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Items: 25

1.

Transcriptional landscape of Mycobacterium tuberculosis infection in macrophages.

Roy S, Schmeier S, Kaczkowski B, Arner E, Alam T, Ozturk M, Tamgue O, Parihar SP, Kawaji H, Itoh M, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Guler R, Bajic VB, Brombacher F, Suzuki H.

Sci Rep. 2018 Apr 30;8(1):6758. doi: 10.1038/s41598-018-24509-6.

2.

Integrative CAGE and DNA Methylation Profiling Identify Epigenetically Regulated Genes in NSCLC.

Horie M, Kaczkowski B, Ohshima M, Matsuzaki H, Noguchi S, Mikami Y, Lizio M, Itoh M, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest ARR, Takai D, Yamaguchi Y, Micke P, Saito A, Nagase T.

Mol Cancer Res. 2017 Oct;15(10):1354-1365. doi: 10.1158/1541-7786.MCR-17-0191. Epub 2017 Jul 11.

PMID:
28698358
3.

Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers.

Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR; FANTOM5 Consortium.

Cancer Res. 2016 Jan 15;76(2):216-26. doi: 10.1158/0008-5472.CAN-15-0484. Epub 2015 Nov 9.

4.

CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors.

Hashimoto K, Suzuki AM, Dos Santos A, Desterke C, Collino A, Ghisletti S, Braun E, Bonetti A, Fort A, Qin XY, Radaelli E, Kaczkowski B, Forrest AR, Kojima S, Samuel D, Natoli G, Buendia MA, Faivre J, Carninci P.

Genome Res. 2015 Dec;25(12):1812-24. doi: 10.1101/gr.191031.115. Epub 2015 Oct 28.

5.

Batf2/Irf1 induces inflammatory responses in classically activated macrophages, lipopolysaccharides, and mycobacterial infection.

Roy S, Guler R, Parihar SP, Schmeier S, Kaczkowski B, Nishimura H, Shin JW, Negishi Y, Ozturk M, Hurdayal R, Kubosaki A, Kimura Y, de Hoon MJ, Hayashizaki Y, Brombacher F, Suzuki H.

J Immunol. 2015 Jun 15;194(12):6035-44. doi: 10.4049/jimmunol.1402521. Epub 2015 May 8.

6.

Cancers of unknown primary origin (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin.

Vikeså J, Møller AK, Kaczkowski B, Borup R, Winther O, Henao R, Krogh A, Perell K, Jensen F, Daugaard G, Nielsen FC.

BMC Cancer. 2015 Mar 19;15:151. doi: 10.1186/s12885-015-1128-x.

7.

Down-Regulation of miR-129-5p and the let-7 Family in Neuroendocrine Tumors and Metastases Leads to Up-Regulation of Their Targets Egr1, G3bp1, Hmga2 and Bach1.

Døssing KB, Binderup T, Kaczkowski B, Jacobsen A, Rossing M, Winther O, Federspiel B, Knigge U, Kjær A, Friis-Hansen L.

Genes (Basel). 2014 Dec 24;6(1):1-21. doi: 10.3390/genes6010001.

8.

A promoter-level mammalian expression atlas.

