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Items: 1 to 50 of 106

1.

MRX Increases Chromatin Accessibility at Stalled Replication Forks to Promote Nascent DNA Resection and Cohesin Loading.

Delamarre A, Barthe A, de la Roche Saint-André C, Luciano P, Forey R, Padioleau I, Skrzypczak M, Ginalski K, Géli V, Pasero P, Lengronne A.

Mol Cell. 2020 Jan 16;77(2):395-410.e3. doi: 10.1016/j.molcel.2019.10.029. Epub 2019 Nov 20.

PMID:
31759824
2.

Correction to: Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.

Matelska D, Shabalin IG, Jabłońska J, Domagalski MJ, Kutner J, Ginalski K, Minor W.

BMC Psychiatry. 2019 Jul 16;19(1):221. doi: 10.1186/s12888-019-2207-3.

3.

Poly-Saturated Dolichols from Filamentous Fungi Modulate Activity of Dolichol-Dependent Glycosyltransferase and Physical Properties of Membranes.

Gryz E, Perlińska-Lenart U, Gawarecka K, Jozwiak A, Piłsyk S, Lipko A, Jemiola-Rzeminska M, Bernat P, Muszewska A, Steczkiewicz K, Ginalski K, Długoński J, Strzalka K, Swiezewska E, Kruszewska JS.

Int J Mol Sci. 2019 Jun 21;20(12). pii: E3043. doi: 10.3390/ijms20123043.

4.

qDSB-Seq is a general method for genome-wide quantification of DNA double-strand breaks using sequencing.

Zhu Y, Biernacka A, Pardo B, Dojer N, Forey R, Skrzypczak M, Fongang B, Nde J, Yousefi R, Pasero P, Ginalski K, Rowicka M.

Nat Commun. 2019 May 24;10(1):2313. doi: 10.1038/s41467-019-10332-8.

5.

Transposable elements contribute to fungal genes and impact fungal lifestyle.

Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska M, Ginalski K.

Sci Rep. 2019 Mar 13;9(1):4307. doi: 10.1038/s41598-019-40965-0.

6.

Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.

Matelska D, Shabalin IG, Jabłońska J, Domagalski MJ, Kutner J, Ginalski K, Minor W.

BMC Evol Biol. 2018 Dec 22;18(1):199. doi: 10.1186/s12862-018-1309-8. Erratum in: BMC Psychiatry. 2019 Jul 16;19(1):221.

7.

i-BLESS is an ultra-sensitive method for detection of DNA double-strand breaks.

Biernacka A, Zhu Y, Skrzypczak M, Forey R, Pardo B, Grzelak M, Nde J, Mitra A, Kudlicki A, Crosetto N, Pasero P, Rowicka M, Ginalski K.

Commun Biol. 2018 Oct 31;1:181. doi: 10.1038/s42003-018-0165-9. eCollection 2018.

8.

Comprehensive Mapping of Histone Modifications at DNA Double-Strand Breaks Deciphers Repair Pathway Chromatin Signatures.

Clouaire T, Rocher V, Lashgari A, Arnould C, Aguirrebengoa M, Biernacka A, Skrzypczak M, Aymard F, Fongang B, Dojer N, Iacovoni JS, Rowicka M, Ginalski K, Côté J, Legube G.

Mol Cell. 2018 Oct 18;72(2):250-262.e6. doi: 10.1016/j.molcel.2018.08.020. Epub 2018 Sep 27.

9.

Exome scale map of genetic alterations promoting metastasis in colorectal cancer.

Goryca K, Kulecka M, Paziewska A, Dabrowska M, Grzelak M, Skrzypczak M, Ginalski K, Mroz A, Rutkowski A, Paczkowska K, Mikula M, Ostrowski J.

BMC Genet. 2018 Sep 19;19(1):85. doi: 10.1186/s12863-018-0673-0.

10.

Predicting proteome dynamics using gene expression data.

Kuchta K, Towpik J, Biernacka A, Kutner J, Kudlicki A, Ginalski K, Rowicka M.

Sci Rep. 2018 Sep 14;8(1):13866. doi: 10.1038/s41598-018-31752-4.

