ZBO Seminars (in English)
Time: Thursdays 11.00PM. Location: IPI PAN building, 3rd floor, room 334.

Seminars 2019

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June 13th 2019
A talk given by Agata Dziedzic entitled "CytoMeth - additional functionalities". Summary provided by the author: CytoMeth is going to be a tool for DNA methylation data analysis. Its main purpose is to take raw bisulphite (fastq) data as input and return beta value as result. On this seminar the author will present suggestions and ideas for additional functionalities of Cythometh, including figures with genomic annotation for batch samples input and broad quality control statistics together with biological explanation of it.

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May 30th 2019
A presentation and discussion leaded by Michal Dramiński entitled "CytoMeth - The current beta version". Summary provided by the author: CytoMeth is a new upcoming tool implemented by ZBO team. The author is going to present the current beta version of the tool that compiles a set of open source software named in the Roche pipeline guidelines to perform SeqCap Epi data analysis.

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May 23rd 2019
A discussion leaded by Michal J. Dąbrowski entitled "Discussion of the conference in CSH". Summary provided by the author: Because of my participation in the Cold Spring Harbor Laboratory conference about “The Biology of Genomes”, I would like to share my observations regarding computational biology in the field of molecular biology, newly acquired knowledge and the possibilities of applying newly discovered tools in our research.

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May 16th 2019
A talk given by Marta Jardanowska entitled "Identification of transcription factor motifs in three different regions influenced by significant DNA methylations in breast cancer". Summary provided by the author: During the previous presentation, the author presented results in 1454 sequences. This time the author decided to use sequences +/- 20bp around all 2023 significant methylations that predict breast cancer and have been identified in the previous analysis. These sequences were divided into three groups depending on the localisation - in promoter regions, gene body regions or intergenic regions. While this talk, the result of the TF motifs search, functional analysis and expression changes will be presented.

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May 9th 2019
A talk given by Agata Dziedzic entitled "DNA methylation of transcription factor motifs within promoters - glioma grades comparison". Summary provided by author: DNA methylation within promoter is knows to affect gene expression. This study aimed to find differentially methylated DNA transcription factor motifs within promoters and to combine obtained results with gene expression changes between glioma grades. Two different approaches were used to find differentially methylated motifs between grades: 1) single methylation site comparison and 2) mean methylation value of whole motif. As a result we raport differentially expressed genes whose expression might be regulated by DNA methylation in their promoters as well as set of specific transcription factors that would be involved in this process.

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April 18th 2019
A discussion leaded by prof. Jacek Koronacki entitled "British Biologist Denis Noble Debunks Neo Darwinism".

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April 4th 2019
A talk given by Marta Jardanowska entitled "Identification of transcription factor motifs influenced by significant DNA methylations in breast cancer". Summary provided by the author: Significant methylations that predict breast cancer have been identified in the previous analysis. In order to check if these methylations could affect any transcription factor (TF), the reference genome was used to determine the sequence +/- 20bp around these methylations. During this talk, the result of the TF motif search will be presented.

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March 28th 2019
A talk given by dr Adam Filip entitled "BRCA - past, presence and future of the project". Summary: During the talk, author will present recent updates to the project together with future plans. In particular new analysis of methylations involved in predicting cancer will be presented.

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March 21st 2019
A talk given by dr Michał J. Dąbrowski entitled "How to select meaningful regulatory regions – the case study of promoter methylations in various glioma tumours". Summary: DNA methylation patterns of genomic regulatory regions affect gene expression levels. In consequence genes that in normal tissue should be silenced are enhanced, and those which should be enhanced are repressed. The change of genes expression results in tumour progression and it seems that epigenetic changes play an important role in this process. Here we confirmed the association of promoter methylation level and gene expression and with use of relevant biological filter we selected the true positive examples.

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March 14th 2019
A talk given by Ilona Grabowicz entitled "Analysis of methylation of cytosines localized within the TAD boundaries". Summary: During this seminar, the results of my latest analyzes on cytosine methylation within the TAD boundaries will be presented. The investigated topics included comparing levels of cytosines methylations depending on the: IDH mutation status, glioma WHO grade and CTCF binding regions. Moreover, it will be shown how methylation levels differ between TAD border and non-border cytosines and whether differentially methylated cytosines influence levels of co-regulation of gene expression within and accross neighboring TADs.

