My Bibliography

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Mikhail FM, Sathienkijkanchai A, Robin NH, Prucka S, Biggerstaff JS, Komorowski J, Andersson R, Bruder CE, Piotrowski A, Diaz de Ståhl T, Dumanski JP, Carroll AJ. Overlapping phenotype of Wolf-Hirschhorn and Beckwith-Wiedemann syndromes in a girl with der(4)t(4;11)(pter;pter). Am J Med Genet A. 2007 Aug 1;143A(15):1760-6. doi: 10.1002/ajmg.a.31821. PubMed PMID: 17603794.

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Mikhail FM, Descartes M, Piotrowski A, Andersson R, Diaz de Ståhl T, Komorowski J, Bruder CE, Dumanski JP, Carroll AJ. A previously unrecognized microdeletion syndrome on chromosome 22 band q11.2 encompassing the BCR gene. Am J Med Genet A. 2007 Sep 15;143A(18):2178-84. doi: 10.1002/ajmg.a.31882. PubMed PMID: 17676630.

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Bruder CE, Piotrowski A, Gijsbers AA, Andersson R, Erickson S, Diaz de Ståhl T, Menzel U, Sandgren J, von Tell D, Poplawski A, Crowley M, Crasto C, Partridge EC, Tiwari H, Allison DB, Komorowski J, van Ommen GJ, Boomsma DI, Pedersen NL, den Dunnen JT, Wirdefeldt K, Dumanski JP. Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am J Hum Genet. 2008 Mar;82(3):763-71. doi: 10.1016/j.ajhg.2007.12.011. Epub 2008 Feb 14. PubMed PMID: 18304490; PubMed Central PMCID: PMC2427204.

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Díaz de Ståhl T, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CE, Dumanski JP. Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. Hum Mutat. 2008 Mar;29(3):398-408. doi: 10.1002/humu.20659. PubMed PMID: 18058796.

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Andersson R, Bruder CE, Piotrowski A, Menzel U, Nord H, Sandgren J, Hvidsten TR, Diaz de Ståhl T, Dumanski JP, Komorowski J. A segmental maximum a posteriori approach to genome-wide copy number profiling. Bioinformatics. 2008 Mar 15;24(6):751-8. doi: 10.1093/bioinformatics/btn003. Epub 2008 Jan 19. PubMed PMID: 18204059.

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Piotrowski A, Bruder CE, Andersson R, Diaz de Ståhl T, Menzel U, Sandgren J, Poplawski A, von Tell D, Crasto C, Bogdan A, Bartoszewski R, Bebok Z, Krzyzanowski M, Jankowski Z, Partridge EC, Komorowski J, Dumanski JP. Somatic mosaicism for copy number variation in differentiated human tissues. Hum Mutat. 2008 Sep;29(9):1118-24. doi: 10.1002/humu.20815. PubMed PMID: 18570184.

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Rada-Iglesias A, Enroth S, Andersson R, Wanders A, Påhlman L, Komorowski J, Wadelius C. Histone H3 lysine 27 trimethylation in adult differentiated colon associated to cancer DNA hypermethylation. Epigenetics. 2009 Feb 16;4(2):107-13. doi: 10.4161/epi.4.2.8038. Epub 2009 Mar 1. PubMed PMID: 19276669.

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Björkholm P, Daniluk P, Kryshtafovych A, Fidelis K, Andersson R, Hvidsten TR. Using multi-data hidden Markov models trained on local neighborhoods of protein structure to predict residue-residue contacts. Bioinformatics. 2009 May 15;25(10):1264-70. doi: 10.1093/bioinformatics/btp149. Epub 2009 Mar 16. PubMed PMID: 19289446; PubMed Central PMCID: PMC2677742.

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Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res. 2009 Oct;19(10):1732-41. doi: 10.1101/gr.092353.109. Epub 2009 Aug 17. PubMed PMID: 19687145; PubMed Central PMCID: PMC2765275.

