Albin Gustav Sandelin
Professor
Computational and RNA Biology
Ole Maaløes Vej 5
2200 København N.
- Published
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data
Vitting-Seerup, K., Porse, Bo Torben, Sandelin, Albin Gustav & Waage, J., 2014, In: B M C Bioinformatics. 15, p. 1-7 7 p., 81.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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 others, , 2017, In: Nucleic Acids Research. 45, D1, p. D737-D743 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcriptome analysis of recurrently deregulated genes across multiple cancers identifies new pan-cancer biomarkers
Kaczkowski, B., Tanaka, Y., Kawaji, H., Sandelin, Albin Gustav, Andersson, Robin, Itoh, M., Lassmann, T., the FANTOM5 consortium, Hayashizaki, Y., Carninci, P. & Forrest, A. R. R., 2016, In: Cancer Research. 76, 2, p. 216-226Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury
Ryge, J., Winther, Ole, Wienecke, Jacob, Sandelin, Albin Gustav, Westerdahl, A., Hultborn, Hans & Kiehn, O., 2010, In: BMC Genomics. 11, 1, p. 365 22 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcriptional profiling of the human fibrillin/LTBP gene family, key regulators of mesenchymal cell functions
Davis, M. R., Andersson, Robin, Severin, J., de Hoon, M., Bertin, N., Baillie, J. K., Kawaji, H., Sandelin, Albin Gustav, Forrest, A. R. R. & Summers, K. M., 2014, In: Molecular Genetics and Metabolism. 112, 3, p. 73-83 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcriptional dynamics during human adipogenesis and its link to adipose morphology and distribution
Ehrlund, A., Mejhert, N., Björk, C., Andersson, Robin, Kulyté, A., Åström, G., Itoh, M., Kawaji, H., Lassmann, T., Daub, C. O., Carninci, P., Forrest, A. R. R., Hayashizaki, Y., Sandelin, Albin Gustav, Ingelsson, E., FANTOM Consortium, Rydén, M., Laurencikiene, J., Arner, P. & Arner, E., 2017, In: Diabetes. 66, 1, p. 218-230 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Transcriptional and epigenomic profiling identifies YAP signaling as a key regulator of intestinal epithelium maturation
Pikkupeura, Laura Maarit, Bardini Bressan, Raul, Guiu, J., Chen, Y., Maimets, Martti, Mayer, Daniela, Schweiger, P. J., Hansen, Stine Lind, Maciag, Grzegorz Jerzy, Larsen, Hjalte List, Lõhmussaar, Kadi, Pedersen, M. T., Teves, Joji Marie Yap, Lange, Jette Bornholdt, Benes, V., Sandelin, Albin Gustav & Jensen, Kim Bak, 2023, In: Science Advances. 9, 28, 16 p., eadf9460.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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 others, , 2015, In: Science (New York, N.Y.). 347, 6225, p. 1010-1014 5 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
TrancriptomeReconstructoR: data-driven annotation of complex transcriptomes
Ivanov, M., Sandelin, Albin Gustav & Marquardt, Sebastian, 2021, In: BMC Bioinformatics. 22, 15 p., 290.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line
Suzuki, H., Forrest, A. R. R., van Nimwegen, E., Daub, C. O., Balwierz, P. J., Irvine, K. M., Lassmann, T., Ravasi, T., Hasegawa, Y., de Hoon, M. J. L., Katayama, S., Schroder, K., Carninci, P., Tomaru, Y., Kanamori-Katayama, M., Kubosaki, A., Akalin, A., Ando, Y., Arner, E., Asada, M. & 31 others, , 2009, In: Nature Genetics. 41, 5, p. 553-62 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The landscape of isoform switches in human cancers
Vitting-Seerup, K. & Sandelin, Albin Gustav, Sep 2017, In: Molecular Cancer Research. 15, 9, p. 1206-1220 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The genome landscape of ER{alpha}- and ER{beta}-binding DNA regions.
