Katedra Biometrii - Department of Biometry
Strona główna > Strony domowe > Krzysztof Pawłowski  
Krzysztof Pawłowski

Pawłowski Lab webpage

Research profile

  • Structure and function predictions for uncharacterised proteins potentially important in human disease;
  • Novel gene/protein families with unexpected evolutionary histories;
  • Systems biology analysis of high throughput biological data;

Current research activities

  • In silico structure / function analysis and evolutionary history of novel protein kinase-like, protease and oxidoreductase families 
    in humans, and throughout the tree of life;
  • Experimental characterisation of novel protein kinase-like families;
  • Systems biology analysis of melanoma proteomics data;

Current and recent grants

  • Biological function of the evolutionarily conserved kinase SELO, common to most living organisms - study in bacterial and yeast models.
    National Science Center (NCN, Poland), 2015-2018
  • The role of the FAM69 protein family in the nervous system. Analysis of a novel family with potential protein kinase function.
    National Science Center (NCN, Poland), 2013-2016
  • Analysis of gene expression correlation in the context of nucleus structure.
    National Science Center (NCN, Poland), 2010-2011
  • In silico analysis of structure, function and evolution of CLCA proteins - a novel human protein family with potential therapeutic applications.
    National Science Center (NCN, Poland), 2007-2010

Scientific career

from 2006 Warsaw University of Life Sciences SGGW
Head, Dept. of Experimental Design and Bioinformatics (from 2017)
associate professor, earlier assistant professor
2016-2018 Lund University (Medical Faculty), Lund, Sweden
2007 - 2012 Nencki Institute of Experimental Biology, PAS, Warszawa, Poland
Head, laboratory of Bioinformatics and Systems Biology
(Dr Habil. [D. Sc.] in biology, 2008)
assistant professor, docent, later associate professor
2001 - 2006 AstraZeneca R&D Lund, Respiratory & Inflammation Research, Sweden
Senior Scientist
1999 - 2001 The Burnham Institute, La Jolla, CA, USA
postdoc (Adam Godzik's lab)
1998 - 1999 The Scripps Research Institute, La Jolla, CA, USA
postdoc (Adam Godzik's lab)
1990 - 1998 Institute of Biochemistry and Biophysics, PAS, Warsaw (Ph.D. in biology, 1997)
Ph.D. student, later assistant professor


Publication list on ResearchGate

Publication list on Google Scholar: 2318 citations, h-index: 22




58. Bacterial pseudokinase catalyzes protein polyglutamylation to inhibit the SidE-family ubiquitin ligases.
M. H. Black, A. Osinski, M. Gradowski, K. A. Servage, K. Pawłowski, D. R. Tomchick, V. S. Tagliabracci.
Science (2019) 364, 787–792.

57. Quantitative Proteomics Identifies Brain Acid Soluble Protein 1 (BASP1) as a Prognostic Biomarker in Pancreatic Cancer.
Q. Zhou, R. Andersson, D. Hu, M. Bauden, A. Sasor, K. Pawłowski, I. Pla Parada, K. Said Hilmersson, M. Zhou, F. Lu, G. Marko-Varga, D. Ansari.
EBioMedicine (2019) in the press.

56. A novel conserved family of Macro-like domains––putative new players in ADP-ribosylation signalling.
M. Dudkiewicz, K. Pawłowski.
PeerJ (2019), 7, e6863.

55. Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data.
L. H. Betancourt, K. Pawłowski, J. Eriksson, A. M. Szasz, S. Mitra, I. Pla, C. Welinder, H. Ekedahl, P. Broberg, R. Appelqvist, M. Yakovleva, Y. Sugihara, K. Miharada, C. Ingvar, L. Lundgren, B. Baldetorp, H. Olsson, M. Rezeli, E. Wieslander, P. Horvatovich, J. Malm, G. Jönsson, G. Marko-Varga
Scientific Reports (2019), 9, 5154.

