Albin Gustav Sandelin

2020

Determinants of enhancer and promoter activities of regulatory elements

Andersson, R. & Sandelin, A., 1 Feb 2020, In: Nature Reviews Genetics. 17 p.

Research output: Contribution to journal › Review › peer-review

78 Citations (Scopus)

JASPAR 2020: update of the open-access database of transcription factor binding profiles

Fornes, O., Castro-Mondragon, J. A., Khan, A., van der Lee, R., Zhang, X., Richmond, P. A., Modi, B. P., Correard, S., Gheorghe, M., Baranašić, D., Santana-Garcia, W., Tan, G., Chèneby, J., Ballester, B., Parcy, F., Sandelin, A., Lenhard, B., Wasserman, W. W. & Mathelier, A., 1 Jan 2020, In: Nucleic Acids Research.

Research output: Contribution to journal › Journal article › Research › peer-review

247 Citations (Scopus)

2019

A Functional Link between Nuclear RNA Decay and Transcriptional Control Mediated by the Polycomb Repressive Complex 2

Garland, W., Comet, I., Wu, M., Radzisheuskaya, A., Rib, L., Vitting-Seerup, K., Lloret-Llinares, M., Sandelin, A., Helin, K. & Jensen, T. H., 12 Nov 2019, In: Cell Reports. 29, 7, p. 1800-1811 12 p.

Research output: Contribution to journal › Journal article › Research › peer-review

11 Citations (Scopus)

4 Downloads (Pure)

A step-by-step guide to analyzing CAGE data using R/Bioconductor

Thodberg, M. & Sandelin, A., 18 Jun 2019, In: F1000Research. 8, 49 p., 886.

Research output: Contribution to journal › Journal article › Research › peer-review

3 Citations (Scopus)

14 Downloads (Pure)

CAGEfightR: analysis of 5'-end data using R/Bioconductor

Thodberg, M., Thieffry, A., Vitting-Seerup, K., Andersson, R. & Sandelin, A., 4 Oct 2019, In: BMC Bioinformatics. 20, 13 p., 487.

Research output: Contribution to journal › Journal article › Research › peer-review

5 Citations (Scopus)

8 Downloads (Pure)

Comprehensive profiling of the fission yeast transcription start site activity during stress and media response

Thodberg, M., Thieffry, A., Bornholdt, J., Boyd, M., Holmberg, C., Azad, A., Workman, C. T., Chen, Y., Ekwall, K., Nielsen, O. & Sandelin, A., 28 Feb 2019, In: Nucleic Acids Research. 47, 4, p. 1671-1691 21 p.

Research output: Contribution to journal › Journal article › Research › peer-review

14 Citations (Scopus)

IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences

Vitting-Seerup, K. & Sandelin, A., 1 Nov 2019, In: Bioinformatics. 35, 21, p. 4469-4471

Research output: Contribution to journal › Journal article › Research › peer-review

PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells

Agrawal-Singh, S., Lerdrup, M., Gomes, A-L. R., van de Werken, H. J. G., Johansen, J. V., Andersson, R., Sandelin, A., Helin, K. & Hansen, K., 23 Jan 2019, In: eLife. 8, p. 1-32 32 p., e40364.

Research output: Contribution to journal › Journal article › Research › peer-review

14 Citations (Scopus)

85 Downloads (Pure)

2018

Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies

Boyd, M., Thodberg, M., Vitezic, M., Lange, J. B., Vitting-Seerup, K., Chen, Y., Coskun, M., Li, Y., Lo, B. Z. S., Klausen, P., Schweiger, P., Pedersen, A. G., Rapin, N. P. J-P., Skovgaard, K., Dahlgaard, K., Andersson, R., Terkelsen, T. B., Lilje, B., Troelsen, J. T., Petersen, A. M., & 7 othersJensen, K. B., Gögenur, I., Thielsen, P., Seidelin, J. B., Nielsen, O. H., Bjerrum, J. T. & Sandelin, A. G., 1 Dec 2018, In: Nature Communications. 9, 19 p., 1661.

Research output: Contribution to journal › Journal article › Research › peer-review

20 Citations (Scopus)

120 Downloads (Pure)

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

Khan, A., Fornes, O., Stigliani, A., Gheorghe, M., Castro-Mondragon, J. A., van der Lee, R., Bessy, A., Chèneby, J., Kulkarni, S. R., Tan, G., Baranasic, D., Arenillas, D. J., Sandelin, A. G., Vandepoele, K., Lenhard, B., Ballester, B., Wasserman, W. W., Parcy, F. & Mathelier, A., 1 Jan 2018, In: Nucleic Acids Research. 46, D1, p. D260-D266 7 p., gkx1126.