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March 7th 2019
A talk given by dr Michał Dramiński entitled "Introduction to object-oriented programming (OOP)". Summary: During this talk object-oriented programming concept will be presented. OOP model is organized around objects rather than "actions" and data rather than logic. Together with the introduction to the paradigm, a real life and some low level (source code) examples will be shown.

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February 28th 2019
A talk given by Agata Dziedzic entitled "An update on methylation of TFs motifs and its influence on gene expression - mean methylation instead of single CpG analysis". Summary: I kindly invite everybody who is interested in methylation of transcription factor motifs for my seminar that I prepared together with Marta J and Michał JD. Let's see which genes turned out to be statistically significant when using a different statistical method for detection and discuss how detected genes might explain biological processes in glioma. This time results were obtained by Wilcoxon test based on comparing different glioma grades. I look forward to your scientific criticism!.

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February 21st 2019
A talk given by prof Jacek Koronacki entitled "From Modeling to Model-free Data Mining and Back". Summary: For a long time statistics had been a hypothesis-driven endeavor, tightly connected with modeling paradigm. Somewhere around 1975 the "Age of Tukey" followed under the banner of "Let tha data speak for themselves". Indeed, with more and more data at hand, modeling proved infeasible unless all too oversimplifying assumptions were made. As was expected, with Data Flood coming in, model-free Data Mining has brought much success to research and development, this being due to breathtaking increase in processing power and memory capacity of our PC's, not to mention HPC systems and cloud computing. However, by the very same token, our modeling abilities have also increased "almost infinitely". In this talk, we'll summarize briefly this process and make some remarks on the power of forward simulation studies (by examples from oncology and portfolio selection) and data-driven causal reasoning.

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February 14th 2019
A talk given by Marta Jardanowska entitled "Identification of DNA motifs regulated by DNA methylation in glioma samples - preliminary study". Summary: Transcription factors (TF) regulate gene expression. TF binding affinity to its DNA motif might be affected by the methylation level of cytosines within that motif. The aim of this presentation will be showing the results of examining the methylation patterns of various TF motifs.

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February 7th 2019
A talk given by dr Paweł Teisseyre entitled "A deeper look at two concepts of measuring gene-gene interactions: logistic regression and interaction information revisited". Summary: Detection of gene–gene interactions is one of the most important challenges in genome-wide case–control studies. Besides traditional logistic regression analysis, recently the entropy-based methods attracted a significant attention. Among entropy- based methods, interaction information is one of the most promising measures having many desirable properties. Although both logistic regression and interaction information have been used in several genome-wide association studies, the relationship between them has not been thoroughly investigated theoretically. The present paper attempts to fill this gap. We show that although certain connections between the two methods exist, in general they refer two different concepts of dependence and looking for interactions in those two senses leads to different approaches to interaction detection. The numerical experiments illustrate the theoretical findings indicating that interaction information and its modified version are more universal tools for detecting various types of interaction than logistic regression and linkage disequilibrium measures.

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January 17th 2019
A talk given by dr Adam Filip entitled "Genomic features predicting presence of breast invasive carcinoma (BRCA)". Summary: During the talk results of analysis of breast cancer data from TCGA (The Cancer Genome Atlas) will be presented. The author will also present a set of mRNAs, methylations, miRNAs and their interplay that determines presence of cancer.

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January 10th 2019
A talk given by dr Michał J. Dąbrowski entitled "Specific DNA methylation level of promoter regions detected for specific group of genes for pilocytic astrocytoma and glioblastoma tumor samples". Summary: DNA methylation is a well-known epigenetic element that regulates genes expression. It was shown that DNA methylation significantly affects glioma tumour development and is associated with patient’s prognosis. Here it was studied whether gene promoter various levels of methylation were correlated with expression of those genes. It was confirmed that a number of 74 genes differed in promoter level methylation as well as in gene expression between pilocytic astrocytoma samples and glioblastoma.

Seminars 2018

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December 10th 2018
A talk given by Ilona Grabowicz entitled "Methylation of CpGs present within borders of Topologically Associating Domains". Summary: Within TAD borders there were found CpGs that can be methylated. The observed levels of methylation differed between glioma patients classified with different WHO grades and between patients carrying mutations in IDH genes and non-carriers.

