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Items: 1 to 50 of 77

1.

Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics.

Makałowski W, Gotea V, Pande A, Makałowska I.

Methods Mol Biol. 2019;1910:177-207. doi: 10.1007/978-1-4939-9074-0_6.

PMID:
31278665
2.

Towards a deeper annotation of human lncRNAs.

Szcześniak MW, Wanowska E, Mukherjee N, Ohler U, Makałowska I.

Biochim Biophys Acta Gene Regul Mech. 2019 May 22. pii: S1874-9399(18)30525-X. doi: 10.1016/j.bbagrm.2019.05.003. [Epub ahead of print]

PMID:
31128317
3.

CANTATAdb 2.0: Expanding the Collection of Plant Long Noncoding RNAs.

Szcześniak MW, Bryzghalov O, Ciomborowska-Basheer J, Makałowska I.

Methods Mol Biol. 2019;1933:415-429. doi: 10.1007/978-1-4939-9045-0_26.

PMID:
30945201
4.

Comparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species.

Golanowska M, Potrykus M, Motyka-Pomagruk A, Kabza M, Bacci G, Galardini M, Bazzicalupo M, Makalowska I, Smalla K, Mengoni A, Hugouvieux-Cotte-Pattat N, Lojkowska E.

Front Microbiol. 2018 Aug 31;9:1940. doi: 10.3389/fmicb.2018.01940. eCollection 2018.

5.

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.

6.

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
7.

Natural antisense transcripts in diseases: From modes of action to targeted therapies.

Wanowska E, Kubiak MR, Rosikiewicz W, Makałowska I, Szcześniak MW.

Wiley Interdiscip Rev RNA. 2018 Mar;9(2). doi: 10.1002/wrna.1461. Epub 2018 Jan 17. Review.

8.

Transcriptional interference by small transcripts in proximal promoter regions.

Pande A, Brosius J, Makalowska I, Makalowski W, Raabe CA.

Nucleic Acids Res. 2018 Feb 16;46(3):1069-1088. doi: 10.1093/nar/gkx1242.

9.

RetrogeneDB-a database of plant and animal retrocopies.

Rosikiewicz W, Kabza M, Kosinski JG, Ciomborowska-Basheer J, Kubiak MR, Makalowska I.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax038.

10.

OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes.

Rosikiewicz W, Suzuki Y, Makalowska I.

Nucleic Acids Res. 2018 Jan 4;46(D1):D186-D193. doi: 10.1093/nar/gkx948.

11.

Protein-Coding Genes' Retrocopies and Their Functions.

Kubiak MR, Makałowska I.

Viruses. 2017 Apr 13;9(4). pii: E80. doi: 10.3390/v9040080. Review.

12.

Retroposition as a source of antisense long non-coding RNAs with possible regulatory functions.

Bryzghalov O, Szcześniak MW, Makałowska I.

Acta Biochim Pol. 2016;63(4):825-833. doi: 10.18388/abp.2016_1354. Epub 2016 Nov 2.

13.

Biological functions of natural antisense transcripts.

Rosikiewicz W, Makałowska I.

Acta Biochim Pol. 2016;63(4):665-673. doi: 10.18388/abp.2016_1350. Epub 2016 Oct 21. Review.

14.

Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii.

Jąkalski M, Takeshita K, Deblieck M, Koyanagi KO, Makałowska I, Watanabe H, Makałowski W.

Biol Direct. 2016 Aug 4;11:35. doi: 10.1186/s13062-016-0138-1.

15.

lncRNA-RNA Interactions across the Human Transcriptome.

Szcześniak MW, Makałowska I.

PLoS One. 2016 Mar 1;11(3):e0150353. doi: 10.1371/journal.pone.0150353. eCollection 2016.

16.

siRNA release from pri-miRNA scaffolds is controlled by the sequence and structure of RNA.

Galka-Marciniak P, Olejniczak M, Starega-Roslan J, Szczesniak MW, Makalowska I, Krzyzosiak WJ.

Biochim Biophys Acta. 2016 Apr;1859(4):639-49. doi: 10.1016/j.bbagrm.2016.02.014. Epub 2016 Feb 26.

PMID:
26921501
17.

CANTATAdb: A Collection of Plant Long Non-Coding RNAs.

Szcześniak MW, Rosikiewicz W, Makałowska I.

Plant Cell Physiol. 2016 Jan;57(1):e8. doi: 10.1093/pcp/pcv201. Epub 2015 Dec 12.

18.

Sequence-non-specific effects generated by various types of RNA interference triggers.

Olejniczak M, Urbanek MO, Jaworska E, Witucki L, Szczesniak MW, Makalowska I, Krzyzosiak WJ.