Research output: Contribution to journal › Journal article › Research › peer-review

605 Citations (Scopus)

79 Downloads (Pure)

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease

Baillie, J. K., Bretherick, A., Haley, C. S., Clohisey, S., Gray, A., Neyton, L. P. A., Barrett, J., Stahl, E. A., Tenesa, A., Andersson, R., Brown, J. B., Faulkner, G. J., Lizio, M., Schaefer, U., Daub, C., Itoh, M., Kondo, N., Lassmann, T., Kawai, J., Mole, D., & 14 othersBajic, V. B., Heutink, P., Rehli, M., Kawaji, H., Sandelin, A. G., Suzuki, H., Satsangi, J., Wells, C. A., Hacohen, N., Freeman, T. C., Hayashizaki, Y., Carninci, P., Forrest, A. R. R. & Hume, D. A., Mar 2018, In: PLoS Computational Biology. 14, 3, 24 p., e1005934.

Research output: Contribution to journal › Journal article › Research › peer-review

5 Citations (Scopus)

74 Downloads (Pure)

The RNA exosome contributes to gene expression regulation during stem cell differentiation

Llinares, M. L., Karadoulama, E., Chen, Y., Wojenski, L. A., Villafano, G. J., Bornholdt, J., Andersson, R., Core, L., Sandelin, A. & Jensen, T. H., 30 Nov 2018, In: Nucleic Acids Research. 46, 21, p. 11502-11513

Research output: Contribution to journal › Journal article › Research › peer-review

19 Citations (Scopus)

44 Downloads (Pure)

2017

An integrated expression atlas of miRNAs and their promoters in human and mouse

de Rie, D., Abugessaisa, I., Alam, T., Arner, E., Arner, P., Ashoor, H., Åström, G., Babina, M., Bertin, N., Burroughs, A. M., Carlisle, A. J., Daub, C. O., Detmar, M., Deviatiiarov, R., Fort, A., Gebhard, C., Goldowitz, D., Guhl, S., Ha, T. J., Harshbarger, J., & 31 othersHasegawa, A., Hashimoto, K., Herlyn, M., Heutink, P., Hitchens, K. J., Hon, C. C., Huang, E., Ishizu, Y., Kai, C., Kasukawa, T., Klinken, P., Lassmann, T., Lecellier, C-H., Lee, W., Lizio, M., Makeev, V., Mathelier, A., Medvedeva, Y. A., Mejhert, N., Mungall, C. J., Noma, S., Ohshima, M., Okada-Hatakeyama, M., Persson, H., Rizzu, P., Roudnicky, F., Sætrom, P., Sato, H., Vitting-Seerup, K., Sandelin, A. G. & FANTOM Consortium, 1 Sept 2017, In: Nature Biotechnology. 35, 9, p. 872-878 7 p.

Research output: Contribution to journal › Journal article › Research › peer-review

183 Citations (Scopus)

Identification of gene transcription start sites and enhancers responding to pulmonary carbon nanotube exposure in Vivo

Lange, J. B., Saber, A. T., Lilje, B., Boyd, M., Jørgensen, M., Chen, Y., Vitezic, M., Jacobsen, N. R., Poulsen, S. S., Berthing, T., Bressendorff, S., Vitting-Seerup, K., Andersson, R., Hougaard, K. S., Yauk, C. L., Halappanavar, S., Wallin, E. H. R., Vogel, U. & Sandelin, A. G., 25 Apr 2017, In: A C S Nano. 11, 4, p. 3597-3613 17 p.

Research output: Contribution to journal › Journal article › Research › peer-review

12 Citations (Scopus)

Regulation of laminin γ2 expression by CDX2 in colonic epithelial cells is impaired during active inflammation

Coskun, M., Soendergaard, C., Joergensen, S., Dahlgaard, K., Riis, L. B., Nielsen, O. H., Sandelin, A. G. & Troelsen, J. T., 1 Feb 2017, In: Journal of Cellular Biochemistry. 118, 2, p. 298-307 10 p.

Research output: Contribution to journal › Journal article › Research › peer-review

2 Citations (Scopus)

Relation between NOD2 genotype and changes in innate signaling in Crohn's disease on mRNA and miRNA levels

Chen, Y., Salem, M., Boyd, M., Bornholdt, J., Li, Y., Coskun, M., Seidelin, J. B., Sandelin, A. & Nielsen, O. H., 2017, In: npj Genomic Medicine. 2, 11 p., 3.