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Mantripragada KK, Díaz de Ståhl T, Patridge C, Menzel U, Andersson R, Chuzhanova N, Kluwe L, Guha A, Mautner V, Dumanski JP, Upadhyaya M. Genome-wide high-resolution analysis of DNA copy number alterations in NF1-associated malignant peripheral nerve sheath tumors using 32K BAC array. Genes Chromosomes Cancer. 2009 Oct;48(10):897-907. doi: 10.1002/gcc.20695. PubMed PMID: 19603524.

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Nord H, Hartmann C, Andersson R, Menzel U, Pfeifer S, Piotrowski A, Bogdan A, Kloc W, Sandgren J, Olofsson T, Hesselager G, Blomquist E, Komorowski J, von Deimling A, Bruder CE, Dumanski JP, Díaz de Ståhl T. Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array. Neuro Oncol. 2009 Dec;11(6):803-18. doi: 10.1215/15228517-2009-013. PubMed PMID: 19304958; PubMed Central PMCID: PMC2802400.

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Popławski AB, Jankowski M, Erickson SW, Díaz de Ståhl T, Partridge EC, Crasto C, Guo J, Gibson J, Menzel U, Bruder CE, Kaczmarczyk A, Benetkiewicz M, Andersson R, Sandgren J, Zegarska B, Bała D, Srutek E, Allison DB, Piotrowski A, Zegarski W, Dumanski JP. Frequent genetic differences between matched primary and metastatic breast cancer provide an approach to identification of biomarkers for disease progression. Eur J Hum Genet. 2010 May;18(5):560-8. doi: 10.1038/ejhg.2009.230. Epub 2010 Jan 6. PubMed PMID: 20051991; PubMed Central PMCID: PMC2987320.

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Sandgren J, Andersson R, Rada-Iglesias A, Enroth S, Akerstrom G, Dumanski JP, Komorowski J, Westin G, Wadelius C. Integrative epigenomic and genomic analysis of malignant pheochromocytoma. Exp Mol Med. 2010 Jul 31;42(7):484-502. doi: 10.3858/emm.2010.42.7.050. PubMed PMID: 20534969; PubMed Central PMCID: PMC2912476.

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Enroth S, Andersson R, Wadelius C, Komorowski J. SICTIN: Rapid footprinting of massively parallel sequencing data. BioData Min. 2010 Aug 13;3(1):4. doi: 10.1186/1756-0381-3-4. PubMed PMID: 20707885; PubMed Central PMCID: PMC2928217.

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Sandgren J, Diaz de Ståhl T, Andersson R, Menzel U, Piotrowski A, Nord H, Bäckdahl M, Kiss NB, Brauckhoff M, Komorowski J, Dralle H, Hessman O, Larsson C, Akerström G, Bruder C, Dumanski JP, Westin G. Recurrent genomic alterations in benign and malignant pheochromocytomas and paragangliomas revealed by whole-genome array comparative genomic hybridization analysis. Endocr Relat Cancer. 2010 Sep;17(3):561-79. doi: 10.1677/ERC-09-0310. Print 2010 Sep. PubMed PMID: 20410162.

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Enroth S, Rada-Iglesisas A, Andersson R, Wallerman O, Wanders A, Påhlman L, Komorowski J, Wadelius C. Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa. BMC Cancer. 2011 Oct 19;11:450. doi: 10.1186/1471-2407-11-450. PubMed PMID: 22011431; PubMed Central PMCID: PMC3216894.

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Enroth S, Andersson CR, Andersson R, Wadelius C, Gustafsson MG, Komorowski J. A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements. Algorithms Mol Biol. 2012 Jan 16;7(1):2. doi: 10.1186/1748-7188-7-2. PubMed PMID: 22248020; PubMed Central PMCID: PMC3371767.

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Ntini E, Järvelin AI, Bornholdt J, Chen Y, Boyd M, Jørgensen M, Andersson R, Hoof I, Schein A, Andersen PR, Andersen PK, Preker P, Valen E, Zhao X, Pelechano V, Steinmetz LM, Sandelin A, Jensen TH. Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat Struct Mol Biol. 2013 Aug;20(8):923-8. doi: 10.1038/nsmb.2640. Epub 2013 Jul 14. PubMed PMID: 23851456.