FANTOM Consortium and the RIKEN PMI and CLST (DGT), Forrest AR, Kawaji H, Rehli M, Baillie JK, de Hoon MJ, Haberle V, Lassmann T, Kulakovskiy IV, Lizio M, Itoh M, Andersson R, Mungall CJ, Meehan TF, Schmeier S, Bertin N, Jørgensen M, Dimont E, Arner E, Schmidl C, Schaefer U, Medvedeva YA, Plessy C, Vitezic M, Severin J, Semple C, Ishizu Y, Young RS, Francescatto M, Alam I, Albanese D, Altschuler GM, Arakawa T, Archer JA, Arner P, Babina M, Rennie S, Balwierz PJ, Beckhouse AG, Pradhan-Bhatt S, Blake JA, Blumenthal A, Bodega B, Bonetti A, Briggs J, Brombacher F, Burroughs AM, Califano A, Cannistraci CV, Carbajo D, Chen Y, Chierici M, Ciani Y, Clevers HC, Dalla E, Davis CA, Detmar M, Diehl AD, Dohi T, Drabløs F, Edge AS, Edinger M, Ekwall K, Endoh M, Enomoto H, Fagiolini M, Fairbairn L, Fang H, Farach-Carson MC, Faulkner GJ, Favorov AV, Fisher ME, Frith MC, Fujita R, Fukuda S, Furlanello C, Furino M, Furusawa J, Geijtenbeek TB, Gibson AP, Gingeras T, Goldowitz D, Gough J, Guhl S, Guler R, Gustincich S, Ha TJ, Hamaguchi M, Hara M, Harbers M, Harshbarger J, Hasegawa A, Hasegawa Y, Hashimoto T, Herlyn M, Hitchens KJ, Ho Sui SJ, Hofmann OM, Hoof I, Hori F, Huminiecki L, Iida K, Ikawa T, Jankovic BR, Jia H, Joshi A, Jurman G, Kaczkowski B, Kai C, Kaida K, Kaiho A, Kajiyama K, Kanamori-Katayama M, Kasianov AS, Kasukawa T, Katayama S, Kato S, Kawaguchi S, Kawamoto H, Kawamura YI, Kawashima T, Kempfle JS, Kenna TJ, Kere J, Khachigian LM, Kitamura T, Klinken SP, Knox AJ, Kojima M, Kojima S, Kondo N, Koseki H, Koyasu S, Krampitz S, Kubosaki A, Kwon AT, Laros JF, Lee W, Lennartsson A, Li K, Lilje B, Lipovich L, Mackay-Sim A, Manabe R, Mar JC, Marchand B, Mathelier A, Mejhert N, Meynert A, Mizuno Y, de Lima Morais DA, Morikawa H, Morimoto M, Moro K, Motakis E, Motohashi H, Mummery CL, Murata M, Nagao-Sato S, Nakachi Y, Nakahara F, Nakamura T, Nakamura Y, Nakazato K, van Nimwegen E, Ninomiya N, Nishiyori H, Noma S, Noma S, Noazaki T, Ogishima S, Ohkura N, Ohimiya H, Ohno H, Ohshima M, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov DA, Pain A, Passier R, Patrikakis M, Persson H, Piazza S, Prendergast JG, Rackham OJ, Ramilowski JA, Rashid M, Ravasi T, Rizzu P, Roncador M, Roy S, Rye MB, Saijyo E, Sajantila A, Saka A, Sakaguchi S, Sakai M, Sato H, Savvi S, Saxena A, Schneider C, Schultes EA, Schulze-Tanzil GG, Schwegmann A, Sengstag T, Sheng G, Shimoji H, Shimoni Y, Shin JW, Simon C, Sugiyama D, Sugiyama T, Suzuki M, Suzuki N, Swoboda RK, 't Hoen PA, Tagami M, Takahashi N, Takai J, Tanaka H, Tatsukawa H, Tatum Z, Thompson M, Toyodo H, Toyoda T, Valen E, van de Wetering M, van den Berg LM, Verado R, Vijayan D, Vorontsov IE, Wasserman WW, Watanabe S, Wells CA, Winteringham LN, Wolvetang E, Wood EJ, Yamaguchi Y, Yamamoto M, Yoneda M, Yonekura Y, Yoshida S, Zabierowski SE, Zhang PG, Zhao X, Zucchelli S, Summers KM, Suzuki H, Daub CO, Kawai J, Heutink P, Hide W, Freeman TC, Lenhard B, Bajic VB, Taylor MS, Makeev VJ, Sandelin A, Hume DA, Carninci P, Hayashizaki Y.

Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182.

9.

MicroRNA expression analysis and Multiplex ligation-dependent probe amplification in metastatic and non-metastatic uveal melanoma.

Larsen AC, Holst L, Kaczkowski B, Andersen MT, Manfé V, Siersma VD, Kolko M, Kiilgaard JF, Winther O, Prause JU, Gniadecki R, Heegaard S.

Acta Ophthalmol. 2014 Sep;92(6):541-9. doi: 10.1111/aos.12322. Epub 2013 Dec 24.

10.

A Decade of Global mRNA and miRNA Profiling of HPV-Positive Cell Lines and Clinical Specimens.

Kaczkowski B, Morevati M, Rossing M, Cilius F, Norrild B.

Open Virol J. 2012;6:216-31. doi: 10.2174/1874357901206010216. Epub 2012 Dec 28.

11.

HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis.

Bagger FO, Rapin N, Theilgaard-Mönch K, Kaczkowski B, Thoren LA, Jendholm J, Winther O, Porse BT.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1034-9. doi: 10.1093/nar/gks1021. Epub 2012 Nov 9.

12.

The rectal cancer microRNAome--microRNA expression in rectal cancer and matched normal mucosa.

Gaedcke J, Grade M, Camps J, Søkilde R, Kaczkowski B, Schetter AJ, Difilippantonio MJ, Harris CC, Ghadimi BM, Møller S, Beissbarth T, Ried T, Litman T.

Clin Cancer Res. 2012 Sep 15;18(18):4919-30. Epub 2012 Jul 31.

13.

Integrative analyses reveal novel strategies in HPV11,-16 and -45 early infection.

