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Items: 38

1.

Benchmarking of alignment-free sequence comparison methods.

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.

Genome Biol. 2019 Jul 25;20(1):144. doi: 10.1186/s13059-019-1755-7.

2.

Sequence Dynamics of Pre-mRNA G-Quadruplexes in Plants.

Kopec PM, Karlowski WM.

Front Plant Sci. 2019 Jun 27;10:812. doi: 10.3389/fpls.2019.00812. eCollection 2019.

3.

StarSeeker: an automated tool for mature duplex microRNA sequence identification based on secondary structure modeling of precursor molecule.

Natsidis P, Kappas I, Karlowski WM.

J Biol Res (Thessalon). 2018 Jun 15;25:11. doi: 10.1186/s40709-018-0081-7. eCollection 2018 Dec.

4.

Annotation and profiling of barley GLYCOGEN SYNTHASE3/Shaggy-like genes indicated shift in organ-preferential expression.

Groszyk J, Yanushevska Y, Zielezinski A, Nadolska-Orczyk A, Karlowski WM, Orczyk W.

PLoS One. 2018 Jun 19;13(6):e0199364. doi: 10.1371/journal.pone.0199364. eCollection 2018.

5.

A stable tRNA-like molecule is generated from the long noncoding RNA GUT15 in Arabidopsis.

Plewka P, Thompson A, Szymanski M, Nuc P, Knop K, Rasinska A, Bialkowska A, Szweykowska-Kulinska Z, Karlowski WM, Jarmolowski A.

RNA Biol. 2018;15(6):726-738. doi: 10.1080/15476286.2018.1445404. Epub 2018 Mar 21.

6.

Efficiency of PacBio long read correction by 2nd generation Illumina sequencing.

Mahmoud M, Zywicki M, Twardowski T, Karlowski WM.

Genomics. 2019 Jan;111(1):43-49. doi: 10.1016/j.ygeno.2017.12.011. Epub 2017 Dec 18.

PMID:
29268960
7.

tRex: A Web Portal for Exploration of tRNA-Derived Fragments in Arabidopsis thaliana.

Thompson A, Zielezinski A, Plewka P, Szymanski M, Nuc P, Szweykowska-Kulinska Z, Jarmolowski A, Karlowski WM.

Plant Cell Physiol. 2018 Jan 1;59(1):e1. doi: 10.1093/pcp/pcx173.

PMID:
29145635
8.

Alignment-free sequence comparison: benefits, applications, and tools.

Zielezinski A, Vinga S, Almeida J, Karlowski WM.

Genome Biol. 2017 Oct 3;18(1):186. doi: 10.1186/s13059-017-1319-7. Review.

9.

Identification and Analysis of WG/GW ARGONAUTE-Binding Domains.

Zielezinski A, Karlowski WM.

Methods Mol Biol. 2017;1640:241-256. doi: 10.1007/978-1-4939-7165-7_18.

PMID:
28608348
10.

Dual Role of the Histone Variant H2A.Z in Transcriptional Regulation of Stress-Response Genes.

Sura W, Kabza M, Karlowski WM, Bieluszewski T, Kus-Slowinska M, Pawełoszek Ł, Sadowski J, Ziolkowski PA.

Plant Cell. 2017 Apr;29(4):791-807. doi: 10.1105/tpc.16.00573. Epub 2017 Mar 3.

11.

ORCAN-a web-based meta-server for real-time detection and functional annotation of orthologs.

Zielezinski A, Dziubek M, Sliski J, Karlowski WM.

Bioinformatics. 2017 Apr 15;33(8):1224-1226. doi: 10.1093/bioinformatics/btw825.

PMID:
28057683
12.

Nicotine affects protein complex rearrangement in Caenorhabditis elegans cells.

Sobkowiak R, Zielezinski A, Karlowski WM, Lesicki A.

Drug Chem Toxicol. 2017 Oct;40(4):470-483. doi: 10.1080/01480545.2016.1264411. Epub 2017 Jan 3.

PMID:
28049353
13.

Assessing the 5S ribosomal RNA heterogeneity in Arabidopsis thaliana using short RNA next generation sequencing data.

Szymanski M, Karlowski WM.

Acta Biochim Pol. 2016;63(4):841-844. doi: 10.18388/abp.2016_1367. Epub 2016 Nov 22.

14.

RNAcentral: a comprehensive database of non-coding RNA sequences.

The RNAcentral Consortium, Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell R, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders PJ, Mestdagh P, Wower J, Clark MB, Quek XC, Dinger ME.

Nucleic Acids Res. 2017 Jan 4;45(D1):D128-D134. doi: 10.1093/nar/gkw1008. Epub 2016 Oct 28.

15.

Maf1-mediated regulation of yeast RNA polymerase III is correlated with CCA addition at the 3' end of tRNA precursors.

Foretek D, Nuc P, Żywicki M, Karlowski WM, Kudla G, Boguta M.

Gene. 2017 May 15;612:12-18. doi: 10.1016/j.gene.2016.08.033. Epub 2016 Aug 27.

16.

Promoter-based identification of novel non-coding RNAs reveals the presence of dicistronic snoRNA-miRNA genes in Arabidopsis thaliana.

Qu G, Kruszka K, Plewka P, Yang SY, Chiou TJ, Jarmolowski A, Szweykowska-Kulinska Z, Echeverria M, Karlowski WM.

BMC Genomics. 2015 Nov 25;16:1009. doi: 10.1186/s12864-015-2221-x.

17.

5SRNAdb: an information resource for 5S ribosomal RNAs.

Szymanski M, Zielezinski A, Barciszewski J, Erdmann VA, Karlowski WM.

Nucleic Acids Res. 2016 Jan 4;44(D1):D180-3. doi: 10.1093/nar/gkv1081. Epub 2015 Oct 20.

