Publications and talks

Research in bioinformatics and systems biology

 

Publications:

Link to Google Scholar stats is here.

  1. Betkier A, Szczesny P, Gorecki P, Fast Algorithms for Inferring Gene-Species Associations. Bioinformatics Research and Applications, 2015:36-47. [full text soon]
  2. Chojnacka A, Szczesny P, Blaszczyk MK, Zielenkiewicz U, Detman A, Salamon A, Sikora A. Noteworthy facts about a methane producing microbial community. PLoS One. 2015 doi: 10.1371/journal.pone.0128008. eCollection 2015. PubMed PMID: 26000448, PubMed Central PMCID: PMC4441513 [full text].
  3. Szczesny P, Poznanski J, Paczek L, Zielenkiewicz P. Hypophosphatemia and sudden infant death syndrome (SIDS)–is ATP the link? Ups J Med Sci. 2014 Mar;119(1):55-6. doi: 10.3109/03009734.2013.849317. Epub 2013 Oct 23. PubMed PMID: 24151935; PubMed Central PMCID: PMC3916719. [full text]
  4. Gladki A, Kaczanowski S, Szczesny P, Zielenkiewicz P. The evolutionary rate of antibacterial drug targets. BMC Bioinformatics. 2013 Feb 1;14:36. doi: 10.1186/1471-2105-14-36. PubMed PMID: 23374913; PubMed Central PMCID: PMC3598507. [full text]
  5. Szczesny P, Mykowiecka A, Pawłowski K, Grynberg M. Distinct protein classes in human red cell proteome revealed by similarity of phylogenetic profiles. PLoS One. 2013;8(1):e54471. doi: 10.1371/journal.pone.0054471. Epub 2013 Jan 21.PubMed PMID: 23349899; PubMed Central PMCID: PMC3549994. [full text]
  6. Poznanski J, Szczesny P, Ruszczyńska K, Zielenkiewicz P, Paczek L. Proteins contribute insignificantly to the intrinsic buffering capacity of yeast cytoplasm. Biochem Biophys Res Commun. 2013 Jan 11;430(2):741-4. doi: 10.1016/j.bbrc.2012.11.079. Epub 2012 Dec 1. PubMed PMID: 23206695. [full text]
  7. Moran Y, Fredman D, Szczesny P, Grynberg M, Technau U. Recurrent horizontal transfer of bacterial toxin genes to eukaryotes. Mol Biol Evol. 2012 Sep;29(9):2223-30. doi: 10.1093/molbev/mss089. Epub 2012 Mar 12. PubMed PMID:22411854; PubMed Central PMCID: PMC3424411. [full text]
  8. Alegría A, Szczesny P, Mayo B, Bardowski J, Kowalczyk M. Biodiversity in Oscypek, a traditional Polish cheese, determined by culture-dependent and -independent approaches. Appl Environ Microbiol. 2012 Mar;78(6):1890-8. doi:10.1128/AEM.06081-11. Epub 2012 Jan 13. PubMed PMID: 22247135; PubMed Central PMCID: PMC3298175. [full text]
  9. Chojnacka A, Błaszczyk MK, Szczęsny P, Nowak K, Sumińska M, Tomczyk-Żak K, Zielenkiewicz U, Sikora A. Comparative analysis of hydrogen-producing bacterial biofilms and granular sludge formed in continuous cultures of fermentative bacteria. Bioresour Technol. 2011 Nov;102(21):10057-64. doi:10.1016/j.biortech.2011.08.063. Epub 2011 Aug 22. PubMed PMID: 21908188. [full text]
  10. Potato Genome Sequencing Consortium, Xu X, Pan S, Cheng S, Zhang B, Mu D, Ni P, Zhang G, Yang S, Li R, Wang J, Orjeda G, Guzman F, Torres M, Lozano R, Ponce O, Martinez D, De la Cruz G, Chakrabarti SK, Patil VU, Skryabin KG, Kuznetsov BB, Ravin NV, Kolganova TV, Beletsky AV, Mardanov AV, Di Genova A, Bolser DM, Martin DM, Li G, Yang Y, Kuang H, Hu Q, Xiong X, Bishop GJ, Sagredo B, Mejía N, Zagorski W, Gromadka R, Gawor J, Szczesny P, Huang S, Zhang Z, Liang C, He J, Li Y, He Y, Xu J, Zhang Y, Xie B, Du Y, Qu D, Bonierbale M, Ghislain M, Herrera Mdel R, Giuliano G, Pietrella M, Perrotta G, Facella P, O’Brien K, Feingold SE, Barreiro LE, Massa GA, Diambra L, Whitty BR, Vaillancourt B, Lin H, Massa AN, Geoffroy M, Lundback S, DellaPenna D, Buell CR, Sharma SK, Marshall DF, Waugh R, Bryan GJ,Destefanis M, Nagy I, Milbourne D, Thomson SJ, Fiers M, Jacobs JM, Nielsen KL, S?nderk?r M, Iovene M, Torres GA, Jiang J, Veilleux RE, Bachem CW, de Boer J, Borm T, Kloosterman B, van Eck H, Datema E, Hekkert Bt, Goverse A, van Ham RC, Visser RG. Genome sequence and analysis of the tuber crop potato. Nature. 2011 Jul 10;475(7355):189-95. doi: 10.1038/nature10158. PubMed PMID: 21743474. [full text]