54. Clinical Protein Science in Translational Medicine Targeting Malignant Melanoma.
J. Gil, L. Betancourt, I. Pla, A. Sanchez, R. Appelqvist, T. Miliotis, M. Kuras, H. Oskolas, Y. Kim, Z. Horvath, J. Eriksson, E. Berge, E. Burestedt, G. Jönsson, B. Baldetorp, C. Ingvar, H. Olsson, L. Lundgren, P. Horvatovich, J. Rodriguez Murillo, Y. Sugihara, C. Welinder, E. Wieslander, B. Lee, H. Lindberg, K. Pawłowski, H. Jeong Kwon, V. Doma, J. Timar, S. Karpati, A.M. Szasz, I. Nemeth, T. Nishimura, G. Corthals, M. Rezeli, B. Knudsen, J. Malm, G. Marko-Varga.
Cell Biology and Toxicology (2019) in the press.


53. Genome-wide functional analyses of plant coiled–coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity.
T. Wróblewski, L. Spiridon, E. C. Martin, A.-J. Petrescu, K. Cavanaugh, M. Jose-Truco, H. Xu, D. Gozdowski, K. Pawłowski, R. W. Michelmore, F. L. W. Takken.
PLoS Biology (2018)
16, e2005821.

52. Global pentapeptide statistics are far away from expected distributions.
J. Poznański, J. Topiński, A. Muszewska, K. Dębski, M. Hoffman-Sommer, K. Pawłowski, M. Grynberg.
Scientific Reports (2018) 8, 15178

51. Protein AMPylation by an evolutionarily conserved pseudokinase.
A. Sreelatha, S. S. Yee, V. A. Lopez, B. C. Park, L. Kinch, S. Pilch, K. A. Servage, J. Zhang, J. Jiou, M. Karasiewicz, M. Łobocka, N. Grishin, K. Orth, R. Kucharczyk, K. Pawłowski, D. R. Tomchick, V. S. Tagliabracci.
Cell (2018) in the press. doi.org/10.1016/j.cell.2018.08.046

50. Phosphoproteomic insights into processes influenced by the kinase-like protein DIA1/C3orf58.
A. Hareza, M. Bakun, B. Świderska, M. Dudkiewicz, A. Koscielny, A. Bajur, J. Jaworski, M. Dadlez, K. Pawłowski.
PeerJ (2018) 6, e4599.

49. Pseudo-DUBs as allosteric activators and molecular scaffolds of protein complexes.
M. Walden, S. K. Masandi, K. Pawłowski, E. Zeqiraj.
Biochemical Society Transactions (2018), 46, 453-466.

48. Proteomic analyses identify prognostic biomarkers for pancreatic ductal adenocarcinoma.
D. Hu, D. Ansari, K. Pawłowski, Q. Zhou, A. Sasor, C. Welinder, T. Kristl, M. Bauden, M. Rezeli, Y. Jiang, G. Marko-Varga, R. Andersson.
Oncotarget (2018), 9,


47. The Legionella pneumophila effector Lpg1137 is a homologue of mitochondrial SLC25 carrier proteins, not of known serine proteases.
M. Gradowski, K. Pawłowski.
PeerJ (2017), 5,e3849

46. Correlation of histopathologic characteristics to protein expression and function in malignant melanoma.
C. Welinder, K. Pawłowski, A.M. Szasz, M. Yakovleva, Y. Sugihara, J. Malm, G. Jönsson, C. Ingvar, L. Lundgren, B. Baldetorp, H. Olsson, M. Rezeli, T. Laurell, E. Wieslander, G. Marko-Varga.
PLoS ONE (2017), 12, e0176167.

45. STYX: a versatile pseudophosphatase.
V. Reiterer, K. Pawłowski, H. Farhan.

Biochemical Society Transactions (2017), 45, 449-456


44. Comparative proteomic analysis of extracellular vesicles isolated by acoustic trapping or differential centrifugation.
M. Rezeli, O. Gidlöf, M. Evander, P. Bryl-Górecka, R. Sathanoori, P. Gilje, K. Pawłowski, P. Horvatovich, D. Erlinge, G. Marko-Varga, T. Laurell.
Analytical Chemistry (2016), 88, 8577-86.

