Publications

Showcase of Our Recent Papers

2017

  1. Zielezinski A, Dziubek M, Sliski J, Karlowski W. ORCAN—a web-based meta-server for real-time detection and functional annotation of orthologs Bioinforamtics. 2017, doi: 10.1093/bioinformatics/btw825
  2. Sobkowiak R, Zielezinski A, Karlowski W, Lesicki A. Nicotine affects protein complex rearrangement in Caenorhabditis elegans cells Drug Chem Toxicol. 2017, doi: 10.1080/01480545.2016.1264411

2016

  1. Machtel P, Bakowska-Zywicka K, Zywicki M. Emerging applications of riboswitches – from antibacterial targets to molecular tools J ApplGenet. 2016 57: 531-541.
  2. Plucinska M, Bakowska-Zywicka K, Zywicki M Suitability of high-throughput DMS-probing data for constraining the secondary structure prediction of small RNAs. BioTechnologia. 2016 97(3): 161-167.
  3. Foretek D, Nuc P, Zywicki M, Karlowski WM, Kudla G, Boguta M. Maf1-mediated regulation of yeast RNA polymerase III is correlated with CCA addition at the 3' end of tRNA precursors. Gene. 2016 Aug 27: S0378-1119(16)30670-9.
  4. Bąkowska-Żywicka K, Mleczko A, Kasprzyk M, Machtel P, Zywicki M, Twardowski T. The widespread occurrence of tRNA-derived fragments in Saccharomyces cerevisiae FEBS openbio. 2016 12: 1186-1200.
  5. Szymanski M, Zielezinski A, Barciszewski J, Erdmann V, Karlowski W 5SRNAdb: an information resource for 5S ribosomal RNAs. Nucleic Acids Res. 2016 44 (D1): D180-D183.

2015

  1. Zywicki M, Gracz J, Karlowski W, Twardowski T, Tyczewska A Expression of miRNAs involved in phosphate homeostasis and senescence is altered in glyphosate-treated maize. Acta Physiologiae Plantarum. 2015 37(265)
  2. Zielezinski A & Karlowski WM Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals. RNA Biol. 2015 12(7):761-70.
  3. Zielezinski A, Dolata J, Alaba S, Kruszka K, Pacak A, Swida-Barteczka A, Knop K, Stepien A, Bielewicz D, Pietrykowska H, Sierocka I, Sobkowiak L, Lakomiak A, Jarmolowski A, Szweykowska-Kulinska Z, Karlowski WM mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs. BMC Plant Biol. 2015 5:144
  4. Piwecka M, Rolle K, Belter A, Barciszewska AM, Żywicki M, Michalak M, Nowak S, Naskręt-Barciszewska MZ, Barciszewski J. Comprehensive analysis of microRNA expression profile in malignant glioma tissues.Mol Oncol. 2015 Mar 25. pii: S1574-7891(15)00056-3.
  5. Alaba S, Piszczalka P, Pietrykowska H, Pacak AM, Sierocka I, Nuc PW, Singh K, Plewka P, Sulkowska A, Jarmolowski A, Karlowski WM, Szweykowska-Kulinska Z. The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants. New Phytol. 2014 Dec 19. 25530158.
  6. Zielezinski A, Karlowski WM. Integrative data analysis indicates an intrinsic disordered domain character of Argonaute-binding motifs. Bioinformatics. 2015 31(3):332-9.
  7. Książkiewicz M, Zielezinski A, Wyrwa K, Szczepaniak A, Rychel S, Karlowski W, Wolko B, Naganowska B. Remnants of the Legume Ancestral Genome Preserved in Gene-Rich Regions: Insights from Lupinus angustifolius Physical, Genetic, and Comparative Mapping. Plant Mol Biol Report. 2015;33:84-101.

2014

  1. Pircher A, Bakowska-Zywicka K, Schneider L, Zywicki M, Polacek N. An mRNA-derived noncoding RNA targets and regulates the ribosome. Mol Cell. 54(1):147-55.
  2. Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, Sandstrom R, Thurman RE, Neph S, Reynolds AP, Stergachis AB, Vernot B, Johnson AK, Haugen E, Sullivan ST, Thompson A, Neri FV 3rd, Weaver M, Diegel M, Mnaimneh S, Yang A, Hughes TR, Nemhauser JL, Queitsch C, Stamatoyannopoulos JA. Mapping and dynamics of regulatory DNA and transcription factor networks in A. thaliana. Cell Rep. 8(6):2015-30.
  3. Kruszka K, Pacak A, Swida-Barteczka A, Nuc P, Alaba S, Wroblewska Z, Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z. Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley. J Exp Bot. 65(20):6123-35.

