Center of Biostatistics and Bioinformatics Analysis

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WHO WE ARE

A new core facility is being established at the Medical University of Gdańsk in the form of the Center of Biostatistics and Bioinformatics Analysis.

The idea of this Computing Centre is to facilitate the work of research teams by increasing the scientific excellence of the published results. The core facility’s key area of operation is to support the process of scientific research and clinical research in the field of biostatistics and bioinformatics, especially in the context of the Priority Research Areas, implemented under the “Excellence Initiative – Research University” program. The Centre employs biostatisticians and bioinformatists whose work is aimed at strengthening interdisciplinarity in research conducted at the MUG.

The core facility offers a wide range of services related to the broadly understood biostatistical and bioinformatic analysis as well as big data analysis. The activity profile includes mainly support for projects based on high-throughput DNA and RNA sequencing (including single cell analysis), as well as other scientific initiatives that require processing of large amounts of data. Additionally, the activities of the Centre will include the use of artificial intelligence in the processing of imaging data and the classification of patient samples.

One of the key initiatives of the Computing Centre is the Biostatistics Clinic, offering MUG employees and doctoral students the opportunity to discuss the optimal approach to statistical data analysis. The Computing Centre will provide researchers with professional support at every stage of research, from designing the measurement methodology, through data acquisition and analysis, to the final interpretation.

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An important mission of the Computing Centre is to offer scientists support at any level in the field of bioinformatics analysis. The core facility offers services supporting research needs at the interface of biostatistics, bioinformatics and molecular biology, focusing on the analysis of data from high-throughput sequencing: DNA analysis, gene regulation analysis (miRNA, transcription factors, epigenetics), genome stability analysis, genome variability (SNP) as well as the analysis of genes and proteins of prokaryotic and viral origin.

This is made possible by an advanced computer infrastructure, which creates space for ground-breaking scientific research based on sophisticated calculations. On the technical level, high-quality biostatistical analysis allows for the extraction of the maximum amount of objective information, which ultimately translates into high-quality research work. In this spirit, the Centre places particular emphasis on the high quality of computational processes, thus increasing the MUG’s project capacity.

The effective conduct of advanced scientific research is possible thanks to a structure that facilitates the comprehensive collection and processing of biostatistical, bioinformatic and clinical imaging data. This structure provides advanced data processing tools that facilitate the proper design of research projects. Thanks to professional statistical and biostatistical analysis, it enables and significantly accelerates their comprehensive implementation.


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RANGE OF SERVICES

Overview of the services provided

The Computing Centre is a scientific unit that provides comprehensive support for researchers in planning, designing, managing and reporting research projects related to clinical, epidemiological and laboratory research.

Cooperation areas:

- grant projects: designing a scientific research and planning biostatistical analyses (analysis of the sample size/ strength of statistical tests, proposal and description of the statistical methodology),

- scientific publications/abstracts: describing the statistical methodology, statistical analysis of the research questions posed, describing and interpreting the results, presenting the results in graphical and tabular form (in accordance with the recommendations of a scientific journal),

- scientific reviews: writing answers to the questions/ suggestions of reviewers related to statistical analysis,

- medical data: database design and management, data cleaning, data quality maintenance,

- biostatistics consultations: educating in designing scientific research, giving advice on collecting and managing data, supporting the selection of statistical methods, helping in the interpretation of results and in the process of evaluating the quality of scientific publications.


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Detailed description of the services provided

The Centre provides a wide range of comprehensive services in the field of advanced biostatistical and bioinformatic analysis. The services are offered primarily to scientists conducting clinical, epidemiological, population, molecular and translational research. The computational techniques offered by the Centre are listed on the Extranet.

1. Biostatistical/Bioinformatic Analysis

The biostatistics/bioinformatics analysis order form can be found on the Extranet.

2. Biostatistical consultations

The biostatistical consultations order form can be found on the Extranet.



Our publications

1. Environmental exposure to persistent organic pollutants measured in breast milk of lactating women from an urban area in central Poland.
Grešner P, Zieliński M, Ligocka D, Polańska K, Wąsowicz W, Gromadzińska J. Environ Sci Pollut Res Int. 2021 Jan;28(4):4549-4557 doi: 10.1007/s11356-020-10767-3

2. Clustered microRNAs: The molecular mechanism supporting the maintenance of luteal function during early pregnancy.
Przygrodzka E, Sokołowska G, Myszczynski K, Krawczynski K, Kaczmarek MM. FASEB J. 2020 May;34(5):6582-6597 doi: 10.1096/fj.201903007RR

3. Rad51 paralogs and the risk of unselected breast cancer: A case-control study.
Grešner P, Jabłońska E, Gromadzińska J. PLoS One. 2020 Jan 6;15(1):e0226976 doi: 10.1371/journal.pone.0226976

