Hybrid 3rd Symposium of Genomics Platform

Speakers

Krzysztof Poterlowicz, PhD

ELIXIR-UK, University of Bradford

Krzysztof is Associate professor in Bioinformatics and Biostatistics, Academic Lead for High Performance Computing cluster and Director of Research for Computational and Data Driven Science at the Faculty of Life Sciences at the University of Bradford. Krzysztof is the training Co-ordinator and a management committee member of ELIXIR-UK, the national Node of ELIXIR in the United Kingdom, the intergovernmental organisation that brings together life science resources from across Europe. Krzysztof is the Principal Investigator on ELIXIR-UK: FAIR Data Stewardship training project, a UK national fellowship for Life Science Data Managers delivered together with collaborators from Cardiff University, Earlham Institute, University of Manchester, and University of Oxford.

Robert Nowak, PhD

Warsaw University of Technology

Robert Nowak, DSc PhD MSc(CS), is an associate professor and head of the Artificial Intelligence Division in the Institute of Computer Science in the Faculty of Electronics and Information Technology at Warsaw University of Technology. Research areas include software development, bioinformatics, artificial intelligence and data fusion. He is involved in developing software systems with efficient implementation of complex algorithms for WUT, European Defense Agency, Samsung, Braster Co., mBank Co., Octagonet Co., Milton-Essex Co., Filbico Ltd., Plum Ltd., Horizen Ltd., Aspartus Ltd., Shanghai Science and Technology Talents Development Center. Co-author of 160 articles, 3 books, 2 patents. He supervises 60 theses. e-mail: robert.nowak@pw.edu.pl

Pawel Stankiewicz, MD, PhD

Baylor College of Medicine

Genomic Disorders: The focus of our research is pathogenetics of lung development and, in particular, the role of non-coding regulatory elements. We demonstrated that haploinsufficiency of the transcriptional factor FOXF1 gene on 16q24.1 results in a lethal neonatal diffuse developmental lung disorder, alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV). Moreover, we unraveled the role of the TBX4 and FGF10 genes in other developmental lung diseases, including acinar dysplasia and congenital alveolar dysplasia. We found that somatic mosaicism for CNVs that also contribute to germline mosaicism is significantly more common than previously thought. We showed that a considerable number of apparently de novo mutations causing genomic disorders occur in the previous generation as low-level somatic mosaicism and can thus be recurrently transmitted to future offspring. We continue to study the scale and clinical importance of this phenomenon.

Anna Gambin, PhD

University of Warsaw

Professor Anna Gambin is deputy dean for research and international cooperation at the Faculty of Mathematics, Computer Science, and Mechanics at the University of Warsaw (term 2016-2024). In her scientific work, she deals with the mathematical modeling of molecular processes and efficient algorithms for analyzing biomedical data. Recently, her research is focused on computational methods supporting medical diagnostics based on genomic and proteomic data. She is the author of over 100 scientific publications and, to date, has supervised ten PhDs in computational biology.

Aleksandra Gruca, PhD

Silesian University of Technology

Aleksandra Gruca holds the position of Associate Professor in the Department of Computer Networks and Systems at the Silesian University of Technology. In addition, she serves as the Vice President of the Polish Bioinformatics Society. Her research primarily focuses on advancing machine learning techniques for analyzing protein sequences, with a particular interest in methods that search for similar low-complexity protein sequences with the aim to predict their function. She is also interested in application of predictive models for the integrated analysis of large-scale multi-omics datasets.

Program

Abstract Book

Monday 27/02/2023

Time

Speaker

Title of presentation

9:00 - 9:10

Opening ceremony

9:10 - 9:40

Robert Nowak

Assembling de-novo.

9:40 - 9:55

Krzysztof Banecki

Simulation of 3D chromatin conformation using genomic and microscopic data.

9:55 - 10:10

Sevastianos Korsak

Multiscale Modelling of Chromatin.

10:10 - 10:25

Teodor Buchner

Why do we need genomics in cardiology?

10:25 - 10:40

Filip Korzeniewski

Prediction of amino acids mutations in SARS-CoV-2 spike protein using recurrent neural networks.

10:40 - 11:00

Coffee break

11:00 - 12:00

Krzysztof Poterlowicz

ELIXIR-UK: The UK powerhouse for FAIR life sciences data.

12:00 - 12:30

Aleksandra Gruca

Low-complexity protein sequences: what can we learn from their analysis.

12:30 - 14:00

Lunch (on your own)

14:00 - 14:30

Anna Gambin

From 48 to 46 chromosomes: a novel targeted assembler of segmental duplications unravels the complexity of the HSA2 fusion.

14:30-14:45

Alexander Myronov

BERTrand - peptide-TCR binding prediction using BERT and random pairing.

14:45-15:00

Krysztof Kucharczyk

TBD

15:00-15:15

Anup Kumar Halder

Chromatin Loop Prediction using Deep Hybrid Learning.

15:15-15:30

Krzysztof Fornalski

The Avrami-Dobrzyński phase transition model of cellular cancer transformation.

15:30 - 16:00

Coffee break

16:00 - 16:45

Paweł Stankiewicz

Genomic hypermutation phenomenon and low-level somatic mosaicism.

16:45-17:00

Katarzyna Nałęcz-Charkiewicz

De novo assembly as a solution to the Traveling Salesman Problem in bounded-degree graphs - in search of best QUBO formulation.