. You can find the recording of the webinar here on our community page and here on youtube.

My highlight from this presentation is that metagenomics has a whole new set of constraints with data analysis. I could not capture a saying from this one 🙂 but I can say that I am far more interested in computational metagenomics than ever before.

Dr. Renard mentioned to be very happy to meet us and appreciated the project. Participants were also eager to have the slides 🙂

Hope to see Dr. Renard as a guest again in the future!

W#1 Reconstruction of Signaling Network Topology from Steady State and Dynamic Perturbation Data

The first webinar of BioInfoNet series was given by Dr. Tolga Can from METU (Middle East Technical University), Ankara, Turkey. METU is one of the oldest, biggest and best universities in Turkey. Dr. Can has a bioinformatics lab. in the Computer Science Department.

His talk was on reconstruction of signaling networks from steady state perturbation data. You can find the recording of the webinar here on our community page and here on youtube.

My take-home message from this webinar (apart from the scientific part) is Dr. Can’s these words: “As computer scientists we do not say “OK this is a very difficult problem, we can not do that”. We offer a solution.”. This was something I have “noticed” before but never mentioned aloud as a statistician. When Dr. Can solidly stated this, I got it. Eventhough this was a statement about methodology, this sentence is now like a saying to me and I am trying to apply this insight to my everyday work.

Dr. Can and all participants mentioned that they enjoyed the webinar. Hope to see Dr. Can as a guest for many times in the future!