January 2019


Aspects of High Throughput Molecular Data Analysis


Arif Harmancı


The molecular information acquisition is gaining strong presence in every aspect of life. Much of this stems from the decreasing cost of DNA sequencing and computational power. Coupled with the data, computational methods are generating waves of interesting results. Interestingly, we are far from making sense of the extremely complicated molecular data. The more data we generate, the more we realize the complexity of the cellular information processing. These developments bring so many exciting opportunities and challenges. In this presentation, I will review different aspects of how triage of genomics, transcriptomics, epigenetics is changing the way we understand how molecular health translates to individual health. I will also review some of the future challenges related to high throughput data acquisition and data analysis.

Date: 7 January 2019 – 8:00 PM on BioInfoNet

Language: English

2018 Webinars

Türkçe için tıklayın

2018 was very productive in terms of the webinars. In total, we had 8 webinars. We have opened our youtube channel to reach more people. You can find our webinar videos both from our bigmarker and youtube channels.

Also we initiated a collaborative effort with RSG Colombia and started to work together. Have a look at their youtube channel!

January 2018

  • Title: Integrative Modeling of Biomolecular Complexes
  • Presenter: Assoc. Prof. Ezgi Karaca from Dokuz Eylül University
  • Date: January 31, 2018
  • Language: English
  • Abstract: Life is operated at the nanometer scale through orchestrated communications of biomolecules. By dissecting this nanoworld, we can acquire a fundamental understanding of how biological macromolecules function, how they are related to disease-linked pathways and how to design drugs targeting them. This understanding led to the birth and rise of Structural Biology, the study of the structures of biomolecules and their complexes at atomic resolution. In this webinar, Dr. Karaca will briefly introduce the basic Structural Biology techniques and the data types acquired with them. This will be followed by a comprehensive explanation of how to incorporate Structural Biology data into biomolecular simulations, especially into docking. Finally, she will talk about her latest research on integrative modeling, recently published in Nature Methods. For more, please see: https://goo.gl/EdUvBq
  • Bigmarker: https://www.bigmarker.com/bioinfonet/EzgiKaraca
  • Youtube: https://www.youtube.com/watch?v=jmFxZDTmEBo

April 2018

  • Title: An evolutionary genomic framework for tackling problems in conservation and biodiversity.
  • Presenter: Asst. Prof. İsmail K. Sağlam from Hacettepe University
  • Date: April 16, 2018
  • Language: English
  • Abstract: Today, the fıeld of conservation biology has risen to the forefront of scientific endeavors as only with a successful translation of conservation science to conservation practices can we hope to combat threats to the sustainability and well being of our ecosystems. As in all fields of the biological sciences the genomic revolution has the potential to rapidly change how we understand and approach conservation studies. The impact of this revolution has been most felt in the applied fields of medical and agricultural sciences. This has resulted in great advances in these fields as well as ever more refined methods for analyzing genomic data. However, the utilization of genomic data in the third major applied field of biology, conservation and environmental studies, is still in its infancy. Currently, genomic methods for conservation biology revolve mostly around describing spatial patterns of genomic differentiation and very little attention has been given to developing new methods that can utilize the vast amount of information available in the genome. One key insight which can be obtained from genome wide data for conservation biology is how the genomic basis of adaptation can directly inform conservation policy. In this talk, I will concentrate on three examples which show how understanding genomic patterns of speciation, evolutionary history and life history evolution can help us solve real life problems in biodiversity and reshape ongoing conservation policies. I will also detail how this approach can be useful in understanding the complex adaptations taking place in organism that are increasingly forced to live under human dominated landscapes. This framework, which merges adaptation genomics with conservation biology, emphasizes the importance of structuring conservation efforts around key adaptive units that strengthen species survival under changing conditions and demonstrates the potential of evolutionary genomics in informing conservation strategies facilitating the preservation of keystone species and ecosystems.
  • Bigmarker: https://www.bigmarker.com/bioinfonet/IsmailKSaglam
  • Youtube: https://www.youtube.com/watch?v=PzRpvKu8GMk