43. Phosphorylation of spore coat proteins by a family of atypical protein kinases.
K. B. Nguyen, A. Sreelatha, E. S. Durrant, J. Lopez-Garrido, A. Muszewska, M. Dudkiewicz, M. Grynberg, S. Yee, K. Pogliano, D. R. Tomchick, K. Pawłowski, J. E. Dixon, and V. S. Tagliabracci.
Proceedings of the National Academy of Sciences USA (2016), 113, E3482-E3491.

42. FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases.
K. Kuchta, A. Muszewska, L. Knizewski, K. Steczkiewicz, L.S. Wyrwicz, K. Pawłowski, L. Rychlewski, K. Ginalski.
Nucleic Acids Research (2016), 44, 3534-48.


41. Workflow for large-scale analysis of melanoma tissue samples.
M.E. Yakovleva, C. Welinder, Y. Sugihara, K. Pawłowski, M. Rezeli, E. Wieslander, J. Malm and G. Marko-Varga.
EuPA Open Proteomics (2015), 8, 78.

40. A Protein Deep Sequencing Evaluation of Metastatic Melanoma Tissues.
C. Welinder, K. Pawłowski, Y. Sugihara, M. Yakovleva, G. Jönsson, C. Ingvar, L. Lundgren, B. Baldetorp, H. Olsson, M. Rezeli,
B. Jansson, T. Laurell, T. Fehniger, B. Döme, J. Malm, E. Wieslander, T. Nishimura
and G. Marko-Varga.
PLoS ONE (2015), 10, e0123661.


39. Analysis of Alpha-Synuclein in Malignant Melanoma – Development of a SRM Quantification Assay.
C. Welinder, G.B. Jönsson, C. Ingvar, L. Lundgren, B. Baldetorp, H. Olsson, T. Breslin, M. Rezeli, B. Jansson,
T. E. Fehniger, T. Laurell, E. Wieslander, K. Pawłowski
and G. Marko-Varga.
PLoS ONE (2014), 9, e110804.

38. Feasibility Study on Measuring Selected Proteins in Malignant Melanoma Tissue by SRM Quantification.
C. Bratt-Welinder, G. Jönsson, C. Ingvar, L. Lundgren, B. Baldetorp, H. Olsson, T. Breslin, M. Rezeli, B. Jansson,
T. Laurell, T. Fehniger, E. Wieslander, K. Pawłowski
and G. Marko-Varga.
Journal of Proteome Research (2014),  13, 1315-1326.

37. Probabilistic approach to predicting substrate specificity of methyltransferases.
T. Szczepińska, J. Kutner, M. Kopczynski, K. Pawłowski, A. Dziembowski, A. Kudlicki, K. Ginalski
and M. Rowicka.
PLoS Comp Biol (2014), 10, e1003514.

36. Bioinformatics analysis of bacterial annexins - putative ancestral relatives of eukaryotic annexins. 
P. K. Kodavali, M. Dudkiewicz, S. Pikuła
and K. Pawłowski.
PLoS ONE (2014), 9, e85428.


35. Structural and functional characterization of annexin 1 from Medicago truncatula.
P. K. Kodavali, K. Skowronek, I. Koszela-Piotrowska, A. Strzelecka-Kiliszek, K. Pawłowski
and S. Pikuła.
Plant Physiology and Biochemistry (2013), 73, 56-62.

34. Genomic positions of co-expressed genes: Echoes of chromosome organisation in gene expression data.
T. Szczepińska
and K. Pawłowski.
BMC Research Notes (2013), 6, 229.

33. A novel predicted calcium-regulated kinase family implicated in neurological disorders.
M. Dudkiewicz, A. Lenart
and K. Pawłowski.
PLoS ONE (2013), 8, e66427.
preprint: Nature Precedings (2012), hdl:10101/npre.2012.7015.1,

32. CLCAs - a family of metalloproteases of intriguing phylogenetic distribution and with cases of substituted catalytic sites.
A. Lenart, M. Dudkiewicz, M. Grynberg
and K. Pawłowski.
PLoS ONE (2013), 8, e62272.