Research output: Contribution to journal › Journal article › Research › peer-review

4 Citations (Scopus)

21 Downloads (Pure)

The landscape of isoform switches in human cancers

Vitting-Seerup, K. & Sandelin, A. G., 1 Sept 2017, In: Molecular Cancer Research. 15, 9, p. 1206-1220 15 p.

Research output: Contribution to journal › Journal article › Research › peer-review

50 Citations (Scopus)

Transcriptional dynamics during human adipogenesis and its link to adipose morphology and distribution

Ehrlund, A., Mejhert, N., Björk, C., Andersson, R., Kulyté, A., Åström, G., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., Sandelin, A. G., Ingelsson, E., FANTOM Consortium, Rydén, M., Laurencikiene, J., Arner, P. & Arner, E., 1 Jan 2017, In: Diabetes. 66, 1, p. 218-230 13 p.

Research output: Contribution to journal › Journal article › Research › peer-review

15 Citations (Scopus)

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

Lizio, M., Harshbarger, J., Abugessaisa, I., Noguchi, S., Kondo, A., Severin, J., Mungall, C., Arenillas, D., Mathelier, A., Medvedeva, Y. A., Lennartsson, A., Drabløs, F., Ramilowski, J. A., Rackham, O., Gough, J., Andersson, R., Sandelin, A. G., Ienasescu, H-I., Ono, H., Bono, H., & 5 othersHayashizaki, Y., Carninci, P., Forrest, A. R. R., Kasukawa, T. & Kawaji, H., 1 Jan 2017, In: Nucleic Acids Research. 45, D1, p. D737-D743 7 p.

Research output: Contribution to journal › Journal article › Research › peer-review

57 Citations (Scopus)

75 Downloads (Pure)

2016

Identification of a nuclear exosome decay pathway for processed transcripts

Meola, N., Domanski, M., Karadoulama, E., Chen, Y., Gentil, C. A. J., Pultz, D., Vitting-Seerup, K., Lykke-Andersen, S., Andersen, J. S., Sandelin, A. G. & Jensen, T. H., 3 Nov 2016, In: Molecular Cell. 64, 3, p. 520-533 14 p.

Research output: Contribution to journal › Journal article › Research › peer-review

99 Citations (Scopus)

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

Mathelier, A., Fornes, O., Arenillas, D. J., Chen, C-Y., Denay, G., Lee, J., Shi, W., Shyr, C., Tan, G., Worsley-Hunt, R., Zhang, A. W., Parcy, F., Lenhard, B., Sandelin, A. G. & Wasserman, W. W., 2016, In: Nucleic Acids Research. 44, D1, p. D110-D115 6 p.

Research output: Contribution to journal › Journal article › Research › peer-review

624 Citations (Scopus)

68 Downloads (Pure)

On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase

Ienasescu, H-I., Li, K., Andersson, R., Vitezic, M., Rennie, S., Chen, Y., Vitting-Seerup, K., Lagoni, E., Boyd, M., Lange, J. B., de Hoon, M. J. L., Kawaji, H., Lassmann, T., FANTOM Consortium, Hayashizaki, Y., Forrest, A. R. R., Carninci, P. & Sandelin, A. G., 1 Jan 2016, In: Database: The Journal of Biological Databases and Curation. 2016, 0, 10 p., baw144.

Research output: Contribution to journal › Journal article › Research › peer-review

10 Citations (Scopus)

85 Downloads (Pure)

Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters

Chen, Y., Pai, A. A., Herudek, J., Lubas, M., Meola, N., Järvelin, A. I., Andersson, R., Pelechano, V., Steinmetz, L. M., Jensen, T. H. & Sandelin, A. G., 1 Sept 2016, In: Nature Genetics. 48, 9, p. 984-994 11 p.

Research output: Contribution to journal › Journal article › Research › peer-review

41 Citations (Scopus)

Regulating retrotransposon activity through the use of alternative transcription start sites

Persson, J., Steglich, B., Smialowska, A., Boyd, M., Lange, J. B., Andersson, R., Schurra, C., Arcangioli, B., Sandelin, A. G., Nielsen, O. & Ekwall, K., 1 May 2016, In: E M B O Reports. 17, 5, p. 753-768 16 p.