11.

Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer.

Argemi X, Matelska D, Ginalski K, Riegel P, Hansmann Y, Bloom J, Pestel-Caron M, Dahyot S, Lebeurre J, Prévost G.

BMC Genomics. 2018 Aug 20;19(1):621. doi: 10.1186/s12864-018-4978-1.

12.

Hypermethylation of TRIM59 and KLF14 Influences Cell Death Signaling in Familial Alzheimer's Disease.

Wezyk M, Spólnicka M, Pośpiech E, Pepłońska B, Zbieć-Piekarska R, Ilkowski J, Styczyńska M, Barczak A, Zboch M, Filipek-Gliszczynska A, Skrzypczak M, Ginalski K, Kabza M, Makałowska I, Barcikowska-Kotowicz M, Branicki W, Żekanowski C.

Oxid Med Cell Longev. 2018 Apr 4;2018:6918797. doi: 10.1155/2018/6918797. eCollection 2018.

13.

Predicting double-strand DNA breaks using epigenome marks or DNA at kilobase resolution.

Mourad R, Ginalski K, Legube G, Cuvier O.

Genome Biol. 2018 Mar 15;19(1):34. doi: 10.1186/s13059-018-1411-7.

14.

Overactive BRCA1 Affects Presenilin 1 in Induced Pluripotent Stem Cell-Derived Neurons in Alzheimer's Disease.

Wezyk M, Szybinska A, Wojsiat J, Szczerba M, Day K, Ronnholm H, Kele M, Berdynski M, Peplonska B, Fichna JP, Ilkowski J, Styczynska M, Barczak A, Zboch M, Filipek-Gliszczynska A, Bojakowski K, Skrzypczak M, Ginalski K, Kabza M, Makalowska I, Barcikowska-Kotowicz M, Wojda U, Falk A, Zekanowski C.

J Alzheimers Dis. 2018;62(1):175-202. doi: 10.3233/JAD-170830.

PMID:
29439343
15.

Dbf4 recruitment by forkhead transcription factors defines an upstream rate-limiting step in determining origin firing timing.

Fang D, Lengronne A, Shi D, Forey R, Skrzypczak M, Ginalski K, Yan C, Wang X, Cao Q, Pasero P, Lou H.

Genes Dev. 2017 Dec 1;31(23-24):2405-2415. doi: 10.1101/gad.306571.117. Epub 2018 Jan 12.

16.

Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.

Kutner J, Shabalin IG, Matelska D, Handing KB, Gasiorowska O, Sroka P, Gorna MW, Ginalski K, Wozniak K, Minor W.

Biochemistry. 2018 Feb 13;57(6):963-977. doi: 10.1021/acs.biochem.7b01137. Epub 2018 Jan 26.

17.

Cut-and-Paste Transposons in Fungi with Diverse Lifestyles.

Muszewska A, Steczkiewicz K, Stepniewska-Dziubinska M, Ginalski K.

Genome Biol Evol. 2017 Dec 1;9(12):3463-3477. doi: 10.1093/gbe/evx261.

18.

Systematic classification of the His-Me finger superfamily.

Jablonska J, Matelska D, Steczkiewicz K, Ginalski K.

Nucleic Acids Res. 2017 Nov 16;45(20):11479-11494. doi: 10.1093/nar/gkx924.

19.
20.

Fungal lifestyle reflected in serine protease repertoire.

Muszewska A, Stepniewska-Dziubinska MM, Steczkiewicz K, Pawlowska J, Dziedzic A, Ginalski K.

Sci Rep. 2017 Aug 22;7(1):9147. doi: 10.1038/s41598-017-09644-w.

21.

A heterozygous mutation in GOT1 is associated with familial macro-aspartate aminotransferase.

Kulecka M, Wierzbicka A, Paziewska A, Mikula M, Habior A, Janczyk W, Dabrowska M, Karczmarski J, Lazniewski M, Ginalski K, Czlonkowska A, Socha P, Ostrowski J.

