Lukasz P. Kozlowski
Scientometrics
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Individual Publications
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Wons E, ..., Kozlowski LP, ..., et al. A transcription factor from the cryptic Escherichia coli Rac prophage controls both phage and host operons. Nucleic Acids Res. 2025, 53 (5); doi: 10.1093/nar/gkaf113 (Supplementary Data  )  |
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Gucwa, ..., Kozlowski LP, ..., et al. Lethal perturbation of an Escherichia coli regulatory network is triggered by a restriction-modification system’s regulator and can be mitigated by excision of the cryptic prophage Rac. Nucleic Acids Res. 2024; 52 (6), 2942-2960 doi: 10.1093/nar/gkad1234 (Supplementary Data ) |
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Szadkowska M, ..., Kozlowski LP, ..., et al. Molecular characterization of PhiKo endolysin of Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29. Front. Microbiol. 2023 14:1303794; doi: 10.3389/fmicb.2023.1303794 (Supplementary Data ) |
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Dorawa, ..., Kozlowski LP, ..., et al. Molecular Characterization of a DNA Polymerase from Thermus thermophilus MAT72 Phage vB_Tt72: A Novel Type-A Family Enzyme with Strong Proofreading Activity. Int. J. Mol. Sci. 2022, 23, 7945; doi: 10.3390/ijms23147945 (Supplementary Data ) |
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Kozlowski LP Proteome-pI 2.0: Proteome Isoelectric Point Database Update. Nucleic Acids Res. 2022 (Database Issue) 50 (D1): D1535–D1540, doi: 10.1093/nar/gkab944 | |
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Morzywolek, ..., Kozlowski LP, ..., et al. Novel lytic enzyme of prophage origin from Clostridium botulinum E3 strain Alaska E43 with bactericidal activity against clostridial cells. Int. J. Mol. Sci 2021; doi: 10.3390/ijms22179536 (Supplementary Data ) |
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Aevarsson A, ..., Kozlowski LP, ..., et al.Going to extremes - a metagenomic journey into the dark matter of life. FEMS Microbiol. Lett 2021; doi: 10.1093/femsle/fnab067 | |
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Kozlowski LP IPC 2.0 – prediction of isoelectric point and pKa dissociation constants. Nucleic Acids Res. 2021; 49 (W1): W285–W292 | |
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Erijman A, Kozlowski L, Sohrabi-Jahromi S, Fishburn J, Warfield L, Schreiber J, Noble WS, Söding J, Hahn S A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning. Molecular Cell; 78, 1–13. doi: 10.1016/j.molcel.2020.04.020 (Supplementary Data ) |
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Kozlowski LP fCite: a fractional citation tool to quantify an individual’s scientific research output. bioRxiv 2019; 771485. doi: 10.1101/771485  |
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Plotka M, Sancho-Vaello E, Dorawa S, Kaczorowska AK, Kozlowski LP, Kaczorowski
T, Zeth K. Structure and function of the Ts2631 endolysin of Thermus scotoductus phage vB_Tsc2631 with unique N-terminal extension used for peptidoglycan binding. Sci Rep. 2019; 9(1):1261. doi: 10.1038/s41598-018-37417-6 (Suppl. Video - Ts2631 endolysin binding to PGNs ) |
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Kozlowski LP Proteome-pI: Proteome Isoelectric Point Database. Nucleic Acids Res. 2017; 45 (D1): D1112-D1116 |
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Kozlowski LP IPC - Isoelectric Point Calculator. Biology Direct 2016; 11:55. doi: 10.1186/s13062-016-0159-9  |
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Plotka M, Kaczorowska AK, Morzywolek A, Makowska J, Kozlowski LP, et al. Biochemical Characterization and Validation of a Catalytic Site of a Highly Thermostable Ts2631 Endolysin from the Thermus scotoductus Phage vB_Tsc2631. PLoS One 2015; 10(9):e0137374, doi: 10.1371/journal.pone.0137374 | |
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Pietal MJ, Bujnicki JM, Kozlowski LP GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function. Bioinformatics 2015; 31(21), 3499-3505, doi: 10.1093/bioinformatics/btv390 | |
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Pawlowski M, Kozlowski L, Kloczkowski A MQAPsingle: A quasi single model approach for estimation of the quality of individual protein structure models. Proteins: Structure, Function, and Bioinformatics 2015; doi: 10.1002/prot.24787 | |