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Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, Jones PA, Hoover CA, Tikhonov A, Prokhortchouk E, Rubin EM, Sandelin A, Gilbert MT, Krogh A, Willerslev E, Orlando L. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. 2014 Mar;24(3):454-66. doi: 10.1101/gr.163592.113. Epub 2013 Dec 3. PubMed PMID: 24299735; PubMed Central PMCID: PMC3941110.

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Andersson R, Gebhard C, Miguel-Escalada I, Hoof I, Bornholdt J, Boyd M, Chen Y, Zhao X, Schmidl C, Suzuki T, Ntini E, Arner E, Valen E, Li K, Schwarzfischer L, Glatz D, Raithel J, Lilje B, Rapin N, Bagger FO, Jørgensen M, Andersen PR, Bertin N, Rackham O, Burroughs AM, Baillie JK, Ishizu Y, Shimizu Y, Furuhata E, Maeda S, Negishi Y, Mungall CJ, Meehan TF, Lassmann T, Itoh M, Kawaji H, Kondo N, Kawai J, Lennartsson A, Daub CO, Heutink P, Hume DA, Jensen TH, Suzuki H, Hayashizaki Y, Müller F, Forrest ARR, Carninci P, Rehli M, Sandelin A. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-461. doi: 10.1038/nature12787. PubMed PMID: 24670763; PubMed Central PMCID: PMC5215096.

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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. A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. doi: 10.1038/nature13182. PubMed PMID: 24670764; PubMed Central PMCID: PMC4529748.

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Rönnerblad M, Andersson R, Olofsson T, Douagi I, Karimi M, Lehmann S, Hoof I, de Hoon M, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Sandelin A, Ekwall K, Arner E, Lennartsson A. Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. Blood. 2014 Apr 24;123(17):e79-89. doi: 10.1182/blood-2013-02-482893. Epub 2014 Mar 26. PubMed PMID: 24671952.

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Davis MR, Andersson R, Severin J, de Hoon M, Bertin N, Baillie JK, Kawaji H, Sandelin A, Forrest AR, Summers KM. Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions. Mol Genet Metab. 2014 May;112(1):73-83. doi: 10.1016/j.ymgme.2013.12.006. Epub 2013 Dec 16. PubMed PMID: 24703491; PubMed Central PMCID: PMC4019825.

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Enroth S, Andersson R, Bysani M, Wallerman O, Termén S, Tuch BB, De La Vega FM, Heldin CH, Moustakas A, Komorowski J, Wadelius C. Nucleosome regulatory dynamics in response to TGFβ. Nucleic Acids Res. 2014 Jun;42(11):6921-34. doi: 10.1093/nar/gku326. Epub 2014 Apr 25. PubMed PMID: 24771338; PubMed Central PMCID: PMC4066760.

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Fort A, Hashimoto K, Yamada D, Salimullah M, Keya CA, Saxena A, Bonetti A, Voineagu I, Bertin N, Kratz A, Noro Y, Wong CH, de Hoon M, Andersson R, Sandelin A, Suzuki H, Wei CL, Koseki H, Hasegawa Y, Forrest AR, Carninci P. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat Genet. 2014 Jun;46(6):558-66. doi: 10.1038/ng.2965. Epub 2014 Apr 28. PubMed PMID: 24777452.

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Andersson R, Refsing Andersen P, Valen E, Core LJ, Bornholdt J, Boyd M, Heick Jensen T, Sandelin A. Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Nat Commun. 2014 Nov 12;5:5336. doi: 10.1038/ncomms6336. PubMed PMID: 25387874.

