News & Events
November 2021
Dr Malgorzata Perycz from ZBO co-authored a publication on the Impact of C-terminal truncations in the Arabidopsis Rab escort protein (REP) on REP–Rab interaction and plant fertility, published recently in The Plant Journal, where she performed phylogenetic analyses of eukaryotic Rabs and REPs. Rab proteins belong to a large family of small GTPases – regulatory proteins important for vesicular transport and signal transduction in the cell. In all eukaryotes the intracellular trafficking of membranes, proteins, and polysaccharides is dependent on Rab functioning. Rab proteins are geranylgeranylated at their C-termini, a modification which is important for their stable binding to lipid bilayers. The Rab Escort Protein (REP) is an accessory protein of the Rab Geranylgeranyl Transferase (RGT) complex and it is obligatory for Rab prenylation. This work studies plant REP–Rab interactions by combining structural, genetic, and cell biology methods. The presented data show that the mechanism of action of REP in the process of Rab geranylgeranylation is different in plants than in animals or yeast.
June 2021
Dr Malgorzata Perycz from ZBO co-authored a letter addressing the topic of disability in space (Disability in space: Aim high) in reference to the current Parastronaut Feasibility Project run by European Space Agency, that has been published in Science on June 18th.
The astronauts are perceived as ones of the fittest people, and space is often regarded as the destination exclusively for the healthy. This is however a misguided perception: sometimes disability in one environment is hyper ability in another. For example, in no gravity, lack of legs is no longer a problem but can be an asset: a smaller fluid shift in the body, lower oxygen consumption, less caloric demand, less weight. This may mean a better health outcome for an astronaut, and better economy of space travel. Sending supplies to space is costly: a kilogram of cargo to International Space Station is between 3,000 and 20,000 US dollars, depending on the vessel. Also, people who leave Earth healthy are no longer so on their return. Lack of gravity affects muscles, bones and balance. Cosmic radiation may cause DNA damage and increased risk of cancer, vision problems, and more. In addition, the accidents – that may happen everywhere - may leave a person with a transient or permanent disability. Including people with disabilities at a design stage of spacecraft and space habitats, and as astronauts, is just a smart thing to do.
Malgorzata is a former flight director of ICAres-1 analog mission, which was the first mission to include a person with disabilities (blindness and lack of hand) in a crew of a simulated space habitat.
June 2021
The paper "Mapping chromatin accessibility and active regulatory elements reveals new pathological mechanisms in human gliomas" is now available to view on Nature Communications.
Researchers from the Nencki Institute PAS, the University of Warsaw, and the Institute of Computer Science PAS, have developed the first comprehensive "Atlas” of regulatory areas active in gliomas of various degrees of malignancy, which revealed deregulation of mechanisms controlling gene expression and a new mechanism driving the invasion of malignant brain tumors. The research was published in Nature Communications on June 15, 2021.
The interdisciplinary project Symphony 3 entitled "Atlas of regulatory areas specific for the human brain - a new tool for discovering the pathways causing selected brain diseases" has been carried out by the teams of prof. Bożena Kamińska (Nencki Institute of Experimental Biology of the Polish Academy of Sciences), dr. hab. Bartosz Wilczyński (Faculty of Mathematics, Informatics and Mechanics, University of Warsaw), and dr. Michał J Dąbrowski (Institute of Computer Science of the Polish Academy of Sciences). The project was financed by the National Research Center (NCN).
For more information please see: PressReleaseENG, PressReleasePL, Graphical_Abstract.
January 2021
The paper "Mapping chromatin accessibility and active regulatory elements reveals new pathological mechanisms in human gliomas" has bee accepted to publish in Nature Communications under the open access CC BY license.
November 2020
The PTBI Autumn Workshop 2020 took place on November 26/27 2020 and was successfully organised by Polish Bioinformatics Society together with IPI PAN. Over 30 presentations and in the peak time we had over 60 participants.
August 2020
Due to COVID-19 pandemic restrictions XIII Symposium of Polish Bioinformatics Society is postponed to 2021, but instead of it IPI PAN organise the PTBI Autumn Workshop 2020 that will take a place November 26/27 2020.
March 2020
Because of the COVID-19 pandemic restrictions we mainly work from home. Due to the fact that we are highly concerned about the progress of this pandemic, we publish this COVID-19 Charts Page.