June 2018

  • Title: Beyin Metabolizması Genom Ölçeğinde Modellenmesi (Genome-scale brain metabolic networks as scaffolds for mapping disease-related alterations)
  • Presenter:  Assoc. Prof. Tunahan Çakır from Gebze Technical University
  • Date:  June 11, 2018
  • Language: Turkish
  • Abstract: Integrative systems-wide analysis of data and networks at genome-scale enables a holistic understanding of the functionality and working principles of the cell. Metabolic networks are among major cellular network types since it is the metabolism that runs the cellular factory. Therefore, reconstruction of brain-specific metabolic networks is crucial to map the effect of brain-related diseases such as neurodegenerative diseases and brain tumors on cell metabolism. In this talk, I will focus on our efforts on reconstructing brain-specific metabolic networks that take into account neuron-astrocyte specificity and the interactions between these two essential cell types. Then, I will present the use of the reconstructed networks as scaffolds to map transcriptome data for neurodegenerative diseases using a graph-based approach termed reporter pathways. I will also present our work on constraint-based modelling of brain metabolic networks for the analysis of brain tumors. A key point in modelling some neurodegenerative diseases such as Alzheimer’s Disease and Parkinson’s Disease is to take into account the aggregation of disease specific proteins in the cell. I will conclude with our ongoing research on Parkinson’s Disease where we map transcriptome data on the reconstructed brain-specific metabolic networks to demonstrate the effect of alpha-synuclein aggregation on brain metabolism.
  • Bigmarker: https://www.bigmarker.com/bioinfonet/TunahanCakir
  • Youtube: https://www.youtube.com/watch?v=z8MV-eu65zI

July 2018

  • Title: Tümörlerdeki Ardışık Kısa Tekrar Dizileri ve Immünoterapi
  • Presenter: Dr. Tuğçe Bilgin Sonay from  University of Lausanne
  • Date: June 12, 2018
  • Language: Turkish
  • Abstract: Hastalıklara sebep olabilecek fenotipik çeşitliliğin kaynakları günümüzün en önemli araştırma konularının başında geliyor. DNA’daki tek nükleotit değişimleri, ve daha büyük yapısal değişimlerinin yanı sıra kopya sayısı mutasyonları da gelişen dizileme teknolojileri sayesinde daha detaylı araştırılmaya başlandı. Özellikle ardışık kısa tekrar dizilerindeki kopya sayısı değişimleri, tüm genomik mutasyonlar arasında en yüksek hıza sahip olmaları ve sebep oldukları fenotipik değişimin derecesel ve geri dönüşümlü olması sebebiyle son yıllarda oldukça önem kazandılar. Bu tekrar dizileri sadece insandan insana değişmez, tek bir insanda bile farklı kopya sayılarında bulunabilirler. Gen bölgelerinde kopya sayısını değiştiren tekrarlar Huntington, ataksiya gibi hastalıklara sebep olmalarıyla bilinirler. DNA tamir sisteminin işlememesi durumunda tümörlerde çokca bulunan bu mutasyonları anlamak hem kanser oluşumunu anlamamıza yardımcı oluyor hem de bu tümörler için immünoterapilerin geliştirilmesine öncülük eden bir role sahiptirler.
  • Bigmarker: https://www.bigmarker.com/bioinfonet/TugceBilgin
  • Youtube: https://www.youtube.com/watch?v=GmjwyTZinjU

August 2018

  • Title: Computational Analysis and Integration of Large-Scale Biological Data with Deep Learning Approaches
  • Presenter: Dr. Tunca Doğan from EMBI – EBI & METU
  • Date: August 2, 2018
  • Language: English
  • Abstract: Machine learning and data mining techniques are frequently employed to make sense of large-scale and noisy biological/biomedical data accumulated in public servers. A key subject in this endeavour is the prediction of the properties of proteins such as their functions and interactions. Recently, deep learning (DL) based methods have outperformed the conventional machine learning algorithms in the fields of computer vision, natural language processing and artificial intelligence; which brought attention to their application to the biological data. In this talk, I’m going to explain the DL-based probabilistic computational methods we have recently developed in our research center (KanSiL, Graduate School of Informatics, ODTU); first, to predict the functions of the uncharacterised proteins (i.e., DEEPred); and second, to identify novel interacting drug candidate molecules for all potential targets in the human proteome (i.e., DEEPscreen) to serve the purposes of drug discovery and repositioning, together with the aim of biomedical data integration. Apart from the benefits of employing novel DL approaches, I’ll also mention the limitations of DL-based techniques when applied on the biological data, to explain why deep learning alone cannot solve every problem related to bioinformatics.
  • Bigmarker: https://www.bigmarker.com/bioinfonet/TuncaDogan
  • Youtube: https://www.youtube.com/watch?v=ijr0B5oTnuY