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Boyd M, Coskun M, Lilje B, Andersson R, Hoof I, Bornholdt J, Dahlgaard K, Olsen J, Vitezic M, Bjerrum JT, Seidelin JB, Nielsen OH, Troelsen JT, Sandelin A. Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2. DNA Res. 2014 Dec;21(6):569-83. doi: 10.1093/dnares/dsu022. Epub 2014 Jul 2. PubMed PMID: 24990076; PubMed Central PMCID: PMC4263293.

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Vitezic M, Bertin N, Andersson R, Lipovich L, Kawaji H, Lassmann T, Sandelin A, Heutink P, Goldowitz D, Ha T, Zhang P, Patrizi A, Fagiolini M, Forrest AR, Carninci P, Saxena A. CAGE-defined promoter regions of the genes implicated in Rett Syndrome. BMC Genomics. 2014 Dec 24;15:1177. doi: 10.1186/1471-2164-15-1177. PubMed PMID: 25539566; PubMed Central PMCID: PMC4522966.

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Arner E, Daub CO, Vitting-Seerup K, Andersson R, Lilje B, Drabløs F, Lennartsson A, Rönnerblad M, Hrydziuszko O, Vitezic M, Freeman TC, Alhendi AM, Arner P, Axton R, Baillie JK, Beckhouse A, Bodega B, Briggs J, Brombacher F, Davis M, Detmar M, Ehrlund A, Endoh M, Eslami A, Fagiolini M, Fairbairn L, Faulkner GJ, Ferrai C, Fisher ME, Forrester L, Goldowitz D, Guler R, Ha T, Hara M, Herlyn M, Ikawa T, Kai C, Kawamoto H, Khachigian LM, Klinken SP, Kojima S, Koseki H, Klein S, Mejhert N, Miyaguchi K, Mizuno Y, Morimoto M, Morris KJ, Mummery C, Nakachi Y, Ogishima S, Okada-Hatakeyama M, Okazaki Y, Orlando V, Ovchinnikov D, Passier R, Patrikakis M, Pombo A, Qin XY, Roy S, Sato H, Savvi S, Saxena A, Schwegmann A, Sugiyama D, Swoboda R, Tanaka H, Tomoiu A, Winteringham LN, Wolvetang E, Yanagi-Mizuochi C, Yoneda M, Zabierowski S, Zhang P, Abugessaisa I, Bertin N, Diehl AD, Fukuda S, Furuno M, Harshbarger J, Hasegawa A, Hori F, Ishikawa-Kato S, Ishizu Y, Itoh M, Kawashima T, Kojima M, Kondo N, Lizio M, Meehan TF, Mungall CJ, Murata M, Nishiyori-Sueki H, Sahin S, Nagao-Sato S, Severin J, de Hoon MJ, Kawai J, Kasukawa T, Lassmann T, Suzuki H, Kawaji H, Summers KM, Wells C, Hume DA, Forrest AR, Sandelin A, Carninci P, Hayashizaki Y. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27;347(6225):1010-4. doi: 10.1126/science.1259418. Epub 2015 Feb 12. PubMed PMID: 25678556; PubMed Central PMCID: PMC4681433.

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Andersson R. Promoter or enhancer, what's the difference? Deconstruction of established distinctions and presentation of a unifying model. Bioessays. 2015 Mar;37(3):314-23. doi: 10.1002/bies.201400162. Epub 2014 Dec 2. Review. PubMed PMID: 25450156.

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Andersson R, Sandelin A, Danko CG. A unified architecture of transcriptional regulatory elements. Trends Genet. 2015 Aug;31(8):426-33. doi: 10.1016/j.tig.2015.05.007. Epub 2015 Jun 11. Review. PubMed PMID: 26073855.

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Young RS, Hayashizaki Y, Andersson R, Sandelin A, Kawaji H, Itoh M, Lassmann T, Carninci P, Bickmore WA, Forrest AR, Taylor MS. The frequent evolutionary birth and death of functional promoters in mouse and human. Genome Res. 2015 Oct;25(10):1546-57. doi: 10.1101/gr.190546.115. Epub 2015 Jul 30. PubMed PMID: 26228054; PubMed Central PMCID: PMC4579340.