31. Intersection of selenoproteins and kinase signalling.
A. Lenart
and K. Pawłowski.
BBA Proteins and Proteomics (2013), 1834, 1279-1284.

30. Novel higher-order epigenetic regulation of bdnf gene upon seizures,
A. Walczak, A. Szczepankiewicz, B. Ruszczycki, K. Zamłyńska, J. Dzwonek, E. Wilczek, K. Żybura-Broda, M. Rylski, T. Szczepińska,
K. Pawłowski
, J. Włodarczyk, I. Szczerbal, M. Świtoński, M. Cremer
and  G. Wilczyński.
Journal of Neuroscience (2013), 33, 2507-11.

29.  Distinct Protein Classes in Human Red Cell Proteome Revealed by Similarity of Phylogenetic Profiles.
P. Szczesny, A. Mykowiecka, K. Pawłowski
and M. Grynberg.
PLoS ONE (2013), 8, e54471.


28. A Novel Protein Kinase-like Domain in a Selenoprotein, Widespread in the Tree of Life.
M. Dudkiewicz, T. Szczepińska, M. Grynberg
and K. Pawłowski.
PLoS ONE (2012), 7, e32138.

27. A widespread peroxiredoxin-like domain in tumor suppression- and progression-implicated proteins.
K. Pawłowski, A. Muszewska, A. Lenart, T. Szczepińska, A. Godzik
and M. Grynberg.
BMC Genomics (2010), 11, 590.

26. Bioinformatyka w poszukiwaniu nowych leków. [in Polish]
K. Pawłowski.
Kosmos (2009), 58, 127–134.

25. An Approach to Prediction of the Haematopoietic Stem Cell Transplantation Outcome
Using Human Leukocyte Antigen Mismatch Information Mapped on Protein Structure Data.
M.Z. Dudkiewicz, P .Malanowski, J. Czerwiński
and K. Pawłowski.
Biology of Blood and Marrow Transplantation (2009), 15, 1014-1025.


24. Bioinformatics analysis of oligosaccharide phosphorylation effect on the stabilization of the beta-amylase-ligand complex.
M.Z. Dudkiewicz, K. Pawłowski, J. Simińska
and S. Orzechowski.
Journal of Carbohydrate Chemistry (2008) 27, 479-495.

23. Uncharacterised / hypothetical proteins in biomedical "omics" experiments: is novelty being swept under the carpet?
K. Pawłowski.
Briefings in Functional Genomics and Proteomics (2008), 7, 283-90.

22. TNF-α- induced self expression in human lung endothelial cells is inhibited by native and oxidized α1-antitrypsin.
D. Subramaniyam, R. Virtala, K. Pawłowski, I. Groth Clausen, S. Warkentin, T. Stevens
and S. Janciauskiene.
The International Journal of Biochemistry & Cell Biology (2008), 40, 258-71.

21. Expression of genes involved in oxidative stress responses in airway epithelial cells of smokers with chronic obstructive pulmonary disease.
S. Pierrou, P. Broberg, R.A. O'Donnell, K. Pawłowski, R. Virtala, E. Lindqvist, A. Richter, S.J. Wilson, G. Angco, S. Moller, H. Bergstrand,
W. Koopmann, E. Wieslander, P.E. Stromstedt, S.T. Holgate, D.E. Davies, J. Lund
and R. Djukanovic.
American Journal of Respiriratory and Critical Care Medicine (2007), 175, 577-86.

20. Novel conserved hydrolase domain in the CLCA family of alleged calcium-activated chloride channels.
K. Pawłowski, M. Lepisto, N. Meinander, U. Sivars, M. Varga
and E. Wieslander.
Proteins (2006), 63, 424-439.

19. CADD, a Chlamydia Protein that Interacts with Death Receptors.
F. Stenner-Liewen, H. Liewen, J.M. Zapata, K. Pawłowski, A. Godzik and J.C. Reed.
Journal of Biological Chemistry (2002), 277, 9633-6.

18. Identification and characterization of DEDD2, a death effector domain-containing protein.
W. Roth, F. Stenner-Liewen, K. Pawłowski, A. Godzik and J.C. Reed.
Journal of Biological Chemistry (2002), 277, 7501-8.

