Full list of publications: PubMed

Recent publications:
(* denotes equal contribution, § denotes corresponding author)

• Zaugg JB^*, Sahlén P^*, Andersson R^*, Alberich-Jorda M, de Laat W, Deplancke B, Ferrer J, Mandrup S, Natoli G, Plewczynski D, Rada-Iglesias A, Spicuglia S^*,§. 2022. Current challenges in understanding the role of enhancers in disease. Nat Struct Mol Biol. DOI | PubMed
• Einarsson H, Salvatore M, Vaagenso C, Alcaraz N, Bornholdt Lange J, Rennie S, Andersson R^§. 2022. Promoter sequence and architecture determine expression variability and confer robustness to genetic variants. Elife. DOI | PubMed
• van Duin L, Krautz R, Rennie S^§, Andersson R^§. 2022. Transcription factor expression is the main determinant of variability in gene co-activity. preprint
• Salvatore M, Horlacher M, Winther O, Andersson R^§. 2022. Transfer learning reveals sequence determinants of regulatory element accessibility. preprint
• Bakoulis S^*, Krautz R^*, Alcaraz N, Salvatore M, Andersson R^§. 2022. Endogenous retroviruses co-opted as divergently transcribed regulatory elements shape the regulatory landscape of embryonic stem cells. Nucleic Acids Res. 50(4):2111-2127. DOI | PubMed
• Rennie S^§, Magnusson DH, Andersson R^§. 2021. hyperTRIBER: a flexible R package for the analysis of differential RNA editing. preprint
• Arribas-Hernández L^*§, Rennie S^*, Köster T, Porcelli C, Lewinski M, Staiger D^§, Andersson R^§, Brodersen P^§. 2021. Principles of mRNA targeting via the Arabidopsis m⁶A-binding protein ECT2. Elife. 10. DOI | PubMed
• Arribas-Hernández L, Rennie S, Schon M, Porcelli C, Enugutti B, Andersson R, Nodine MD, Brodersen P. 2021. The YTHDF proteins ECT2 and ECT3 bind largely overlapping target sets and influence target mRNA abundance, not alternative polyadenylation. Elife. 10. DOI | PubMed
• Petryk N, Reverón-Gómez N, González-Aguilera C, Dalby M, Andersson R, Groth A. 2021. Genome-wide and sister chromatid-resolved profiling of protein occupancy in replicated chromatin with ChOR-seq and SCAR-seq. Nat Protoc. 16(9):4446-4493. DOI | PubMed
• Alam T, Agrawal S, Severin J, Young RS, Andersson R, Arner E, Hasegawa A, Lizio M, Ramilowski JA, Abugessaisa I, Ishizu Y, Noma S, Tarui H, Taylor MS, Lassmann T, Itoh M, Kasukawa T, Kawaji H, Marchionni L, Sheng G, R R Forrest A, Khachigian LM, Hayashizaki Y, Carninci P, de Hoon MJL. 2020. Comparative transcriptomics of primary cells in vertebrates. Genome Res. 30(7):951-961. DOI | PubMed
• Gazova I, Lefevre L, Bush SJ, Clohisey S, Arner E, de Hoon M, Severin J, van Duin L, Andersson R, Lengeling A, Hume DA, Summers KM. 2020. The Transcriptional Network That Controls Growth Arrest and Macrophage Differentiation in the Human Myeloid Leukemia Cell Line THP-1. Front Cell Dev Biol. 8: 498. DOI | PubMed
• Andersson R^§, Sandelin A^§. 2020. Determinants of enhancer and promoter activities of regulatory elements. Nat Rev Genet 21(2):71-87. DOI | PubMed
• Thodberg M, Thieffry A, Vitting-Seerup K, Andersson R, Sandelin A. 2019. CAGEfightR: analysis of 5′-end data using R/Bioconductor. BMC Bioinformatics 20: 1–13. DOI | PubMed
• Agrawal Singh S, Lerdrup M, Gomes AR, van de Werken HJ, Vilstrup Johansen J, Andersson R, Sandelin A, Helin K, Hansen K. 2019. PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells. Elife. Jan 23;8. DOI | PubMed
• Jefimov K^*, Alcaraz N^*, Kloet S^*, Varv S, Sakya SA, Vaagenso CD, Vermeulen M^§, Aasland R^§ & Andersson R^§. 2018. The GBAF chromatin remodeling complex binds H3K27ac and mediates enhancer transcription. preprint
• Lloret-Llinares M, Karadoulama E, Chen Y, Wojenski LA, Villafano GJ, Bornholdt J, Andersson R, Core L, Sandelin A, Jensen TH. 2018. The RNA exosome contributes to gene expression regulation during stem cell differentiation. Nucleic Acids Res. Sep 13. DOI | PubMed
• Petryk N^*, Dalby M^*, Wenger A, Stromme CB, Strandsby A, Andersson R^§ & Groth A^§. 2018. MCM2 promotes symmetric inheritance of modified histones during DNA replication. Science 3: eaau0294. DOI | PubMed
• Rennie S^*, Dalby M^*, Lloret-Llinares M, Bakoulis S, Dalager Vaagensø C, Heick Jensen T & Andersson R^§. 2018. Transcription start site analysis reveals widespread divergent transcription in D. melanogaster and core promoter-encoded enhancer activities. Nucleic Acids Res. 39: 311. DOI | PubMed | preprint
