Systems biology and genomics


Selected publications

  1. Arner E. et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (2015)
  2. Forrest ARR et al. A promoter level expression atlas. Nature (2014)
  3. Severin J et al. ZENBU: secured scientific collaborations, data integration and omics visualization. Nature Biotechnology  (2014)
  4. Andersson R et al. An atlas of active enhancers across human cell types and tissues Nature (2014)
  5. Fort A, Hashimoto K et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposon in pluripotency maintenance Nature Genetics (2014)
  6. Carrieri C, Cimatti L, Biagioli M, Beugnet A, Zucchelli S, Fedele S, Pesce E, Ferrer I, Collavin L, Santoro C, Forrest ARR, Carninci P, Biffo S, Stupka E, Gustincich S: Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature (2012)
  7. Ravasi T, Cannistraci C, Katayama S, Bajic V, Tan K, Akalin A, Schmeier S, Kamburov A, Kanamori M, Bertin N, Carninci P, Daub C, Forrest A, Gough J, Grimmond S, Han J, Hashimoto T, Hide W, Hofmann O, Kaur M, Kawaji H, Kubosaki A, Lassmann T, van Nimwegen E, MacPherson C, Ogawa C, Radovanovic A, Schwartz A, Teasdale R, Tegnér J, Lenhard B, Teichmann S, Hume D, Ideker T, Arakawa T, Ninomiya N, Murakami K, Tagami M, Fukuda S, Imamura K, Kai C, Ishihara R, Kitazume Y, Kawai J, Suzuki H, Hayashizaki Y. An atlas of combinatorial transcriptional regulation in mouse and man. Cell Mar 5;140(5):744-52 (2010).
  8. Suzuki H, Forrest ARR, van Nimwegen E, et al.: The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics (2009)
  9. Faulkner G, Kimura Y, Daub C, Wani S, Plessy C, Irvine K, Schroder K, Cloonan N, Steptoe A, Lassmann T, Waki K, Hornig N, Arakawa T, Takahashi H, Kawai J, Forrest ARR, Suzuki H, Hayashizaki Y, Hume D, Orlando V, Grimmond S, Carninci P: The regulated retrotransposon transcriptome of mammalian cells. Nature Genetics (2009)
  10. Cloonan N, Forrest ARR, Kolle G, Gardiner BA, Faulkner GJ, Brown MK, Taylor DF, Steptoe AL, Wani S, Bethel G, Robertson AJ, Perkins AC, Bruce SJ, Lee CC, Ranade SS, Peckham HE, Manning JM, McKernan KJ, Grimmond SM. Stem cell transcriptome profiling via massive-scale mRNA sequencing Nature Methods.1223 (2008)

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