Lukasz P. Kozlowski

Publications






Kozlowski LP Proteome-pI: Proteome Isoelectric Point Database. Nucleic Acids Res. 2016; 11:55. doi: 10.1093/nar/gkw978

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 Microbiol2013; 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

Pałyga J, Kozłowski Ł Structure and function of molecular chaperone HSP90. Sowriemiennyj Naucznyj Wiestnik Ser. Biologija Chimija 2007; 15(23), 46-65

- top 1% in Computer Science (WoS)          underscored - single authorship publications

Other

Referee in Scientific Journals

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


Membership in Societies: International Society for Computational Biology (ISCB), Polish Bioinformatics Society, Polish Biochemical Society


Conferences and workshops

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
2008 - 2013        Polish Ministry of Science and Higher Education (grant no. NN301 190139) - main contractor
2012 - 2014        Exgenome Molecular Enzymes (EU, FP7, grant no. 286556) - a contractor
2013 - 2014        Polish Ministry of Science and Higher Education (IUVENTUS PLUS grant no. 0301/IP1/2013/72) - a head
2016 - 2020        Virus-X: Viral Metagenomics for Innovation Value (EU, Horizon 2020, grant no. 685778) - a contractor

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

Contact: Lukasz P. Kozlowski