J Hepatol. 2017 Nov;67(5):1026-1030. doi: 10.1016/j.jhep.2017.07.003. Epub 2017 Jul 15.

22.

Comprehensive classification of the PIN domain-like superfamily.

Matelska D, Steczkiewicz K, Ginalski K.

Nucleic Acids Res. 2017 Jul 7;45(12):6995-7020. doi: 10.1093/nar/gkx494.

23.

Phylogeny-Based Systematization of Arabidopsis Proteins with Histone H1 Globular Domain.

Kotliński M, Knizewski L, Muszewska A, Rutowicz K, Lirski M, Schmidt A, Baroux C, Ginalski K, Jerzmanowski A.

Plant Physiol. 2017 May;174(1):27-34. doi: 10.1104/pp.16.00214. Epub 2017 Mar 15.

24.

Ssb1 and Ssb2 cooperate to regulate mouse hematopoietic stem and progenitor cells by resolving replicative stress.

Shi W, Vu T, Boucher D, Biernacka A, Nde J, Pandita RK, Straube J, Boyle GM, Al-Ejeh F, Nag P, Jeffery J, Harris JL, Bain AL, Grzelak M, Skrzypczak M, Mitra A, Dojer N, Crosetto N, Cloonan N, Becherel OJ, Finnie J, Skaar JR, Walkley CR, Pandita TK, Rowicka M, Ginalski K, Lane SW, Khanna KK.

Blood. 2017 May 4;129(18):2479-2492. doi: 10.1182/blood-2016-06-725093. Epub 2017 Mar 7.

25.

Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes.

Aymard F, Aguirrebengoa M, Guillou E, Javierre BM, Bugler B, Arnould C, Rocher V, Iacovoni JS, Biernacka A, Skrzypczak M, Ginalski K, Rowicka M, Fraser P, Legube G.

Nat Struct Mol Biol. 2017 Apr;24(4):353-361. doi: 10.1038/nsmb.3387. Epub 2017 Mar 6.

26.

Towards Engineering Novel PE-Based Immunotoxins by Targeting Them to the Nucleus.

Borowiec M, Gorzkiewicz M, Grzesik J, Walczak-Drzewiecka A, Salkowska A, Rodakowska E, Steczkiewicz K, Rychlewski L, Dastych J, Ginalski K.

Toxins (Basel). 2016 Nov 10;8(11). pii: E321.

27.

Genome-wide co-localization of active EGFR and downstream ERK pathway kinases mirrors mitogen-inducible RNA polymerase 2 genomic occupancy.

Mikula M, Skrzypczak M, Goryca K, Paczkowska K, Ledwon JK, Statkiewicz M, Kulecka M, Grzelak M, Dabrowska M, Kuklinska U, Karczmarski J, Rumienczyk I, Jastrzebski K, Miaczynska M, Ginalski K, Bomsztyk K, Ostrowski J.

Nucleic Acids Res. 2016 Dec 1;44(21):10150-10164. Epub 2016 Sep 1.

28.

Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study.

Huang R, Ripstein ZA, Augustyniak R, Lazniewski M, Ginalski K, Kay LE, Rubinstein JL.

Proc Natl Acad Sci U S A. 2016 Jul 19;113(29):E4190-9. doi: 10.1073/pnas.1603980113. Epub 2016 Jul 11.

29.

Diverse cap-binding properties of Drosophila eIF4E isoforms.

Zuberek J, Kuchta K, Hernández G, Sonenberg N, Ginalski K.

Biochim Biophys Acta. 2016 Oct;1864(10):1292-303. doi: 10.1016/j.bbapap.2016.06.015. Epub 2016 Jun 29.

PMID:
27374989
30.

FAM46 proteins are novel eukaryotic non-canonical poly(A) polymerases.

Kuchta K, Muszewska A, Knizewski L, Steczkiewicz K, Wyrwicz LS, Pawlowski K, Rychlewski L, Ginalski K.

Nucleic Acids Res. 2016 May 5;44(8):3534-48. doi: 10.1093/nar/gkw222. Epub 2016 Apr 7.

31.