January 2020
On January 8th Michał Dramiński and Michał J. Dąbrowski gave a talk at The Faculty of Electronics and Information Technology, Warsaw University of Technology, entitled 'Massive Feature Selection for dissecting significant regulatory regions for Breast Cancer development, using MCFS-ID algorithm'.
December 2019
We are pleased to announce that XIII Symposium of Polish Bioinformatics Society (September 16-18, 2020) will be hosted by Institute of Computer Science, Polish Academy of Sciences.
October 2019
It is our great pleasure to invite you to a seminar of Prof. Jacek Majewski entitled: "Exploring the Downstream Effects of Epigenetic Driver Mutations in Cancer: Disease informs Basic Science." on October 23rd, at 11.00 in the Nencki Institute of experimental biology in the Centre of Neurobiology conference room. Prof. Jacek Majewski is an Associate Professor at the Department of Human Genetics of McGill University and Genome Quebec Innovation Centre.
Below please find a summary of Prof. Majewski talk:
Several years ago, my lab participated in the identification of mutations in histone genes, specifically the H3K27M variant, as one of the key drivers in pediatric glioblastoma (Shwartzentruber et al. 2012). Our subsequent work has focused on using genomics approaches to study the downstream consequences of the histone mutations and also other epigenetic driver events in cancer. Epigenetic dysregulation seems most important in paediatric cancers, where we believe it is necessary to disrupt a balance between differentiation and proliferation, but we have also identified and studied epigenetic drivers in other cancers, such as bone, head and neck cancers (Papillon-Cavanagh et al. 2017), and leukemias (Boileau et al. 2019). We use CRSIPR genome editing in animal models and cell lines, along with genome-wide approaches such as RNA-seq, ChIP-seq, WGBS, to study the downstream effects of introduction or removal of epigenetic oncogenic mutations on the chromatin landscape. In addition to cancer relevance, I will highlight the insights into basic chromatin biology, and specifically interdependencies of various chromatin modifications, which this research direction has allowed us to elucidate.
September 2019
Michał Dąbrowski gave a talk at the 'XII Symposium of Polish Bioinformatics Society' which took place in September 19-21, 2019 - Kraków, Poland, entitled 'CytoMeth - a tool to perform DNA methylation analysis of bisulfite-converted Next Generation Sequencing data'. Abstract.
July 2019
The article 'Global DNA Methylation Patterns in Human Gliomas and Their Interplay with Other Epigenetic Modifications' has been published in Special Issue of Epigenetics in Metabolic and Neurological Disorders.
July 2019
Marta Jardanowska participated in the 44th FEBS Congress which took place in Kraków on 6-11 July 2019. She presented a poster entitled 'Analysis of transcription factor motifs discovered in glioma grade-specific enhancers'.
June 2019
During the 18th Int. Conf. on Artificial Intelligence and Soft Computing, June 16-20, 2019, Jacek Koronacki delivered an invited talk on 'Empirical Model Building with Monte Carlo Feature Selection and Interdependency Discovery' (prepared in collaboration with Michał Dramiński and Michał J. Dąbrowski). Also during the conference, Professor Koronacki was awarded a diploma "in recognition of his outstanding contribution to the development of computational intelligence" by the Polish Neural Network Society.
June 2019
Marta Jardanowska participated in the 3rd SMB PhD Students Symposium which took place on 14 June 2019 in Dziekanów Leśny. She presented a poster entitled 'Analysis of glioma grade-specific transcription factor motifs in the sequences of the active enhancers'.
June 2019
ZBO welcomes a new PhD scientist! On June 6th, Ilona Grabowicz successfully defended her PhD thesis. Gratz!
May 2019
Michal J. Dabrowski participated in the "Biology of Genomes" conference in Cold Spring Harbor Laboratory 7-11.05.2019. In the first poster section there were presented results of our lab entitled “Genome-wide mapping of DNA methylation variants affecting gene expression levels in gliomas with respect to their grade and IDH gene mutation status”. We are grateful organisers for the excellent meeting.
March 2019
prof. Jacek Koronacki Michał Dramiński and Michał J. Dąbrowski gave a talk at the University of Bialystok, 2019, entitled 'Massive Feature Selection for Breast Cancer Study using MCFS-ID algorithm'.
September 2018
Michał Dramiński gave a talk at the 'XI Symposium of Polish Bioinformatics Society' which took place in September 5-7, 2018 - Wrocław, Poland, entitled 'Monte Carlo Feature Selection and Interdependencies Discovery (MCFS-ID) with rmcfs 1.3.0'.