18.

Pathogen-regulated genes in wheat isogenic lines differing in resistance to brown rust Puccinia triticina.

Dmochowska-Boguta M, Alaba S, Yanushevska Y, Piechota U, Lasota E, Nadolska-Orczyk A, Karlowski WM, Orczyk W.

BMC Genomics. 2015 Oct 5;16:742. doi: 10.1186/s12864-015-1932-3.

19.

mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs.

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.

BMC Plant Biol. 2015 Jun 16;15:144. doi: 10.1186/s12870-015-0533-2.

20.

Early origin and adaptive evolution of the GW182 protein family, the key component of RNA silencing in animals.

Zielezinski A, Karlowski WM.

RNA Biol. 2015;12(7):761-70. doi: 10.1080/15476286.2015.1051302.

21.

The liverwort Pellia endiviifolia shares microtranscriptomic traits that are common to green algae and land plants.

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.

New Phytol. 2015 Apr;206(1):352-67. doi: 10.1111/nph.13220. Epub 2014 Dec 19.

22.

Integrative data analysis indicates an intrinsic disordered domain character of Argonaute-binding motifs.

Zielezinski A, Karlowski WM.

Bioinformatics. 2015 Feb 1;31(3):332-9. doi: 10.1093/bioinformatics/btu666. Epub 2014 Oct 9.

PMID:
25304778
23.

The plant s1-like nuclease family has evolved a highly diverse range of catalytic capabilities.

Lesniewicz K, Karlowski WM, Pienkowska JR, Krzywkowski P, Poreba E.

Plant Cell Physiol. 2013 Jul;54(7):1064-78. doi: 10.1093/pcp/pct061. Epub 2013 Apr 24.

PMID:
23620482
24.

NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis.

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.

Mol Cell. 2012 Oct 12;48(1):121-32. doi: 10.1016/j.molcel.2012.07.027. Epub 2012 Aug 30.

25.

Analysis of OPCRIT results indicate the presence of a novel 'social functioning' domain and complex structure of other dimensions in the Wielkopolska (Poland) population.

Maciukiewicz M, Czerski PM, Leszczynska-Rodziewicz A, Kapelski P, Szczepankiewicz A, Dmitrzak-Weglarz M, Skibinska M, Pawlak J, Hauser J, Karlowski WM.

Schizophr Res. 2012 Jul;138(2-3):223-32. doi: 10.1016/j.schres.2012.03.032. Epub 2012 Apr 21.

PMID:
22521495
26.

mirEX: a platform for comparative exploration of plant pri-miRNA expression data.

Bielewicz D, Dolata J, Zielezinski A, Alaba S, Szarzynska B, Szczesniak MW, Jarmolowski A, Szweykowska-Kulinska Z, Karlowski WM.

Nucleic Acids Res. 2012 Jan;40(Database issue):D191-7. doi: 10.1093/nar/gkr878. Epub 2011 Oct 19.

27.

Agos--a universal web tool for GW Argonaute-binding domain prediction.

Zielezinski A, Karlowski WM.

Bioinformatics. 2011 May 1;27(9):1318-9. doi: 10.1093/bioinformatics/btr128. Epub 2011 Mar 8.

PMID:
21385787
28.

Complex regulation of two target genes encoding SPX-MFS proteins by rice miR827 in response to phosphate starvation.

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.

Plant Cell Physiol. 2010 Dec;51(12):2119-31. doi: 10.1093/pcp/pcq170. Epub 2010 Nov 9.

PMID:
21062869
29.

Genome-wide computational identification of WG/GW Argonaute-binding proteins in Arabidopsis.

Karlowski WM, Zielezinski A, Carrère J, Pontier D, Lagrange T, Cooke R.

Nucleic Acids Res. 2010 Jul;38(13):4231-45. doi: 10.1093/nar/gkq162. Epub 2010 Mar 24.

30.

Identification of precursor transcripts for 6 novel miRNAs expands the diversity on the genomic organisation and expression of miRNA genes in rice.

Lacombe S, Nagasaki H, Santi C, Duval D, Piégu B, Bangratz M, Breitler JC, Guiderdoni E, Brugidou C, Hirsch J, Cao X, Brice C, Panaud O, Karlowski WM, Sato Y, Echeverria M.

BMC Plant Biol. 2008 Dec 2;8:123. doi: 10.1186/1471-2229-8-123.

31.

Sequence composition and genome organization of maize.

Messing J, Bharti AK, Karlowski WM, Gundlach H, Kim HR, Yu Y, Wei F, Fuks G, Soderlund CA, Mayer KF, Wing RA.

Proc Natl Acad Sci U S A. 2004 Oct 5;101(40):14349-54. Epub 2004 Sep 23.

32.
33.

Comparative analysis of the receptor-like kinase family in Arabidopsis and rice.

Shiu SH, Karlowski WM, Pan R, Tzeng YH, Mayer KF, Li WH.

Plant Cell. 2004 May;16(5):1220-34. Epub 2004 Apr 22.

34.
35.

Comparison of rice and Arabidopsis annotation.

Schoof H, Karlowski WM.

Curr Opin Plant Biol. 2003 Apr;6(2):106-12. Review.

PMID:
12667865
36.

MOsDB: an integrated information resource for rice genomics.

Karlowski WM, Schoof H, Janakiraman V, Stuempflen V, Mayer KF.

Nucleic Acids Res. 2003 Jan 1;31(1):190-2.

37.
38.

Lupine leghemoglobin I: expression in transgenic Lotus and tobacco tissues.

Strózycki PM, Karłowski WM, Dessaux Y, Petit A, Legocki AB.

Mol Gen Genet. 2000 Mar;263(2):173-82.

PMID:
10778735

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