Histone H1 Variants in Arabidopsis Are Subject to Numerous Post-Translational Modifications, Both Conserved and Previously Unknown in Histones, Suggesting Complex Functions of H1 in Plants.

Kotliński M, Rutowicz K, Kniżewski Ł, Palusiński A, Olędzki J, Fogtman A, Rubel T, Koblowska M, Dadlez M, Ginalski K, Jerzmanowski A.

PLoS One. 2016 Jan 28;11(1):e0147908. doi: 10.1371/journal.pone.0147908. eCollection 2016.

32.

A Specialized Histone H1 Variant Is Required for Adaptive Responses to Complex Abiotic Stress and Related DNA Methylation in Arabidopsis.

Rutowicz K, Puzio M, Halibart-Puzio J, Lirski M, Kotliński M, Kroteń MA, Knizewski L, Lange B, Muszewska A, Śniegowska-Świerk K, Kościelniak J, Iwanicka-Nowicka R, Buza K, Janowiak F, Żmuda K, Jõesaar I, Laskowska-Kaszub K, Fogtman A, Kollist H, Zielenkiewicz P, Tiuryn J, Siedlecki P, Swiezewski S, Ginalski K, Koblowska M, Archacki R, Wilczynski B, Rapacz M, Jerzmanowski A.

Plant Physiol. 2015 Nov;169(3):2080-101. doi: 10.1104/pp.15.00493. Epub 2015 Sep 8.

33.

Strategies for achieving high sequencing accuracy for low diversity samples and avoiding sample bleeding using illumina platform.

Mitra A, Skrzypczak M, Ginalski K, Rowicka M.

PLoS One. 2015 Apr 10;10(4):e0120520. doi: 10.1371/journal.pone.0120520. eCollection 2015. Erratum in: PLoS One. 2020 Jan 2;15(1):e0227431.

34.

Five eIF4E isoforms from Arabidopsis thaliana are characterized by distinct features of cap analogs binding.

Kropiwnicka A, Kuchta K, Lukaszewicz M, Kowalska J, Jemielity J, Ginalski K, Darzynkiewicz E, Zuberek J.

Biochem Biophys Res Commun. 2015 Jan 2;456(1):47-52. doi: 10.1016/j.bbrc.2014.11.032. Epub 2014 Nov 18.

PMID:
25446076
35.

The histone deacetylases sir2 and rpd3 act on ribosomal DNA to control the replication program in budding yeast.

Yoshida K, Bacal J, Desmarais D, Padioleau I, Tsaponina O, Chabes A, Pantesco V, Dubois E, Parrinello H, Skrzypczak M, Ginalski K, Lengronne A, Pasero P.

Mol Cell. 2014 May 22;54(4):691-7. doi: 10.1016/j.molcel.2014.04.032.

36.

Probabilistic approach to predicting substrate specificity of methyltransferases.

Szczepińska T, Kutner J, Kopczyński M, Pawłowski K, Dziembowski A, Kudlicki A, Ginalski K, Rowicka M.

PLoS Comput Biol. 2014 Mar 20;10(3):e1003514. doi: 10.1371/journal.pcbi.1003514. eCollection 2014 Mar.

37.

The RNase H-like superfamily: new members, comparative structural analysis and evolutionary classification.

Majorek KA, Dunin-Horkawicz S, Steczkiewicz K, Muszewska A, Nowotny M, Ginalski K, Bujnicki JM.

Nucleic Acids Res. 2014 Apr;42(7):4160-79. doi: 10.1093/nar/gkt1414. Epub 2014 Jan 23.

38.

DIRS and Ngaro Retrotransposons in Fungi.

Muszewska A, Steczkiewicz K, Ginalski K.

PLoS One. 2013 Sep 25;8(9):e76319. doi: 10.1371/journal.pone.0076319. eCollection 2013.

39.

Nucleotide-resolution DNA double-strand break mapping by next-generation sequencing.

Crosetto N, Mitra A, Silva MJ, Bienko M, Dojer N, Wang Q, Karaca E, Chiarle R, Skrzypczak M, Ginalski K, Pasero P, Rowicka M, Dikic I.