October 2018

  • Title: The FoundationOne® Assay for Genomic Profiling of Solid Tumor Cancers
  • Presenter: Dr. Abdullah Karaman from  University Hospital Zurich
  • Date: October 5, 2018
  • Language: English
  • Abstract: Comprehensive genomic tumor profiling is the basis of precision medicine in the modern era of cancer diagnosis and treatment. The possibility to profile cancer genomes and identify driver mutations in individual tumors has changed the way how oncologists diagnose cancer, decide on therapies and identify patients for clinical trials. At the University Hospital Zurich and in in collaboration with Roche, Switzerland and Foundation Medicine Inc., Cambridge, USA, we have established the validated diagnostic FoundationOne® assay for solid tumors. The FoundationOne® assay is designed to detect various genomic alterations in 315 cancer related genes including single nucleotide variants, indels and copy number alterations. In addition, fusions and rearrangement events in 28 cancer associated genes are assessed. Besides these alterations, the microsatellite status (MSI) of 114 intronic homopolymer repeat loci and the tumor mutational burden (TMB) is determined as biomarkers for immun-checkpoint inhibitors. For its application in the clinical practice, the assay was designed to work with common FFPE blocks while guaranteeing a specificity of ≥ 99% and sensitivity of 90-99%. To reliably identify driver mutations in highly heterogeneous cancer samples, the assay includes targeted resequencing of exons with a median coverage of 500x. The FoundationOne® has already established itself as an essential element at tumor board meetings, where it supports oncologists in the diagnosis and decision making process for succeeding treatment options. Here, I will introduce the audience to the assay, give an overview of the first results obtained at the UniversityHopsital Zurich, will demonstrate its advantages and give statistics on its performance.
  • Bigmarker: https://www.bigmarker.com/bioinfonet/AbdullahKahraman
  • Youtube: https://www.youtube.com/watch?v=zB5PjaGbrUA

October 2018

  • Title: Cancer Biomarkers Using Integrative Single Cell and Bulk Sequencing
  • Presenter: Akdeş Sevim Harmancı from
  • Date: October 23, 2018
  • Language: English
  • Abstract: Cancer is a disease of genomic and epigenomic alterations. Single nucleotide changes, copy number variations (CNV), chromosomal rearrangements and modification in DNA methylation together drive the formation of a tumor. The integrative ‘omic’ approaches in cancer research have led to a deeper understanding of tumor biology and are establishing the foundation necessary to support the long-term goals of personalized medicine. In this talk, I will talk about identifying brain tumor biomarkers using integrative bulk or single-cell sequencing data. This talk will consist of two parts. The first part will cover our work where we characterized non-NF2 meningiomas through complex integrative analysis of genetic and epigenetic data. I will also explain the epigenetic and genetic mechanisms leading to atypical meningioma and malignant glioma transformation. The second part will introduce our algorithm named CaSpER, that identifies visualizes and integrates CNV events in multiscale resolution using single-cell and bulk RNA-Sequencing data.
  • Bigmarker: https://www.bigmarker.com/bioinfonet/AkdesSerinHarmanci
  • Youtube: https://www.youtube.com/watch?v=FSL3KT8gY2s

December 2018

  • Title: What ancient and modern DNA tells us about our human past?
  • Presenter: Dr. Stephan Schiffels from Max Planck Institute for the Science of Human History
  • Date: December 12, 2018
  • Language: English
  • Abstract: Our human past leaves traces in our genomes, via population size changes, admixture events and migration patterns. Via genetic analyses, we can therefore read human history from our genomes, which adds critically to our growing body of pre-historical evidence from archaeology and linguistics. In this talk, I will introduce the field of historical population genetics, and showcase three examples: First, I will show how our genomes contain information about the origins of our species in Africa, in the deep past. Second, I will demonstrate how we can use ancient DNA from Anglo-Saxon remains in Great Britain to investigate the nature and consequences of the Anglo-Saxon migration period. Third, I will introduce our most recent project, in which we use ancient and modern DNA to investigate the peopling of North America.
  • Bigmarker: https://www.bigmarker.com/bioinfonet/What-ancient-and-modern-DNA-tells-us-about-our-human-past
  • Youtube: Will be available soon

Short Tandem Repeats in Tumours and Immunotherapy


Our July webinar was given by Tugce Bilgin Sonay, from the Department of Computational Biology in the University of Lausanne. In this session, apart from her work, Tugce also explained other studies in this area.

At the beginning of the talk, she gave a general introduction on the detection of short tandem repeats and their impact on phenotype, gene expression and epigenetics. The primary focus of the talk was (1) Microsatellite Instability (MSI) in tumours, which mostly occurs due to the increase in the number of short tandem repeats as a result of a faulty DNA damage repair system, (2) Identification of the effect of the short tandem repeats in these tumours and (3) how these effects can be utilized for immunotherapy.

If you are interested in how short tandem repeats influence cancer and how they can be used for immunotherapy purposes, we strongly suggest you watch this webinar: https://youtu.be/GmjwyTZinjU (unfortunately, this webinar is only available in Turkish)

As ISCB RSG Turkey, we want to thank Tugce again for accepting our invitation and giving this very informative talk!

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!