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December 6th 2018
A talk given by dr Michał Dramiński entitled "Classification of Symfonia patients based on models built on Cecarelli RNASeq data". Summary: This talk is about selection of the most significant genes for several target attributes (e.g. IDH mutant status, grade, survival, GBM subtype etc.) from Cecarelli RNASeq data, later building classification models and application of them on Symfonia RNASeq data. Selection of significant features is performed using MCFS-ID algorithm and classification method is based on application of committee of three different classifiers. Finally, a new set of descriptive features is obtained for Symfonia patients.

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November 29th 2018
A talk given by Agata Dziedzic entitled "Differentially methylated sites and their influence on gene expression". Summary: We performed differentional methylation calling and found 209,260 differentially methylated sites for PA vs. GB and 174,383 differentially methylated sites for IDH wild-type vs. IDH mutant. Then we annotated those sites in respect to the genome parts (promoter, gene body, CpG islands). Additionally, to verify the differentially methylated sites functionality, we investigated expression (RNA-seq) of genes associated with those sites.

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November 22nd 2018
A talk given by prof Jacek Koronacki entitled "AI: What's that, and how it relates to human enhancement and cyber immortality". Summary: The talk will consist of two parts. In the first, a study in progress which offers a novel approach to describe what AI is will be presented. By far, the main author of this novel approach is Andrzej Rabczenko, with the undersigned playing the role of a critical commentator of Andrzej’s work. In the second part, a hype on human enhancement, cyber immortality and the like endeavors will be critically (and with due hostility) assessed.

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November 8th 2018
A talk given by Marta Jardanowska entitled "Motif analysis: detection of transcription factor motifs on promoter and enhancer sequences". Summary: The aim of this presentation will be introduction to motif searching in sequences in promoter and enhancer regions from patients diagnosed with glioma. The author will show common and differential motifs from PA and DA/GB samples using two different approaches of searching - de novo analysis and known motif search. Then the author will be showing some biological relations, especially protein families correlations.

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October 25th 2018
A talk given by Adria Roura entitled "Somatic mutation history of glioblastoma patients with recurrent tumors". Summary: Glioblastoma (GBM, WHO grade IV) is a common and most lethal primary brain tumor which remains largely resistant to current therapies. Despite tumor resection and the following treatment of GBM patients with radiotherapy and chemotherapy, GBM frequently recurs. Dissection of the GBM genetics and understanding intrinsic mechanisms of tumor recurrence may lead to more targeted and effective treatments. Here we report the results of targeted next-generation sequencing of cancer- and epigenetics-related genes in 16 fresh frozen glioma samples of WHO grade IV, collected from Polish population. We employed a second generation DNA sequencing target enrichment design comprising a 600 cancer-related gene panel and 100 epigenetics-related genes, comprising the exomes +/- the promoter regions. The target region spanning 7 MB (1x106 base pairs) was designed to cover meaningful portion of genomic, cancer-related sites with a strong emphasis on epigenetic regulators (histone modifiers, chromatin modelers, histone chaperons). Additionally, RNA sequencing was performed to better understand the transcriptomic profiling in the malignant progression of GBM. Targeted sequencing of GBMs demonstrated different genetic drivers (including well known EGFR, TP53, PDGFR and PTEN mutations) and numerous genetic alterations in genes responsible for histone modifications, chromatin remodeling and DNA damage repair. In recurring GBMs we observed only a subset of mutations coming from primary tumors, suggesting a specific path of clonal evolution.

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October 18th 2018
A talk given by dr Adam Filip entitled "Prognostic markers for Breast Invasive Carcinoma (BRCA)". Summary: In order to find features that predict breast invasive carcinoma, Monte Carlo Feature Selection and Interdependency Discovery (MCFS-ID) algorithm was applied on the Cancer Genome Atlas (TCGA) dataset containing information obtained from tissues of patients suffering from BRCA. The dataset was composed of information about methylation (HumanMethylation450), mRNA and microRNA expression levels. During the talk, a set of features predicting presence of cancer and/or its subtypes will be presented.

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October 10th 2018
A talk given by dr Michał J. Dąbrowski entitled "REST transcription factor ChIP-seq data of glioma tumor patients in the context of their DNA methylation patterns". Summary: The aim of the study is to obtain a better picture of how DNA methylation may affect the binding of REST transcription factor to DNA. This association is studied in the context of discerning glioma patients for PA vs. high grades. We seek for the significant differences that have significant functional effect on specific genes expression. The first preliminary results will be shown as well as plans for the further analysis. I look forward for a fruitful discussion.

