Book of abstracts

Download the book of abstracts of PTBi 2018.

Conference program

Wednesday, Sep 5th
11:00 Registration
12:30 Lunch
13:30 Opening



Keynote lecture B1 (chair M. Kotulska)

Johannes Söding, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
New algorithms and tools for large-scale sequence analysis of metagenomics data





Session B1-1 Linguistic modeling in bioinformatics (chair O. Unold)

Alexander Bolshoy, University of Haifa, Israel
Towards an Encyclopedia of Sequence Biology

Michaela Zemková, Charles University in Prague, Czech Republic
Parasitism and peptide vocabularies

Mateusz Pyzik, Wroclaw University of Science and Technology, Poland
How to measure the topological quality of protein parse trees?

15:30 Coffee break







Session B1-2 (chair W. Rudnicki)

Michał Dramiński, Polish Academy of Sciences, Warsaw, Poland
Monte Carlo Feature Selection and Interdependencies Discovery (MCFS-ID) with rmcfs 1.3.0

Wanda Niemyska, University of Warsaw, Poland
The Wasserstein distance as a dissimilarity measure for mass spectra with application to spectral deconvolution

Michał Burdukiewicz, University of Wroclaw, Poland
predPCR: automated classification of sigmoid curves

Barbara Poszewiecka, University of Warsaw, Poland
TADeus – tool for clinical evaluation of chromosomal rearrangements modifying chromatin organization

Jarosław Chilimoniuk, University of Wroclaw, Poland
PhyMet2: a database and toolkit for phylogenetic and metabolic analyses of methanogens


ICGI Lecture (chair O. Unold)
Colin de la Higuera, University of Nantes, France
Grammatical inference: where did all those good ideas go?

18:15 Posters & snacks
List of posters in the conference book

Best Poster Award:
Wiktor Franus, Warsaw University of Technology
Implementation of a hybrid algorithm for generating scaffolds

 Thursday, Sep 6th



Keynote lecture B2 (chair W. Nowak)

Mounir Tarek, CNRS-University of Lorraine, Vandœuvre-lès-Nancy, France
Exploring the Complex Dynamics of an Ion Channel Voltage Sensor Domain via Computation





Session B2-1 (chair M. Szachniuk)

Katarzyna Walczewska-Szewc, Nicolaus Copernicus University in Torun, Poland
Investigating the dynamics of ATP-sensitive potassium channel gating: a molecular dynamics study

Sebastian Bittrich, University of Applied Sciences, Mittweida, Germany
Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl-tRNA synthetases
(Best Presentation Award)

Mateusz Skrzypecki, Wroclaw University of Science and Technology, Poland
Evaluation of residue-residue contact prediction in metamorphic proteins

10:45 Conference photo & coffee break



Keynote lecture B3 (chair J. Szyda)

Joanna Polańska, Silesian University of Technology, Gliwice, Poland
Single-cell sequencing – new data, new challenge












Session B2-2 Flash (chair B. Wilczyński)

Mariusz Bromke, Wroclaw Medical University, Poland
Drug activity assesment with metabolomics

Tomasz Prejzendanc, Poznan University of Technology, Poland
ModeLang – an approach to model dynamical systems in bioinformatics

Dorota Mackiewicz, University of Wroclaw, Poland
New insights in Y chromosome degeneration

Paweł Sztromwasser, Medical University of Lodz, Poland
Improving detection of gene duplications in whole-genome sequencing data using allelic depth imbalance

Małgorzata Wnętrzak, University of Wroclaw, Poland
The standard genetic code robustness to both point and frameshift mutations

Aleksandra Kroczak, University of Wroclaw, Poland
Bioinformatic analyses of mitochondrial genomes show duplicated regions in many parrot taxa

Mateusz Kudła, Poznan University of Technology, Poland
Detecting Life Signatures with RNA Sequence Similarity Measures

Jakub Wiedemann, Poznan University of Technology, Poland
Bioinformatic study of RNA multi-branched loops

