Laboratory of Genomics and Bioinformatics
Head: Michal Kolář
Prague node
HOME INSTITUTION
Institute of Molecular Genetics of the Czech Academy of Sciences
RESEARCH PROGRAMME(S)
RP 3 - Biomarkers of cancers and cancer diagnostics
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
COLLABORATION WITHIN THE NICR
Meritxell Alberich Jordà
(Prague node, Institute of Molecular Genetics of the Czech Academy of Sciences)
Aleksi Šedo
(Prague node, First Faculty of Medicine CU)
Karel Smetana
(Prague node, First Faculty of Medicine CU)
Helena Kupcová Skalníková
(Prague node, First Faculty of Medicine CU)
Libor Macůrek
(Prague node, Institute of Molecular Genetics of the Czech Academy of Sciences)
Martin Gregor
(Prague node, Institute of Molecular Genetics of the Czech Academy of Sciences)
Martin Sztacho
(Prague node, First Faculty of Medicine CU)
Pavel Klener
(Prague node, First Faculty of Medicine CU)
Vladimír Kořínek
(Prague node, Institute of Molecular Genetics of the Czech Academy of Sciences)
SPECIALIZED EXPERTISE AND TECHNOLOGY
NGS sequencing, both short and long reads
Single-cell transcriptomics, spatially resolved transcriptomics
Bioinformatics