Liu, Y., Gao, H., Marstrand, T. T., Ström, A., Valen, E., Sandelin, Albin Gustav, Gustafsson, J. & Dahlman-Wright, K., 2008, In: Proceedings of the National Academy of Science of the United States of America.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The frequent evolutionary birth and death of functional promoters in mouse and human
Young, R. S., Hayashizaki, Y., Andersson, Robin, Sandelin, Albin Gustav, Kawaji, H., Itoh, M., Lassmann, T., Carninci, P., Bickmore, W. A., Forrest, A. R. & Taylor, M. S., 2015, In: Genome Research. 25, p. 1546-1557 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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 others, , 2015, In: PLoS Biology. 13, 12, 48 p., e1002315.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The adipose transcriptional response to insulin is determined by obesity, not insulin sensitivity
Rydén, M., Hrydziuszko, O., Mileti, E., Raman, A., Lange, Jette Bornholdt, Boyd, M., Toft, E., Qvist, V., Näslund, E., Thorell, A., Andersson, D. P., Dahlman, I., Gao, H., Sandelin, Albin Gustav, Daub, C. O. & Arner, P., 2016, In: Cell Reports. 16, 9, p. 2317-2326 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The Value of Example Solutions in Pharmacy Education: The role of seniority and gender.
Sandelin, Albin Gustav, Hansen, H. R., Baldursdóttir, S. G., Kristensen, Anders Skov, Bak, Lasse Kristoffer, Christiansen, Frederik Voetmann & Selhuber-Unkel, C. J. M., 2011, In: Pharmacy Education. 11, 1, p. 32-37 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The RNA exosome shapes the expression of key protein-coding genes
Wu, M., Karadoulama, Evdoxia, Lloret-llinares, M., Rouviere, J. O., Vaagensø, C. S., Moravec, M., Li, B., Wang, J., Wu, G., Gockert, M. A. M., Pelechano, V., Jensen, T. H. & Sandelin, Albin Gustav, 2020, In: Nucleic Acids Research. 48, 15, p. 8509-8528Research output: Contribution to journal › Journal article › Research › peer-review
- Published
The RNA exosome contributes to gene expression regulation during stem cell differentiation
Llinares, M. L., Karadoulama, Evdoxia, Chen, Y., Wojenski, L. A., Villafano, G. J., Lange, Jette Bornholdt, Andersson, Robin, Core, L., Sandelin, Albin Gustav & Jensen, T. H., 2018, In: Nucleic Acids Research. 46, 21, p. 11502-11513Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
Pauli, A., Valen, E., Lin, M. F., Garber, M., Vastenhouw, N. L., Levin, J. Z., Fan, L., Sandelin, Albin Gustav, Rinn, J. L., Regev, A. & Schier, A. F., 2012, In: Genome Research. 22, p. 577-591 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Systematic clustering of transcription start site landscapes
Zhao, X., Valen, E., Parker, B. J. & Sandelin, Albin Gustav, 2011, In: P L o S One. 6, 8, 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Spatially resolved analysis of microenvironmental gradient impact on cancer cell phenotypes
Auxillos, Jamie Yam, Crouigneau, R., Li, Y. F., Dai, Yifan, Stigliani, Arnaud, Tavernaro, I., Resch-Genger, U., Sandelin, Albin Gustav, Marie, R. & Pedersen, Stine Helene Falsig, 2024, In: Science Advances. 10, 18, 17 p., eadn3448.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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 others, , 2018, In: PLoS Computational Biology. 14, 3, 24 p., e1005934.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors
Lennartsson, A., Arner, E., Fagiolini, M., Saxena, A., Andersson, Robin, Takahashi, H., Noro, Y., Sng, J., Sandelin, Albin Gustav, Hensch, T. K. & Carninci, P., 2015, In: Epigenetics & Chromatin. 8, 15 p., 55.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Relation between NOD2 genotype and changes in innate signaling in Crohn's disease on mRNA and miRNA levels
