Building skills for the future: Masters 4.0 in Bioinformatics

Moderator: Nemanja Bogavac

Introductions: Jelena Ružičić

Panelists:

Prof. Dr. Janko Samardžić
Prof. Dr. Nataša Pržulj
Dr. Nevena Veljković

1. Jelena Karanović, Identifying the cluster of differentiation markers deregulated in colon cancer through analysis of Gene Expression Omnibus database

2. Marat Kazanov, Characterizing Somatic Mutation Clusters in Cancers Enriched with APOBEC Mutagenesis

3. Jovana Despotović, Non-coding transcripts of protein-coding genes as novel biomarkers for colorectal cancer diagnosis

4. Miljana Tanic, Navigating ELSI for FAIR multiomics data management within STEPUPIORS international rectal cancer project

5. Dušan Ušjak, Integration of Whole Exome and Single-Cell Transcriptomic Data Analysis to Identify Potentially Pathogenic Variants in Unicuspid Aortic Valve Disease

6. Marina Andjelkovic, Molecular genetic basis of childhood epilepsy in Serbia: utility of clinical and whole exome sequencing

7. Paula Štancl, Impact of 3D chromatin structure on cancer mutation patterns and tissue-of-origin prediction

8. Lucija Milicic, Machine learning methods for metabolite biomarkers detection

9. Nevena Vukojicic, Enhancing Cancer Genomics: A Pipeline for Spatial Transcriptomics Analysis on the CGC

10. Mila Ljujić, Transcriptome profiling of pharmacological manipulation of zebrafish tailfin regeneration

14:00-14:20 Maja Zivkovic, The genetic pathways of ferroptosis-related processes in multiple sclerosis

14:20-14:30 Rafael Campos-Martin, Epigenome-wide analysis identifies methylome profiles linked to Obsessive-Compulsive Disorder, disease severity, and treatment response

14:30-14:40 Sonja Katz, Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping

14:40-14:50 Marija Stankovic, Interaction between healthy and diseased bronchial epithelial cells with Lactiplantibacillus plantarum BGPKM22 reveals distinct expression profiles by dual RNA sequencing

14:00-14:20 Yuriy Orlov, Bioinformatics tools for reconstruction of gene networks of complex diseases

14:20-14:40 Saša Malkov, Feature Selection For Multi-Source SCT Data

14:40-14:50 Miloš Košprdić, Enhancing Biomedical Information Retrieval with Semantic Search: A Comparative Analysis Using PubMed Data

Introduction to Bioinformatic Tools for Extracting Pharmacogenomics Information from Next-Generation Sequencing Data

10:00-10:25 Xun Xu, DCS: from Reading Genome to Understanding Life

10:25-10:50 Marko Mišić, Spectral Clustering for Transcriptomics Data: an Approximate Column Sampling Approach on the GPU

10:50-11:00 Xin Lin, Advancing Supervised Machine Learning for scRNA-seq Data Analysis

11:00-11:10 Milos Radonjic, STIM: Multipurpose method for spatial transcriptomics data integration across different technologies

10:00-10:25 Alexandre de Brevern, Analysis of unlikely (and rare) local protein conformations

10:25-10:50 Fabio Zobi, Antimicrobial Rhenium Tricarbonyl Complexes: Accelerating their Discovery by Leveraging Machine Learning Models

10:50-11:00 Darya Tsibulskaya, Analysis of AlphaFold2 Predicted Structures of Aggregation Factors in Lactic Acid Bacteria

11:00-11:10 Marija Vidovic, Label-Free Quantitative Proteomics of Pelargonium zonale: Tissue-Specific Differences

11:10-11:20 Matija Marijan, Impact of Protein Representations on Drug-Target Affinity Prediction

11:20-11:30 Aleksandra Divac Rankov, Impact of Electronic Cigarette Components on Lung Cell Proteome: A High-Resolution Mass Spectrometry Analysis

10:00-10:05 Noel Malod-Dognin, Brief Introduction to NetBio Cosi

10:05-10:30 Sam Windels, Graphlet-based higher-order network embeddings: the past, the present and the future

10:30-10:50 Katarina Mihajlovic, MONFIT: Multi-omics factorization-based integration of time-series data sheds light on Parkinson’s disease

10:50-11:10 Carme Zambrana, “Pan-viral” disease mechanisms unveil the sweet spot for therapeutic intervention

11:10-11:30 Federico Melograna, Detecting Genetic Interactions with Visible Neural Networks

