Sandelin group

Core promoter and transcriptomics bioinformatics

Publications

Here is also a link to the relevant PubMed search.

indicates papers affiliated with Copenhagen University

Research papers

2009

• Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, Kanamori-Katayama M, Kubosaki A, Akalin A, Ando Y, Arner E, Asada M, Asahara H, Bailey T, Bajic VB, Bauer D, Beckhouse AG, Bertin N, Bjorkegren J, Brombacher F, Bulger E, Chalk AM, Chiba J, Cloonan N, Dawe A, Dostie J, Engstrom PG, Essack M, Faulkner GJ, Fink JL, Fredman D, Fujimori K, Furuno M, Gojobori T, Gough J, Grimmond SM, Gustafsson M, Hashimoto M, Hashimoto T, Hatakeyama M, Heinzel S, Hide W, Hofmann O, Hornquist M, Huminiecki L, Ikeo K, Imamoto N, Inoue S, Inoue Y, Ishihara R, Iwayanagi T, Jacobsen A, Kaur M, Kawaji H, Kerr MC, Kimura R, Kimura S, Kimura Y, Kitano H, Koga H, Kojima T, Kondo S, Konno T, Krogh A, Kruger A, Kumar A, Lenhard B, Lennartsson A, Lindow M, Lizio M, Macpherson C, Maeda N, Maher CA, Maqungo M, Mar J, Matigian NA, Matsuda H, Mattick JS, Meier S, Miyamoto S, Miyamoto-Sato E, Nakabayashi K, Nakachi Y, Nakano M, Nygaard S, Okayama T, Okazaki Y, Okuda-Yabukami H, Orlando V, Otomo J, Pachkov M, Petrovsky N, Plessy C, Quackenbush J, Radovanovic A, Rehli M, Saito R, Sandelin A, Schmeier S, Schonbach C, Schwartz AS, Semple CA, Sera M, Severin J, Shirahige K, Simons C, St Laurent G, Suzuki M, Suzuki T, Sweet MJ, Taft RJ, Takeda S, Takenaka Y, Tan K, Taylor MS, Teasdale RD, Tegner J, Teichmann S, Valen E, Wahlestedt C, Waki K, Waterhouse A, Wells CA, Winther O, Wu L, Yamaguchi K, Yanagawa H, Yasuda J, Zavolan M, Hume DA, Arakawa T, Fukuda S, Imamura K, Kai C, Kaiho A, Kawashima T, Kawazu C, Kitazume Y, Kojima M, Miura H, Murakami K, Murata M, Ninomiya N, Nishiyori H, Noma S, Ogawa C, Sano T, Simon C, Tagami M, Takahashi Y, Kawai J, Hayashizaki Y: The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line . Nat Genet 2009, 41(5):553-562.
• Valen E, Pascarella G, Chalk A, Maeda N, Kojima M, Kawazu C, Murata M, Nishiyori H, Lazarevic D, Motti D, Marstrand TT, Tang MH, Zhao X, Krogh A, Winther O, Arakawa T, Kawai J, Wells C, Daub C, Harbers M, Hayashizaki Y, Gustincich S, Sandelin A, Carninci P: Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE . Genome Res 2009, 19(2):255-265.
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  2008

• Won KJ, Sandelin A, Marstrand TT, Krogh A: Modeling promoter grammars with evolving hidden Markov models . Bioinformatics 2008, 24(15):1669-1675.
• Kawaji H, Nakamura M, Takahashi Y, Sandelin A, Katayama S, Fukuda S, Daub CO, Kai C, Kawai J, Yasuda J et al: Hidden layers of small RNAs . BMC Genomics 2008, 9(1).
• Liu Y, Gao H, Marstrand TT, Strom A, Valen E, Sandelin A, Gustafsson JA, Dahlman-Wright K: The genome landscape of ER{alpha}- and ER{beta}-binding DNA regions . Proceedings of the National Academy of Sciences of the United States of America 2008, 105(7):2604-2609.
• Gao H, Falt S, Sandelin A, Gustafsson JA, Dahlman-Wright K: Genome-Wide Identification of Estrogen Receptor {alpha}-Binding Sites in Mouse Liver . Mol Endocrinol 2008, 22(1):10-22.
• Frith MC, Valen E, Krogh A, Hayashizaki Y, Carninci P, Sandelin A: A code for transcription initiation in mammalian genomes . Genome Res 2008, 18(1):1-12.