Chen, Y., Salem, M., Boyd, M., Lange, Jette Bornholdt, Li, Yuan, Coskun, M., Seidelin, Jakob Benedict, Sandelin, Albin Gustav & Nielsen, Ole Haagen, 2017, In: npj Genomic Medicine. 2, 11 p., 3.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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, Lene Buhl, Nielsen, Ole Haagen, Sandelin, Albin Gustav & Troelsen, J. T., 2017, In: Journal of Cellular Biochemistry. 118, 2, p. 298-307 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Regulating retrotransposon activity through the use of alternative transcription start sites
Persson, J., Steglich, B., Smialowska, A., Boyd, M., Lange, Jette Bornholdt, Andersson, Robin, Schurra, C., Arcangioli, B., Sandelin, Albin Gustav, Nielsen, Olaf & Ekwall, K., 2016, In: E M B O Reports. 17, 5, p. 753-768 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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, Robin, Pelechano, V., Steinmetz, L. M., Jensen, T. H. & Sandelin, Albin Gustav, 2016, In: Nature Genetics. 48, 9, p. 984-994 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Prediction of regulatory elements
Sandelin, Albin Gustav, 2008, In: Methods in Molecular Biology. 453, p. 233-44 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data
Chen, Y., Jørgensen, M., Kolde, R., Zhao, X., Parker, B., Valen, E., Wen, J. & Sandelin, Albin Gustav, 2011, In: BMC Genomics. 12, 1, 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Polyadenylation site-induced decay of upstream transcripts enforces promoter directionality
Ntini, E., Järvelin, A. I., Lange, Jette Bornholdt, Chen, Y., Boyd, M., Jørgensen, M., Andersson, Robin, Hoof, I., Schein, A., Andersen, P. R., Andersen, P. K., Preker, P., Valen, E., Zhao, X., Pelechano, V., Steinmetz, L. M., Sandelin, Albin Gustav & Jensen, T. H., 2013, In: Nature Structural and Molecular Biology. 20, p. 923-928 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Personalized B cell response to the Lactobacillus rhamnosus GG probiotic in healthy human subjects: a randomized trial
Lange, Jette Bornholdt, Chen, Y., Rago, Alfredo, Sloth, S., Hendel, J., Melsæther, C., Müller, C. V., Juul Nielsen, M., Strickertsson, J., Engelholm, Lars Henning, Vitting-Seerup, K., Jensen, Kim Bak, Baker, A. & Sandelin, Albin Gustav, 9 Nov 2020, In: Gut Microbes. 12, 1, p. 1-14 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
PROMoter uPstream Transcripts share characteristics with mRNAs and are produced upstream of all three major types of mammalian promoters
Preker, P., Almvig, K., Christensen, M. S., Valen, E., Mapendano, C. K., Sandelin, Albin Gustav & Jensen, T. H., 19 May 2011, In: Nucleic Acids Research.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells
Agrawal-Singh, S., Lerdrup, Mads, Gomes, A. R., van de Werken, H. J. G., Johansen, Jens Vilstrup, Andersson, Robin, Sandelin, Albin Gustav, Helin, K. & Hansen, K., 2019, In: eLife. 8, p. 1-32 32 p., e40364.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave
Thieffry, A., López Márquez, Diego, Lange, Jette Bornholdt, Gholami Malekroudi, M., Bressendorff, Simon, Barghetti, A., Sandelin, Albin Gustav & Brodersen, Peter, 2022, In: The Plant Cell. 34, 7, 23 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Organismal benefits of transcription speed control at gene boundaries
Leng, Xueyuan, Ivanov, M., Kindgren, P., Malik, I., Thieffry, A., Brodersen, Peter, Sandelin, Albin Gustav, Kaplan, C. D. & Marquardt, Sebastian, 2020, In: EMBO Reports. 21, 4, 16 p., e49315.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase
Ienasescu, H., Li, K., Andersson, Robin, Vitezic, M., Rennie, Sarah, Chen, Y., Vitting-Seerup, K., Lagoni, E., Boyd, M., Lange, Jette Bornholdt, de Hoon, M. J. L., Kawaji, H., Lassmann, T., FANTOM Consortium, F. C., Hayashizaki, Y., Forrest, A. R. R., Carninci, P. & Sandelin, Albin Gustav, 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
- Published