4. The Discovery of a LEMD2-Associated Nuclear Envelopathy with Early Progeroid Appearance Suggests Advanced Applications for AI-Driven Facial Phenotyping.
Marbach F, Rustad CF, Riess A, Đukić D, Hsieh TC, Jobani I, Prescott T, Bevot A, Erger F, Houge G, Redfors M, Altmueller J, Stokowy T, Gilissen C, Kubisch C, Scarano E, Mazzanti L, Fiskerstrand T, Krawitz PM, Lessel D, Netzer C. Am J Hum Genet. 2019 Apr 4;104(4):749-757 doi: 10.1016/j.ajhg.2019.02.021

5. Spectrum of Epithelial-Mesenchymal Transition Phenotypes in Circulating Tumour Cells from Early Breast Cancer Patients.
Markiewicz A, Topa J, Nagel A, Skokowski J, Seroczynska B, Stokowy T, Welnicka-Jaskiewicz M, Zaczek AJ. Cancers (Basel). 2019 Jan 9;11(1):59 doi: 10.3390/cancers11010059

6. Comparison of three variant callers for human whole genome sequencing.
Supernat A, Vidarsson OV, Steen VM, Stokowy T. Sci Rep. 2018 Dec 14;8(1):17851 doi: 10.1038/s41598-018-36177-7

7. Sequencing of organellar genomes of Gymnomitrion concinnatum (Jungermanniales) revealed the first exception in the structure and gene order of evolutionary stable liverworts mitogenomes.
Myszczyński K, Górski P, Ślipiko M, Sawicki J. BMC Plant Biol. 2018 Dec 3;18(1):321 doi: 10.1186/s12870-018-1558-0

8. Enhanced detection of circulating tumor DNA by fragment size analysis.
Mouliere F, Chandrananda D, Piskorz AM, Moore EK, Morris J, Ahlborn LB, Mair R, Goranova T, Marass F, Heider K, Wan JCM, Supernat A, Hudecova I, Gounaris I, Ros S, Jimenez-Linan M, Garcia-Corbacho J, Patel K, Østrup O, Murphy S, Eldridge MD, Gale D, Stewart GD, Burge J, Cooper WN, van der Heijden MS, Massie CE, Watts C, Corrie P, Pacey S, Brindle KM, Baird RD, Mau-Sørensen M, Parkinson CA, Smith CG, Brenton JD, Rosenfeld N. Sci Transl Med. 2018 Nov 7;10(466):eaat4921 doi: 10.1126/scitranslmed.aat4921

9. Copy number signatures and mutational processes in ovarian carcinoma.
Macintyre G, Goranova TE, De Silva D, Ennis D, Piskorz AM, Eldridge M, Sie D, Lewsley LA, Hanif A, Wilson C, Dowson S, Glasspool RM, Lockley M, Brockbank E, Montes A, Walther A, Sundar S, Edmondson R, Hall GD, Clamp A, Gourley C, Hall M, Fotopoulou C, Gabra H, Paul J, Supernat A, Millan D, Hoyle A, Bryson G, Nourse C, Mincarelli L, Sanchez LN, Ylstra B, Jimenez-Linan M, Moore L, Hofmann O, Markowetz F, McNeish IA, Brenton JD. Nat Genet. 2018 Sep;50(9):1262-1270 doi: 10.1038/s41588-018-0179-8

10. Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa).
Krawczyk K, Nobis M, Myszczyński K, Klichowska E, Sawicki J. Sci Rep. 2018 Jan 31;8(1):1924 doi: 10.1038/s41598-018-20399-w

11. Duplicated Enhancer Region Increases Expression of CTSB and Segregates with Keratolytic Winter Erythema in South African and Norwegian Families.
Ngcungcu T, Oti M, Sitek JC, Haukanes BI, Linghu B, Bruccoleri R, Stokowy T, Oakeley EJ, Yang F, Zhu J, Sultan M, Schalkwijk J, van Vlijmen-Willems IMJJ, von der Lippe C, Brunner HG, Ersland KM, Grayson W, Buechmann-Moller S, Sundnes O, Nirmala N, Morgan TM, van Bokhoven H, Steen VM, Hull PR, Szustakowski J, Staedtler F, Zhou H, Fiskerstrand T, Ramsay M. Am J Hum Genet. 2017 May 4;100(5):737-750 doi: 10.1016/j.ajhg.2017.03.012

12. Lipid peroxidation and glutathione peroxidase activity relationship in breast cancer depends on functional polymorphism of GPX1.
Jablonska E, Gromadzinska J, Peplonska B, Fendler W, Reszka E, Krol MB, Wieczorek E, Bukowska A, Gresner P, Galicki M, Zambrano Quispe O, Morawiec Z, Wasowicz W. BMC Cancer. 2015 Oct 7;15:657 doi: 10.1186/s12885-015-1680-4

