Magda Mielczarek

  • Position: Assistant Professor
  • Contact:✉: magda.mielczarek@upwr.edu.pl
  • Address: Office no. 302, Kozuchowska 7, 51-631 Wroclaw
  • Consultations: — (onsite or online).
  • LinkedIn 

Teaching:

  • Tutoring
  • Basics of Bioinformatics / Podstawy Bioinformatyki
  • Bioinformatics / Bioinformatyka
  • Programming lab (Bash course)  / Pracownia informatyczna
  • NGS data analysis / Analiza danych NGS
  • Data analysis / Analiza danych
  • Bioinformatics seminar / Seminarium bioinformatyczne
  • Bachelor and master thesis supervision
  • Bioinformatics Student Association supervision 2017- 2021 (SKN Bioinformatyków)

Publications:

  1. K. Kotlarz, M. Mielczarek, P. Biecek, K. Wojdak-Maksymiec, T. Suchocki, P. Topolski, W. Jagusiak, J. Szyda. An explainable deep learning classifier of bovine mastitis based on whole genome sequence data – circumventing the p>>n problemInternational Journal of Molecular Sciences 2024. (IF=5.600)
  2. M. Sztuka, K. Kotlarz, M. Mielczarek, P. Hajduk, J. Liu, J. Szyda. NextFlow vs. plain Bash: Different Approaches to the Parallelisation of SNP Calling from the Whole Genome Sequence Data.  NAR Genomics and Bioinformatics 2024 (IF=4.6).
  3. B. Hofman, J. Szyda, M. Frąszczak, M. Mielczarek. Long non-coding RNAs Variability in Porcine Skeletal Muscle Journal of Applied Genetics 2024 (IF=2.4).
  4. Liu J., Mroczek M., Mach A., Stępień M., Aplas A., Pronobis-Szczylik B., Bukowski S., Mielczarek M., Gajewska E., Topolski P., Król Z.J., Szyda J., Dobosz P. Genetics, Genomics and Emerging Molecular Therapies of Pancreatic Cancer.  Cancers 2023; 15(3):779 (IF=6.575).
  5. Mielczarek M., Frąszczak M., Zielak-Steciwko A.E., Nowak B., Hofman B., Pierścińska J., Kruszyńsk W.,Szyda J.
    An effect of large-scale deletions and duplications on transcript expression.  Functional and Integrative Genomics 2022, 23, 19(IF=3.674)
  6. Kołomański, M., Szyda, J., Frąszczak, M., Mielczarek, M. DNA sequence features underlying large-scale duplications and deletions in human Journal of Applied Genetics 202263, 527–533. (IF = 3.240)
  7. Kotlarz, K., Mielczarek, M., Wang, Y., Dou, J., Suchocki, T., Szyda, J. Identification of functional features underlying heat stress response in Sprague–Dawley rats using mixed linear models Scientific Reports 2022, 12, 7671. (IF = 4.379)
  8. M. Mielczarek, B. CzechJ. StańczykJ. SzydaB. Guldbrandtsen. Extraordinary Command Line: Basic Data Editing Tools for Biologists Dealing with Sequence DataThe Open Bioinformatics Journal 2020. IF(2019)=1.50.
  9. Kotlarz K, Mielczarek M, Suchocki T, Czech B, Guldbrandtsen B, and Szyda J. The application of deep learning for the classification of correct and incorrect SNP genotypes from whole-genome DNA sequencing pipelines. Journal of Applied Genetics 2020
  10. Kosińska-Selbi B, Mielczarek M, Szyda  J. Review: Long Non-Coding RNA in Livestock. Animal 2020 
  11. Szyda J, Mielczarek M, Minozzi G, Williams J.L, Wojdak-Maksymiec K. The Genetic Background of Clinical Mastitis in Holstein-Friesian cattle. Animal 2019
  12. P. Barski, M. Mielczarek, M. Frąszczak, J. Szyda. Assessing DNA sequence features underlying copy number variants. ASP Zootechnica 2019
  13. Mielczarek M. Frąszczak M, Williams J, Nicolazzi EL,  Szyda J, Landscape of Copy Number Variations in Bos taurus: individual – and inter-breed variability. BMC Genomics 2018. IF(2016/2017)= 3.729
  14. Czech B, Frąszczak M, Mielczarek M, Szyda J. Identification and annotation of breed-specific single nucleotide polymorphisms in Bos taurus genomes. PLOS One 2018. IF(2016/2017)= 2.806
  15. Mielczarek M., Frąszczak M., Giannico R., Minozzi G., Williams J.L., Wojdak-Maksymiec K., and Szyda, J. Analysis of Copy Number Variations in Holstein-Friesian Cow Genomes Based on Whole Genome Sequence Data. Journal of Dairy Science 2017, 100:7, pp 5515-5525, IF(2016)=2.474
  16. Mielczarek M. and Szyda J. Review of alignment and SNP calling algorithms for next-generation sequencing data. Journal of Applied Genetics 2016 57(1), pp. 71-79, IF(2015)=1.477
  17. Szyda J., Frąszczak, M. Mielczarek, M., Giannico, R., Minozzi, G., Nicolazzi, E.L., Kamiński, S. and Wojdak-Maksymiec, K. The assessment of inter-individual variation of whole-genome DNA sequence in 32 cows. Mammalian Genome 2015, 28(11), pp. 658-665, IF(2014)=3.068

Education:

  1. 2012-2016 Biology, Wroclaw University of Environmental and Life Sciences, The Faculty of Biology and Animal Science. PhD studies; area of study: genomics, genetics, and bioinformatics; The main goal of the PhD thesis was the investigation of CNVs across 155 individuals belonging to 13 different breeds of domestic cattle (Bos taurus Linnaeus, 1758). In particular, the study comprised: (i) detecting CNV polymorphisms including their validation using different algorithms, (ii) identifying the functional and biological annotations of CNVs, (iii) describing the distribution of these polymorphisms across the genome and assessing the inter-breed and inter-individual variation in the number and distribution of CNVs.
  2. 2010-2012 Biotechnology, specialization: bioinformatics, University of Wrocław, Faculty of Biotechnology. Graduate studies; an individual programme with emphasis on bioinformatics techniques and programming;
  3. 2005-2010 Biology, specialization: zoology, University of Wrocław, Faculty of Biological Sciences. Master’s degree, Biology.

Membership:

  • Polish Bioinformatics Society (PTBI)
  • Member of the European Federation for Animal Science (EAAP). EAAP is an international non-governmental organisation which aims to improve the farming of domestic animals.

Interests: Bioinformatics, genomics, NGS, multiomics.