Nuclear stability and transcriptional directionality separate functionally distinct RNA species
Andersson, Robin, Refsing Andersen, P., Valen, E., Core, L. J., Lange, Jette Bornholdt, Boyd, M., Jensen, T. H. & Sandelin, Albin Gustav, 2014, In: Nature Communications. 5, 10 p., 5336.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
New histone supply regulates replication fork speed and PCNA unloading
Mejlvang, J., Feng, Y., Alabert, C., Neelsen, K. J., Jasencakova, Zuzana, Zhao, X., Lees, M., Sandelin, Albin Gustav, Pasero, P., Lopes, M. & Groth, Anja, 6 Jan 2014, In: Journal of Cell Biology. 204, 1, p. 29-43 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Multivariate Hawkes process models of the occurrence of regulatory elements
Carstensen, L., Sandelin, Albin Gustav, Winther, Ole & Hansen, Niels Richard, 2010, In: BMC Bioinformatics. 11, p. 456Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Molecular architecture of transcription factor hotspots in early adipogenesis
Siersbæk, R., Baek, S., Rabiee, A., Nielsen, R., Traynor, S., Clarke, N., Sandelin, Albin Gustav, Jensen, O. N., Sung, M., Hager, G. L. & Mandrup, S., 2014, In: Cell Reports. 7, 5, p. 1434-1442 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Modeling promoter grammars with evolving hidden Markov models
Won, K., Sandelin, Albin Gustav, Marstrand, T. T. & Krogh, Anders, 2008, In: Bioinformatics. 24, 15, p. 1669-75 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Metazoan promoters: emerging characteristics and insights into transcriptional regulation
Lenhard, B., Sandelin, Albin Gustav & Carninci, P., 2012, In: Nature Reviews. Genetics. 13, 4, p. 233-245 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Mesenchymal-epithelial crosstalk shapes intestinal regionalisation via Wnt and Shh signalling
Maimets, Martti, Pedersen, M. T., Guiu, J., Dreier, J., Thodberg, Malte, Antoku, Yasuko, Schweiger, P. J., Rib, Leonor, Bardini Bressan, Raul, Miao, Y., Garcia, K. C., Sandelin, Albin Gustav, Serup, Palle & Jensen, Kim Bak, 2022, In: Nature Communications. 13, 12 p., 715.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Mammalian RNA polymerase II core promoters: insights from genome-wide studies.
Sandelin, Albin Gustav, Carninci, P., Lenhard, B., Ponjavic, J., Hayashizaki, Y. & Hume, D. A., 2007, In: Nature Reviews. Genetics. 8, 6, p. 424-36 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Lactate receptor GPR81 drives breast cancer growth and invasiveness through regulation of ECM properties and Notch ligand DLL4
Jørgensen, Kathrine Lundø, Dmytriyeva, O., Spøhr, L., Alves, Eliana Carolina Goncalves, Yao, Jiayi, Puig Blasco, Laia, Trauelsen, Mette, Ponniah, M., Severin, M., Sandelin, Albin Gustav, Kveiborg, Marie, Schwartz, Thue W. & Pedersen, Stine Helene Falsig, 2023, In: BMC Cancer. 23, 1, 20 p., 1136.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.
Bryne, J. C., Valen, E., Tang, M. E., Marstrand, T., Winther, Ole, da Piedade, I., Krogh, Anders, Lenhard, B. & Sandelin, Albin Gustav, 2008, In: Nucleic Acids Research. 36, Database issue, p. D102-6Research output: Contribution to journal › Journal article › Research › peer-review
- Published
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles
Rauluseviciute, I., Riudavets-puig, R., Blanc-mathieu, R., Castro-mondragon, J., Ferenc, K., Kumar, V., Lemma, R. B., Lucas, J., Chèneby, J., Baranasic, D., Khan, A., Fornes, O., Gundersen, S., Johansen, M., Hovig, E., Lenhard, B., Sandelin, Albin Gustav, Wasserman, W., Parcy, F. & Mathelier, A., 2024, In: Nucleic Acids Symposium Series. 52, D1, p. D174–D182 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles
Castro-Mondragon, J. A., Riudavets-Puig, R., Rauluseviciute, I., Lemma, R. B., Turchi, L., Blanc-Mathieu, R., Lucas, J., Boddie, P., Khan, A., Perez, N. M., Fornes, O., Leung, T. Y., Aguirre, A., Hammal, F., Schmelter, D., Baranasic, D., Ballester, B., Sandelin, A., Lenhard, B., Vandepoele, K. & 3 others, , 2022, In: Nucleic acids symposium series. 50, D1, p. D165-D173 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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, Albin Gustav, Lenhard, B., Wasserman, W. W. & Mathelier, A., 2020, In: Nucleic Acids Research. 48, D1, p. D87-D92 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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, Albin Gustav, Vandepoele, K., Lenhard, B., Ballester, B., Wasserman, W. W., Parcy, F. & Mathelier, A., 2018, In: Nucleic Acids Research. 46, D1, p. D260-D266 7 p., gkx1126.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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., Denay, G., Lee, J., Shi, W., Shyr, C., Tan, G., Worsley-Hunt, R., Zhang, A. W., Parcy, F., Lenhard, B., Sandelin, Albin Gustav & 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
- Published
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., Lim, J., Shyr, C., Tan, G., Zhou, M., Lenhard, B., Sandelin, Albin Gustav & Wasserman, W. W., 2014, In: Nucleic Acids Research. 42, p. D142-D147 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles
Portales-Casamar, E., Thongjuea, S., Kwon, A. T., Arenillas, D., Zhao, X., Valen, E., Yusuf, D., Lenhard, B., Wasserman, W. W. & Sandelin, Albin Gustav, 2009, In: Nucleic Acids Research.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences
Vitting-Seerup, K. & Sandelin, Albin Gustav, 2019, In: Bioinformatics. 35, 21, p. 4469-4471Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Interaction of antidepressants with the serotonin and norepinephrine transporters: mutational studies of the S1 substrate binding pocket
Sørensen, L., Andersen, J., Thomsen, M., Hansen, S. M. R., Zhao, X., Sandelin, Albin Gustav, Strømgaard, Kristian & Kristensen, Anders Skov, 2012, In: The Journal of Biological Chemistry. 287, 52, p. 43694-43707 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Interaction of antidepressants with the serotonin and norepinephrine transporters: mutational studies of the S1 substrate binding pocket
Sørensen, L., Andersen, J., Thomsen, M., Hansen, S. M. R., Zhao, X., Sandelin, Albin Gustav, Strømgaard, Kristian & Kristensen, Anders Skov, 2012, In: Journal of Biological Chemistry. 287, p. 43694-43707 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Identification of gene transcription start sites and enhancers responding to pulmonary carbon nanotube exposure in Vivo
Lange, Jette Bornholdt, Saber, A. T., Lilje, B., Boyd, M., Jørgensen, M., Chen, Y., Vitezic, M., Jacobsen, N. R., Poulsen, S. S., Berthing, T., Bressendorff, Simon, Vitting-Seerup, K., Andersson, Robin, Hougaard, K. S., Yauk, C. L., Halappanavar, S., Wallin, E. H. R., Vogel, U. & Sandelin, Albin Gustav, 2017, In: A C S Nano. 11, 4, p. 3597-3613 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Identification of a nuclear exosome decay pathway for processed transcripts
Meola, N., Domanski, M., Karadoulama, Evdoxia, Chen, Y., Gentil, C. A. J., Pultz, D., Vitting-Seerup, K., Lykke-Andersen, S., Andersen, J. S., Sandelin, Albin Gustav & 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
- Published
Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2
