Zoe Cournia
Physics-Based and AI Methods for Protein Interaction Analysis
An exploration of simulation and machine learning methods for predicting protein-ligand, protein-protein, and protein-membrane interactions.
Webinars
Talks and seminars featuring experts from around the world, open to everyone.
Student Presenters
Open Student Webinars
Student-led research presentations and discussions
Dr. Elisa Frezza
Modeling RNA and Protein-RNA Complexes Using Different Computational Approaches
Dr. Elisa Frezza walks through computational strategies for modeling RNA structures and protein-RNA interactions, covering molecular dynamics simulations, normal mode analysis, and coarse-grained methods.
Serbulent Unsal
Language Models Can Learn Complex Functional Properties of Proteins
Serbulent Unsal received her B.Sc. degree in Statistics and Computer Sciences from Karadeniz Technical University in Turkey.
Dr. Ömer Ali Bayraktar
Mapping Human Tissue Architecture and Pathology Using Spatial Transcriptomics
Dr. Bayraktar presents cell2location, a Bayesian model for resolving fine-grained cell types in spatial transcriptomic data, and GBM-space, a multi-modal genomics approach to mapping tumour tissue architecture in glioblastoma.
Asst. Prof. Yaron Orenstein
Computational Challenges in Protein-RNA Interactions
Yaron Orenstein is a Senior Lecturer and the head of the Computational Biology lab at the School of Electrical and Computer Engineering at Ben-Gurion University of the Negev.
Dr. Ayesha Fatima
Understanding Disease Mechanistic for Better Drug Design
An overview of how bioinformatics tools provide the basis for constructing mathematical models of diseases to understand disease mechanisms and design rational drugs on a whole-systems basis.
Dilara Uzuner, Ecehan Abdik, Hatice Büşra Lüleci, Müberra Fatma Cesur
Open Student Webinars – Gebze Technical University
Four graduate students from Gebze Technical University present their research in cancer dormancy, Parkinson's disease metabolism, Alzheimer's disease, and Klebsiella pneumoniae drug targets.
Barış Ekim
Minimizer-space de Bruijn Graphs
Barış Ekim introduces minimizer-space sequencing data analysis (mdBG), achieving orders-of-magnitude improvements in genome assembly speed and memory usage over existing methods.
Hatice Ülkü Osmanbeyoğlu
Predictive Cell-Specific Gene Regulatory Models
Presentation of SPaRTAN, a computational method to link cell-surface receptors to transcription factors using CITE-seq datasets, applied to predict signaling-coupled TF states in tumor infiltrating CD8+ T cells.
Dr. Gülşah Merve Kılınç
Palaeogenomic Investigation of the Past Human Populations in Northeast Asia
Ancient DNA analysis of 40 individuals spanning 17,000–550 years from Yakutia and Lake Baikal, revealing gene flow events, Palaeo-Inuit ancestors, and Yersinia pestis in ancient Northeast Asia.
Reyhan Metin / Metehan Çelebi
Species-Specific Allosteric Drug Design on Glycolytic Enzymes and Analysis by Molecular Dynamics Simulations
A study using Constraint Molecular Dynamics simulation to clarify how glycolytic enzymes are allosterically inhibited in a species-specific manner, enabling targeted drug design.
Özlen Konu
The Role of Cholinergic Signals in Cancer Biology
An in silico, in vitro, and in vivo investigation of cholinergic signals in cancer progression, including the role of CHRNA5 in breast cancer and zebrafish xenograft models for liver cancer.
Mohammad Asif Khan
Understanding Viral Diversity Dynamics
An exploration of viral diversity dynamics at the protein sequence level, focusing on how viruses evade host immune responses through rapid mutation and the implications for vaccine design.
Cansu Dinçer
CEN-tools: An Integrative Platform to Identify the 'Contexts' of Essential Genes
Presentation of CEN-tools, a website and Python package for interrogating gene essentiality from large-scale CRISPR screens across biological contexts including tissue of origin, mutation profiles, and drug response levels.
Vidit Goyal
Early Detection of Various Types of Skin Cancer Using Deep Learning CNN – Vidit Goyal
A convolutional neural network approach using Modified Inception and MobileNet models to detect and classify skin cancer types, evaluated on the HAM10000 dataset.
Begüm Serra Büyüktarakçı
Sex, Genes and Diplomonads: The Evolution of Sex-related Genes in Hexamita inflata – Begüm Serra Büyüktarakçı
A comparative phylogenomic study of sex-related genes in Hexamita inflata, showing evidence for nuclear fusion and meiotic inter-homolog recombination in this diplomonad.
Julien Y. Dutheil
The Impact of Protein Structure on Sequence Evolution – Julien Y. Dutheil
Investigation of how protein structure influences sequence evolution, focusing on the distribution of adaptive mutations along 3D protein structures and coevolution between positions.