How to analyze and interpret RNA-seq data

Screen 1 Alexej Abyzov, Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline

Screen 1 Anita Skakić, WGS approach to identify potential genetic modifiers in Glycogen Storage Disease Ib

Screen 1 Anna Dorofeeva, Bioinformatics insights into genes encoding heat-resistant obscure (Hero) proteins and their role in cardiovascular diseases: a regulatory SNP analysis

Screen 1 Anđelo Beletić, Advances in a comprehensive understanding of alpha-1 antitrypsin glycosylation-data mining within recent publications

Screen 1 Dragana Bosnic, Silicon Affects The Expression Of Conserved And Novel Cucumber miRNAs In Response To Copper Stress

Screen 1 Dragana Dudic, Towards Head and Neck Myeloid Cells Atlas

Screen 1 Dušan Lazić, A comparative transcriptomic analysis of mouse DM1 models’ skeletal muscles

Screen 2 Fedor Kazanov, Analysis of RNA Secondary Structural Elements Using the RNAsselem Python Package

Screen 2 Ilma Mujkovic, Detection, identification and quantification of target DNA sequence in soybean event GTS 40-3-2

Screen 2 Jelena Kusic-Tisma, Fine-tuning RNA-seq alignment parameters for Danio rerio genome

Screen 2 Katarina Kruščić, Exploring Genetic Variant Selection Algorithms for Enhanced Genotyping Assays in Personalized Medicine

Screen 2 Ljiljana Rakičević, Pharmacogenetics-based Dosing Algorithm for Acenocoumarol in the Serbian Population

Screen 2 Lou Chitkushev, Enhancing Immunogenicity Assessment of C57BL/6 T-cell Epitopes

Screen 2 Marija Vidovic, Aggregation of LEA proteins from Ramonda serbica: in silico vs. in vitro

Screen 3 Marina Jelovac, Pharmacogenomic landscape of Serbian population

Screen 3 Marko Ćosić, The morphological analysis of a Holter Electrocardiogram

Screen 3 Martina Mia Mitic, Identification of Synonymous Genetic Variants Associated with Idiopathic Thrombosis using whole exome sequencing

Screen 3 Mikhail Potievskiy, Machine learning approach for risk factors detection of pancreatic fistula and AI diagnostic systems development

Screen 3 Milana Djonovic, Viral presence in the 1000 Genomes Project data​

Screen 3 Milica Ciric, Exploring biotechnological potential of LLDPE- and mixed plastics-degrading bacteria from contaminated soils

Screen 3 Minjie Lyu, Improvement of PBMC Cell Types Classification in Healthy Samples

Screen 4 Miodrag Dragoj, Integrating functional screening and bioinformatics for personalized medicine approaches in NSCLC

Screen 4 Nataša Mačak, A Transcriptomic Meta-analysis of Carbon Nanomaterials Toxicity on Lung Tissue

Screen 4 Nenad Vesić, Two different methods to assess PSA-test results in patients with prostate cancer

Screen 4 Nevena Ćirić, Sequence-based Hierarchical Classification of Tandem Repeats using Neural Network Models

Screen 4 Nikita Yolshin, Analysis of Influenza Virus Sequences in Russia for the Current Epidemic Season 2023-2024

Screen 4 Nikita Yolshin, Analysis of SARS-CoV-2 Variant Sequences for Identification of Unique Insertions and Deletions for qPCR Detection of Emerging Variants

Screen 4 Nikola Djordjevic, A Graphical User Interface for Automated BLAST Analysis and Phylogenetic Tree Construction

Screen 5 Polina Kanevska, DNA Mechanics peculiarities: Model for Twist and Stretch Coupling

Screen 5 Yuriy Orlov, Analysis of structural features of DNA in tRNA genes

Screen 5 Yuriy Orlov, GWAS study for severe COVID-19 linked with thromboinflammation syndrome

Screen 5 Yuriy Orlov, Integration of bioinformatics data for crop plant breeding

Screen 5 Yuriy Orlov, The sequence complexity estimates: algorithms and applications

Screen 5 Yuriy Orlov, Trends for Artificial Intelligence, Machine Learning, and Deep Learning applications in plant breeding

12:00-12:25 Marco Gerdol, Evidence of widespread hemizygosity and gene presence/absence variation in invertebrate pangenomes: are we overlooking the impact of genomic structural variation in metazoans?