Biochim Biophys Acta. 2016 Feb;1859(2):306-14. doi: 10.1016/j.bbagrm.2015.11.005. Epub 2015 Nov 22.

PMID:
26612823
19.

Inter-population Differences in Retrogene Loss and Expression in Humans.

Kabza M, Kubiak MR, Danek A, Rosikiewicz W, Deorowicz S, Polański A, Makałowska I.

PLoS Genet. 2015 Oct 16;11(10):e1005579. doi: 10.1371/journal.pgen.1005579. eCollection 2015 Oct.

20.

RetrogeneDB--a database of animal retrogenes.

Kabza M, Ciomborowska J, Makałowska I.

Mol Biol Evol. 2014 Jul;31(7):1646-8. doi: 10.1093/molbev/msu139. Epub 2014 Apr 16.

21.

miRNEST 2.0: a database of plant and animal microRNAs.

Szczesniak MW, Makalowska I.

Nucleic Acids Res. 2014 Jan;42(Database issue):D74-7. doi: 10.1093/nar/gkt1156. Epub 2013 Nov 15.

22.

Characterization of the mitochondrial genome of Rousettus leschenaulti.

Szcześniak M, Yoneda M, Sato H, Makałowska I, Kyuwa S, Sugano S, Suzuki Y, Makałowski W, Kai C.

Mitochondrial DNA. 2014 Dec;25(6):443-4. doi: 10.3109/19401736.2013.809451. Epub 2013 Jul 2.

PMID:
23815317
23.

HuntMi: an efficient and taxon-specific approach in pre-miRNA identification.

Gudyś A, Szcześniak MW, Sikora M, Makałowska I.

BMC Bioinformatics. 2013 Mar 5;14:83. doi: 10.1186/1471-2105-14-83.

24.

ERISdb: a database of plant splice sites and splicing signals.

Szcześniak MW, Kabza M, Pokrzywa R, Gudyś A, Makałowska I.

Plant Cell Physiol. 2013 Feb;54(2):e10. doi: 10.1093/pcp/pct001. Epub 2013 Jan 7.

PMID:
23299413
25.

[MicroRNA databases].

Szcześniak MW, Owczarkowska E, Gapski J, Makałowska I.

Postepy Biochem. 2012;58(1):91-9. Review. Polish.

PMID:
23214133
26.

"Orphan" retrogenes in the human genome.

Ciomborowska J, Rosikiewicz W, Szklarczyk D, Makałowski W, Makałowska I.

Mol Biol Evol. 2013 Feb;30(2):384-96. doi: 10.1093/molbev/mss235. Epub 2012 Oct 12.

27.

Transposable elements and their identification.

Makałowski W, Pande A, Gotea V, Makałowska I.

Methods Mol Biol. 2012;855:337-59. doi: 10.1007/978-1-61779-582-4_12. Review.

PMID:
22407715
28.

Rootstock-regulated gene expression patterns associated with fire blight resistance in apple.

Jensen PJ, Halbrendt N, Fazio G, Makalowska I, Altman N, Praul C, Maximova SN, Ngugi HK, Crassweller RM, Travis JW, McNellis TW.

BMC Genomics. 2012 Jan 9;13:9. doi: 10.1186/1471-2164-13-9.

29.

miRNEST database: an integrative approach in microRNA search and annotation.

Szcześniak MW, Deorowicz S, Gapski J, Kaczyński Ł, Makalowska I.

Nucleic Acids Res. 2012 Jan;40(Database issue):D198-204. doi: 10.1093/nar/gkr1159. Epub 2011 Dec 1.

30.

Primate and rodent specific intron gains and the origin of retrogenes with splice variants.

Szcześniak MW, Ciomborowska J, Nowak W, Rogozin IB, Makałowska I.

Mol Biol Evol. 2011 Jan;28(1):33-7. doi: 10.1093/molbev/msq260. Epub 2010 Oct 1.

31.

Genome evolution.

Makałowska I, Rogozin IB, Makałowski W.

Adv Bioinformatics. 2010;2010:643701. doi: 10.1155/2010/643701. Epub 2011 Jul 21. No abstract available.

32.

Plant pathogen culture collections: it takes a village to preserve these resources vital to the advancement of agricultural security and plant pathology.

Kang S, Blair JE, Geiser DM, Khang CH, Park SY, Gahegan M, O'Donnell K, Luster DG, Kim SH, Ivors KL, Lee YH, Lee YW, Grünwald NJ, Martin FM, Coffey MD, Veeraraghavan N, Makalowska I.