Boyd, M., Coskun, M., Lilje, B., Andersson, Robin, Hoof, I., Lange, Jette Bornholdt, Dahlgaard, K., Olsen, Jørgen, Vitezic, M., Bjerrum, Jakob Tveiten , Seidelin, Jakob Benedict, Nielsen, Ole Haagen, Troelsen, J. & Sandelin, Albin Gustav, 2014, In: D N A Research. 21, 6, p. 569-583 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Birney, E., Stamatoyannopoulos, J. A., Dutta, A., Guigó, R., Gingeras, T. R., Margulies, E. H., Weng, Z., Snyder, M., Dermitzakis, E. T., Thurman, R. E., Kuehn, M. S., Taylor, C. M., Neph, S., Koch, C. M., Asthana, S., Malhotra, A., Adzhubei, I., Greenbaum, J. A., Andrews, R. M., Flicek, P. & 36 others, , 2007, In: Nature. 447, 7146, p. 799-816 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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, Albin Gustav & Jensen, T. H., 2014, In: Genes & Development. 28, p. 2498-2517 20 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Human gene promoters are intrinsically bidirectional
Andersson, Robin, Chen, Y., Core, L., Lis, J. T., Sandelin, Albin Gustav & Jensen, T. H., 2015, In: Molecular Cell. 60, 3, p. 346-347 2 p.Research output: Contribution to journal › Letter › Research › peer-review
- Published
Hidden layers of human small RNAs
Kawaji, H., Nakamura, M., Takahashi, Y., Sandelin, Albin Gustav, Katayama, S., Fukuda, S., Daub, C. O., Kai, C., Kawai, J., Yasuda, J., Carninci, P. & Hayashizaki, Y., 2008, In: BMC Genomics. 9, p. 157Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic and chromatin signals underlying transcription start-site selection
Valen, E. & Sandelin, Albin Gustav, 2011, In: Trends in Genetics. 27, 11, p. 475-485 11 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genomic Stability and Phenotypic Characteristics of Industrially Produced Lacticaseibacillus rhamnosus GG in a Yogurt Matrix
Strickertsson, Marianne Stage, Hui, Y., Nielsen, Dennis Sandris, Vera-Jimenéz, N. I., Olsen, J., Sandelin, Albin Gustav & Wichmann, A., 2021, In: Applied and Environmental Microbiology. 87, 24, 18 p., e01575-21.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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 others, , 2014, In: Genome Research. 24, 3, p. 454-466 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genome-wide identification of estrogen receptor alpha-binding sites in mouse liver.
Gao, H., Fält, S., Sandelin, Albin Gustav, Gustafsson, J. & Dahlman-Wright, K., 2007, In: Molecular Endocrinology. 22, 1, p. 10-22 12 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
Valen, E., Pascarella, G., Chalk, A., Maeda, N., Kojima, M., Kawazu, C., Murata, M., Nishiyori, H., Lazarevic, D., Motti, D., Marstrand, T. T., Tang, M-H. E., Zhao, X., Krogh, A., Winther, O., Arakawa, T., Kawai, J., Wells, C., Daub, C., Harbers, M. & 4 others, , 2009, In: Genome Research. 19, 2, p. 255-65 10 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Gene expression analysis of the emergence of epileptiform activity after focal injection of kainic acid into mouse hippocampus
Motti, D., Le Duigou, C., Eugène, E., Chemaly, N., Wittner, L., Lazarevic, D., Krmac, H., Marstrand, T., Valen, E., Sanges, R., Stupka, E., Sandelin, Albin Gustav, Cherubini, E., Gustincich, S. & Miles, R., 2010, In: European Journal of Neuroscience. 32, 8, p. 1364-79 15 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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 others, , 2015, In: Genome Biology (Online Edition). 16, 14 p., 22.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
GMD: measuring the distance between histograms with applications on high-throughput sequencing reads
Zhao, X. & Sandelin, Albin Gustav, 2012, In: Bioinformatics. 28, 8, p. 1164-1165 2 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Functional annotation of human long noncoding RNAs via molecular phenotyping
Ramilowski, J. A., Yip, C. W., Agrawal, S., Chang, J-C., Ciani, Y., Kulakovskiy, I. V., Mendez, M., Ooi, J. L. C., Ouyang, J. F., Parkinson, N., Petri, A., Roos, L., Severin, J., Yasuzawa, K., Abugessaisa, I., Akalin, A., Antonov, I. V., Arner, E., Bonetti, A., Bono, H. & 96 others, , 2020, In: Genome Research. 30, 7, p. 1060-1072 13 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Dynamic usage of transcription start sites within core promoters.