Research output: Contribution to journal › Journal article › Research › peer-review

13 Citations (Scopus)

83 Downloads (Pure)

The adipose transcriptional response to insulin is determined by obesity, not insulin sensitivity

Rydén, M., Hrydziuszko, O., Mileti, E., Raman, A., Lange, J. B., Boyd, M., Toft, E., Qvist, V., Näslund, E., Thorell, A., Andersson, D. P., Dahlman, I., Gao, H., Sandelin, A. G., Daub, C. O. & Arner, P., 30 Aug 2016, In: Cell Reports. 16, 9, p. 2317-2326 10 p.

Research output: Contribution to journal › Journal article › Research › peer-review

23 Citations (Scopus)

138 Downloads (Pure)

Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers

Kaczkowski, B., Tanaka, Y., Kawaji, H., Sandelin, A. G., Andersson, R., Itoh, M., Lassmann, T., the FANTOM5 consortium, Hayashizaki, Y., Carninci, P. & Forrest, A. R. R., 15 Jan 2016, In: Cancer Research. 76, 2, p. 216-226

Research output: Contribution to journal › Journal article › Research › peer-review

44 Citations (Scopus)

2015

A unified architecture of transcriptional regulatory elements

Andersson, R., Sandelin, A. G. & Danko, C. G., 1 Aug 2015, In: Trends in Genetics. 31, 8, p. 426-433 8 p.

Research output: Contribution to journal › Journal article › Research › peer-review

87 Citations (Scopus)

Gateways to the FANTOM5 promoter level mammalian expression atlas

Lizio, M., Harshbarger, J., Shimoji, H., Severin, J., Kasukawa, T., Sahin, S., Abugessaisa, I., Fukuda, S., Hori, F., Ishikawa-Kato, S., Mungall, C. J., Arner, E., Baillie, J. K., Bertin, N., Bono, H., de Hoon, M., Diehl, A. D., Dimont, E., Freeman, T. C., Fujieda, K., & 21 othersHide, W., Kaliyaperumal, R., Katayama, T., Lassmann, T., Meehan, T. F., Nishikata, K., Ono, H., Rehli, M., Sandelin, A. G., Schultes, E. A., 't Hoen, P. A. C., Tatum, Z., Thompson, M., Toyoda, T., Wright, D. W., Daub, C. O., Itoh, M., Carninci, P., Hayashizaki, Y., Forrest, A. R. R. & Kawaji, H., 5 Jan 2015, In: Genome Biology (Online Edition). 16, 14 p., 22.

Research output: Contribution to journal › Journal article › Research › peer-review

319 Citations (Scopus)

561 Downloads (Pure)

Human gene promoters are intrinsically bidirectional

Andersson, R., Chen, Y., Core, L., Lis, J. T., Sandelin, A. G. & Jensen, T. H., 5 Nov 2015, In: Molecular Cell. 60, 3, p. 346-347 2 p.

Research output: Contribution to journal › Letter › peer-review

35 Citations (Scopus)

Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors

Lennartsson, A., Arner, E., Fagiolini, M., Saxena, A., Andersson, R., Takahashi, H., Noro, Y., Sng, J., Sandelin, A. G., Hensch, T. K. & Carninci, P., 14 Dec 2015, In: Epigenetics & Chromatin. 8, 15 p., 55.

Research output: Contribution to journal › Journal article › Research › peer-review

23 Citations (Scopus)

210 Downloads (Pure)

The constrained maximal expression level owing to haploidy shapes gene content on the mammalian X chromosome