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Andersson R, Chen Y, Core L, Lis JT, Sandelin A, Jensen TH. Human Gene Promoters Are Intrinsically Bidirectional. Mol Cell. 2015 Nov 5;60(3):346-7. doi: 10.1016/j.molcel.2015.10.015. PubMed PMID: 26545074; PubMed Central PMCID: PMC5485825.

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Lennartsson A, Arner E, Fagiolini M, Saxena A, Andersson R, Takahashi H, Noro Y, Sng J, Sandelin A, Hensch TK, Carninci P. Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors. Epigenetics Chromatin. 2015;8:55. doi: 10.1186/s13072-015-0043-3. eCollection 2015. PubMed PMID: 26673794; PubMed Central PMCID: PMC4678690.

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Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, Itoh M, Lassmann T, Hayashizaki Y, Carninci P, Forrest AR. Transcriptome Analysis of Recurrently Deregulated Genes across Multiple Cancers Identifies New Pan-Cancer Biomarkers. Cancer Res. 2016 Jan 15;76(2):216-26. doi: 10.1158/0008-5472.CAN-15-0484. Epub 2015 Nov 9. PubMed PMID: 26552699.

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Persson J, Steglich B, Smialowska A, Boyd M, Bornholdt J, Andersson R, Schurra C, Arcangioli B, Sandelin A, Nielsen O, Ekwall K. Regulating retrotransposon activity through the use of alternative transcription start sites. EMBO Rep. 2016 May;17(5):753-68. doi: 10.15252/embr.201541866. Epub 2016 Feb 22. PubMed PMID: 26902262; PubMed Central PMCID: PMC5341516.

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Chen Y, Pai AA, Herudek J, Lubas M, Meola N, Järvelin AI, Andersson R, Pelechano V, Steinmetz LM, Jensen TH, Sandelin A. Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nat Genet. 2016 Sep;48(9):984-94. doi: 10.1038/ng.3616. Epub 2016 Jul 25. PubMed PMID: 27455346; PubMed Central PMCID: PMC5008441.

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Ienasescu H, Li K, Andersson R, Vitezic M, Rennie S, Chen Y, Vitting-Seerup K, Lagoni E, Boyd M, Bornholdt J, de Hoon MJ, Kawaji H, Lassmann T, Hayashizaki Y, Forrest AR, Carninci P, Sandelin A. On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. Database (Oxford). 2016;2016. doi: 10.1093/database/baw144. Print 2016. PubMed PMID: 28025337; PubMed Central PMCID: PMC5199134.

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Ehrlund A, Mejhert N, Björk C, Andersson R, Kulyté A, Åström G, Itoh M, Kawaji H, Lassmann T, Daub CO, Carninci P, Forrest AR, Hayashizaki Y, Sandelin A, Ingelsson E, Rydén M, Laurencikiene J, Arner P, Arner E. Transcriptional Dynamics During Human Adipogenesis and Its Link to Adipose Morphology and Distribution. Diabetes. 2017 Jan;66(1):218-230. doi: 10.2337/db16-0631. Epub 2016 Nov 1. PubMed PMID: 27803022; PubMed Central PMCID: PMC5860264.

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Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drabløs F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest AR, Kasukawa T, Kawaji H. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res. 2017 Jan 4;45(D1):D737-D743. doi: 10.1093/nar/gkw995. Epub 2016 Oct 27. PubMed PMID: 27794045; PubMed Central PMCID: PMC5210666.

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Bornholdt J, Saber AT, Lilje B, Boyd M, Jørgensen M, Chen Y, Vitezic M, Jacobsen NR, Poulsen SS, Berthing T, Bressendorff S, Vitting-Seerup K, Andersson R, Hougaard KS, Yauk CL, Halappanavar S, Wallin H, Vogel U, Sandelin A. Identification of Gene Transcription Start Sites and Enhancers Responding to Pulmonary Carbon Nanotube Exposure in Vivo. ACS Nano. 2017 Apr 25;11(4):3597-3613. doi: 10.1021/acsnano.6b07533. Epub 2017 Mar 31. PubMed PMID: 28345861.