17. Fold prediction for bacterial genomes.
K. Pawłowski, L. Rychlewski, B. Zhang and A. Godzik.
Journal of Structural Biology (2001), 134, 219-31.

16. Surface map comparison. Studying function diversity of homologous proteins.
K. Pawłowski and A. Godzik.
Journal of Molecular Biology (2001), 309, 793-806.

15. A diverse family of proteins containing tumor necrosis factor receptor-associated factor domains.
J.M. Zapata, K. Pawłowski, A. Godzik and J.C. Reed.
Journal of Biological Chemistry (2001), 276, 24242-52.

14. PAAD – a new protein domain associated with apoptosis, cancer and autoimmune diseases.
K. Pawłowski, F. Pio, Z.-L. Chu, J.C. Reed and A. Godzik.
Trends in Biochemical Sciences (2001), 26, 85-87.

13. Saturated Blast: detecting distant homology using automated multiple intermediate sequence search.
W. Li, F. Pio, K. Pawłowski and A. Godzik.
Bioinformatics (2000), 16, 1105-1110.

12. BAR: a novel apoptosis regulator at the intersection of caspases and Bcl-2 family proteins.
H. Zhang, Q. Xu, S. Krajewski, M. Krajewska, Z. Xie, S. Fuess, S. Kitada, A. Godzik,
K. Pawłowski, A. Shabaik, L. Bubendorf and J.C. Reed.
Proceedings of the National Academy of Sciences USA (2000), 97, 2591-2596.

11. From fold to function predictions: an apoptosis regulator protein BID.
K. Pawłowski, L. Rychlewski, J. C. Reed and A. Godzik.
Computers & Chemistry (2000), 5, 42-53.

10. Sensitive sequence comparison as protein function predictor.
K. Pawłowski, L. Jaroszewski, L. Rychlewski and A. Godzik.
Pacific Symposium on Biocomputing (2000), 5, 42-53.


9. The Helicobacter pylori genome: from sequence analysis to structural and functional predictions.
K. Pawłowski, B. Zhang, L. Rychlewski and A. Godzik
Proteins (1999), 36, 20-30.

8. From fold predictions to function predictions:
Automation of functional site conservation analysis for functional genome predictions.
B. Zhang, L. Rychlewski, K. Pawłowski, J. S. Fetrow, J. Skolnick and A. Godzik
Protein Science (1999), 8, 1104-1115.

7. Ion-channel activity of the BH3 only Bcl-2 Family Member, BID.
S. L. Schendel, R. Azimov, K. Pawłowski, A. Godzik, B. L. Kagan and J. C. Reed
Journal of Biological Chemistry (1999), 274, 21932-6.

6. CAFASP-1: Critical Assessment of Fully Automated Structure Prediction Methods.
D. Fischer, C. Barret, K. Bryson, A. Elofsson, A. Godzik, D. Jones, K. Karplus, L. A. Kelley, R. M. MacCallum, K. Pawłowski, B. Rost, L. Rychlewski, M. Sternberg
Proteins (1999), Suppl 3, 209-217.

5. Multiple Model Approach – Exploring the limits of comparative modelling.
L. Jaroszewski, K. Pawłowski and A. Godzik
Journal of Molecular Modeling (1998), 4, 294-309.

4. Multiple model approach-dealing with alignment ambiguities in protein modeling.
K. Pawłowski, L. Jaroszewski, A. Bierzynski and A. Godzik
Pacific Symposium on Biocomputing, (1997), 2, 328-339.

3. Isolated calcium binding loops from EF-hand proteins can dimerize forming a native-like structure.
J. Wojcik, J. Goral, K. Pawłowski and A. Bierzynski
Biochemistry, (1997), 36, 680-687.

2 .Helix-coil transition theories – how correct they are?
A. Bierzynski and K. Pawłowski
Acta Biochimica Polonica, (1997), 44, 423-432.

1. Structural diversity in a family of homologous proteins.
K. Pawłowski, A. Bierzynski and A. Godzik
Journal of Molecular Biology, (1996), 259, 349-366.

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