About Me

I am currently a researcher working in the group of Prof Bozena Kaminska at Nencki Institute. I received a master's degree in mathematics and applied statistics in 2008 from the Warsaw University. My thesis work was on technical aspects of gene expression microarray data analyses. I got interested in brain tumor biology and gene regulation, and those interests directed me to a biological laboratory where in 2013 I did my PhD. In years 2013-2016 as a research postdoctoral fellow in Genetics at Harvard Medical School I have been involved in projects focused on epigenetic factors influencing chromatin states. In particular, I co-developed a novel method to assess DNA accessibility and confirmed that changes in nucleosome accessibility may predominate over changes in nucleosome occupancy during rapid transcriptional induction.

Contact Details

Jakub Mieczkowski
ul. Ludwika Pasteura 3
02-093 Warsaw, Poland

(48 22) 589 25 24


Nencki Institute of Experimental Biology

PhD in biology with speciality in bioinformatics (with honors) Mar 2013

Warsaw University

MSc Degree in Mathematics with speciality in Applied Statistics Sep 2008


Nencki Institute of Experimental Biology
Neurobiology Center

Research Fellow August 2016 - Present

Massachusetts General Hospital
Harvard Medical School

Research Fellow June 2013 - June 2016

Nencki Institute of Experimental Biology

Specialist March 2013 - June 2013



  • Mieczkowski J, Tolstorukov MY, Bioinformatic Analysis of Nucleosome and Histone Variant Positioning, Histone Variants Methods and Protocols, Springer 2018, Methods in Molecular Biology series

  • 2018

  • Walentynowicz KA, Ochocka N, Pasierbinska M, Wojnicki K, Stepniak K, Mieczkowski J, Ciechomska IA, Kaminska B, In Search for Reliable Markers of Glioma-Induced Polarization of Microglia, Front Immunol, 2018 Jan 15;9:1329
  • 2017

  • Garofalo S, Porzia A, Mainiero F, Di Angelantonio S, Cortese B, Basilico B, Pagani F, Cignitti G, Chece G, Maggio R, Tremblay ME, Savage J, Bisht K, Esposito V, Bernardini G, Seyfried T, Mieczkowski J, Stepniak K, Kaminska B, Santoni A, Limatola C, Environmental stimuli shape microglial plasticity in glioma, Elife, 2017 Dec 29;6
  • Gieryng A, Pszczolkowska D, Bocian K, Dabrowski M, Rajan WD, Kloss M, Mieczkowski J, Kaminska B, Immune microenvironment of experimental rat C6 gliomas resembles human glioblastomas, Sci Rep., 2017 Dec 14;7(1):17556
  • Cook A*, Mieczkowski J*, Tolstorukov MY, Single-Assay Profiling of Nucleosome Occupancy and Chromatin Accessibility, Current Protocols in Molecular Biology, 2017 Oct 2;120, 21.34.1–21.34.18
  • Mueller B*, Mieczkowski J*, Kundu S, Wang P, Sadreyev R, Tolstorukov MY, Kingston RE, Widespread changes in nucleosome accessibility without changes in nucleosome occupancy during a rapid transcriptional induction, Genes & Dev., 2017 Mar 1; 31(5):451, 2017.
  • Wang X*, Lee RS*, Alver BH*, Haswell JR, Wang S, Mieczkowski J, Drier Y, Gillespie SM, Archer TC, Wu JN, Tzvetkov EP, Troisi EC, Pomeroy SL, Biegel JA, Tolstorukov MY, Bernstein BE, Park PJ, Roberts CW, SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation, Nat Genet., 2017 Feb;49(2):289-295.
  • 2016

  • Deaton AM, Gómez-Rodríguez M, Mieczkowski J, Tolstorukov MY, Kundu S, Sadreyev RI, Jansen LE, Kingston RE, Enhancer regions show high histone H3.3 turnover that changes during differentiation, eLife, 2016 Jun 15;5. pii: e15316.
  • Mieczkowski J*, Cook A*, Bowman SK*, Mueller B, Alver BH, Kundu S, Deaton AM, Urban JA, Larschan E, Park PJ, Kingston RE, Tolstorukov MY, MNase titration reveals differences between nucleosome occupancy and chromatin accessibility, Nat Commun., 2016 May 6;7:11485.
  • 2015

  • Mieczkowski J*, Kocyk M*, Nauman P, Gabrusiewicz K, Sielska M, Przanowski P, Maleszewska M, Rajan WD, Pszczolkowska D, Tykocki T, Grajkowska W, Kotulska K, Roszkowski M, Kostkiewicz B, Kaminska B, Down-regulation of IKKβ expression in glioma-infiltrating microglia/macrophages is associated with defective inflammatory/immune gene responses in glioblastoma, Oncotarget, 2015 Oct 20;6(32):33077-90.
  • 2014

  • Kruczyk M*, Przanowski P*, Dabrowski M, Swiatek-Machado K, Mieczkowski J, Wallerman O, Ronowicz A, Piotrowski A, Wadelius C, Kaminska B, Komorowski J, Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells, Biochim Biophys Acta., 2014 Nov;1839(11):1341-50.
  • Przanowski P, Dabrowski M, Ellert-Miklaszewska A, Kloss M, Mieczkowski J, Kaza B, Ronowicz A, Hu F, Piotrowski A, Kettenmann H, Komorowski J, Kaminska B, The signal transducers Stat1 and Stat3 and their novel target Jmjd3 drive the expression of inflammatory genes in microglia, J Mol Med (Berl). 2014 Mar;92(3):239-54.
  • 2013

  • Kruczyk M, Baltzer N, Mieczkowski J, Draminski M, Koronacki J, Komorowski J, Random reducts: A monte carlo rough set-based method for feature selection in large datasets, Fundamenta Informaticae, 2013; 127 (1-4), 273-88.
  • 2012

  • Mieczkowski J*, Swiatek-Machado K*, Kaminska B, Identification of pathway deregulation--gene expression based analysis of consistent signal transduction, PLoS One, 2012;7(7):e41541.
  • Swiatek-Machado K, Mieczkowski J, Ellert-Miklaszewska A, Swierk P, Fokt I, Szymanski S, Skora S, Szeja W, Grynkiewicz G, Lesyng B, Priebe W, Kaminska B, Novel small molecular inhibitors disrupt the JAK/STAT3 and FAK signaling pathways and exhibit a potent antitumor activity in glioma cells, Cancer Biol Ther., 2012 Jun;13(8):657-70.
  • 2010

  • Dabrowski M, Dojer N, Zawadzka M, Mieczkowski J, Kaminska B, Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems, BMC Syst Biol. 2010 Jun 17;4:86.
  • Tyburczy ME, Kotulska K, Pokarowski P, Mieczkowski J, Kucharska J, Grajkowska W, Roszkowski M, Jozwiak S, Kaminska B, Novel proteins regulated by mTOR in subependymal giant cell astrocytomas of patients with tuberous sclerosis complex and new therapeutic implications, Am J Pathol., 2010 Apr;176(4):1878-90.
  • Mieczkowski J, Tyburczy ME, Dabrowski M, Pokarowski P, Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements, BMC Bioinformatics, 2010 Feb 24;11:104.
*equal contributors


Identification of epigenetic mechanisms contributing to glioma drug resistance

This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 665778. Learn more.

Disclosing chromatin accessibility in brain tumor cells after treatment by cracking a ‘nucleosomal code’

This project has received funding from the National Science Centre in Poland.