Hurst, L. D., Ghanbarian, A. T., Forrest, A. R. R., Huminiecki, L., Rehli, M., Kenneth Baillie, J., de Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E., & 243 othersSchmidl, C., Schaefer, U., Medvedeva, Y. A., Plessy, C., Vitezic, M., Severin, J., Semple, C. A., Ishizu, Y., Young, R. S., Francescatto, M., Alam, I., Albanese, D., Altschuler, G. M., Arakawa, T., Archer, J. A. C., Arner, P., Babina, M., Baker, S., Balwierz, P. J., Beckhouse, A. G., Pradhan, S. B., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Maxwell Burroughs, A., Califano, A., Cannistraci, C. V., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H. C., Dalla, E., Davis, C. A., Detmar, M., Diehl, A. D., Dohi, T., Drabløs, F., Edge, A. S. B., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G. J., Favorov, A. V., Fisher, M. E., Frith, M. C., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J. I., Geijtenbeek, T. B., Gibson, A., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Hitchens, K. J., Ho Sui, S. J., Hofmann, O. M., Hoof, I., Hori, F., Huminiecki, L., Iida, K., Ikawa, T., Jankovic, B. R., Jia, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori, M. K., Kasianov, A. S., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawamoto, H., Kawamura, Y. I., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L. M., Kitamura, T., Peter Klinken, S., Knox, A. J., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kwon, A. T., Laros, J. F. J., Lee, W., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Mackay, A. S., Manabe, R., Mar, J. C., Marchand, B., Mathelier, A., Mejhert, N., Meynert, A., Mizuno, Y., de Lima Morais, D. A., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C. L., Murata, M., Nagao, S. S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., van Nimwegen, E., Ninomiya, N., Nishiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada, M. H., Okazaki, Y., Orlando, V., Ovchinnikov, D. A., Pain, A., Passier, R., Patrikakis, M., Persson, H., Piazza, S., Prendergast, J. G. D., Rackham, O. J. L., Ramilowski, J. A., Rashid, M., Ravasi, T., Rizzu, P., Roncador, M., Roy, S., Rye, M. B., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schneider, C., Schultes, E. A., Schulze-Tanzil, G. G., Schwegmann, A., Sengstag, T., Sheng, G., Shimoji, H., Shimoni, Y., Shin, J. W., Simon, C., Sugiyama, D., Sugiyama, T., Suzuki, M., Suzuki, N., Swoboda, R. K., 't Hoen, P. A. C., Tagami, M., Takahashi, N., Takai, J., Tanaka, H., Tatsukawa, H., Tatum, Z., Thompson, M., Toyoda, H., Toyoda, T., Valen, E., van de Wetering, M., van den Berg, L. M., Verardo, R., Vijayan, D., Vorontsov, I. E., Wasserman, W. W., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Zabierowski, S. E., Zhang, P. G., Zhao, X., Zucchelli, S., Summers, K. M., Suzuki, H., Daub, C. O., Kawai, J., Heutink, P., Hide, W., Freeman, T. C., Lenhard, B., Bajic, V. B., Taylor, M. S., Makeev, V. J., Sandelin, A. G., Hume, D. A., Carninci, P. & Hayashizaki, Y., 2015, In: PLoS Biology. 13, 12, 48 p., e1002315.

Research output: Contribution to journal › Journal article › Research › peer-review

15 Citations (Scopus)

129 Downloads (Pure)

The frequent evolutionary birth and death of functional promoters in mouse and human

Young, R. S., Hayashizaki, Y., Andersson, R., Sandelin, A. G., Kawaji, H., Itoh, M., Lassmann, T., Carninci, P., Bickmore, W. A., Forrest, A. R. & Taylor, M. S., 1 Oct 2015, In: Genome Research. 25, p. 1546-1557 12 p.

Research output: Contribution to journal › Journal article › Research › peer-review

25 Citations (Scopus)

151 Downloads (Pure)

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells

Arner, E., Daub, C. O., Vitting-Seerup, K., Andersson, R., Lilje, B., Drabløs, F., Lennartsson, A., Rönnerblad, M., Hrydziuszko, O., Vitezic, M., Freeman, T. C., Alhendi, A. M. N., Arner, P., Axton, R., Baillie, J. K., Beckhouse, A., Bodega, B., Briggs, J., Brombacher, F., Davis, M., & 89 othersDetmar, M., Ehrlund, A., Endoh, M., Eslami, A., Fagiolini, M., Fairbairn, L., Faulkner, G. J., Ferrai, C., Fisher, M. E., Forrester, L., Goldowitz, D., Guler, R., Ha, T., Hara, M., Herlyn, M., Ikawa, T., Kai, C., Kawamoto, H., Khachigian, L. M., Klinken, S. P., Kojima, S., Koseki, H., Klein, S., Mejhert, N., Miyaguchi, K., Mizuno, Y., Morimoto, M., Morris, K. J., Mummery, C., Nakachi, Y., Ogishima, S., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D., Passier, R., Patrikakis, M., Pombo, A., Qin, X-Y., Roy, S., Sato, H., Savvi, S., Saxena, A., Schwegmann, A., Sugiyama, D., Swoboda, R., Tanaka, H., Tomoiu, A., Winteringham, L. N., Wolvetang, E., Yanagi-Mizuochi, C., Yoneda, M., Zabierowski, S., Zhang, P., Abugessaisa, I., Bertin, N., Diehl, A. D., 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, T. F., Mungall, C. J., Murata, M., Nishiyori-Sueki, H., Sahin, S., Nagao-Sato, S., Severin, J., de Hoon, M. J. L., Kawai, J., Kasukawa, T., Lassmann, T., Suzuki, H., Kawaji, H., Summers, K. M., Wells, C., Hume, D. A., Forrest, A. R. R., Sandelin, A. G., Carninci, P. & Hayashizaki, Y., 27 Feb 2015, In: Science (New York, N.Y.). 347, 6225, p. 1010-1014 5 p.