  11. Muszewska A, Taylor JW, Szczesny P, Grynberg M. Independent subtilases expansions in fungi associated with animals. Mol Biol Evol. 2011 Dec;28(12):3395-404. doi: 10.1093/molbev/msr176. Epub 2011 Jul 4. PubMed PMID: 21727238; PubMed Central PMCID: PMC3247792. [full text]
  12. Szczesny P, Iacovache I, Muszewska A, Ginalski K, van der Goot FG, Grynberg M. Extending the aerolysin family: from bacteria to vertebrates. PLoS One. 2011;6(6):e20349. doi: 10.1371/journal.pone.0020349. Epub 2011 Jun 8. PubMed PMID: 21687664; PubMed Central PMCID: PMC3110756. [full text]
  13. Nguyen KA, Zylicz J, Szczesny P, Sroka A, Hunter N, Potempa J. Verification of a topology model of PorT as an integral outer-membrane protein in Porphyromonas gingivalis. Microbiology. 2009 Feb;155(Pt 2):328-37. doi: 10.1099/mic.0.024323-0. PubMed PMID: 19202082; PubMed Central PMCID: PMC2729710. [full text]
  14. Szczesny P, Linke D, Ursinus A, Bär K, Schwarz H, Riess TM, Kempf VA, Lupas AN, Martin J, Zeth K. Structure of the head of the Bartonella adhesin BadA. PLoS Pathog. 2008 Aug 8;4(8):e1000119. doi: 10.1371/journal.ppat.1000119. PubMed PMID: 18688279; PubMed Central PMCID: PMC2483945. [full text]
  15. Szczesny P, Lupas A. Domain annotation of trimeric autotransporter adhesins–daTAA. Bioinformatics. 2008 May 15;24(10):1251-6. doi: 10.1093/bioinformatics/btn118. Epub 2008 Apr 8. PubMed PMID: 18397894; PubMed Central PMCID: PMC2373917. [full text]
  16. Grosskinsky U, Schütz M, Fritz M, Schmid Y, Lamparter MC, Szczesny P, Lupas AN, Autenrieth IB, Linke D. A conserved glycine residue of trimeric autotransporter domains plays a key role in Yersinia adhesin A autotransport. J Bacteriol. 2007 Dec;189(24):9011-9. Epub 2007 Oct 5. PubMed PMID: 17921300; PubMed Central PMCID: PMC2168626. [full text]
  17. Koretke KK, Szczesny P, Gruber M, Lupas AN. Model structure of the prototypical non-fimbrial adhesin YadA of Yersinia enterocolitica. J Struct Biol. 2006 Aug;155(2):154-61. Epub 2006 Apr 3. PubMed PMID: 16675268. [full text]
  18. Szczesny P, Wieczorek G, Zielenkiewicz P. MOFOID–not only the protein modeling server. Acta Biochim Pol. 2005;52(1):267-9. PubMed PMID: 15827624. [full text]

 

On open science

 

Publications (as a single author, in Polish):

  1. Otwarta nauka, czyli dobre praktyki uczonych (title in English: Open science – good research practices), Wydawnictwa Zwarte Stowarzyszenia EBIB, Volume 7, 2013. [full text ]
  2. Otwieranie nauki – lekcja z globalizacji (title in English: Opening science – the lesson from globalisation), Biuletyn Polskiego Towarzystwa Ekonomicznego, Volume 56, 2012. [full text of the issue]
  3. Nauka 2.0 – świadome współtworzenie (title in English: Science 2.0 – concious co-creation), Instytut Obywatelski, 2012. [full text]

Talks (video)

  1. Science 2.0 Conference. Hamburg, Germany, 2014 [video]
  2. ENVIMPACT – Open Innovation. Warsaw, Poland, 2013 [video]
  3. Forum Nowej Nauki (talk in Polish). Krakow, Poland, 2012 [video]
  4. TEDxWarsaw. Warsaw, Poland, 2010 [video]

Slides from the talks above, plus several others from lectures that were not recorded are available at Slideshare

 

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