• 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. 2018. Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies. Nat Commun. 9(1):1661. DOI | PubMed
• 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. 2018. Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PLoS Comput Biol. 14(3):e1005934. DOI | PubMed
• Rennie S, Dalby M, van Duin L, Andersson R^§. 2018. Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions. Nat Comms 9: 487. DOI | PubMed | preprint | Data
• 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. 2018. Loss-of-function variants in ADCY3 increase risk of obesity and type 2 diabetes. Nat Genet 50: 172–174. DOI | PubMed
• Ehrlund A, Mejhert N, Björk C, Andersson R, et al. 2016. Transcriptional Dynamics During Human Adipogenesis and its Link to Adipose Morphology and Distribution. Diabetes. 2016. DOI | PubMed
• Lizio M, Harshbarger J, Abugessaisa I, Noguchi S, Kondo A, Severin J, Mungall C, Arenillas D, Mathelier A, Medvedeva YA, Lennartsson A, Drablos F, Ramilowski JA, Rackham O, Gough J, Andersson R, Sandelin A, Ienasescu H, Ono H, Bono H, Hayashizaki Y, Carninci P, Forrest ARR, Kasukawa T, Kawaji H. 2016. Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals. Nucleic Acids Res. 2016. DOI | PubMed
• 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 | PubMed
• Persson J, Steglich B, Smialowska A, Boyd M, Bornholdt J, Andersson R, et al. Regulating retrotransposon activity through the use of alternative transcription start sites. EMBO reports. 2016; 17(5):753-68. DOI | PubMed
• Kaczkowski B, Tanaka Y, Kawaji H, Sandelin A, Andersson R, et al. Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers. Cancer research. 2016; 76(2):216-26. DOI | PubMed
• Lennartsson A, Arner E, Fagiolini M, Saxena A, Andersson R, et al. Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors. Epigenetics & chromatin. 2015; 8:55. DOI | PubMed
• 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):346-347. DOI | PubMed
• Andersson R^§, Sandelin A, Danko CG^§. A Unified Architecture of Transcriptional Regulatory Elements. Trends Genet. 2015 Aug;31(8):426-33. DOI | PubMed | preprint
• Young RS, Hayashizaki Y, Andersson R, et al. The frequent evolutionary birth and death of functional promoters in mouse and human. Genome Res. 2015 Jul 30. pii: gr.190546.115. DOI | PubMed
• 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 | PubMed
• Arner E^*, Daub CO^*, Vitting-Seerup K^*, Andersson R^*, et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science. 2015 Feb 27;347(6225):1010-4. DOI | PubMed
• Vitezic M, Bertin N, Andersson R, et al. CAGE-defined promoter regions of the genes implicated in Rett Syndrome. BMC Genomics. 2014 Dec 24;15(1):1177. DOI | PubMed
• Boyd M, Coskun M, Lilje B, Andersson R, et al. 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 | PubMed.
• Andersson R^*, Refsing Andersen P^*, et al. Nuclear stability and transcriptional directionality separate functionally distinct RNA species. Nat Commun. 2014 Nov 12;5:5336. DOI | PubMed | preprint
• 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, et al. 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 | PubMed
• Davis MR, Andersson R, et al. 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 | PubMed
• Rönnerblad M, Andersson R, et al. 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 | PubMed
• FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature. 2014 Mar 27;507(7493):462-70. DOI | PubMed | Data
• Andersson R^*, Gebhard C^*, et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014 Mar 27;507(7493):455-61. DOI | PubMed | Data
• Pedersen JS, Valen E, Velazquez AM, Parker BJ, Rasmussen M, Lindgreen S, Lilje B, Tobin DJ, Kelly TK, Vang S, Andersson R, et al. Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res. 2014 Mar;24(3):454-66. DOI | PubMed
• Enroth S^*, Andersson R^*, et al. Nucleosome regulatory dynamics in response to TGFβ. Nucleic Acids Res. 2014;42(11):6921-34. DOI | PubMed
• Ntini E, Järvelin AI, Bornholdt J, Chen Y, Boyd M, Jørgensen M, Andersson R, et al. Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality. Nat Struct Mol Biol. 2013 Aug;20(8):923-8. DOI | PubMed