Systems Biology and Genomics (Associate Director Scientific, Co-Chair Research Leadership Team)
Professor Alistair Forrest
Research Overview
Professor Forrest’s research focuses on using cutting-edge genomic techniques, in particular next generation DNA sequencing and computational approaches (bioinformatics) to understand how cells work at a system level. He has extensive experience in next generation sequencing (NGS) and has published using a variety of platforms (Roche, SOLiD, Illumina and Helicos) and protocols (RNA-seq, CAGE, small RNA, ChIP-seq). The move to Perkins has allowed him to translate his basic research on mammalian systems onto clinically relevant questions such as identification of novel cancer biomarkers and drug targets.
Research Projects
- Mammalian transcriptional networks defining cellular states
- Broken transcriptional regulatory networks in cancer
- Pan-cancer and mesothelioma biomarkers
- Non-coding RNA biology
- Tissue specificity of drug targets
Selected Publications
1. Hon C. et al. An atlas of human long non-coding RNAs with accurate 5′ ends. Nature (2017)
2. de Rie D. et al. An integrated expression atlas of miRNAs and their promoters in human and mouse. Nature Biotechnology (2017)
3. Arner E. et al. Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (2015).
4. Forrest ARR et al. A promoter level expression atlas. Nature (2014)
5. Severin J et al. ZENBU: secured scientific collaborations, data integration and omics visualization. Nature Biotechnology (2014)
6. Andersson R et al. An atlas of active enhancers across human cell types and tissues Nature (2014)
7. 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)
8. 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)
9. 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).
10. 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)