2007

• Bryne JC, Valen E, Tang MH, Marstrand T, Winther O, da Piedade I, Krogh A, Lenhard B, Sandelin A: JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update . Nucleic Acids Res 2007.
• The_ENCODE_Consortium: Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project . Nature 2007, 447(7146):799-816.

2006

• Kawaji H, Frith MC, Katayama S, Sandelin A, Kai C, Kawai J, Carninci P, Hayashizaki Y: Dynamic usage of transcription start sites within core promoters . Genome Biol 2006, 7(12):R118.
• Vlieghe D, Sandelin A, De Bleser PJ, Vleminckx K, Wasserman WW, van Roy F, Lenhard B: A new generation of JASPAR, the open-access repository for transcription factor binding site profiles . Nucleic Acids Res 2006, 34(Database issue):D95-97.
• Ponjavic J, Lenhard B, Kai C, Kawai J, Carninci P, Hayashizaki Y, Sandelin A: Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters . Genome Biol 2006, 7(8):R78.
• Frith MC, Ponjavic J, Fredman D, Kai C, Kawai J, Carninci P, Hayshizaki Y, Sandelin A: Evolutionary turnover of mammalian transcription start sites . Genome Res 2006, 16(6):713-722.
• Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, Semple CA, Taylor MS, Engstrom PG, Frith MC et al: Genome-wide analysis of mammalian promoter architecture and evolution . Nat Genet 2006.
• Bailey PJ, Klos JM, Andersson E, Karlen M, Kallstrom M, Ponjavic J, Muhr J, Lenhard B, Sandelin A, Ericson J: A global genomic transcriptional code associated with CNS-expressed genes . Exp Cell Res 2006.

2005

• Stahlberg N, Merino R, Hernandez LH, Fernandez-Perez L, Sandelin A, Engstrom P, Tollet-Egnell P, Lenhard B, Flores-Morales A: Exploring hepatic hormone actions using a compilation of gene expression profiles . BMC Physiol 2005, 5(1):8.
• Sandelin A, Wasserman WW: Prediction of nuclear hormone receptor response elements . Mol Endocrinol 2005, 19(3):595-606.
• Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J et al: Antisense transcription in the mammalian transcriptome . Science 2005, 309(5740):1564-1566.
• Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C et al: The transcriptional landscape of the mammalian genome . Science 2005, 309(5740):1559-1563.

2004

• Sandelin A, Wasserman WW, Lenhard B: ConSite: web-based prediction of regulatory elements using cross-species comparison . Nucleic Acids Res 2004, 32(Web Server issue):W249-252.
• Sandelin A, Wasserman WW: Constrained Binding Site Diversity within Families of Transcription Factors Enhances Pattern Discovery Bioinformatics . J Mol Biol 2004, 338(2):207-215.
• Sandelin A, Bailey P, Bruce S, Engstrom PG, Klos JM, Wasserman WW, Ericson J, Lenhard B: Arrays of ultraconserved non-coding regions span the loci of key developmental genes in vertebrate genomes . BMC Genomics 2004, 5(1):99.
• Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B: JASPAR: an open-access database for eukaryotic transcription factor binding profiles . Nucleic Acids Res 2004, 32(1):D91-94.

2003

• Sandelin A, Hoglund A, Lenhard B, Wasserman WW: Integrated analysis of yeast regulatory sequences for biologically linked clusters of genes . Funct Integr Genomics 2003, 3(3):125-134.
• Lenhard B, Sandelin A, Mendoza L, Engstrom P, Jareborg N, Wasserman WW: Identification of conserved regulatory elements by comparative genome analysis . J Biol 2003, 2(2):13.

2002

• Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S, Nikaido I, Osato N, Saito R, Suzuki H et al: Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs . Nature 2002, 420(6915):563-573.

Reviews and book chapters

• Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA: Mammalian RNA polymerase II core promoters: insights from genome-wide studies . Nat Rev Genet 2007, 8(6):424-436.
• Gustincich S, Sandelin A, Plessy C, Katayama S, Simone R, Lazarevic D, Hayashizaki Y, Carninci P: The complexity of the mammalian transcriptome . J Physiol 2006, 575(Pt 2):321-332.
• Wasserman WW, Sandelin A: Applied Bioinformatics for the Identification of Regulatory Elements . Nat Rev Genet 2004, 5:276-287.
• Sandelin A: In silico prediction of cis-regulatory elements. Stockholm: Karolinska Institutet; 2004.
• Sandelin A: Prediction of Regulatory Elements. In: Bioinformatics Vol II : structure, function and applications. Edited by Keith JM, vol. 2: Humana Press; 2008: 233-244.