Julia Pelc, Wroclaw University of Science and Technology, Poland
Analysis of gplmDCA tool and created filters performance for contact site prediction in knotted and metamorphic proteins

Joanna Miśkiewicz, Poznan University of Technology, Poland
G-quadruplex Topology from Bioinformatics Perspective

12:40 Lunch







Session B2-3 (chair P. Mackiewicz)

Juan Francisco Carrascoza Mayen, Poznan University of Technology, Poland
Origins of Life: Nano-confinement of Prebiotic Soup in Montmorillonite Clay Car–Parrinello Quantum Dynamics Study

Paweł Błażej, University of Wroclaw, Poland
The structure of the genetic code as an optimal graph clustering problem

Patryk Jarnot, Silesian University of Technology, Gliwice, Poland
GBSC: Method for clustering proteins by repeats in sequences

Kaja Chmielewska, Poznan University of Technology, Poland
Aortic aneurysm formation and progression analyzed using Petri net-based approach

Jarosław Synak, Poznan University of Technology, Poland
Parallel RNA World Simulator

15:20 Coffee break
15:30 General Assembly of Polish Bioinformatics Society
17:30 Depart to social event
18:00 Visit to Africarium
19:00 Dinner at Laguna Bistro
 Friday, Sep 7th






Session B3-1 Best PhD & MSc thesis awards 2017 (chairs A. Gambin & A. Gruca)

Michał Ciach, University of Warsaw, Poland
Modelling of protein dissociation in mass spectrometry (MSc, 1st prize)

Jagoda Jabłońska, University of Warsaw, Poland
Systematic classification of the His-Me finger superfamily (MSc, distinction)

Grzegorz Skoraczyński, University of Warsaw, Poland
A challenge of automatic classification organic reactions yield and duration (MSc, distinction)

Wojciech Rosikiewicz, Adam Mickiewicz University, Poznan, Poland
(In)Stability of protein-coding genes’5’end overlap (PhD, 1st prize)

10:20 Coffee break








Session B3-2 (chair W. A. Sokalski)

Wiesław Nowak, Nicolaus Copernicus University in Torun, Poland
Photoinduced Structural Rearrangements in Proteins Involved in Insulin Release. Computer and Bioinformatics Modeling

Krzysztof Pawłowski, Warsaw University of Life Sciences – SGGW, Poland
Bioinformatics discovery of novel kinase families – unexpected biology and biochemistry in a well-known enzyme superfamily

Dominik Gront, University of Warsaw, Poland
SURPASS: Low-Resolution Coarse-Grained Protein Model

Joanna Szyda,Wroclaw University of Environmental and Life Sciences, Poland
Understanding unmapped reads using Bos taurus whole genome DNA sequence

Robert Nowak, Warsaw University of Technology
dnaasm – de-novo assembler generation sequencing data for second and third generation sequencing data

Michał Boniecki, International Institute of Molecular and Cell Biology, Warsaw, Poland
SimRNP: a new method for fully flexible modeling of protein-RNA complexes and for simulations of RNA-protein binding

12:40 Closing remarks
13:00 Lunch

General information

All lectures take place in room 10AC. Lunches are served in the foyer. The poster session and coffee breaks are held in the mezzanine. Depart to the social event (a 20-minutes walk) is from the reception desk.

Presentation guidelines

Please note that the duration of the regular talk is 15min + 5min for discussion. Duration of the flash talk is 4min + 1min for a quick question and answer.

We ask all the speakers to load and check their presentations before the start of their session – for assistance please contact the chair of your session or the conference staff. The conference room is equipped with a computer with Windows. Speakers willing to present using their own Mac laptop are kindly asked to bring their own Mac-to-VGA adapter. We apologize for the inconvenience.

The maximum poster size is 90x120cm (portrait orientation), which is equivalent to the A0 format. Posters can be put up from 11am on 5th September and have to be taken down by 3pm on 7th September. Posters left after that time will be destroyed.