12:25-12:50 Vladimir Babenko, Alternatively spliced exons manifest coordinated multi-domain alteration in synapse specific genes

12:00-12:20 Milena Stojić, Estimating the dimensionality of omics network embedding space

12:20-12:40 Alexandros Xenos, Towards a linearly organised embedding space of biological networks

12:40-13:00 Noel Malod-Dognin, The axes of biology: a novel axes-based network embedding paradigm to decipher the functional mechanisms of the cell

How to analyze and interpret RNA-seq data

10:00-10:25 Fotis Psomopoulos, FAIR Research Software as the catalyst for trustworthy AI in Life Sciences

10:25-10:50 Bojana Stanic, Toxicology Transformed: Harnessing Artificial Intelligence for Advanced Research

10:50-11:00 Zuqi Li, INMTD: integrative clustering with 2D genotypes and 3D facial images in the presence of confounders

11:00-11:10 Ivan Lorencin, Application of Kolmogorov-Arnold Networks in Cervical Cancer Diagnostics

11:10-11:20 Nazar Beknazarov, Z-Flipons conserved between human and mouse are associated with increased transcription initiation rates

MICOS-EU Competition

Fabio Stella Transportability and precision medicine: A Causal Networks Perspective

Benjamin Dizier Bioinformatics Beyond Pills: Transforming Health for All

Erwin Dreesen Pharmacometric models for improved therapeutic drug Monitoring

Andrew Walkira Unravelling MAFLD: From Molecular Mechanisms to Targeted Solutions

Katarina Mihajlović Towards curing Parkinson’s disease with AI

Daniel Becker, From Data to Insights: Transforming Genomic Analysis with DRAGEN and Emedgene

Screen 1 Alexej Abyzov, Transgenerational transmission of post-zygotic mutations suggests symmetric contribution of first two blastomeres to human germline

Screen 1 Anita Skakić, WGS approach to identify potential genetic modifiers in Glycogen Storage Disease Ib

Screen 1 Anna Dorofeeva, Bioinformatics insights into genes encoding heat-resistant obscure (Hero) proteins and their role in cardiovascular diseases: a regulatory SNP analysis

Screen 1 Anđelo Beletić, Advances in a comprehensive understanding of alpha-1 antitrypsin glycosylation-data mining within recent publications

Screen 1 Dragana Bosnic, Silicon Affects The Expression Of Conserved And Novel Cucumber miRNAs In Response To Copper Stress

Screen 1 Dragana Dudic, Towards Head and Neck Myeloid Cells Atlas

Screen 1 Dušan Lazić, A comparative transcriptomic analysis of mouse DM1 models’ skeletal muscles

Screen 2 Fedor Kazanov, Analysis of RNA Secondary Structural Elements Using the RNAsselem Python Package

Screen 2 Ilma Mujkovic, Detection, identification and quantification of target DNA sequence in soybean event GTS 40-3-2

Screen 2 Jelena Kusic-Tisma, Fine-tuning RNA-seq alignment parameters for Danio rerio genome

Screen 2 Katarina Kruščić, Exploring Genetic Variant Selection Algorithms for Enhanced Genotyping Assays in Personalized Medicine

Screen 2 Ljiljana Rakičević, Pharmacogenetics-based Dosing Algorithm for Acenocoumarol in the Serbian Population

Screen 2 Lou Chitkushev, Enhancing Immunogenicity Assessment of C57BL/6 T-cell Epitopes

Screen 2 Marija Vidovic, Aggregation of LEA proteins from Ramonda serbica: in silico vs. in vitro

Screen 3 Marina Jelovac, Pharmacogenomic landscape of Serbian population

Screen 3 Marko Ćosić, The morphological analysis of a Holter Electrocardiogram

Screen 3 Martina Mia Mitic, Identification of Synonymous Genetic Variants Associated with Idiopathic Thrombosis using whole exome sequencing

Screen 3 Mikhail Potievskiy, Machine learning approach for risk factors detection of pancreatic fistula and AI diagnostic systems development

Screen 3 Milana Djonovic, Viral presence in the 1000 Genomes Project data​

Screen 3 Milica Ciric, Exploring biotechnological potential of LLDPE- and mixed plastics-degrading bacteria from contaminated soils

Screen 3 Minjie Lyu, Improvement of PBMC Cell Types Classification in Healthy Samples

Screen 4 Miodrag Dragoj, Integrating functional screening and bioinformatics for personalized medicine approaches in NSCLC

Screen 4 Nataša Mačak, A Transcriptomic Meta-analysis of Carbon Nanomaterials Toxicity on Lung Tissue