Phytopathology. 2006 Sep;96(9):920-5. doi: 10.1094/PHYTO-96-0920.

33.

Comparative analysis of an unusual gene arrangement in the human chromosome 1.

Makałowska I.

Gene. 2008 Nov 1;423(2):172-9. doi: 10.1016/j.gene.2008.06.030. Epub 2008 Jul 11.

PMID:
18672041
34.

Phytophthora Database: A Forensic Database Supporting the Identification and Monitoring of Phytophthora.

Park J, Park B, Veeraraghavan N, Jung K, Lee YH, Blair JE, Geiser DM, Isard S, Mansfield MA, Nikolaeva E, Park SY, Russo J, Kim SH, Greene M, Ivors KL, Balci Y, Peiman M, Erwin DC, Coffey MD, Rossman A, Farr D, Cline E, Grünwald NJ, Luster DG, Schrandt J, Martin F, Ribeiro OK, Makalowska I, Kang S.

Plant Dis. 2008 Jun;92(6):966-972. doi: 10.1094/PDIS-92-6-0966.

PMID:
30769728
35.

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.

Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T.

Nucleic Acids Res. 2008 Jan;36(Database issue):D793-9. Epub 2007 Dec 18.

36.

Birth and death of gene overlaps in vertebrates.

Makałowska I, Lin CF, Hernandez K.

BMC Evol Biol. 2007 Oct 16;7:193.

37.

Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA Leu (CAA).

Brzezicha B, Schmidt M, Makalowska I, Jarmolowski A, Pienkowska J, Szweykowska-Kulinska Z.

Nucleic Acids Res. 2006;34(20):6034-43. Epub 2006 Oct 27.

38.

ChloroplastDB: the Chloroplast Genome Database.

Cui L, Veeraraghavan N, Richter A, Wall K, Jansen RK, Leebens-Mack J, Makalowska I, dePamphilis CW.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D692-6.

39.

SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans.

Lamason RL, Mohideen MA, Mest JR, Wong AC, Norton HL, Aros MC, Jurynec MJ, Mao X, Humphreville VR, Humbert JE, Sinha S, Moore JL, Jagadeeswaran P, Zhao W, Ning G, Makalowska I, McKeigue PM, O'donnell D, Kittles R, Parra EJ, Mangini NJ, Grunwald DJ, Shriver MD, Canfield VA, Cheng KC.

Science. 2005 Dec 16;310(5755):1782-6.

40.

Origin and evolution of the chicken leukocyte receptor complex.

Nikolaidis N, Makalowska I, Chalkia D, Makalowski W, Klein J, Nei M.

Proc Natl Acad Sci U S A. 2005 Mar 15;102(11):4057-62. Epub 2005 Mar 7.

41.

Overlapping genes in vertebrate genomes.

Makalowska I, Lin CF, Makalowski W.

Comput Biol Chem. 2005 Feb;29(1):1-12. Review.

PMID:
15680581
42.

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Imanishi T, Itoh T, Suzuki Y, O'Donovan C, Fukuchi S, Koyanagi KO, Barrero RA, Tamura T, Yamaguchi-Kabata Y, Tanino M, Yura K, Miyazaki S, Ikeo K, Homma K, Kasprzyk A, Nishikawa T, Hirakawa M, Thierry-Mieg J, Thierry-Mieg D, Ashurst J, Jia L, Nakao M, Thomas MA, Mulder N, Karavidopoulou Y, Jin L, Kim S, Yasuda T, Lenhard B, Eveno E, Suzuki Y, Yamasaki C, Takeda J, Gough C, Hilton P, Fujii Y, Sakai H, Tanaka S, Amid C, Bellgard M, Bonaldo Mde F, Bono H, Bromberg SK, Brookes AJ, Bruford E, Carninci P, Chelala C, Couillault C, de Souza SJ, Debily MA, Devignes MD, Dubchak I, Endo T, Estreicher A, Eyras E, Fukami-Kobayashi K, Gopinath GR, Graudens E, Hahn Y, Han M, Han ZG, Hanada K, Hanaoka H, Harada E, Hashimoto K, Hinz U, Hirai M, Hishiki T, Hopkinson I, Imbeaud S, Inoko H, Kanapin A, Kaneko Y, Kasukawa T, Kelso J, Kersey P, Kikuno R, Kimura K, Korn B, Kuryshev V, Makalowska I, Makino T, Mano S, Mariage-Samson R, Mashima J, Matsuda H, Mewes HW, Minoshima S, Nagai K, Nagasaki H, Nagata N, Nigam R, Ogasawara O, Ohara O, Ohtsubo M, Okada N, Okido T, Oota S, Ota M, Ota T, Otsuki T, Piatier-Tonneau D, Poustka A, Ren SX, Saitou N, Sakai K, Sakamoto S, Sakate R, Schupp I, Servant F, Sherry S, Shiba R, Shimizu N, Shimoyama M, Simpson AJ, Soares B, Steward C, Suwa M, Suzuki M, Takahashi A, Tamiya G, Tanaka H, Taylor T, Terwilliger JD, Unneberg P, Veeramachaneni V, Watanabe S, Wilming L, Yasuda N, Yoo HS, Stodolsky M, Makalowski W, Go M, Nakai K, Takagi T, Kanehisa M, Sakaki Y, Quackenbush J, Okazaki Y, Hayashizaki Y, Hide W, Chakraborty R, Nishikawa K, Sugawara H, Tateno Y, Chen Z, Oishi M, Tonellato P, Apweiler R, Okubo K, Wagner L, Wiemann S, Strausberg RL, Isogai T, Auffray C, Nomura N, Gojobori T, Sugano S.