Research output: Contribution to journal › Journal article › Research › peer-review

299 Citations (Scopus)

2014

Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation

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, A. R. R., Sandelin, A. G., Ekwall, K., Arner, E. & Lennartsson, A., 24 Apr 2014, In: Blood. 123, 17

Research output: Contribution to journal › Journal article › Research › peer-review

52 Citations (Scopus)

An atlas of active enhancers across human cell types and tissues

Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Lange, J. B., 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, F. O., & 30 othersJørgensen, M., Andersen, P. R., Bertin, N., Rackham, O., Burroughs, A. M., Baillie, J. K., Ishizu, Y., Shimizu, Y., Furuhata, E., Maeda, S., Negishi, Y., Mungall, C. J., Meehan, T. F., Lassmann, T., Itoh, M., Kawaji, H., Kondo, N., Kawai, J., Lennartsson, A., Daub, C. O., Heutink, P., Hume, D. A., Jensen, T. H., Suzuki, H., Hayashizaki, Y., Mueller, F., Forrest, A. R. R., Carninci, P., Rehli, M. & Sandelin, A. G., 2014, In: Nature. 507, 7493, p. 455-461 7 p.

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1216 Citations (Scopus)

A promoter-level mammalian expression atlas

Forest, A. R. R., Kawaji, H., Rehli, M., Baillie, J. K., De Hoon, M. J. L., Haberle, V., Lassmann, T., Kulakovskiy, I. V., Lizio, M., Itoh, M., Andersson, R., Mungall, C. J., Meehan, T. F., Schmeier, S., Bertin, N., Jørgensen, M., Dimont, E., Arner, E., Schmidl, C., Schaefer, U., & 241 othersMedvedeva, Y. A., Plessy, C., Vitezic, M., Severin, J., Semple, C. A., Ishizu, Y., Young, R. S., Francescatto, M., Altschuler, I. A., Albanese, D., Altschule, G. M., Arakawa, T., Archer, J. A. C., Arner, P., Babina, M., Rennie, S., Balwierz, P. J., Beckhouse, A. G., Pradhan-Bhatt, S., Blake, J. A., Blumenthal, A., Bodega, B., Bonetti, A., Briggs, J., Brombacher, F., Burroughs, A. M., Califano, A., Cannistraci, C. V., Carbajo, D., Chen, Y., Chierici, M., Ciani, Y., Clevers, H. C., Dalla, E., Davis, C. A., Detmar, M., Diehl, A. D., Dohi, T., Drabløs, F., Edge, A. S. B., Edinger, M., Ekwall, K., Endoh, M., Enomoto, H., Fagiolini, M., Fairbairn, L., Fang, H., Farach-Carson, M. C., Faulkner, G. J., Favorov, A. V., Fisher, M. E., Frith, M. C., Fujita, R., Fukuda, S., Furlanello, C., Furuno, M., Furusawa, J. I., Geijtenbeek, T. B., Gibson, A. P., Gingeras, T., Goldowitz, D., Gough, J., Guhl, S., Guler, R., Gustincich, S., Ha, T. J., Hamaguchi, M., Hara, M., Harbers, M., Harshbarger, J., Hasegawa, A., Hasegawa, Y., Hashimoto, T., Herlyn, M., Hitchens, K. J., Sui, S. J. H., Hofmann, O. M., Hoof, I., Hori, F., Huminiecki, L., Iida, K., Ikawa, T., Jankovic, B. R., Jia, H., Joshi, A., Jurman, G., Kaczkowski, B., Kai, C., Kaida, K., Kaiho, A., Kajiyama, K., Kanamori-Katayama, M., Kasianov, A. S., Kasukawa, T., Katayama, S., Kato, S., Kawaguchi, S., Kawamoto, H., Kawamura, Y. I., Kawashima, T., Kempfle, J. S., Kenna, T. J., Kere, J., Khachigian, L. M., Kitamura, T., Klinken, S. P., Knox, A. J., Kojima, M., Kojima, S., Kondo, N., Koseki, H., Koyasu, S., Krampitz, S., Kubosaki, A., Kwon, A. T., Laros, J. F. J., Lee, W., Lennartsson, A., Li, K., Lilje, B., Lipovich, L., Mackay-sim, A., Manabe, R. I., Mar, J. C., Marchand, B., Mathelier, A., Mejhert, N., Meynert, A., Mizuno, Y., De