Screen 4 Nenad Vesić, Two different methods to assess PSA-test results in patients with prostate cancer

Screen 4 Nevena Ćirić, Sequence-based Hierarchical Classification of Tandem Repeats using Neural Network Models

Screen 4 Nikita Yolshin, Analysis of Influenza Virus Sequences in Russia for the Current Epidemic Season 2023-2024

Screen 4 Nikita Yolshin, Analysis of SARS-CoV-2 Variant Sequences for Identification of Unique Insertions and Deletions for qPCR Detection of Emerging Variants

Screen 4 Nikola Djordjevic, A Graphical User Interface for Automated BLAST Analysis and Phylogenetic Tree Construction

Screen 5 Polina Kanevska, DNA Mechanics peculiarities: Model for Twist and Stretch Coupling

Screen 5 Yuriy Orlov, Analysis of structural features of DNA in tRNA genes

Screen 5 Yuriy Orlov, GWAS study for severe COVID-19 linked with thromboinflammation syndrome

Screen 5 Yuriy Orlov, Integration of bioinformatics data for crop plant breeding

Screen 5 Yuriy Orlov, The sequence complexity estimates: algorithms and applications

Screen 5 Yuriy Orlov, Trends for Artificial Intelligence, Machine Learning, and Deep Learning applications in plant breeding

MICOS-EU Competition

Ritchie Head Patients as partners in EC research

Hanna Boëthius Effective precision health serving the needs of diverse patient populations

Lara Andreoli Beyond the Score: Navigating Polygenic Risk in Healthcare

Hélène Antoine-Poirel Unlocking Precision Medicine: Synergizing Genetic Insights, Patient Engagement, and AI for Ethical Healthcare Advancements

Integrative multi-omics data analysis for precision medicine

14:00-14:25 Oxana Galzitskaya, What do amyloidosis, antimicrobial peptides, and the Spike RBD of SARS-CoV-2 have in common?

14:25-14:50 Suzana Blesic, Data analysis and modelling of climate and environmental drivers of vector borne diseases – some methodological approaches and challenges of OneHealth data

14:50-15:15 Anđela Rodić, Understanding the natural activation mechanism of the CRISPR-Cas immune system in Escherichia coli: A Computational Modeling Perspective

15:15-15:25 Iva Sabolić, Bioinformatic workflow to analyse Multiome ATAC + Gene Expression data

15:25-15:35 Nenad Mitic, A novel approach to SARS CoV-2 classification

15:35-15:45 Alexander Skupin, Mechanism-based classification of SARS-CoV-2 Variants by Molecular Dynamics Resembles Phylogenetic Tree

14:00-14:10 Yury Barbitoff, A systematic characterization of genotype-to-phenotype relationships in mouse and human

14:10-14:20 Yury Gusarov, The danger of powerful mitochondria: life-history traits shape the evolution of bird mtDNA

14:20-14:30 Lazar Vasović, Intrinsic disorder of proteins associated with diseases

14:30-14:40 Alexey Starostin, Determining the efficiency of the miTAR neural network in searching for microRNA target genes

Stefan Delic, Created by scientists for scientists – New England Biolabs, Next Generation Sequencing Library Preparation Products

Gökhan Ertaylan Dynamic Paths to Personalized Health: Navigating Transitions with Care

Diana Trutschel Nurse-Led Precision Care: Empowering Patients with Automated Excellences

Federico Melograna Discovering Your Health Blueprint: The Power of Personalized Networks

Martijn Ludwig Automating Precision Health: Revolutionizing Therapeutic Discovery and Patient Communication

Integrative multi-omics data analysis for precision medicine

10:00-10:25 Nataša Sladoje, Just feed it to the network – what can go wrong? Towards AI-supported early cancer detection from cytological image data

10:25-10:50 Vladimir Brusic, Sleep Apnea Monitoring using Wearable Heart Rate Sensors

10:50-11:00 Joakim Lindblad, Efficient Large Scale Multimodal Image Registration

11:00-11:10 Bogdan Kirillov, Leveraging Open Source Hardware and Physics-Informed Machine Learning for Accurate Experimental Identification of Bioink Thermophysical Properties in 3D Bioprinting

10:00-10:25 Andrea Gelemanovic, Elucidating the role of cellular parabiosis in determining the preferential site of metastasis

10:25-10:50 Marija Mihailovic, Multi-scale modeling uncovers 7q11.23 copy number variation-dependent alterations in ribosomal biogenesis, mTOR and neuronal maturation and excitability

