Laboratory of Bioinformatics and Systems Biology

The research interest includes development of new theoretical and experimental tools and their application to investigate structure, function and evolution of proteins and their interaction with ligands. Research is also focused on application of next generation sequencing to a wide range of genomic, metagenomic and transcriptomic studies.

Prof. Krzysztof Ginalski
phone: +48 22 55 40833
room: 2151 (II building)

Overactive BRCA1 Affects Presenilin 1 in Induced Pluripotent Stem Cell-Derived Neurons in Alzheimer’s Disease
Wezyk, M., Szybinska, A., Wojsiat, J., Szczerba, M., Day, K., Ronnholm, H., ... & Ilkowski, J. (2018).
Journal of Alzheimer's Disease, 62(1), 175-202.
Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies
Kutner, J., Shabalin, I. G., Matelska, D., Handing, K. B., Gasiorowska, O., Sroka, P., ... & Minor, W. (2018).
Biochemistry, 57(6), 963-977.
Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution
Mourad, R., Ginalski, K., Legube, G., & Cuvier, O. (2018).
Genome biology, 19(1), 34
Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer
Argemi, X., Matelska, D., Ginalski, K., Riegel, P., Hansmann, Y., Bloom, J., . . . Prévost, G.
BMC Genomics, 19(1)
Predicting proteome dynamics using gene expression data
Kuchta, K., Towpik, J., Biernacka, A., Kutner, J., Kudlicki, A., Ginalski, K., & Rowicka, M.
Scientific Reports, 8(1)
Exome scale map of genetic alterations promoting metastasis in colorectal cancer
Goryca, K., Kulecka, M., Paziewska, A. ... & Ostrowski, J. (2019)
BMC Genetics, 19(1)
i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks
Biernacka, A., Zhu, Y., Skrzypczak, M. ... & Ginalski, K. (2018)
Communications Biology, 1(1)
Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures
Clouaire, T., Rocher, V., Lashgari, A. ... & Legube, G. (2018)
Molecular Cell, 72(2), 250-262.e6
Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase
Matelska, D, Shabalin, I. G., Jablonska, J. (2018)
BMC Evolutionary Biology, 18(1)
Hypermethylation of TRIM59 and KLF14 influences cell death signaling in familial Alzheimer’s disease
Wezyk, M., Spólnicka, M., Pośpiech, E., Pepłońska, B., Zbieć-Piekarska, R., Ilkowski, J., ... & Skrzypczak, M. (2018).
Oxidative medicine and cellular longevity, 2018
Phylogenetic and Phylogenomic Definition of Rhizopus Species
Gryganskyi, A. P., Golan, J., Dolatabadi, S., Mondo, S., Robb, S., Idnurm, A., . . . Stajich, J. E.
Genes|Genomes|Genetics, 8(6), 2007-2018
The microbial toxicity of quaternary ammonium ionic liquids is dependent on the type of lipopolysaccharide
Kowalczyk, P., Borkowski, A., Czerwonka, G., Cłapa, T., Cieśla, J., Misiewicz, A., . . . & Szala, M.
Journal of Molecular Liquids, 266, 540-547.
Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes.
Aymard, F., Aguirrebengoa, M., Guillou, E., Javierre, B. M., Bugler, B., Arnould, C., ... & Ginalski, K. (2017).
Nature Structural and Molecular Biology, 24(4), 353.
Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress.
Shi, W., Vu, T., Boucher, D., Biernacka, A., Nde, J., Pandita, R. K., ... & Jeffery, J. (2017).
Blood, 129(18), 2479-2492.
Phylogeny-based systematization of Arabidopsis proteins with histone H1 globular domain.
Kotliński, M., Knizewski, L., Muszewska, A., Rutowicz, K., Lirski, M., Schmidt, A., ... & Jerzmanowski, A. (2017).
Plant physiology, 174(1), 27-34.
Comprehensive classification of the PIN domain-like superfamily.
Matelska, D., Steczkiewicz, K., & Ginalski, K. (2017).
Nucleic acids research, 45(12), 6995-7020.
A heterozygous mutation in GOT1 is associated with familial macro-aspartate aminotransferase.
Kulecka, M., Wierzbicka, A., Paziewska, A., Mikula, M., Habior, A., Janczyk, W., ... & Czlonkowska, A. (2017).
Journal of hepatology, 67(5), 1026-1030.
Fungal lifestyle reflected in serine protease repertoire.
Muszewska, A., Stepniewska-Dziubinska, M. M., Steczkiewicz, K., Pawlowska, J., Dziedzic, A., & Ginalski, K. (2017).
Scientific reports, 7(1), 9147.
Systematic classification of the His-Me finger superfamily
Jablonska, J., Matelska, D., Steczkiewicz, K., & Ginalski, K. (2017).
Nucleic acids research, 45(20), 11479-11494.
Cut-and-paste transposons in fungi with diverse lifestyles
Muszewska, A., Steczkiewicz, K., Stepniewska-Dziubinska, M., & Ginalski, K. (2017).
Genome biology and evolution, 9(12), 3463-3477.
Dbf4 recruitment by forkhead transcription factors defines an upstream rate-limiting step in determining origin firing timing