Morais, D. A. L., Morikawa, H., Morimoto, M., Moro, K., Motakis, E., Motohashi, H., Mummery, C. L., Murata, M., Nagao-Sato, S., Nakachi, Y., Nakahara, F., Nakamura, T., Nakamura, Y., Nakazato, K., Van Nimwegen, E., Ninomiya, N., Nishiyori, H., Noma, S., Nozaki, T., Ogishima, S., Ohkura, N., Ohmiya, H., Ohno, H., Ohshima, M., Okada-Hatakeyama, M., Okazaki, Y., Orlando, V., Ovchinnikov, D. A., Pain, A., Passier, R., Patrikakis, M., Persson, H., Piazza, S., Prendergast, J. G. D., Rackham, O. J. L., Ramilowski, J. A., Rashid, M., Ravasi, T., Rizzu, P., Roncador, M., Roy, S., Rye, M. B., Saijyo, E., Sajantila, A., Saka, A., Sakaguchi, S., Sakai, M., Sato, H., Satoh, H., Savvi, S., Saxena, A., Schneider, C., Schultes, E. A., Schulze-Tanzil, G. G., Schwegmann, A., Sengstag, T., Sheng, G., Shimoji, H., Shimoni, Y., Shin, J. W., Simon, C., Sugiyama, D., Sugiyama, T., Suzuki, M., Suzuki, N., Swoboda, R. K., 'T Hoen, P. A. C., Tagami, M., Tagami, N. T., Takai, J., Tanaka, H., Tatsukawa, H., Tatum, Z., Thompson, M., Toyoda, H., Toyoda, T., Valen, E., Van De Wetering, M., Van Den Berg, L. M., Verardo, R., Vijayan, D., Vorontsov, I. E., Wasserman, W. W., Watanabe, S., Wells, C. A., Winteringham, L. N., Wolvetang, E., Wood, E. J., Yamaguchi, Y., Yamamoto, M., Yoneda, M., Yonekura, Y., Yoshida, S., Zabierowski, S. E., Zhang, P. G., Zhao, X., Zucchelli, S., Summers, K. M., Suzuki, H., Daub, C. O., Kawai, J., Heutink, P., Hide, W., Freeman, T. C., Lenhard, B., Bajic, L. V. B., Taylor, M. S., Makeev, V. J., Sandelin, A. G., Hume, D. A., Carninci, P. & Hayashizaki, Y., 1 Jan 2014, In: Nature. 507, 7493, p. 462-470 9 p.

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1011 Citations (Scopus)

CAGE-defined promoter regions of the genes implicated in Rett Syndrome

Vitezic, M., Bertin, N., Andersson, R., Lipovich, L., Kawaji, H., Lassmann, T., Sandelin, A. G., Heutink, P., Goldowitz, D., Ha, T., Zhang, P., Patrizi, A., Fagiolini, M., Forrest, A. R., Carninci, P. & Saxena, A., 24 Dec 2014, In: BMC Genomics. 15, 16 p., 1177.

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6 Citations (Scopus)

913 Downloads (Pure)

Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance

Fort, A., Hashimoto, K., Yamada, D., Salimullah, M., Keya, C. A., Saxena, A., Bonetti, A., Voineagu, I., Bertin, N., Kratz, A., Noro, Y., Wong, C-H., de Hoon, M., Andersson, R., Sandelin, A. G., Suzuki, H., Wei, C-L., Koseki, H., Hasegawa, Y., Forrest, A. R. R., & 2 othersCarninci, P. & FANTOM Consortium, Jun 2014, In: Nature Genetics. 46, 6, p. 558-566 9 p.

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174 Citations (Scopus)

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

Pedersen, J. S., Valen, E., Velazquez, A. M. V., Parker, B. J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D. J., Kelly, T. K., Vang, S., Andersson, R., Jones, P. A., Hoover, C. A., Tikhonov, A., Prokhortchouk, E., Rubin, E. M., Sandelin, A. G., Gilbert, M. T. P., Krogh, A., Willerslev, E., & 1 othersOrlando, L. A. A., Mar 2014, In: Genome Research. 24, 3, p. 454-466 13 p.

