Karolina Jodkowska PhD

Research Assistant Professor


Karolina Jodkowska completed her BSc and MSc in Biology at the University of Warsaw. She received her PhD degree in molecular biology at Autonomous University of Madrid (Spain). She has extensive experimental experience in the field of biochemistry, molecular biology and genomics, which she gained in prestigious Polish and foreign research centers. She is a laureate of an international scholarship program for doctoral students sponsored by the "La Caixa" foundation. Research for her PhD dissertation was carried out at the National Cancer Research Center (CNIO) in Madrid and was focused on studying the mechanisms regulating replication start sites in mammalian cells. She obtained a travel grant from Boehringer Ingelheim Fonds to learn state-of-the-art techniques to investigate the 3D structure of the genome in the cell nucleus at Emory University (Atlanta, USA). She has extensive experience in high-throughput techniques using whole-genome sequencing (Hi-C, HiChIP, SNS-seq, Pore-C, ChIP-seq, RNA-seq), using platforms such as Illumina and Oxford Nanopore. Her research interests are focused on understanding how basic cellular processes such as replication, transcription and DNA repair are coordinated in the context of three-dimensional organization of chromatin with the nucleus.

Selected publications

  1. 3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome, Nucleic Acids Research. Wlasnowolski M, Sadowski M, Czarnota T, Jodkowska K, Szalaj P, Tang Z, Ruan Y, Plewczynski D. Volume 48, Issue W1, 02 July 2020, Pages W170–W176, https://doi.org/10.1093/nar/gkaa388
  2. Three-dimensional connectivity and chromatin environment mediate the activation efficiency of mammalian DNA replication origins. Jodkowska K, Pancaldi V, Almeida R, Maria Rigau, Graña-Castro O, Fernández-Justel JM, Rodríguez-Acebes S, Rubio-Camarillo M, Carrillo-de Santa Pau E, Pisano D, Al-Shahrour F, Valencia A, Gómez M, Méndez J. bioRxiv 644971; doi: https://doi.org/10.1101/644971
  3. Super resolution imaging of a distinct chromatin loop in human lymphoblastoid cells. Zhu J, Parteka Z, Lee B, Szalaj P, Wang P, Jodkowska K, Aaron J, Chew T-L, Plewczynski D, Ruan Y. bioRxiv 621920; doi: https://doi.org/10.1101/621920
  4. A short G1 phase imposes constitutive replication stress and fork remodelling in mouse embryonic stem cells. Ahuja AK, Jodkowska K, Teloni F, Bizard AH, Zellweger R, Herrador R, Ortega S, Hickson ID, Altmeyer M, Mendez J, Lopes M. Nat Commun. 2016 Feb 15;7:10660.
  5. Multilayer OMIC data in medullary thyroid carcinoma identifies the STAT3 pathway as a potential therapeutic target in RETM918T tumors. Mancikova V, Montero-Conde C, Perales-Paton J, Fernandez AF, Santacana M, Jodkowska K, Inglada-Pérez L, Castelblanco E, Borrego S, Encinas M, Matias-Guiu X, Fraga MF, Robledo M. Clin Cancer Res. 2016 Sep 12
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