Fang, D., Lengronne, A., Shi, D., Forey, R., Skrzypczak, M., Ginalski, K., Yan, Ch., Wang, X. Cao, Q, Pasero, P, Lou, H. (2017).
Genes & development, 31(23-24), 2405-2415.
Histone H1 variants in Arabidopsis are subject to numerous post-translational modifications, both conserved and previously unknown in histones, suggesting complex functions of H1 in plants.
Kotliński, M., Rutowicz, K., Kniżewski, Ł., Palusiński, A., Olędzki, J., Fogtman, A., ... & Jerzmanowski, A. (2016).
PloS one 11, no. 1 (2016): e0147908.
Diverse cap-binding properties of Drosophila eIF4E isoforms.
Zuberek, J., Kuchta, K., Hernández, G., Sonenberg, N., & Ginalski, K. (2016).
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics, 1864(10), 1292-1303.
FAM46 proteins are novel eukaryotic non-canonical poly (A) polymerases.
Kuchta, K., Muszewska, A., Knizewski, L., Steczkiewicz, K., Wyrwicz, L. S., Pawlowski, K., ... & Ginalski, K. (2016).
Nucleic acids research 44, no. 8 (2016): 3534-3548.
Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study
Huang, R., Ripstein, Z. A., Augustyniak, R., Lazniewski, M., Ginalski, K., Kay, L. E., & Rubinstein, J. L. (2016).
Proceedings of the National Academy of Sciences, 113(29), E4190-E4199.
Towards engineering novel PE-based immunotoxins by targeting them to the nucleus
Borowiec, M., Gorzkiewicz, M., Grzesik, J., Walczak-Drzewiecka, A., Salkowska, A., Rodakowska, E., ... & Ginalski, K. (2016).
Toxins, 8(11), 321.
Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy
Mikula, M., Skrzypczak, M., Goryca, K., Paczkowska, K., Ledwon, J. K., Statkiewicz, M., ... & Karczmarski, J. (2016).
Nucleic acids research, 44(21), 10150-10164.
A specialized histone H1 variant is required for adaptive responses to complex abiotic stress and related DNA methylation in Arabidopsis
Rutowicz, K., Ginalski K., Puzio, M., Halibart-Puzio, J., Lirski, M., Kroteń, M. A., Kotliński, M., ... & Kościelniak, J. (2015)
Plant physiology, pp-00493
Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using Illumina platform
Mitra, A., Skrzypczak, M., Ginalski, K., & Rowicka, M. (2015)
PloS one, 10(4), e0120520
Five eIF4E isoforms from Arabidopsis thaliana are characterized by distinct features of cap analogs binding.
Kropiwnicka, A., Kuchta, K., Lukaszewicz, M., Kowalska, J., Jemielity, J., Ginalski, K., ... & Zuberek, J. (2015).
Biochemical and biophysical research communications, 456(1), 47-52.
The histone deacetylases sir2 and rpd3 act on ribosomal DNA to control the replication program in budding yeast.
Yoshida, K., Bacal, J., Desmarais, D., Padioleau, I., Tsaponina, O., Chabes, A., ... & Ginalski, K. (2014).
Molecular cell, 54(4), 691-697.
HarmonyDOCK: the structural analysis of poses in protein-ligand docking.
Plewczynski, D., Philips, A., Grotthuss, M. V., Rychlewski, L., & Ginalski, K. (2014).
Journal of Computational Biology, 21(3), 247-256.
The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification
Majorek, K. A., Dunin-Horkawicz, S., Steczkiewicz, K., Muszewska, A., Nowotny, M., Ginalski, K., & Bujnicki, J. M. (2014).
Nucleic acids research, 42(7), 4160-4179
Probabilistic Approach to Predicting Substrate Specificity of Methyltransferases
Szczepińska, T., Kutner, J., Kopczyński, M., Pawłowski, K., Dziembowski, A., Kudlicki, A., Ginalski K., ... & Rowicka, M. (2014).
PLoS computational biology, 10(3), e1003514.
Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.
Crosetto, N., Mitra, A., Silva, M. J., Bienko, M., Dojer, N., Wang, Q., ... & Pasero, P. (2013).
Nature methods, 10(4), 361.
Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels.
Szczesny, R. J., Hejnowicz, M. S., Steczkiewicz, K., Muszewska, A., Borowski, L. S., Ginalski, K., & Dziembowski, A. (2013).
Nucleic acids research, 41(5), 3144-3161.
DIRS and Ngaro Retrotransposons in Fungi
Muszewska, A., Steczkiewicz, K., & Ginalski, K. (2013)
PLoS one, 8(9), e76319
C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3′ end modification.
Mroczek, S., Krwawicz, J., Kutner, J., Lazniewski, M., Kuciński, I., Ginalski, K., & Dziembowski, A. (2012).
Genes & development, 26(17), 1911-1925.
Novel AlkB dioxygenases—alternative models for in silico and in vivo studies.
Mielecki, D., Zugaj, D. Ł., Muszewska, A., Piwowarski, J., Chojnacka, A., Mielecki, M., ... & Grzesiuk, E. (2012)
PLoS One 7, no. 1 (2012): e30588
Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily
Steczkiewicz, K., Muszewska, A., Knizewski, L., Rychlewski, L., & Ginalski, K. (2012)
Nucleic acids research, 40(15), 7016-7045.
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