Nat Methods. 2013 Apr;10(4):361-5. doi: 10.1038/nmeth.2408. Epub 2013 Mar 17.

40.

Identification of a novel human mitochondrial endo-/exonuclease Ddk1/c20orf72 necessary for maintenance of proper 7S DNA levels.

Szczesny RJ, Hejnowicz MS, Steczkiewicz K, Muszewska A, Borowski LS, Ginalski K, Dziembowski A.

Nucleic Acids Res. 2013 Mar 1;41(5):3144-61. doi: 10.1093/nar/gkt029. Epub 2013 Jan 28.

41.

C16orf57, a gene mutated in poikiloderma with neutropenia, encodes a putative phosphodiesterase responsible for the U6 snRNA 3' end modification.

Mroczek S, Krwawicz J, Kutner J, Lazniewski M, Kuciński I, Ginalski K, Dziembowski A.

Genes Dev. 2012 Sep 1;26(17):1911-25. doi: 10.1101/gad.193169.112. Epub 2012 Aug 16.

42.

Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily.

Steczkiewicz K, Muszewska A, Knizewski L, Rychlewski L, Ginalski K.

Nucleic Acids Res. 2012 Aug;40(15):7016-45. doi: 10.1093/nar/gks382. Epub 2012 May 25.

43.

The C2H2 zinc finger transcription factors are likely targets for Ni(II) toxicity.

Kurowska E, Sasin-Kurowska J, Bonna A, Grynberg M, Poznański J, Knizewski L, Ginalski K, Bal W.

Metallomics. 2011 Nov;3(11):1227-31. doi: 10.1039/c1mt00081k. Epub 2011 Aug 25.

PMID:
21869994
44.

Comprehensive structural and substrate specificity classification of the Saccharomyces cerevisiae methyltransferome.

Wlodarski T, Kutner J, Towpik J, Knizewski L, Rychlewski L, Kudlicki A, Rowicka M, Dziembowski A, Ginalski K.

PLoS One. 2011;6(8):e23168. doi: 10.1371/journal.pone.0023168. Epub 2011 Aug 9.

45.

Extending the aerolysin family: from bacteria to vertebrates.

Szczesny P, Iacovache I, Muszewska A, Ginalski K, van der Goot FG, Grynberg M.

PLoS One. 2011;6(6):e20349. doi: 10.1371/journal.pone.0020349. Epub 2011 Jun 8.

46.

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

Steczkiewicz K, Zimmermann MT, Kurcinski M, Lewis BA, Dobbs D, Kloczkowski A, Jernigan RL, Kolinski A, Ginalski K.

Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9443-8. doi: 10.1073/pnas.1015399108. Epub 2011 May 23.

47.

Novel transmembrane lipases of alpha/beta hydrolase fold.

Lazniewski M, Steczkiewicz K, Knizewski L, Wawer I, Ginalski K.

FEBS Lett. 2011 Mar 23;585(6):870-4. doi: 10.1016/j.febslet.2011.02.016. Epub 2011 Feb 17.

48.

Detailed mechanism of squalene epoxidase inhibition by terbinafine.

Nowosielski M, Hoffmann M, Wyrwicz LS, Stepniak P, Plewczynski DM, Lazniewski M, Ginalski K, Rychlewski L.

J Chem Inf Model. 2011 Feb 28;51(2):455-62. doi: 10.1021/ci100403b. Epub 2011 Jan 13.

PMID:
21229992
49.

HarmonyDOCK: the structural analysis of poses in protein-ligand docking.

Plewczynski D, Philips A, Von Grotthuss M, Rychlewski L, Ginalski K.

J Comput Biol. 2014 Mar;21(3):247-56. doi: 10.1089/cmb.2009.0111. Epub 2010 Nov 20.

PMID:
21091053
50.

VoteDock: consensus docking method for prediction of protein-ligand interactions.

Plewczynski D, Łaźniewski M, von Grotthuss M, Rychlewski L, Ginalski K.

J Comput Chem. 2011 Mar;32(4):568-81. doi: 10.1002/jcc.21642. Epub 2010 Sep 1.

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