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Głów D, Pianka D, Sulej AA, Kozłowski ŁP, et al. Sequence-specific cleavage of dsRNA by Mini-III RNase Nucleic Acids Res. 2015; 43(5):2864-73, doi: 10.1093/nar/gkv009 | |
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Sierocka I, Kozlowski LP, Bujnicki JM, Jarmolowski A, Szweykowska-Kulinska Z Female-specific gene expression in dioecious liverwort Pellia endiviifolia is developmentally regulated and connected to archegonia production BMC Plant Biol. 2014; 14:168 doi: 10.1186/1471-2229-14-168 | |
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Plotka M, Kaczorowska AK, Stefanska A, Morzywolek A, Fridjonsson O, Dunin-Horkawicz S, Kozlowski L, et al. Discovery and characterization of a novel highly thermostable endolysin from Thermus scotoductus MAT2119 bacteriophage Ph2119 that shows amino-acid sequence similarity to eukaryotic peptidoglycan recognition proteins (PGRPs). Appl Env Microbiol 2013; 80(3):886-95, doi: 10.1128/AEM.03074-13 | |
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Tuszynska I, Matelska D, Magnus M, Chojnowski G, Kasprzak JM, Kozlowski LP, et al. Computational modeling of protein-RNA complex structures. Methods 2013; 65(3):310-9. doi: 10.1016/j.ymeth.2013.09.014 | |
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Puton T, Kozlowski L, Rother KM, Bujnicki JM CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction. Nucleic Acids Res 2013; 41(7):4307-23. doi: 10.1093/nar/gkt101 | |
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Kozlowski LP, Bujnicki JM MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. BMC Bioinformatics 2012; 13:111. doi: 10.1186/1471-2105-13-111 |
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Al-Haggar M, Madej-Pilarczyk A, Kozlowski L, et al. A novel homozygous p.Arg527Leu LMNA mutation in two unrelated Egyptian families causes overlapping mandibuloacral dysplasia and progeria syndrome. Eur J Human Genet 2012;20 (11), 1134-1140. doi: 10.1038/ejhg.2012.77 | |
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Puton* T, Kozlowski* L, Tuszynska I, Rother K, Bujnicki JM Computational methods for prediction of protein-RNA interactions. J Struct Biol 2012; 179 (3), 261-268 doi: 10.1016/j.jsb.2011.10.001 | |
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Nakagome S, Mano S, Kozlowski L, Bujnicki JM, Shibata H, Fukumaki Y, Kidd JR, Kidd KK, Kawamura S, Oota H Crohn’s disease risk alleles on the NOD2 locus have been maintained by natural selection on standing variation. Mol Biol Evol. 2012; 29(6):1569-85. doi: 10.1093/molbev/mss006 | |
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Kozłowski Ł, Orłowski J, Bujnicki JM "Structure prediction of alternatively spliced proteins" in "Alternative pre-mRNA Splicing: Theory and Protocols" Editors: Stamm S, Smith Ch, Luehrmann R Wiley-Blackwell, 2012, 582-591 Book chapter | |
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Majorek K, Kozłowski Ł, Jakalski M, Bujnicki JM "First steps of protein structure prediction" in "Prediction of Protein Structures, Functions and Interactions" Editors: Bujnicki JM. Wiley & Sons, 2008, chapter 2, 39–62 Book chapter | |
Referee in Scientific Journals
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Research & Development Assessment
Member of an expert panel in the National Centre of Research and Development (NCRD, pol. NCBiR), Poland. Occasionally, the assessment for other institutions e.g. Polish National Agency for Academic Exchange (NAWA), Polish Agency for Enterprise Development (PARP), Register of Expert Peer Reviewers for Italian Scientific Evaluation (REPRISE), Fonds de la Recherche Scientifique (F.R.S.–FNRS). The evaluation of R&D projects with total valuation over $100M.
Membership in Societies: International Society for Computational Biology (ISCB), Polish Bioinformatics Society, Polish Biochemical Society
Conferences and workshops
2024 ISMB 2024, Jul 12-16 (Montreal, Canada),
2024 SCP24 (Single-Cell Proteomics Conference), May 28-29 (online),
2024 NVIDIA GTC Spring 2024 Conference and Expo March, March 18–21 (online),
2023 NVIDIA GTC Spring 2023 Conference, March 18–21 (online),
2022 MLCB 2022 (Machine Learning in Computational Biology), November 21-22 (online),
2022 APFED-22 (Advances in Protein Folding, Evolution and Design), April 6-8 (online),
2022 SCP22 (Single-Cell Proteomics Conference), June 15-16 (online),
2022 UK BioBank Scientific Conference, June 21 (online),