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90 Citations (Scopus)

274 Downloads (Pure)

Human nonsense-mediated RNA decay initiates widely by endonucleolysis and targets snoRNA host genes

Lykke-Andersen, S., Chen, Y., Ardal, B., Lilje, B., Waage, J. E., Sandelin, A. G. & Jensen, T. H., 15 Nov 2014, In: Genes & Development. 28, p. 2498-2517 20 p.

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91 Citations (Scopus)

Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2

Boyd, M., Coskun, M., Lilje, B., Andersson, R., Hoof, I., Lange, J. B., Dahlgaard, K., Olsen, J., Vitezic, M., Bjerrum, J. T., Seidelin, J. B., Nielsen, O. H., Troelsen, J. & Sandelin, A. G., 1 Dec 2014, In: D N A Research. 21, 6, p. 569-583 15 p.

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9 Citations (Scopus)

1750 Downloads (Pure)

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles

Mathelier, A., Zhao, X., Zhang, A. W., Parcy, F., Worsley-Hunt, R., Arenillas, D. J., Buchman, S., Chen, C., Chou, A., Ienasescu, H-I., Lim, J., Shyr, C., Tan, G., Zhou, M., Lenhard, B., Sandelin, A. G. & Wasserman, W. W., 1 Jan 2014, In: Nucleic Acids Research. 42, p. D142-D147 6 p.

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728 Citations (Scopus)

528 Downloads (Pure)

Molecular architecture of transcription factor hotspots in early adipogenesis

Siersbæk, R., Baek, S., Rabiee, A., Nielsen, R., Traynor, S., Clarke, N., Sandelin, A. G., Jensen, O. N., Sung, M-H., Hager, G. L. & Mandrup, S., 12 Jun 2014, In: Cell Reports. 7, 5, p. 1434-1442 9 p.

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41 Citations (Scopus)

1227 Downloads (Pure)

New histone supply regulates replication fork speed and PCNA unloading

Mejlvang, J., Feng, Y., Alabert, C., Neelsen, K. J., Jasencakova, Z., Zhao, X., Lees, M., Sandelin, A., Pasero, P., Lopes, M. & Groth, A., 6 Jan 2014, In: Journal of Cell Biology. 204, 1, p. 29-43 15 p.

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87 Citations (Scopus)

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

Andersson, R., Refsing Andersen, P., Valen, E., Core, L. J., Lange, J. B., Boyd, M., Jensen, T. H. & Sandelin, A. G., 2014, In: Nature Communications. 5, 10 p., 5336.

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88 Citations (Scopus)

spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data

Vitting-Seerup, K., Porse, B. T., Sandelin, A. & Waage, J., 23 Mar 2014, In: B M C Bioinformatics. 15, p. 1-7 7 p., 81.

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50 Citations (Scopus)

3196 Downloads (Pure)

Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions

Davis, M. R., Andersson, R., Severin, J., de Hoon, M., Bertin, N., Baillie, J. K., Kawaji, H., Sandelin, A. G., Forrest, A. R. R. & Summers, K. M., May 2014, In: Molecular Genetics and Metabolism. 112, 3, p. 73-83 11 p.

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19 Citations (Scopus)

2013

Acute Genome-wide effects of Rosiglitazone on PPARγ transcriptional networks in Adipocytes

Haakonsson, A. K., Madsen, M. S., Nielsen, R., Sandelin, A. G. & Mandrup, S., 1 Sept 2013, In: Molecular Endocrinology. 27, 9, p. 1536-1549 14 p.

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30 Citations (Scopus)

Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing

Kielpinski, L. J., Boyd, M., Sandelin, A. & Vinther, J., 2013, In: Methods in molecular biology (Clifton, N.J.). 1038, p. 213-31 19 p.

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11 Citations (Scopus)

Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality

Ntini, E., Järvelin, A. I., Lange, J. B., Chen, Y., Boyd, M., Jørgensen, M., Andersson, R., Hoof, I., Schein, A., Andersen, P. R., Andersen, P. K., Preker, P., Valen, E., Zhao, X., Pelechano, V., Steinmetz, L. M., Sandelin, A. G. & Jensen, T. H., Aug 2013, In: Nature Structural and Molecular Biology. 20, p. 923-928 6 p.

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171 Citations (Scopus)

Albin Gustav Sandelin

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