Publications

Showcase of Our Recent Papers

2021

  • RNAcentral Consortium RNAcentral 2021: secondary structure integration, improved sequence search and new member databases. Nucleic Acids Res. 49(D1):D212-D220 [PubMed]
  • Dolata J, Zielezinski A, Stepien A, Kruszka K, Bielewicz D, Pacak A, Jarmolowski A, Karlowski WM, Szweykowska-Kulinska Z. Quantitative Analysis of Plant miRNA Primary Transcripts. Methods Mol Biol. 2170:53-77 [PubMed]

2020

  • Baranek J, Pogodzinski B, Szipluk N, Zielezinski A. TOXiTAXi: a web resource for toxicity of Bacillus thuringiensis protein compositions towards species of various taxonomic groups. Sci Rep. 10(1):19767 [PubMed]
  • Kloc Y, Dmochowska-Boguta, Zielezinski A, Nadolska-Orczyk A, Karlowski WM, Orczyk W. Silencing of HvGSK1.1-A GSK3/SHAGGY-Like Kinase-Enhances Barley ( Hordeum vulgare L.) Growth in Normal and in Salt Stress Conditions. Int J Mol Sci. 21(18):6616 [PubMed]
  • Walczak M, Lykowska-Szuber L, Plucinska M et al. Is Polymorphism in the Apoptosis and Inflammatory Pathway Genes Associated With a Primary Response to Anti-TNF Therapy in Crohn's Disease Patients? Front Pharmacol. 14 August 2020 [PubMed]
  • Sierocka I, Alaba S, Jarmolowski A, Karlowski WM, Szweykowska-Kulinska Z. The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach. Planta 252(2):21 [PubMed]
  • Smoczynska A, Pacak A, Nuc P, Swida-Barteczka A, Kruszka K, Karlowski WM, Jarmolowski, Szweykowska-Kulinska Z. A Functional Network of Novel Barley MicroRNAs and Their Targets in Response to Drought. Genes 11(5):488 [PubMed]
  • Zmienko A, Marszalek-Zenczak M, Wojciechowski P, Samelak-Czajk A, Luczak M, Kozlowski P, Karlowski WM, Figlerowicz M. AthCNV: A Map of DNA Copy Number Variations in the Arabidopsis Genome. Plant Cell 32(6):1797-1819 [PubMed]
  • Dmochowska-Boguta, Kloc Y, Zielezinski A, Werecki P, Nadolska-Orczyk A, Karlowski WM, Orczyk W. TaWAK6 encoding wall-associated kinase is involved in wheat resistance to leaf rust similar to adult plant resistance. PLOS ONE 15(1):e0227713 [PubMed]

2019

  • Zielezinski A, Girgis HZ, Bernard G, Leimeister CA, Tang K, Dencker T, Lau AK, Röhling S, Choi JJ, Waterman MS, Comin M, Kim SH, Vinga S, Almeida JS, Chan CX, James BT, Sun F, Morgenstern B, Karlowski WM. Benchmarking of alignment-free sequence comparison methods. Genome Biol. 20(1):144. [PubMed]
  • Fricker R, Brogli R, Luidalepp H, Wyss L, Fasnacht M, Joss O, Zywicki M, Helm M, Schneider A, Cristodero M, Polacek N. A tRNA half modulates translation as stress response in Trypanosoma brucei. Nat Commun. 10(1):118 [PubMed]
  • Kopec PM, Karlowski WM. Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants. Front Plant Sci. 10:812 [PubMed]
  • Mahmoud M, Zywicki M, Twardowski T, Karlowski WM. Efficiency of PacBio long read correction by 2nd generation Illumina sequencing. Genomics 111(1):43-49 [PubMed]
  • The RNAcentral Consortium. RNAcentral: a hub of information for non-coding RNA sequences. Nucleic Acids Res. 47(D1):D1250-D1251 [PubMed]

2018

  • Groszyk J, Yanushevska Y, Zielezinski A, Nadolska-Orczyk A, Karlowski WM, Orczyk W. Annotation and profiling of barley GLYCOGEN SYNTHASE3/Shaggy-like genes indicated shift in organ-preferential expression. PLOS ONE 13(6):e0199364 [PubMed]
  • Plewka P, Thompson A, Szymanski M, Nuc P, Knop K, Rasinska A, Bialkowska A, Szweykowska-Kulinska Z, Karlowski WM, Jarmolowski A. A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis. RNA Biol. 15(6):726-738 [PubMed]
  • Thompson A, Zielezinski A, Plewka P, Szymanski M, Nuc P, Szweykowska-Kulinska Z, Jarmolowski A, Karlowski WM. tRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana. Plant Cell Physiol. 59(1):e1 [PubMed]
  • Natsidis P, Kappas I, Karlowski WM. StarSeeker: an automated tool for mature duplex microRNA sequence identification based on secondary structure modeling of precursor molecule J Biol Res (Thessalon) 25:11. [PubMed]
  • Wyss L, Waser M, Gebetsberger J, Zywicki M, Polacek N. mRNA-specific translation regulation by a ribosome-associated ncRNA in Haloferax volcanii. Sci Rep. 8(1):12502 [PubMed]

