What ancient and modern DNA tells us about our human past?

  • 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

Cancer Biomarkers Using Integrative Single Cell and Bulk Sequencing

  • 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

The FoundationOne® Assay for Genomic Profiling of Solid Tumor Cancers

  • 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

Computational Analysis and Integration of Large-Scale Biological Data with Deep Learning Approaches

  • 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

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!!

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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 evolutionary genomic framework for tackling problems in conservation and biodiversity.

  • 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

An easy way to understand a study: Student Presentations

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

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!

RSG-Turkey is a member of The International Society for Computational Biology (ISCB) Student Council (SC) Regional Student Groups (RSG). We are a non-profit community composed of early career researchers interested in computational biology and bioinformatics.

Contact: turkey.rsg@gmail.com

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