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Items: 12

1.

Presence of TMPRSS2-ERG is associated with alterations of the metabolic profile in human prostate cancer.

Hansen AF, Sandsmark E, Rye MB, Wright AJ, Bertilsson H, Richardsen E, Viset T, Bofin AM, Angelsen A, Selnæs KM, Bathen TF, Tessem MB.

Oncotarget. 2016 Jul 5;7(27):42071-42085. doi: 10.18632/oncotarget.9817.

2.

A Balanced Tissue Composition Reveals New Metabolic and Gene Expression Markers in Prostate Cancer.

Tessem MB, Bertilsson H, Angelsen A, Bathen TF, Drabløs F, Rye MB.

PLoS One. 2016 Apr 21;11(4):e0153727. doi: 10.1371/journal.pone.0153727.

3.

Phosphatase of regenerating liver 3 (PRL-3) is overexpressed in human prostate cancer tissue and promotes growth and migration.

Vandsemb EN, Bertilsson H, Abdollahi P, Størkersen Ø, Våtsveen TK, Rye MB, Rø TB, Børset M, Slørdahl TS.

J Transl Med. 2016 Mar 15;14:71. doi: 10.1186/s12967-016-0830-z.

4.

Gene signatures ESC, MYC and ERG-fusion are early markers of a potentially dangerous subtype of prostate cancer.

Rye MB, Bertilsson H, Drabløs F, Angelsen A, Bathen TF, Tessem MB.

BMC Med Genomics. 2014 Aug 12;7:50. doi: 10.1186/1755-8794-7-50.

5.

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.

6.

The Genomic HyperBrowser: an analysis web server for genome-scale data.

Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W133-41. doi: 10.1093/nar/gkt342.

7.

The Triform algorithm: improved sensitivity and specificity in ChIP-Seq peak finding.

Kornacker K, Rye MB, Håndstad T, Drabløs F.

BMC Bioinformatics. 2012 Jul 24;13:176. doi: 10.1186/1471-2105-13-176.

8.

A ChIP-Seq benchmark shows that sequence conservation mainly improves detection of strong transcription factor binding sites.

Håndstad T, Rye MB, Drabløs F, Sætrom P.

PLoS One. 2011 Apr 14;6(4):e18430. doi: 10.1371/journal.pone.0018430.

9.

A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs.

Rye MB, Sætrom P, Drabløs F.

Nucleic Acids Res. 2011 Mar;39(4):e25. doi: 10.1093/nar/gkq1187.

10.

An improved pixel-based approach for analyzing images in two-dimensional gel electrophoresis.

Rye MB, Faergestad EM, Martens H, Wold JP, Alsberg BK.

Electrophoresis. 2008 Mar;29(6):1382-93. doi: 10.1002/elps.200700419.

PMID:
18348214
11.

A multivariate spot filtering model for two-dimensional gel electrophoresis.

Rye MB, Alsberg BK.

Electrophoresis. 2008 Mar;29(6):1369-81. doi: 10.1002/elps.200700417.

PMID:
18348213
12.

A new method for assigning common spot boundaries for multiple gels in two-dimensional gel electrophoresis.

Rye MB, Faergestad EM, Alsberg BK.

Electrophoresis. 2008 Mar;29(6):1359-68. doi: 10.1002/elps.200700418.

PMID:
18348212
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