Genomics Platform@WUT Symposium 2022
To celebrate the second anniversary of its foundation, Genomics Platform@WUT organizes its second symposium on 24-06-2022 as a hybrid conference. We cordially invite all researchers from Warsaw University of Technology interested in genomics and bioinformatics to participate in this event. Our venue is Faculty of Mathematics and Information Sciences of the Warsaw University of Technology (Koszykowa 75, 00-662 Warszawa, Poland), Lecture Room 101.
Abstract book
The abstract book is available here.
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About
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:
- Dariusz Plewczyński (Laboratory of Bioinformatics and Computational Genomics).
- Robert Nowak (Artificial Intelligence Division).
- Przemysław Biecek (MI2 Data Lab).
- Małgorzata Adamczyk (Laboratory of Systems and Synthetic Biology).
- Tomasz Gambin (biodatageeks).
- 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.
Keynote Speakers
Professor Sanghamitra Bandyopadhyay
About Speaker
- Professor, Machine Intelligence Unit
- Director, Indian Statistical Institute
- Fellow: FNA, FIEEE, FTWAS, FNAE, FNASc, FIAPR
- URL: http://www.isical.ac.in/~sanghami
Machine Learning in Computational Biology
Abstract: In this talk, we will focus on some Machine Learning Solutions in Computational Biology. In particular, we will first focus on a method of microRNA target prediction. Next, we will show its utilization for building a microRNA induced gene regulatory network, whose analysis reveals some novel markers for breast and colon cancer. We will then provide a brief overview of a single cell RNA-seq data clustering algorithm. Finally, we will conclude with an application of optimization technique for the drug design problem.
Professor Ujjwal Maulik
About Speaker
- Professor, Jadavpur University, Kolkata, India
- Former Chair Department of Computer Science and Engineering
- Fellow: IEEE, INAE, IAPR, Humboldt, ICTP
- URL: https://sites.google.com/site/drujjwalmaulik/
Dr. Ujjwal Maulik is a Professor in the Department of Computer Science and Engineering, Jadavpur University since 2004. He was also the former Head of the same Department. He held the position of the Principal in charge and the Head of the Department of Computer Science and Engineering, Kalayni Government Engineering College. Dr. Maulik completed B. Sc. in Physics and B. Tech in Computer Science from Calcutta University, Kolkata, and West Bengal, India in 1986 and 1989 respectively. He also received his M. Tech in Computer Science and Ph. D. in Engineering in 1992 and 1997 both at Jadavpur University, Kolkata, West Bengal, India.
Dr. Maulik worked in many universities and research laboratories around the world as visiting Professor/ Scientist including Los Alamos National Lab., USA in 1997, University of New South Wales, Australia in 1999, Universities of Texas at Arlington, USA in 2001, University of Maryland at Baltimore County, USA in 2004, Fraunhofer Institute for Autonome Intelligent Systems, St. Augustin, Germany in 2005, Tsinghua University, China in 2007, Sapienza University, Rome, Italy in 2008, University of Heidelberg, Germany in 2009, German Cancer Research Center (DKFZ), Germany in 2010, 2011 and 2012, Grenoble INP, France in 2010, 2013 and 2016, University of Warsaw in 2013 and 2019, University of Padova, Italy in 2014 and 2016, Corvinus University, Budapest, Hungary in 2015 and 2016, University of Ljubljana, Slovenia in 2015 and 2017, International Center for Theoretical Physics (ICTP), Trieste, Italy in 2014, 2017 and 2018. He is the recipient of Alexander von Humboldt Fellowship during 2010, 2011 and 2012 and Senior Associate of ICTP, Italy during 2012-2018. He is the Fellow of Indian National Academy of Engineers (INAE), India, International Association for Pattern Recognition (IAPR), USA and The Institute of Electrical and Electronics Engineers (IEEE), USA. His research interest include Machine Learning, Pattern Analysis, Data Science, Bioinformatics, Multi-objective Optimization, Social Networking, IoT and Autonomous Car. In these areas he has published ten books, more than three hundred fifty papers, filed several patents and already guided twenty doctoral students.
Artificial Intelligence for Healthcare
Abstract: In this lecture first we will discuss some current trends in Artificial Intelligence (AI). We will briefly introduce advantages of Deep Learning Techniques and In this regard we will demonstrate applications of different machine learning algorithms including Deep Learning in real life situation. We will demonstrate how Deep Learning Techniques and Graph Neural Network. Subsequently we will demonstrate how these techniques can be used for healthcare applications.
Schedule
| Time | Title | Speaker |
|---|---|---|
| 11:00 - 11:10 | Opening talk | Dariusz Plewczyński |
| 11:10 - 11:25 | Drug repurposing for identification of potential spike inhibitors for SARS-CoV-2 using molecular docking and molecular dynamics simulations | Michał Łaźniewski |
| 11:25 - 11:40 | ConsensuSV - HPC-ready, ML-enhanced automated pipeline for Illumina-based variant detection | Mateusz Chiliński |
| 11:40 - 11:55 | Comparative analysis of the 3D structure of the genome of selected human lymphoblastoid cells based on ChIA-PET and HiChIP data | Anastasiya Gurova |
| 11:55 - 12:10 | The dynamic role of Cohesin in the maintaining the genome architecture | Ashutosh Choudhury |
| 12:10 - 12:25 | Compartmentalisation detected by Hi-C and GAM - orthogonal methods in 3D structural genomics | Teresa Szczepińska |
| 12:25 - 12:40 | The cohesin-mediated looping of the human genome across cell lines. | Abhishek Agarwal |
| 12:40 - 12:50 | Break | |
| 12:50 - 13:05 | Intrinsic linking of chromatin in human cells | Michał Denkiewicz |
| 13:05 - 13:20 | Multi-scale phase separation by explosive percolation with single chromatin loop resolution | Kaustav Sengupta |
| 13:20 - 13:35 | Computational modeling of human-nCoV interaction network | Anup Kumar Halder |
| 13:35 - 13:50 | 3D genome structures reconstruction | Krzysztof Banecki |
| 13:50 - 14:05 | A Stochastic Monte-Carlo model for Loop Extrusion of Chromatin | Sevastianos Korsak |
| 14:05 - 14:20 | Comparative Analysis of Long Versus Short-Read Sequencing Technologies in Terms of SV Inference of TRIOS | Sachin Gadakh |
| 14:20 - 14:30 | Break | |
| 14:30 - 14:45 | Super-resolution visualization of chromatin loop folding in human lymphoblastoid cells using interferometric photoactivated localization microscopy | Zofia Tojek |
| 14:45 - 15:00 | Generative Adversarial Networks for Dataset Augmentation | Jakub Józefowicz |
| 15:00 - 15:15 | PartSeg - tool for reproducible segmentation of chromatin | Grzegorz Bokota |
| 15:15 - 17:00 | Break | |
| 17:00 - 18:00 | Keynote: Machine Learning in Computational Biology | Sanghamitra Bandyopadhyay |
| 18:00 - 19:00 | Keynote: Artificial Intelligence for Healthcare | Ujjwal Maulik |