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September 27th 2018
A talk given by dr Rafał Guzik entitled "IDH in Glioma". Summary: IDH1/2 genes suddenly “Big Banged” cancer genetics in 2008. They are continuously being found mutated in 80 % of grade 2 – 3 glioma and secondary glioblastoma (also in 16 to 75 % tumors of other tissues). Why? What is the mechanism? Let’s review the basics...

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September 20th 2018
A talk given by dr Magdalena Mozolewska entitled "Implementation and tests of carbon nanoparticles in coarse-grained UNRES force field.". Summary: Nanoparticles are relatively new, but a rapidly increasing area of interest by scientists. Due to their unique properties, Carbon Nanotubes (CN) and fullerenes can be used in a variety of fields e.g. an industry, military or in a medicine, as carriers of small ligands into target cells e.g. in a cancer therapy, or CNs themselves can be used as ligands, interacting with receptors as their antagonists. Very high computational cost of all-atom force fields limits severely a time-scale of the simulations and a size of the investigated systems. Therefore, in this work, we introduce the implementation of CNs and fullerenes into the physics-based, coarse-grained UNited RESidue (UNRES) force field, which due to the reduction of the number of interaction sites, provides 3-4 order of magnitude speed-up comparing to the all-atom force fields. We simplified representations of CNs and fullerenes to the immobile outer field with adjustable dimensions, which interacts with proteins through Kihara potential. Simulations of protein-nanoparticle systems were tested for the ability to keep constant energy and influence of nanoparticle on temperature stability of the thermostats. Then new potential was utilized to study interactions of various sizes of CNs and fullerenes with different proteins. Our results show that the extended UNRES force field can predict binding of these proteins to CNs correctly and observed the influence of carbon nanoparticles on the protein-structure stability is in a good agreement with the experimental observations.

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September 6th 2018
A talk given by Ilona Grabowicz entitled "Towards finding hyperactive TADs in glioma.". Summary: In development of glioma, various genes whose expression becomes altered, play a different roles. Majority of genes are localized within TADs and in this talk the author will present a method for finding hyperactive TADs in glioma and how this method can be applied to other datasets.

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June 14th 2018
A talk given by dr inż. Michał Dramiński entitled "dmUtils: a new R helper package to support mcfs analysis.". Summary: During this talk the author of rmcfs package will present practical usage of the new dmUtils package together with new version of rmcfs. The package implements set of functions that simplifies analysis of decision tables as well as more advanced analysis of the top features obtained from MCFS. Some information about upcoming version of rmcfs 1.3 will be also discussed. Entire talk will be more live demo than typical presentation.

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May 24th 2018
A talk given by Agata Dziedzic entitled "Overview of DNA methylation analysis - from raw sequencing data to first results.". Summary: We investigated 21 brain tumour samples representing various glioma grades: pilocytic astrocytoma (PA; grade I; n = 7), diffuse astrocytoma (DA; grades II and III; n = 7) and glioblastoma (GB; grade IV; n = 7). We used SeqCap Epi CpGiant Methylation panel and performed bisulphite conversion followed by Illumina sequencing. We obtained at average 23 mln sites per each sample. From those 23 mln sites ~ 3.3 mln were in CpG context and ~ 19.7 mln were in non-CpG context. For further study we only selected sites that were in CpG context and with coverage above 10 reads. We will present first results of differentional methylation calling and methylation patterns across samples form various tumor grade.

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May 17th 2018
A talk given by prof. dr hab. Jacek Koronacki entitled "Neo-Darwinism is wrong ...". Summary: Neo-Darwinism is wrong with its emphasis on blind chance as the origin of variation. "Blind chance is necessary, but the origin of functional variation is not at the molecular level" writes Denis Noble in his survey published in Interface Focus 7 (2017), http://dx.doi.org/10.1098/rsfs.2016.0159. He writes also: "Stochasticity is harnessed by organisms to generate functionality. Random-ness does not, therefore, necessarily imply lack of function or ‘blind chance’ at higher levels. [...] The order originates at higher levels, which constrain the components at lower levels. We now know that this includes the genome, which is controlled by patterns of tran-scription factors and various epigenetic and reorganization mechanisms." In my talk, borrowing from Noble's paper, I'll sketch where to look for justification of those claims.