PLoS Biol. 2004 Jun;2(6):e162. Epub 2004 Apr 20. Erratum in: PLoS Biol. 2004 Jul;2(7):e256.

43.

Mammalian overlapping genes: the comparative perspective.

Veeramachaneni V, Makałowski W, Galdzicki M, Sood R, Makałowska I.

Genome Res. 2004 Feb;14(2):280-6.

44.

Identification and characterization of mouse Rab32 by mRNA and protein expression analysis.

Cohen-Solal KA, Sood R, Marin Y, Crespo-Carbone SM, Sinsimer D, Martino JJ, Robbins C, Makalowska I, Trent J, Chen S.

Biochim Biophys Acta. 2003 Sep 23;1651(1-2):68-75.

PMID:
14499590
45.

Cloning and characterization of a novel gene, SHPRH, encoding a conserved putative protein with SNF2/helicase and PHD-finger domains from the 6q24 region.

Sood R, Makalowska I, Galdzicki M, Hu P, Eddings E, Robbins CM, Moses T, Namkoong J, Chen S, Trent JM.

Genomics. 2003 Aug;82(2):153-61.

PMID:
12837266
46.

Melanoma mouse model implicates metabotropic glutamate signaling in melanocytic neoplasia.

Pollock PM, Cohen-Solal K, Sood R, Namkoong J, Martino JJ, Koganti A, Zhu H, Robbins C, Makalowska I, Shin SS, Marin Y, Roberts KG, Yudt LM, Chen A, Cheng J, Incao A, Pinkett HW, Graham CL, Dunn K, Crespo-Carbone SM, Mackason KR, Ryan KB, Sinsimer D, Goydos J, Reuhl KR, Eckhaus M, Meltzer PS, Pavan WJ, Trent JM, Chen S.

Nat Genet. 2003 May;34(1):108-12.

PMID:
12704387
47.

GALA, a database for genomic sequence alignments and annotations.

Giardine B, Elnitski L, Riemer C, Makalowska I, Schwartz S, Miller W, Hardison RC.

Genome Res. 2003 Apr;13(4):732-41.

48.

Mutant deoxynucleotide carrier is associated with congenital microcephaly.

Rosenberg MJ, Agarwala R, Bouffard G, Davis J, Fiermonte G, Hilliard MS, Koch T, Kalikin LM, Makalowska I, Morton DH, Petty EM, Weber JL, Palmieri F, Kelley RI, Schäffer AA, Biesecker LG.

Nat Genet. 2002 Sep;32(1):175-9. Epub 2002 Aug 19.

PMID:
12185364
49.

Identification of six novel genes by experimental validation of GeneMachine predicted genes.

Makalowska I, Sood R, Faruque MU, Hu P, Robbins CM, Eddings EM, Mestre JD, Baxevanis AD, Carpten JD.

Gene. 2002 Feb 6;284(1-2):203-13.

PMID:
11891061
50.

Physical and transcript map of the hereditary prostate cancer region at xq27.

Stephan DA, Howell GR, Teslovich TM, Coffey AJ, Smith L, Bailey-Wilson JE, Malechek L, Gildea D, Smith JR, Gillanders EM, Schleutker J, Hu P, Steingruber HE, Dhami P, Robbins CM, Makalowska I, Carpten JD, Sood R, Mumm S, Reinbold R, Bonner TI, Baffoe-Bonnie A, Bubendorf L, Heiskanen M, Kallioneimi OP, Baxevanis AD, Joseph SS, Zucchi I, Burk RD, Isaacs W, Ross MT, Trent JM.

Genomics. 2002 Jan;79(1):41-50.

PMID:
11827456

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