2013

  1. Lesniewicz K, Karlowski WM, Pienkowska JR, Krzywkowski P, Poreba E. The plant s1-like nuclease family has evolved a highly diverse range of catalytic capabilities. Plant Cell Physiol. 54(7):1064-78.
  2. Książkiewicz M, Wyrwa K, Szczepaniak A, Rychel S, Majcherkiewicz K, Przysiecka Ł, Karlowski W, Wolko B, Naganowska B. Comparative genomics of Lupinus angustifolius gene-rich regions: BAC library exploration, genetic mapping and cytogenetics. BMC Genomics. 2013 14:79.
  3. Kruszka K, Pacak A, Swida-Barteczka A, Stefaniak AK, Kaja E, Sierocka I, Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z. Developmentally regulated expression and complex processing of barley pri-microRNAs. BMC Genomics. 2013 14:34.

2012

  1. Bielewicz D, Dolata J, Zielezinski A, Alaba S, Szarzynska B, Szczesniak MW, Jarmolowski A, Szweykowska-Kulinska Z, Karlowski WM. mirEX: a platform for comparative exploration of plant pri-miRNA expression data. Nucleic Acids Res. 2012 40(Database issue):D191-7.
  2. Sobkowiak L, Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z. Non-Canonical Processing of Arabidopsis pri-miR319a/b/c Generates Additional microRNAs to Target One RAP2.12 mRNA Isoform. Front Plant Sci. 2012 3:46.
  3. Maciukiewicz M, Czerski PM, Leszczynska-Rodziewicz A, Kapelski P, Szczepankiewicz A, Dmitrzak-Weglarz M, Skibinska M, Pawlak J, Hauser J, Karlowski WM. Analysis of OPCRIT results indicate the presence of a novel 'social functioning' domain and complex structure of other dimensions in the Wielkopolska (Poland) population. Schizophr Res. 2012 138(2-3):223-32.
  4. Pontier D, Picart C, Roudier F, Garcia D, Lahmy S, Azevedo J, Alart E, Laudié M, Karlowski WM, Cooke R, Colot V, Voinnet O, Lagrange T. NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis. Mol Cell. 2012 48(1):121-32.
  5. Gebetsberger J, Zywicki M, Künzi A, Polacek N. tRNA-derived fragments target the ribosome and function as regulatory non-coding RNA in Haloferax volcanii. Archaea. 2012:260909.
  6. Skreka K, Schafferer S, Nat IR, Zywicki M, Salti A, Apostolova G, Griehl M, Rederstorff M, Dechant G, Hüttenhofer A. Identification of differentially expressed non-coding RNAs in embryonic stem cell neural differentiation. Nucleic Acids Res. 2012 40(13):6001-15.
  7. Zywicki M, Bakowska-Zywicka K, Polacek N. Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res. 2012 40(9):4013-24.
  8. Skreka K, Zywicki M, Karbiener M, Hüttenhofer A, Scheideler M, Rederstorff M. Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray. J Nucleic Acids. 2012:283560.

2011

  1. Zielezinski A, Karlowski WM. Agos--a universal web tool for GW Argonaute-binding domain prediction. Bioinformatics. 2011 27(9):1318-9.
  2. Sierocka I, Rojek A, Bielewicz D, Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z. Novel genes specifically expressed during the development of the male thalli and antheridia in the dioecious liverwort Pellia endiviifolia. Gene. 2011 485(1):53-62.
  3. Karlowski WM. Beyond sequence similarity – the curious case of GW/WG protein domain. BioTechnologia. 92(4):303-305

2010

  1. Karlowski WM, Zielezinski A, Carrère J, Pontier D, Lagrange T, Cooke R. Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis. Nucleic Acids Res. 2010 38(13):4231-45.
  2. Lin SI, Santi C, Jobet E, Lacut E, El Kholti N, Karlowski WM, Verdeil JL, Breitler JC, Périn C, Ko SS, Guiderdoni E, Chiou TJ, Echeverria M. Complex regulation of two target genes encoding SPX-MFS proteins by rice miR827 in response to phosphate starvation. Plant Cell Physiol. 2010 51(12):2119-31.
  3. Chirkova A, Erlacher MD, Clementi N, Zywicki M, Aigner M, Polacek N. The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center. Nucleic Acids Res. 2010 38(14):4844-55.