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February 22nd 2018
ZBO seminars: A talk given by prof. Jacek Koronacki entitled "Issues in Big Data Analysis: Dealing with Data Streams". Summary: After a short intro explaining what is usually meant under the term "Big Data", I shall confine myself to dealing with data streams. I shall report on: (i) current approaches to building classification trees for stationary series; (ii) a simple way to adjust an ensemble size in stream data classification; and (iii) a not so simple way to develop regression models for nonstationary data streams. My emphasis will be on methods with sound mathematical foundation (albeit with all the proofs and mathematical details skipped). The talk will be based on the work of Prof. Leszek Rutkowski and his research group at Częstochowa University of Technology.

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February 1st 2018
ZBO seminars: A talk given by Paweł Teisseyre entitled "Introduction to multi-label classification". Summary: Recently multi-label classification has attracted a significant attention in machine learning community. In standard classification problem we investigate the relationship between response variable (e.g. occurrence of cancer) and features (e.g. expressions of genes, SNPs or methylations). In multi-label problem we consider many response variables (labels) simultaneously (e.g. different diseases). The goal is to build a model which predicts response variables (labels) based on feature values. Multi-label methods has been successfully applied in many domains, an interesting example is modeling mulimorbidity (co-occurence of many diseases in one patient). In my talk I will introduce the basic methods: Binary Relevance, Label Powerset and Classifier Chains and discuss the available software.

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January 18th 2018
ZBO seminars: A talk given by Bartosz Wojtaś entitled "Next generation sequencing focused on transcriptomics". Summary: Next generation sequencing technology has emerged as a leading biomedical technology of XXI century. It has revolutionized modern science and medicine. In my talk I want to explain basics of that technology for non-expert audience and discuss in details potential of transcriptomics analysis. In my talk I will also discuss differences between two most commonly used global transcriptomics analysis - microarrays and RNAseq.

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January 4th 2018
ZBO seminars: A talk given by Marta Jardanowska entitled "Network activity of selected neurons of the C. elegans nematode in interaction processess of the organism with its environment". Summary: Caenorhabditis elegans is a popular model organism in studies of embryogenesis, morphogenesis, development and neurobiology. Because of the good knowledge of anatomy of this nematode, understanding its neural networks can provide many valuable solutions to today's problems referring to the functioning of nervous systems and the functioning of the human brain. Because C. elegans is a simple organism, therefore, in the current state of the knowledge, leading both experimental and computational research, we have a real possibility of obtaining reliable and accurate results.

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December 21st 2017
ZBO seminars: A talk given by Ilona Grabowicz entitled "Investigating brain gene expression and gut microbiome changes and its interactions with the host upon diet-induced behaviour changes". Summary: Diet is influencing organisms in numerous ways. In the seminar, it will be described how 'cafeteria diet' can affect behavior of mice and gene expression in a TAD-dependent manner in different parts of the brain. Moreover, it will be shortly discussed how the high-fat diet and differences in mice strains can affect also behavior of mice and also composition of their gut microbiota.

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December 7th 2017
ZBO seminars: A talk given by Agata Dziedzic entitled "Fungal lifestyle reflected in serine protease repertoire". Summary: Fungi are able to switch between different lifestyles in order to adapt to environmental changes. Their ecological strategy is connected to their secretome as fungi obtain nutrients by secreting hydrolytic enzymes to their surrounding and acquiring the digested molecules. We focus on fungal serine proteases (SPs), the phylogenetic distribution of which is barely described so far. In order to collect a complete set of fungal proteases, we searched over 600 fungal proteomes. Obtained results suggest that serine proteases are more ubiquitous than expected. Our study present a comprehensive evolutionary history of fungal SP families in the context of fungal ecology and fungal tree of life.

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November 30th 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).

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November 9th 2017
ZBO seminars: A talk given by Dr Michał J. Dąbrowski entitled "Methylation patterns in cancer patients". Summary: DNA methylation is one of the most frequently studied epigenetic elements in mammals. It regulates gene expression in cells – activation and silencing depending on the cell function specificity. It is also associated with histone modifications and by that with the architecture of a chromatin. The covalent addition of a methyl group is most frequently present in cystosine within CpG dinucleotides. The concentration of (CpG)n is called CpG islands. The majority (~70%) of human promoters located near transcription start site (TSS) of a gene contain a CpG island. During an organism development many epigenetic factors may change, including CpG methylation and chromatin reorganization. DNA methylation is known to be abnormal in all studied forms of cancer. This talk is focused on how this occurs, what is its role in tumorigenesis and how is it used for cancer classification purposes and prediction of patients prognosis.

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October 26th 2017
ZBO seminars: A talk given by Dr Magdalena Mozolewska entitled "Molecular modeling of protein systems". Summary: The Iron-Sulfur Clusters (ISCs) are highly spread among the organisms from prokaryote to eukaryote. They are the crucial part of many cellular processes like electron transfer, redox reactions, and catalysis of chemical reactions. Many proteins require presence of chaperons to achieve and stabilize their structures. In yeast Saccharomyces cerevisiae the Fe/S cluster biogenesis cycle is one of the mechanisms, which are necessary for the organism, but despite the numerous studies, still not well known. To investigate such intricate system coarse-grained UNRES force field was used to obtain the structure and dynamics of the Isu1-Jac1 and Isu1-Jac1-Ssq1 complexes.

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October 19th 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.

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October 12th 2017
ZBO seminars: A talk given by Dr Michał Dramiński entitled "Monte Carlo Feature Selection and Interdependencies Discovery (MCFS-ID). Theory and practical usage of the algorithm". Summary: The aim of the lecture was to present and teach an innovative approach (MCFS-ID) to select informative features from high dimensional complex Life Science data sets using R. R is powerful environment and language for data processing and it supports various machine learning, statistical, optimization and data mining functions. The package rmcfs is not only MCFS-ID implementation for R – it is a complex solution for feature selection, discovery of feature interdependencies (ID) as well as evaluation and later processing of the obtained result.

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August 30th 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.

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July 20th 2017
PhD student scholarship competition is over. We selected best candidates to join to our team.

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July 2nd 2017
New applications are no longer accepted. Notification of results of the competition will take place on 2017-07-20.

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June 7th 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)

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June 5th 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.

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May 16-17th 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.

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May 1st 2017
ZBO Web Page is alive.

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April 3rd 2017
A visit of Magdalena Mozolewska to Komorowski's Lab in Uppsala.

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March 14th 2017
Michał Dąbrowski and Jan Komorowski visited Cold Spring Harbor Laboratory. They attended and contributed to the 'Systems Biology: Networks Conference'.