Michal Kolář

Laboratory of Genomics and Bioinformatics

Malicious messages shall not pass!

  • Mission: To describe intercellular communication in the tumor microenvironment and its impact on cancer development. We focus in particular on communication between cancer cells and cancer-associated fibroblasts.
  • Vision: To modulate this communication in the way that arrests cancer cell proliferation.

Our laboratory focuses on advanced applications of genomics, transcriptomics and bioinformatics, the most dynamically developing disciplines in the life sciences today. In our research, we perform transcriptomic and epigenomic analyses both at bulk and single-cell level and operate a spatially resolved transcriptomics laboratory. We develop bioinformatics tools and protocols to analyze data generated in our lab or available in public databases. 

SELECTED PUBLICATIONS
  • Kubovčiak J, Kolář M, Novotnný J: Scdrake: a reproducible and scalable pipeline for scRNA-seq data analysis. Bioinform Adv 2023 3(1): vbad089. DOI: 10.1093/bioadv/vbad089
  • Taborska P, Lukac P, Stakheev D, Rajsiglova L, Kalkusova K, Strnadova K, Lacina L, Dvorankova B, Novotny J, Kolar M, Vrana M, Cechova H, Ransdorfova S, Valerianova M, Smetana K, Vannucci L, Smrz D: Novel PD-L1- and collagen-expressing patient-derived cell line of undifferentiated pleomorphic sarcoma (JBT19) as a model for cancer immunotherapy. Sci Rep 2023 13(1): 19079. DOI: 10.1038/s41598-023-46305-7
  • Rasl J, Grušanovic J, Klímová Z, Čáslavský J, Groušl T, Novotný J, Kolář M, Vomastek T: ERK2 signaling regulates cell-cell adhesion of epithelial cells and enhances growth factor-induced cell scattering. Cell Signal 2022 99: 110431. DOI: 10.1016/j.cellsig.2022.110431
  • Strnadová K, Pfeiferová L, Přikryl P, Dvořánková B, Vlčák E, Frýdlová J, Vokurka M, Novotný J, Šáchová J, Hradilová M, Brábek J, Šmigová J, Rösel D, Smetana K Jr, Kolář M, Lacina L. Exosomes produced by melanoma cells significantly influence the biological properties of normal and cancer-associated fibroblasts. Histochem Cell Biol. 2022 Feb;157(2):153-172. DOI: 10.1007/s00418-021-02052-2
  • Novotný J, Strnadová K, Dvořánková B, Kocourková Š, Jakša R, Dundr P, Pačes V, Smetana K Jr, Kolář M, Lacina L. Single-Cell RNA Sequencing Unravels Heterogeneity of the Stromal Niche in Cutaneous Melanoma Heterogeneous Spheroids. Cancers (Basel). 2020 Nov 10;12(11):3324. DOI: 10.3390/cancers12113324
SPECIALIZED EXPERTISE AND TECHNOLOGY

NGS sequencing, both short and long reads

Single-cell transcriptomics, spatially resolved transcriptomics 

Bioinformatics

COLLABORATION WITH LARGE RESEARCH INFRASTRUCTURES AND RESEARCH CENTRES

European and national infrastructure for life science data ELIXIR and ELIXIR CZ

Biotechnology and Biomedicine Centre of the Czech Academy of Sciences and the Charles University BIOCEV