Lukasz P. Kozlowski

Publications






Kozlowski LP Proteome-pI 2.0: Proteome Isoelectric Point Database Update. (Accepted) 2021

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 )

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

Kozlowski LP IPC 2.0 – prediction of isoelectric point and pKa dissociation constants. Nucleic Acids Res. 2021; 49 (W1): W285–W292

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 )

Kozlowski LP fCite: a fractional citation tool to quantify an individual’s scientific research output. bioRxiv 2019; 771485. doi: 10.1101/771485

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 )

Kozlowski LP Proteome-pI: Proteome Isoelectric Point Database. Nucleic Acids Res. 2017; 45 (D1): D1112-D1116

Kozlowski LP IPC - Isoelectric Point Calculator. Biology Direct 2016; 11:55. doi: 10.1186/s13062-016-0159-9

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

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

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

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

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

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

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

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

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

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

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

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

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

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




Nucleic Acid Res., Bioinformatics, BMC Bioinformatics, Peer J., Knowledge-Based Systems, Scientometrics, Acta Biochimica Pol., IJMS and few others


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


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
2008                  Masovian Fellowship for Ph.D. Students
2015 - 2017       Max Planck Institute Fellowship

Contact: Lukasz P. Kozlowski