Kaczkowski B, Rossing M, Andersen DK, Dreher A, Morevati M, Visser MA, Winther O, Nielsen FC, Norrild B.

Sci Rep. 2012;2:515. doi: 10.1038/srep00515. Epub 2012 Jul 17.

14.

HemaExplorer: a Web server for easy and fast visualization of gene expression in normal and malignant hematopoiesis.

Bagger FO, Rapin N, Theilgaard-Mönch K, Kaczkowski B, Jendholm J, Winther O, Porse B.

Blood. 2012 Jun 28;119(26):6394-5. doi: 10.1182/blood-2012-05-427310. No abstract available.

15.

How the RNA isolation method can affect microRNA microarray results.

Podolska A, Kaczkowski B, Litman T, Fredholm M, Cirera S.

Acta Biochim Pol. 2011;58(4):535-40. Epub 2011 Dec 6.

16.

Differential expression of cellular microRNAs in HPV 11, -16, and -45 transfected cells.

Dreher A, Rossing M, Kaczkowski B, Andersen DK, Larsen TJ, Christophersen MK, Nielsen FC, Norrild B.

Biochem Biophys Res Commun. 2011 Aug 19;412(1):20-5. doi: 10.1016/j.bbrc.2011.07.011. Epub 2011 Jul 18.

PMID:
21782796
17.

MicroRNA expression profiling of the porcine developing brain.

Podolska A, Kaczkowski B, Kamp Busk P, Søkilde R, Litman T, Fredholm M, Cirera S.

PLoS One. 2011 Jan 6;6(1):e14494. doi: 10.1371/journal.pone.0014494.

18.

Global microRNA analysis of the NCI-60 cancer cell panel.

Søkilde R, Kaczkowski B, Podolska A, Cirera S, Gorodkin J, Møller S, Litman T.

Mol Cancer Ther. 2011 Mar;10(3):375-84. doi: 10.1158/1535-7163.MCT-10-0605. Epub 2011 Jan 20.

19.

The microRNA molecular signature of atypic and common acquired melanocytic nevi: differential expression of miR-125b and let-7c.

Holst LM, Kaczkowski B, Glud M, Futoma-Kazmierczak E, Hansen LF, Gniadecki R.

Exp Dermatol. 2011 Mar;20(3):278-80. doi: 10.1111/j.1600-0625.2010.01163.x. Epub 2010 Dec 17.

PMID:
21166724
20.

Differential expression of cellular microRNAs in HPV-11 transfected cells. An analysis by three different array platforms and qRT-PCR.

Dreher A, Rossing M, Kaczkowski B, Nielsen FC, Norrild B.

Biochem Biophys Res Commun. 2010 Dec 17;403(3-4):357-62. doi: 10.1016/j.bbrc.2010.11.035. Epub 2010 Nov 13.

PMID:
21078297
21.

A simple procedure for routine RNA extraction and miRNA array analyses from a single thyroid in vivo fine needle aspirate.

Rossing M, Kaczkowski B, Futoma-Kazmierczak E, Glud M, Klausen M, Faber J, Nygaard B, Kiss K, Sørensen CH, Nielsen FC, Bennedbæk FN, Friis-Hansen L.

Scand J Clin Lab Invest. 2010 Dec;70(8):529-34. doi: 10.3109/00365513.2010.522250. Epub 2010 Oct 15.

PMID:
20950121
22.

MicroRNAs and potential target interactions in psoriasis.

Zibert JR, Løvendorf MB, Litman T, Olsen J, Kaczkowski B, Skov L.

J Dermatol Sci. 2010 Jun;58(3):177-85. doi: 10.1016/j.jdermsci.2010.03.004. Epub 2010 Mar 17.

PMID:
20417062
23.

Changes in oncomiR expression in CTCL cell lines during apoptosis induced by Notch inhibition.

Manfè V, Holst LM, Rosbjerg A, Kamstrup MR, Kaczkowski B, Gniadecki R.

Leuk Res. 2010 Sep;34(9):e235-6. doi: 10.1016/j.leukres.2010.03.035. Epub 2010 Apr 22. No abstract available.

PMID:
20416947
24.

Reproducible pattern of microRNA in normal human skin.

Holst LM, Kaczkowski B, Gniadecki R.

Exp Dermatol. 2010 Aug;19(8):e201-5. doi: 10.1111/j.1600-0625.2009.01049.x.

25.

Structural profiles of human miRNA families from pairwise clustering.

Kaczkowski B, Torarinsson E, Reiche K, Havgaard JH, Stadler PF, Gorodkin J.

Bioinformatics. 2009 Feb 1;25(3):291-4. doi: 10.1093/bioinformatics/btn628. Epub 2008 Dec 4.

PMID:
19059941

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