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Grarup N, Moltke I, Andersen MK, Dalby M, Vitting-Seerup K, Kern T, Mahendran Y, Jørsboe E, Larsen CVL, Dahl-Petersen IK, Gilly A, Suveges D, Dedoussis G, Zeggini E, Pedersen O, Andersson R, Bjerregaard P, Jørgensen ME, Albrechtsen A, Hansen T. Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes. Nat Genet. 2018 Feb;50(2):172-174. doi: 10.1038/s41588-017-0022-7. Epub 2018 Jan 8. PubMed PMID: 29311636; PubMed Central PMCID: PMC5828106.

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Rennie S, Dalby M, van Duin L, Andersson R. Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions. Nat Commun. 2018 Feb 5;9(1):487. doi: 10.1038/s41467-017-02798-1. PubMed PMID: 29402885; PubMed Central PMCID: PMC5799294.

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Baillie JK, Bretherick A, Haley CS, Clohisey S, Gray A, Neyton LPA, Barrett J, Stahl EA, Tenesa A, Andersson R, Brown JB, Faulkner GJ, Lizio M, Schaefer U, Daub C, Itoh M, Kondo N, Lassmann T, Kawai J, Mole D, Bajic VB, Heutink P, Rehli M, Kawaji H, Sandelin A, Suzuki H, Satsangi J, Wells CA, Hacohen N, Freeman TC, Hayashizaki Y, Carninci P, Forrest ARR, Hume DA. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS Comput Biol. 2018 Mar;14(3):e1005934. doi: 10.1371/journal.pcbi.1005934. eCollection 2018 Mar. PubMed PMID: 29494619; PubMed Central PMCID: PMC5849332.

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Boyd M, Thodberg M, Vitezic M, Bornholdt J, Vitting-Seerup K, Chen Y, Coskun M, Li Y, Lo BZS, Klausen P, Jan Schweiger P, Pedersen AG, Rapin N, Skovgaard K, Dahlgaard K, Andersson R, Terkelsen TB, Lilje B, Troelsen JT, Petersen AM, Jensen KB, Gögenur I, Thielsen P, Seidelin JB, Nielsen OH, Bjerrum JT, Sandelin A. Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. Nat Commun. 2018 Apr 25;9(1):1661. doi: 10.1038/s41467-018-03766-z. PubMed PMID: 29695774; PubMed Central PMCID: PMC5916929.

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Rennie S, Dalby M, Lloret-Llinares M, Bakoulis S, Dalager Vaagensø C, Heick Jensen T, Andersson R. Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities. Nucleic Acids Res. 2018 Jun 20;46(11):5455-5469. doi: 10.1093/nar/gky244. PubMed PMID: 29659982; PubMed Central PMCID: PMC6009668.

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Petryk N, Dalby M, Wenger A, Stromme CB, Strandsby A, Andersson R, Groth A. MCM2 promotes symmetric inheritance of modified histones during DNA replication. Science. 2018 Sep 28;361(6409):1389-1392. doi: 10.1126/science.aau0294. Epub 2018 Aug 16. PubMed PMID: 30115746.

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Lloret-Llinares M, Karadoulama E, Chen Y, Wojenski LA, Villafano GJ, Bornholdt J, Andersson R, Core L, Sandelin A, Jensen TH. The RNA exosome contributes to gene expression regulation during stem cell differentiation. Nucleic Acids Res. 2018 Nov 30;46(21):11502-11513. doi: 10.1093/nar/gky817. PubMed PMID: 30212902; PubMed Central PMCID: PMC6265456.

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Agrawal Singh S, Lerdrup M, Gomes AR, van de Werken HJ, Vilstrup Johansen J, Andersson R, Sandelin A, Helin K, Hansen K. PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells. Elife. 2019 Jan 23;8. doi: 10.7554/eLife.40364. PubMed PMID: 30672466; PubMed Central PMCID: PMC6344081.

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