2017

  • Zielezinski A, Vinga S, Almeida J, Karlowski WM. Alignment-free sequence comparison: benefits, applications, and tools. Genome Biol. 18(1):186 [PubMed]
  • Sura W, Kabza M, Karlowski WM, Bieluszewski T, Kus-Slowinska M, Pawełoszek Ł, Sadowski J, Ziolkowski PA. Dual Role of the Histone Variant H2A.Z in Transcriptional Regulation of Stress-Response Genes. Plant Cell. 29(4):791-807 [PubMed]
  • Foretek D, Nuc P, Żywicki 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 612:12-18 [PubMed]
  • The RNAcentral Consortium. RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res. 45(D1):D128-D134 [PubMed]
  • Zielezinski A, Karlowski W. Identification and Analysis of WG/GW ARGONAUTE-Binding Domains. Methods Mol Biol. 1640:241-256 [PubMed]
  • Zielezinski A, Dziubek M, Sliski J, Karlowski W. ORCAN—a web-based meta-server for real-time detection and functional annotation of orthologs. Bioinformatics. 33(8):1224-1226 [PubMed]
  • Sobkowiak R, Zielezinski A, Karlowski W, Lesicki A. Nicotine affects protein complex rearrangement in Caenorhabditis elegans cells. Drug Chem Toxicol. 40(4):470-483. [PubMed]

2016

  • Machtel P, Bakowska-Zywicka K, Zywicki M. Emerging applications of riboswitches – from antibacterial targets to molecular tools. J ApplGenet. 57(4):531-541. [PubMed]
  • Plucinska M, Bakowska-Zywicka K, Zywicki M. Suitability of high-throughput DMS-probing data for constraining the secondary structure prediction of small RNAs. BioTechnologia 97(3):161-167.
  • 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 612:12-18. [PubMed]
  • Bąkowska-Żywicka K, Mleczko A, Kasprzyk M, Machtel P, Zywicki M, Twardowski T. The widespread occurrence of tRNA-derived fragments in Saccharomyces cerevisiae. FEBS Open Bio. 6(12):1186-1200. [PubMed]
  • Szymanski M, Zielezinski A, Barciszewski J, Erdmann V, Karlowski WM. 5SRNAdb: an information resource for 5S ribosomal RNAs. Nucleic Acids Res. 44(D1):D180-D183. [PubMed]

2015

  • 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 37(265).
  • Zielezinski A & Karlowski WM. Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals. RNA Biol. 12(7):761-70. [PubMed]
  • 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. 5:144. [PubMed]
  • 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. 9(7):1324-40. [PubMed]
  • 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. 206(1):352-67. [PubMed]
  • Zielezinski A, Karlowski WM. Integrative data analysis indicates an intrinsic disordered domain character of Argonaute-binding motifs. Bioinformatics. 31(3):332-9. [PubMed]
  • Książkiewicz M, Zielezinski A, Wyrwa K, Szczepaniak A, Rychel S, Karlowski WM, 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 33:84-101. [PubMed]

2014

  • 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 [PubMed]
  • 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. [PubMed]
  • Kruszka K, Pacak A, Swida-Barteczka A, Nuc P, Alaba S, Wroblewska Z, Karlowski WM, Jarmolowski A, Szweykowska-Kulinska Z. Transcriptionally and post-transcriptionally regulated microRNAs in heat stress response in barley. J Exp Bot. 65(20):6123-35. [PubMed]

2013

  • 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. [PubMed]
  • 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. 14:79. [PubMed]
  • Kruszka K, Pacak A, Swida-Barteczka A, Stefaniak AK, Kaja E, Sierocka I, Karlowski WM, Jarmolowski A, Szweykowska-Kulinska Z. Developmentally regulated expression and complex processing of barley pri-microRNAs. BMC Genomics. 14:34. [PubMed]

2012

  • 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. 40(Database issue):D191-7. [PubMed]
  • Sobkowiak L, Karlowski WM, 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. 3:46. [PubMed]
  • 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. 138(2-3):223-32. [PubMed]
  • 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. 48(1):121-32. [PubMed]
  • 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. [PubMed]
  • 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. 40(13):6001-15. [PubMed]
  • Zywicki M, Bakowska-Zywicka K, Polacek N. Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis. Nucleic Acids Res. 40(9):4013-24. [PubMed]
  • 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. [PubMed]

2011

  • Zielezinski A, Karlowski WM. Agos--a universal web tool for GW Argonaute-binding domain prediction. Bioinformatics 27(9):1318-9. [PubMed]
  • Sierocka I, Rojek A, Bielewicz D, Karlowski WM, 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. [PubMed]
  • Karlowski WM. Beyond sequence similarity – the curious case of GW/WG protein domain. BioTechnologia. 92(4):303-305

2010

  • 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. 38(13):4231-45. [PubMed]
  • 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. 51(12):2119-31. [PubMed]
  • 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. 38(14):4844-55. [PubMed]