Kawaji, H., Frith, M. C., Katayama, S., Sandelin, Albin Gustav, Kai, C., Kawai, J., Carninci, P. & Hayashizaki, Y., 2006, In: Genome Biology. 7, 12, p. R118Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network
Grapotte, M., Saraswat, M., Bessière, C., Menichelli, C., Ramilowski, J. A., Severin, J., Hayashizaki, Y., Itoh, M., Tagami, M., Murata, M., Kojima-Ishiyama, M., Noma, S., Noguchi, S., Kasukawa, T., Hasegawa, A., Suzuki, H., Nishiyori-Sueki, H., Frith, M. C., Abugessaisa, I., Aitken, S. & 31 others, , 2021, In: Nature Communications. 12, 18 p., 3297.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Discovery of regulatory elements is improved by a discriminatory approach
Valen, E., Sandelin, Albin Gustav, Winther, Ole & Krogh, Anders, 2009, In: PLoS Computational Biology. 5, 11, p. e1000562Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Dioxin increases the interaction between aryl hydrocarbon receptor and estrogen receptor alpha at human promoters
Ahmed, S., Valen, E., Sandelin, Albin Gustav & Matthews, J., 2009, In: Toxicological Sciences. 111, 2, p. 254-266Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Determinants of enhancer and promoter activities of regulatory elements
Andersson, Robin & Sandelin, Albin Gustav, 2020, In: Nature Reviews Genetics. 21, 2, p. 71-87 17 p.Research output: Contribution to journal › Review › Research › peer-review
- Published
Detection of reverse transcriptase termination sites using cDNA ligation and massive parallel sequencing
Kielpinski, L. J., Boyd, M., Sandelin, Albin Gustav & Vinther, Jeppe, 2013, In: Methods in molecular biology (Clifton, N.J.). 1038, p. 213-31 19 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Detecting host responses to microbial stimulation using primary epithelial organoids
Lange, Jette Bornholdt, Müller, C. V., Nielsen, M. J., Strickertsson, J., Rago, D., Chen, Y., Maciag, Grzegorz Jerzy, Skov, Jonathan, Wellejus, A., Schweiger, P. J., Hansen, Stine Lind, Broholm, C., Gögenur, Ismail, Maimets, Martti, Sloth, S., Hendel, J., Baker, A., Sandelin, Albin Gustav & Jensen, Kim Bak, 2023, In: Gut Microbes. 15, 2, 16 p., 2281012.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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 others, , 2014, In: Nature Genetics. 46, 6, p. 558-566 9 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Crosstalk between tumor acidosis, p53 and extracellular matrix regulates pancreatic cancer aggressiveness
Czaplinska, D., Ialchina, Renata, Andersen, Henriette Berg, Yao, Jiayi, Stigliani, Arnaud, Dannesboe, Johs, Flinck, M., Chen, X., Mitrega, J., Gnosa, S. P., Dmytriyeva, O., Alves, F., Napp, J., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2023, In: International Journal of Cancer. 152, 6, p. 1210-1225 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cross-species ChIP-seq studies provide insights into regulatory strategies of PPAR¿ in adipocytes
Schmidt, S. F., Jørgensen, M., Sandelin, Albin Gustav & Mandrup, S., 2012, In: Transcription. 3, 1, p. 19-24 6 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cross species comparison of C/EBPa and PPAR¿ profiles in mouse and human adipocytes reveals interdependent retention of binding sites
Schmidt, S. F., Jørgensen, M., Chen, Y., Nielsen, R., Sandelin, Albin Gustav & Mandrup, S., 2011, In: BMC Genomics. 12, 16 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Computational identification of signals predictive for nuclear RNA exosome degradation pathway targeting
Wu, M., Schmid, M., Jensen, T. H. & Sandelin, Albin Gustav, 2022, In: NAR Genomics and Bioinformatics. 4, 3, 18 p., lqac071.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Comprehensive profiling of the fission yeast transcription start site activity during stress and media response
Thodberg, Malte, Thieffry, A., Lange, Jette Bornholdt, Boyd, M., Holmberg, Christian, Azad, A., Workman, C. T., Chen, Y., Ekwall, K., Nielsen, Olaf & Sandelin, Albin Gustav, 28 Feb 2019, In: Nucleic Acids Research. 47, 4, p. 1671-1691 21 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Chronic acidosis rewires cancer cell metabolism through PPARα signaling