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May 10th 2018
A talk given by dr Michał J. Dąbrowski entitled "Unveiling informative DNA methylation site and gene expression profiles that contribute to glioma patients survival". Summary: There is a grooving evidence that molecular markers are important for diagnosis and prognosis of glioma patients. In the Central Nervous System tumor classification provided by World Health Organization in 2016 there is a number of molecular features that were included in the classification together with histology. In this project in order to find clinically useful prognostic markers for glioma patients’ survival, we employed Monte Carlo Feature Selection and Interdependencies Discovery (MCFS-ID) algorithm on DNA methylation (HumanMethylation450 platform) and RNA-seq datasets from The Cancer Genome Atlas (TCGA) for 88 patients observed until death. Using the machine learning methods, we discovered a set of significant features, mainly DNA methylation sites that enable for an accurate distinction between glioma patients with short and long overall survival (OS) i.e. days to death. The significance of the discovered features was confirmed on an independent glioma study cohort. We found that those features are much better predictors of patients’ OS than the previously described molecular markers (such as, e.g., IDH, ATRX, DAXX mutation status). Finally, we found that the most important methylation feature (cg15072976) overlaps with RE1 Silencing Transcription Factor (REST) binding site, is functional and its methylation status affects transcription factor binding in U87glioma cells as evidenced by gel shift assay.

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April 26th 2018
A talk given by dr Rafał Guzik entitled "IDH (isocitrate dehydrogenase) in glioma". Summary: IDH1/2 genes suddenly “Big Banged” in cancer genetics in 2008. They have being continuously found to be mutated in about 80 % of grade 2 – 3 gliomas and secondary glioblastoma, in 75 % of cartilaginous tumors, intrahepatic cholangiocarcinoma (23 %), close to 20 % of acute myeloid leukaemia, thyroid carcinomas (16 %), and other tumors. Why? What is the mechanism? Let’s review the basics...

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April 19th 2018
A talk given by dr Magdalena Mozolewska entitled "De novo motif search". Summary: De novo motif search is a commonly used method in bioinformatical studies to search and identify specific sequences in a given DNA sequence for further analysis, e.g. an identification of transcription factors motifs. The main hypothesis is that specific transcription factors of the selected genes promotor regions, can distinguish the grade of the glioma tumor. In this study, the DNA sequences were obtained from glioma patients and cover active promotors that are used in the de novo motif prediction to identify transcription factors important in development of glioma.

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April 5th 2018
A talk given by Ilona Grabowicz entitled "Investigating microbiome of Down's Syndrome model mice and its changes induced by high-fat diet". Summary: People suffering from Down's syndrome are characterized by malfunctioning of the gastrointestinal tract and are more prone to obesity than healthy ones. Recent advances in sequencing technology made it possible to study microbiomes. In my talk I will present results of the analysis of microbiomes of the Down's syndrome mouse models, which are also subjected to high-fat diet, which promotes obesity and has addictive properties. I will show which bacterial species are differentially abundant between these two mouse strains and also diets. I will show the pros and cons of sequencing microbial DNA and RNA. Moreover I will show the results and pitfalls of analyzing the microbial gene expression.

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March 22nd 2018
A talk given by dr Michał Dramiński entitled "Analysis of IDH and gene expression levels of Symfonia patients". Summary: This talk is about selection of the most significant genes for IDH status, tumor grade and survival for set of TCGA and Symfonia patients.

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March 15th 2018
A talk given by Marta Jardanowska entitled "Motif analysis: Detection of transcription factor motifs within the grade specific active promoters marked by histone methylation". Summary: The talk is about the latest research related to detection of motifs of transcription factors in a set of DNA sequences marked with specific histone methylation in the promotor region of transcribed genes. The first set of methylated promoters comes from the following selection: promotors active in grade one and non-active in the higher grades. The other set is opposite to the first one. There are active promoters from higher grades and non-active in the grade one. The aim of this presentation is to describe biological background of the research and methods used. Some preliminary results will be presented as well as the encounter difficulties and further steps of this analysis.

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February 22nd 2018
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
A talk given by dr 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
A talk given by dr 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
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.

Seminars 2017

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December 21st 2017
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
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 9th 2017
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
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 12th 2017
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.