Genomics Platform@WUT Symposium 2021

To celebrate the first anniversary of its foundation, Genomics Platform@WUT organizes its first symposium on 23-06-2021 as a virtual conference. We cordially invite all researchers from Warsaw University of Technology interested in genomics and bioinformatics to participate in this event.

The abstract book is available here.


To register, please use this form. The Symposium happens on the Google Meet platform, so to participate you need only a valid Google account and a modern web browser.


The Genomics Platform@WUT was established on 11-05-2020 to integrate and promote the genomics-oriented community at Warsaw University of Technology. Coordinated by a Scientific Advisory Board headed by Dariusz Plewczyński (Laboratory of Bioinformatics and Computational Genomics), Genomics Platform@WUT consists of six research groups with diverse research areas:

  1. Dariusz Plewczyński (Laboratory of Bioinformatics and Computational Genomics).
  2. Robert Nowak (Artificial Intelligence Division).
  3. Przemysław Biecek (MI2 Data Lab).
  4. Małgorzata Adamczyk (Laboratory of Systems and Synthetic Biology).
  5. Tomasz Gambin (biodatageeks).
  6. Krzysztof Kaczmarski (GPU Programming Team).

Secretary of the Scientific Advisory Board: Michał Burdukiewicz.

The Platform is open to both experimental and computational scientists interested in genomics. It aims to integrate the genomics-oriented community of Warsaw University of Technology and promote its achievements.


Opening session (09:00 - 10:00)

IntroductionDariusz Plewczyński (Warsaw University of Technology)09:00 - 09:10
IntroductionMariusz Malinowski09:10 - 09:20
New High Performance Computing Center at Faculty of Mathematics and Information Science.Krzysztof Kaczmarski (Warsaw University of Technology)09:20 - 09:50
Break09:50 - 10:00

Session 1 (10:00 - 11:00)

How can we use mathematical modelling to complete understanding of cellular metabolism in living organismsMałgorzata Adamczyk (Warsaw University of Technology)10:00 - 10:35
The 13C metabolic flux analysis as a tool in validating the interplay of gene expression networks and metabolismRóża Szatkowska (Chair of Drug and Cosmetics Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland)10:35 - 10:50
Break10:50 - 11:00

Session 2 (11:00 - 13:20)

Comparison of 3D Chromatin Contacts in Human ESC-H1 Mapped Using GAM or Hi-CTeresa Szczepińska (Warsaw University of Technology, and Max-Delbrück Centre for Molecular Medicine)11:00 - 11:15
Optimisation of HiChIP method to generate high-resolution map of chromatin contacts mediated by CTCF and cohesin in the human genomeKarolina Jodkowska (Warsaw University of Technology, University of Warsaw)11:15 - 12:35
Comparative Analysis of Long (Oxford Nanopore Technologies 1D) Versus Short-Read Sequencing Technologies in Terms of SV InferenceSachin Gadakh (Centre of New Technologies, University of Warsaw ; Doctoral School of Exact and Natural Sciences, University of Warsaw)11:30 - 11:40
Molecular modeling and simulation of potential drug-repurposing for SARS-CoV-2 (COVID-19) coronavirusDoni Dermawan (Faculty of Chemistry, Warsaw University of Technology)11:40 - 11:50
Bat Coronaviruses as an emerging threat for human populationMichał Łaźniewski (Centre for Advanced Materials and Technologies, Warsaw University of Technology, Warsaw, Poland )11:50 - 12:05
Break12:05 - 13:45
The cohesin-mediated looping of the human genome across cell lines.Abhishek Agarwal (Warsaw University of Technology)12:10 - 12:20
Super-resolution imaging of chromatin loop structures in human cellsZofia Parteka (MiNI, Warsaw University of Technology, CeNT University of Warsaw)12:20 - 12:30
Structural Variants Detection by Consensus AlgorithmMateusz Chiliński (Warsaw University of Technology)12:30 - 12:40
Network analysis of 3D genomic data from population-averaged and single cell experimentsMichał Denkiewicz (Faculty of Mathematics and Information Science, Warsaw University of Technology)12:40 - 12:50
Identification of potential mechanisms of gene expression regulated by DNA methylations within transcription factor binding sites for breast cancerMichal Wlasnowolski (Warsaw University of Technology)12:50 - 13:00
3D chromatin methodsMichał Kadlof (Warsaw University of Technology)13:00 - 13:10
Chromatin phase separation simulations by percolation and loop extrusion model at single loop resolutionKaustav Sengupta (University of Warsaw)13:10 - 13:20

Session 3 (13:45 - 15:30)

De-novo assemblyRobert Nowak (Warsaw University of Technology)13:45 - 14:10
Estimated nucleotide reconstruction quality symbols of basecalling tools for Oxford Nanopore sequencingWiktor Kuśmirek (Warsaw University of Technology, Institute of Computer Science)14:10 - 14:25
Break14:25 - 15:35
Genomic map assembly algorithm utilizing binary sequencesPrzemysław Stawczyk (Warsaw University of Technology)14:30 - 14:45
Algorithm for DNA sequence assembly by quantum annealingKatarzyna Nałęcz-Charkiewicz (Warsaw University of Technology)14:45 - 15:00
Analysis of Oxford Nanopore output signal data for basecallingAdam Napieralski (Warsaw University of Technology)15:00 - 15:15
Nucleotide methylation classification using machine learning methods on the Oxford Nanopore based dataŁukasz Neumann (Warsaw University of Technology)15:15 - 15:30

Session 4 (15:35 - 16:15)

Negative data set sampling as the source of bias in prediction of antimicrobial peptidesMichał Burdukiewicz (Medical University of Białystok)15:35 - 15:50
Towards cloud-native, big data ready and efficient population-scale analyses of sequencing dataTomasz Gambin, Marek Wiewiórka (Warsaw University of Technology)15:50 - 16:10
Closing remarksMichał Burdukiewicz16:10 - 16:15