September 2018
We are still looking to hire one PhD student to join the team. If you are dynamic and committed young researcher working or specializing in one or more of the various fields of our interest you are highly welcome to apply. For information on open positions in the Lab please see (open positions)
July 2018
The article 'rmcfs: An R Package for Monte Carlo Feature Selection and Interdependency Discovery' has been published in Journal of Statistical Software.
July 2018
ZBO extends interests about a new "research field" ;)
June 2018
ZBO team have participated in the conference: 'BioInformatics in Torun 2018 - BIT18' which took place in 28-30 June 2018. We presented three posters: 'Analysis of the eQTLs and differentially expressed genes in the RNA-Seq data from glioma patients.' by Ilona E. Grabowicz et al., second 'Motif search in promoter regions from patients diagnosed with glioma' by Marta Jardanowska & Magdalena Mozolewska et al. and the third one by Agata Dziedzic et al.
June 2018
We are looking to hire one PhD student to join the team. If you are dynamic and committed young researcher working or specializing in one or more of the various fields of our interest you are highly welcome to apply. For information on open positions in the Lab please see (open positions)
March 2018
The article 'Unveiling new interdependencies between significant DNA methylation sites, gene expression profiles and glioma patients survival' has been published in Nature - Scientific Reports.
March 2018
On 8th and 9th of March Agata Dziedzic and Ilona Grabowicz have attended the 8th Clinical Epigenetics International Meeting in Düsseldorf, Germany. They have presented posters entitled “Analysis of the Single Nucleotide Polymorphisms in the RNA-Seq data from glioma patients” and “A tool for DNA methylation analysis - case study of 26 glioma patients representing various tumour grades”.
November 2017
Enthusiasts R Meetup: A talk given by dr Michał Dramiński entitled "Monte Carlo Feature Selection and Interdependencies Discovery (MCFS-ID)". More information about this event is (here).
October 2017
dr Michał J. Dąbrowski and dr Michał Dramiński gave a talk at IPI PAN entitled "Feature selection in life sciences" for the Ministry of Science and Technology of Taiwan.
August 2017
dr Magdalena Mozolewska gave a talk at the "2nd International Conference on Computational Genomics and Proteomics" held in Playa Blanca, Panama from August 14 to August 18, 2017 entitled "Carbon nanotubes in UNRES force field". She presented the results of implementing the simplified Carbon Nanotube into the physics-based, coarse-grained UNited RESidue (UNRES) force field. Simulations of protein-CN systems were tested for the ability to keep constant energy and influence of CN on temperature stability of the thermostats. Then new potential was utilized to study interactions of various sizes of CNs with three model proteins: BSE, CT, and SBP. Her results show that the extended UNRES force field can predict binding of these proteins to CNs correctly, and observed influence of CN on the protein-structure stability is in a good agreement with the experimental observations.
July 2017
PhD student scholarship competition is over. We selected best candidates to join to our team.
July 2017
New applications are no longer accepted. Notification of results of the competition will take place on 2017-07-20.
June 2017
We are looking to hire three PhD students to join the team. If you are dynamic and committed young researcher working or specializing in one or more of the various fields of our interest you are highly welcome to apply.
For information on open positions in the Lab please see (open positions)
June 2017
dr Michal J. Dabrowski gave a talk at the IPI PAN seminar entitled “DNA methylation impact on the glioma patients overall survival”. The aim of our study is to establish a highly accurate prediction of patients’ survival using the classification-based feature selection and rule-based modeling. Moreover, we aim at obtaining specific interdependencies between genes and methylation sites. At the same time, we verify feasibility of the Monte Carlo Feature Selection and Interdependency Discovery (MSFS-ID) algorithm to efficiently process large scale data consisting of almost half million features.
May 2017
Atlas of brain regulatory regions meeting May 16-17th 2017 in Wierzba. This was an annual meeting that entire consortium participated to update working progress.
ZBO presented there: simulation of transcription factor binding to specific DNA regions,
semiautomatic analysis of genes significantly related to glioma patients prognosis,
application of a pipeline for methylom data analysis.
May 2017
ZBO Web Page is alive.
April 2017
A visit of Magdalena Mozolewska to Komorowski's Lab in Uppsala.
March 2017
Michał Dąbrowski and Jan Komorowski visited Cold Spring Harbor Laboratory. They attended and contributed to the 'Systems Biology: Networks Conference'.