13. Dysregulation of markers of oxidative stress and DNA damage among nail technicians despite low exposure to volatile organic compounds.
Grešner P, Stepnik M, Król MB, Swiercz R, Smok-Pieniazek A, Twardowska E, Gromadzińska J, Wasowicz W. Scand J Work Environ Health. 2015 Nov;41(6):579-93 doi: 10.5271/sjweh.3523

14. Expression of selenoprotein-coding genes SEPP1, SEP15 and hGPX1 in non-small cell lung cancer.
Gresner P, Gromadzinska J, Jablonska E, Kaczmarski J, Wasowicz W. Lung Cancer. 2009 Jul;65(1):34-40 doi: 10.1016/j.lungcan.2008.10.023


Contact


Anna Supernat, PhD
Coordinator of the Center of Biostatistics and Bioinformatics Analysis
Medical University of Gdańsk
Dębinki 1 Street
80-211 Gdańsk
Phone: 58 349 14 38
centrum.obliczeniowe@gumed.edu.pl



The Computing Centre Events Forum

09.02.2021 – II. R programming and biomedical analytics workshop

16.12.2020 – Inspiring conversations EIT Health of the MUG – Out of the box – Medical innovations

25.11.2020 – R programming workshop

TEAM

Main staff


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Anna Supernat, PhD – coordinator

A graduate of the Intercollegiate Faculty of Biotechnology at the University of Gdansk and the Medical University of Gdansk. She completed her doctoral thesis at the Department of Cell Biology of the Medical University of Gdansk, under the supervision of Professor Anna Żaczek, PhD, MUG. The subject of her interest is the molecular basis of tumours, especially in the field of liquid biopsies analysed by high-throughput sequencing. Author of 19 publications in peer-reviewed journals, participant of numerous international conferences, expert of the National Centre for Research and Development (NCBR), manager of grants awarded by the National Science Centre (NCN) and NCBR.


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Tomasz Stokowy, PhD, Eng. – consultant

A graduate of the Faculty of Automatic Control, Electronics and Computer Science at the Silesian University of Technology, specializing in medical bioinformatics. Author of over 40 scientific publications on topics related to medical genetics and oncology. He works at the Genomics Core Facility at the University of Bergen (Norway), where he completed a postdoctoral fellowship. He is a consultant of the Centre for Biostatistics and Bioinformatics in the field of data analysis from large-scale scientific experiments and clinical trials.


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Peter Grešner, PhD – specialist biostatistician

Biophysicist, specialist in biomedical physics and methods of statistical analysis in biomedical research. A graduate of the Faculty of Mathematics, Physics and Computer Science at the Comenius University in Bratislava (Slovakia). In 2006-2020, he was professionally associated with the Department of Toxicology and Carcinogenesis of the J. Nofer Institute of Occupational Medicine in Lodz. Scientific interests include issues related to biochemistry, molecular biology, biostatistics and bioinformatics, mainly in the context of neoplastic processes caused by environmental conditions. Author or co-author of over 20 scientific publications and numerous conference reports. Manager or co-contractor of several scientific projects, including prestigious projects financed by the European Union, NATO Science Program and the National Science Centre (NCN).


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Kamil Myszczyński, PhD – specialist bioinformatician

A graduate of the Faculty of Biology and Biotechnology at the University of Warmia and Mazury in Olsztyn. Specialist in analysis of biological data obtained from high-throughput methods. He is interested in the development and implementation of bioinformatic analysis protocols, directions of development of sequencing techniques and the role of individual fractions of nucleic acids in the organism. Co-contractor of over a dozen projects related to genomics and transcriptomics including humans, mammals, plants, bacteria and fungus. Author or co-author of over 20 scientific publications.


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Sebastian Cygert, MSc. Eng. – Artificial Intelligence consultant

A graduate of the Faculty of Cryptology at Military University of Technology and of the Applied Computer Science at Warsaw University of Technology. The subject of his master’s thesis was the simulation of relativistic heavy ion collisions. Currently he is a PhD student at Gdańsk University of Technology, where he works on the ability to generalize visual perception models and using compression methods for neural networks. He has broad experience in industrial sector (Samsung, Amazon, Moody’s Analitycs). He worked on the Amazon Scout autonomous vehicle project. Author of many publications on parallel computing and machine learning (including image and speech recognition, detection of surgical instruments, methods of uncertainty estimation).


Young staff mentored by the Centre


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Maksym Jopek, Eng. – bioinformatist-trainee

Analyst and software engineer. A graduate of Automation and Robotics at the Faculty of Electrical and Control Engineering at the Gdansk University of Technology. Passionate about machine learning and data analysis. Member of IAESTE Gdansk and the GRADIENT science club. Currently employed as a bioinformatist-trainee at the Centre for Biostatistics and Bioinformatics, where he participates in the implementation of projects related to high-throughput sequencing of liquid biopsies taken from oncology patients.