Rolver, M. G., Holland, L. K. K., Ponniah, M., Prasad, N. S., Yao, Jiayi, Schnipper, J., Kramer, S., Elingaard-Larsen, L., Pedraz-Cuesta, E., Liu, B., Pardo, L. A., Maeda, K., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2023, In: International Journal of Cancer. 152, 8, 17 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Chromatin modifier HUSH co-operates with RNA decay factor NEXT to restrict transposable element expression
Garland, W., Müller, I., Wu, M., Schmid, M., Imamura, K., Rib, Leonor, Sandelin, Albin Gustav, Helin, K. & Jensen, T. H., 2022, In: Molecular Cell. 82, 9, p. 1691-1707.e8Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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 others, , 2018, In: Nature Communications. 9, 19 p., 1661.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Characterization of Arabidopsis thaliana Promoter Bidirectionality and Antisense RNAs by Inactivation of Nuclear RNA Decay Pathways
Thieffry, A., Vigh, Maria Louisa, Lange, Jette Bornholdt, Ivanov, M., Brodersen, Peter & Sandelin, Albin Gustav, 2020, In: The Plant Cell. 32, 6, p. 1845-1867 23 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Cancer Cell Acid Adaptation Gene Expression Response is Correlated to Tumor-Specific Tissue Expression Profiles and Patient Survival
Yao, Jiayi, Czaplinska, D., Ialchina, Renata, Schnipper, J., Liu, B., Sandelin, Albin Gustav & Pedersen, Stine Helene Falsig, 2020, In: Cancers. 12, 8, 27 p., 2183.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
- Published
CAGEfightR: analysis of 5'-end data using R/Bioconductor
Thodberg, Malte, Thieffry, A., Vitting-Seerup, K., Andersson, Robin & Sandelin, Albin Gustav, 2019, In: BMC Bioinformatics. 20, 13 p., 487.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
CAGE-defined promoter regions of the genes implicated in Rett Syndrome
Vitezic, M., Bertin, N., Andersson, Robin, Lipovich, L., Kawaji, H., Lassmann, T., Sandelin, Albin Gustav, Heutink, P., Goldowitz, D., Ha, T., Zhang, P., Patrizi, A., Fagiolini, M., Forrest, A. R., Carninci, P. & Saxena, A., 2014, In: BMC Genomics. 15, 16 p., 1177.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Biogenic mechanisms and utilization of small RNAs derived from human protein-coding genes
Valen, E., Preker, P., Andersen, P. R., Zhao, X., Chen, Y., Ender, C., Dueck, A., Meister, G., Sandelin, Albin Gustav & Jensen, T. H., 2011, In: Nature Structural and Molecular Biology. 18, 9, p. 1075–1082 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Analysis of the DNA methylome and transcriptome in granulopoiesis reveal timed changes and dynamic enhancer methylation
Rönnerblad, M., Andersson, Robin, 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, Albin Gustav, Ekwall, K., Arner, E. & Lennartsson, A., 2014, In: Blood. 123, 17Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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 others, , 21 Aug 2017, In: Nature Biotechnology. 35, 9, p. 872-878 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
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 others, , 2014, In: Nature. 507, 7493, p. 455-461 7 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
Acute Genome-wide effects of Rosiglitazone on PPARγ transcriptional networks in Adipocytes
Haakonsson, A. K., Madsen, M. S., Nielsen, R., Sandelin, Albin Gustav & Mandrup, S., 2013, In: Molecular Endocrinology. 27, 9, p. 1536-1549 14 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A unified architecture of transcriptional regulatory elements
Andersson, Robin, Sandelin, Albin Gustav & Danko, C. G., Aug 2015, In: Trends in Genetics. 31, 8, p. 426-433 8 p.Research output: Contribution to journal › Journal article › Research › peer-review
- Published
A step-by-step guide to analyzing CAGE data using R/Bioconductor
Thodberg, Malte & Sandelin, Albin Gustav, 18 Jun 2019, In: F1000Research. 8, 49 p., 886.Research output: Contribution to journal › Journal article › Research › peer-review
ID: 5007
Most downloads
-
3507
downloads
spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
3347
downloads
Prediction of RNA Polymerase II recruitment, elongation and stalling from histone modification data
Research output: Contribution to journal › Journal article › Research › peer-review
Published -
2993
downloads
Multivariate Hawkes process models of the occurrence of regulatory elements
Research output: Contribution to journal › Journal article › Research › peer-review
Published