2022 CMSB 2022 (20th conference on Computational Methods in Systems Biology), Sep 14-16 (online),
2021 MLCB 2021 (Machine Learning in Computational Biology), Nov 22-23 (online),
2021 HUPO ReCONNECT 2021 (Human Proteome Organization Congress), Nov 15-19 (online),
2021 ML in PL 2021 (Machine Learning in Poland), Nov 5-7 (online),
2021 STI2021 (Conference on Science, Technology and Innovation Indicators), Sep 13,15,17 (online),
2021 RECOMB 2021, Aug 29 - Sep 1 (online),
2021 ISMB 2021, Jul 25-30 (online),
2021 ICCS 2021 (International Conference on Computational Science), Jun 16-18 (online),
2021 AI in Healthcare, Jun 8 (online),
2020 ECCB 2020, Sep 7-8 (online),
2020 ISMB 2020, Jul 13-16 (online),
2020 RECOMB 2020 (24th Annual International Conference on Research in Computational Molecular Biology), Jun 22-25 (online),
2020 SCFE20 (Supercomputer Frontiers 2020), Mar 23-26 (online),
2019 ISMB/ECCB 2019, Basel, Switzerland, Jul 21-25 (poster & talk),
2017 ISMB/ECCB 2017, Praque, Czech Republic, July 21-25 (poster),
2016 FRET 2, International Discussion Meeting on Förster Resonance Energy Transfer in the Life Sciences, Gottingen, Germany, April 3-6,
2016 DAGStat2016, 4th Joint Statistical Meeting, Gottingen, Germany, March 14-18,
2015 RECOMB 2015, the 19th Annual International Conference on Research in Computational Molecular Biology, Warsaw, Poland, April 12-15,
2014 BIO 2014 Congress - 1st Congress of the Polish Biochemistry, Cell Biology, Biophysics and Bioinformatics, Warsaw, Poland, September 9-12,
2014 ECCB'14 – European Conference on Computational Biology, Strasburg, France, September 7-10,
2014 Advanced RNA-Seq and ChiP-Seq Data Analysis Course, EMBL-EBI, UK,May 12-15
2013 Automated and Reproducible Analysis of NGS data (ARANGS13) Course, Oeiras, Portugal, October 21-24th
2013 RNA 3' ends: Mechanism and biological function in eukaryotic genomes, Oxford, UK, September 25-29
2013 SocBiN Bioinformatics /BIT13, Torun, June 26-29
2013 Cancer genetics for medical community, Warsaw, June17
2012 Critical Assessment of Techniques for Protein Structure Prediction (CASP10), Gaeta, Italy, December 9-12
2012 Bioinformatics in Torun – BIT12, Torun, Poland, September 27-29
2012 10th Workshop on Bioinformatics and 5th Symposium of the Polish Bioinformatics Society, Poland, May 25-27
2011 MultiPole Approach to Structural Biology, Warsaw, November 16-19
2011 4th Annual Meeting of Polish Bioinformatics Society, Krakow, September 30 - October 2, 2011
2011 EMBO Young Scientists Forum, Warsaw, June 30 -July 01
2011 Bioinformatics in Torun – BIT11, Torun, June 2-4
2010 Critical Assessment of Techniques for Protein Structure Prediction (CASP9), Pacific Groove, USA, December 5-9
2010 Workshop on Interdisciplinary Grant Application, Warsaw, October 6
2010 HealthProt workshop, Warsaw, August 27-30
2010 EURASNET, Frontiers in Structural Biology of RNAs and RNPs, Poznan, August 16-19
2010 Workshop, Grid Computing and Bioinformatics, PL-GRID, Toruń, June 12
2010 Bioinformatics in Toruń - BIT10, Toruń, June 10-12
2010 Workshop on Scientific Communication, Warsaw, April 26-30
2010 EMBO workshop: RNA and RNA-processing enzymes. Warsaw, April 14-16
2010 School of Molecular Medicine. Warsaw, April 12-15
2010 CambridgePYTHON's Innovation Academy, Warsaw, March 6, March 20, May 29
2009 2nd Annual Meeting of Polish Bioinformatics Society, Poznań, October 2-4
2009 ISMB/ECCB 2009, Stockholm, Sweden, June 27 – July 2
2009 Bioinformatics in Toruń - BIT09, Toruń, May 21-23
2008 Critical Assessment of Techniques for Protein Structure Prediction (CASP8), Sardinia, Italy, December 3-7
2008 1st Annual Meeting of Polish Bioinformatics Society, Jadwisin, October 3-5
2008 SocBin Bioinformatics 2008, Warsaw, April 24-27
Grants
2019 - 2021 National Science Centre (PL, grant OPUS no. 2018/29/B/NZ2/01403) – a principal investigator, ~150k Euro
2016 - 2020 Virus-X: Viral Metagenomics for Innovation Value (EU, Horizon 2020, grant no. 685778) - a contractor
2013 - 2014 Polish Ministry of Science and Higher Education (IUVENTUS PLUS grant no. 0301/IP1/2013/72) - a principal investigator, ~40k Euro
2012 - 2014 Exgenome Molecular Enzymes (EU, FP7, grant no. 286556) - a contractor
2008 - 2013 Polish Ministry of Science and Higher Education (grant no. NN301 190139) - a main contractor, grant for PhD, ~10k Euro
Fellowships & Awards
2023 Individual award of the Rector of the University of Warsaw for scientific achievements
2015 - 2017 Max Planck Institute Fellowship
2008 Masovian Fellowship for Ph.D. Students