10:50-11:00 Evgeniia Maksiutenko, The landscape of point mutations leading to pregnancy loss

11:00-11:10 Milovan Suvakov, Detecting somatic copy number variations in 245,388 participants from All of Us biobank

Marieke Kuijjer Cellular Complexity: Multiomics Integration for Personalized Regulatory Networks

Leen Thielemans Unlocking Success in Life Sciences: Harnessing the Power of Cross-Functional ‘Tiger Teams’

Elle Wilson Multi-omics characterization of Parkinson’s disease patient-derived dopaminergic neurons

Zuqi Li Image-Based Phenotypes as Key Biomarkers for Genetic Influences on Patient Subtypes

Sonja Katz From Bytes to Bedside and Back: Enhancing Clinical Decision Support with Explainable AI

Nahid Taheri, Specific Brain Age Estimation Using MRI

Kariofyllis Karamperis Precision Pharmacogenomics for Europe’s Future Health

Integrative multi-omics data analysis for precision medicine

12:00-12:25 Svetlana Ugarcina Perovic, Challenges in metagenomic annotation of antibiotic resistome

12:25-12:50 Jurica Zucko, Searching for the baseline miCRObiota

Overview of EU Funded Projects or Initiatives. A brief overview of EU-funded projects relevant to precision health and its key focus areas, objectives, and stages in the patient’s health journey.

Identifying Common Challenges and Opportunities – Building Bridges. Common challenges faced by EU-funded projects in precision health and potential opportunities for collaboration and synergy among projects.

Sharing Best Practices and Lessons Learned – Tearing Down Silos. Presentations or case studies from select projects that highlight successful strategies, methodologies, and lessons learned

Integrative multi-omics data analysis for precision medicine

BIO4 Campus: Transforming Science into Business

Moderator: Mladjan Stojanović

Panelists:

Dr. Marin Jukić
Dr. Oskar Marko

Dr. Jelisaveta Lazarević

Prof. dr. Mirjana Pešić

1. Pavle Eric, De novo genome sequencing for endangered bird of prey species

2. Tatiana Ilina, LEA4 protein group member from resurrection plant Ramonda serbica Panč. – production and in silico characterization

3. Jovana Ćurčić, Structural characteristics of YtnP lactonase originating from Stenotrophomonas maltophilia 6960

4. Biljana Stankovic, Genome-wide association study identified genetic signal in cystatin genes associated with Long COVID-19

5. Nikola Kotur, Using Singular Value Decomposition for Extracting Underlying Gene Expression Patterns in Transcriptomic Analysis

6. Sen Lin, Mouse Tissue of Origin Single Cell Classification System

7. Milana Grbić, Exploration of Intrinsic Disorder Regions through Classification of Intrinsically Disordered Proteins Using PPI Network Structure and Sequence Attributes: A Case Study

8. Pavel Latyshev, Unsupervised domain adaptation methods for cross-species transfer of regulatory code signals

9. Aleksandar Danicic, Versatile Multi-Sample Single Cell RNA-Seq Pipeline with Extensive Customization Options

10. Matvei Kolesnik, Transcriptome-wide detection of RNA cleavage sites revealed tRNA cleavage by target-activated CRISPR-Cas13a effector

14:00-14:25 Aleksandar Krstić, Multiomic Profiling of Early Onset Colorectal Cancer

14:25-14:35 Alessandra Vittorini Orgeas, A pipeline for the identification of disease-specific genetic biomarkers using NGS sequencing data of cfDNAs in human plasma

14:35-14:45 Yulia Suvorova, Development of automated pharmacogenetic report for evaluating possible side effects of acute lymphoblastic leukemia therapy

14:45-14:55 Lana Radenkovic, PCR-based nanopore sequencing method for characterizing short tandem repeat expansions

15:00-15:25 Vladimir Jovanović, ZEB2 as a driver of human-specific traits: Insights from comparative ChIP-Seq and RNA-Seq

15:25-15:35 Nevena Milivojević Dimitrijević, Deciphering the effects of nanosized polystyrene particles using lab-on-chip technology and transcriptome profile

14:00-14:25 Branko Dragovich, From physical to biological information and the genetic code

14:25-14:50 Stevan Macesic, Modeling of the Hypothalamic-Pituitary-Adrenal Axis dynamics by Stoichiometric Networks

14:50-15:00 Sofija Markovic, Unraveling Bacterial Persister Formation: Insights from a Type I Toxin-Antitoxin System Model