Bilgenur Baloğlu
Density Based Clustering and Error Correction of Metabarcodes in Nanopore Sequencing Using ASHURE – Bilgenur Baloğlu
Presentation of a new Python pipeline (ASHURE) for density-based clustering and error correction of metabarcodes using Oxford Nanopore sequencing, achieving >99% sequence accuracy for freshwater mock communities.
Hüseyin Cahit Burduroğlu
Projecting the Course of COVID-19 in Turkey: A Probabilistic Modeling Approach – Hüseyin Cahit Burduroğlu
A Bayesian negative binomial multilevel model with mixed effects for projecting COVID-19 confirmed daily and cumulative cases in Turkey, showing a decreasing epidemic curve under compliance with containment measures.
Ergi Deniz Özsoy
Lewontin Paradox and Its Considerations – Ergi Deniz Özsoy
A summary of modern studies and approaches related to the Lewontin Paradox — the contradiction between population size and neutral genetic variation — with emphasis on the Hill-Robertson effect and linked selection.
Kimberly Gilbert
Drivers of Genetic Diversity in Regions of Low Recombination – Kimberly Gilbert
A theoretical and empirical study of how multi-locus associative overdominance can amplify genetic diversity in low-recombination regions, with evidence of this phenomenon in the human genome.
Nazlı S. Kara, Meltem Kutnu, Yasemin Utkueri, Funda Yılmaz, Elif Bozlak, Evrim Fer
Comparison of SARS-CoV-2 Variants with INSaFLU and Galaxyproject – RSG-Turkey Active Members
A comparative study of SARS-CoV-2 genome variants identified by the Galaxy Project and INSaFLU workflows, presented by RSG-Turkey active members.
Aylin Bircan
Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey – Aylin Bircan
A comprehensive phylogenetic analysis of SARS-CoV-2 genomes in Turkey using 15,277 global sequences, revealing early introduction of the virus and multiple independent international transmission events.
Aashil A. Batavia
Accessing Multi-omics Data for the Purposes of Tumour Profiling
An introduction to accessing The Cancer Genome Atlas repository and tools for multi-omics assessment of tumours, focusing on renal cell carcinomas.
David Žihala
Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in Green Algae – David Žihala
An exploration of codon reassignments and unprecedented variants of the mitochondrial genetic code in the green algal order Sphaeropleales.
Seyit Kale
Molecular Simulations as an in silico Experiment
A historical and physical perspective on how molecular simulations can be thought of as in silico experiments, exploring the analogy between simulation and wet-lab experiments in structural biology.
Nikolay Oskolkov
Do We Have Big Data in Life Sciences? – Nikolay Oskolkov
An overview of applications of Artificial Neural Networks to Single Cell Genomics, Microscopy Imaging, and Genomics/Ancient DNA research, addressing the challenges of big data in life sciences.
Ercüment Çiçek
Hercules: Long Read Error Correction Algorithm with Machine Learning
Presentation of Hercules, the first machine learning algorithm for long-read error correction using Hidden Markov Models, achieving higher mapping rates than existing methods.
Arif Harmancı
Aspects of High Throughput Molecular Data Analysis
An overview of how genomics, transcriptomics, and epigenetics are changing our understanding of molecular health, and the future challenges of high-throughput data analysis.
Tugce Bilgin Sonay
Short Tandem Repeats in Tumours and Immunotherapy
A webinar on Microsatellite Instability in tumours — the impact of short tandem repeats on gene expression, epigenetics, and how these effects can be utilized for immunotherapy.
Tunahan Cakir
Genome-scale Brain Metabolic Networks as Scaffolds for Mapping Disease-related Alterations
A webinar covering systems-wide analysis of brain cell metabolism, mapping transcriptome data for neurodegenerative diseases using reporter pathways, and constraint-based modelling of brain metabolic networks.
Ismail Saglam
Evolutionary Genomics for Conservation and Biodiversity – Ismail Saglam
A webinar on how computational approaches and evolutionary genomics can help study conservation and biodiversity, including testing evolutionary models and understanding the evolutionary basis of adaptation.
Ezgi Karaca
The First Webinar of 2018 – Integrative Modeling of Biomolecular Complexes
A recap of the first webinar of 2018, given by Assoc. Prof. Ezgi Karaca on integrative modeling of biomolecular complexes including structural biology techniques and the HADDOCK docking program.
Ezgi Karaca
Integrative Modeling of Biomolecular Complexes
An introduction to structural biology techniques and how to incorporate structural data into biomolecular simulations, especially docking, with discussion of integrative modeling published in Nature Methods.
Bernhard Y. Renard
Computational Metagenomics on the Species Level
A talk on computational metagenomics on the species level, part of the early BioInfoNet webinar series, exploring the challenges and opportunities of metagenomic data analysis.
Tolga Can
Reconstruction of Signaling Network Topology from Steady State and Dynamic Perturbation Data
The first webinar of the BioInfoNet series, presenting methods for reconstructing signaling network topology from steady state and dynamic perturbation data.
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