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Even though all cells of the human body essentially share the same genetic information, the cell types that form the organs and tissues appear very diverse and have distinct properties. The central question of our research is what determines the identity of mammalian cells during development and differentiation; and how cellular identity is impaired in disease. We investigate transcript diversity, alternative splicing, gene regulation, and epigenetics to identify key elements and mechanisms involved in maintenance and conversion of cellular identities. Using machine learning techniques, we study the role of DNA sequence in regulation of cell-type specific expression signatures. We are closely collaborating with wet labs to translate computational models to cellular phenotypes.
PhD projects available starting in August 2018. Highly motivated students with a background in bioinformatics, statistics or computer science are welcome to contact Jonathan Göke.
In the Media
PBS Nova Next (10/2016): The Viruses That Made Us Human
Inside Science (2/2015): Ancient Viral Invaders May Affect Modern Human Embryo Development
National Geographic (4/2014): Ancient Virus DNA Gives Stem Cells the Power to Transform
A*STAR Research (1/2014): Regulating stem cell behavior
Channel News Asia (12/2013): Singapore scientists make breakthrough in regenerative medicine
Today (12/2013): A*STAR scientists find better way to engineer human stem cells
Asian Scientist (12/2013): Researchers Convert Human Embryonic Stem Cells Into Blastocyst-Like Cells
- Demircioğlu D, Cukuroglu E, Kindermans M, Nandi T, Calabrese C, Fonseca NA, Kahles A, Lehmann KV, Stegle O, Brazma A, Brooks AN, Rätsch G, Tan P, Göke J "A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters." Cell 2019 Sep 05 ; 178(6) : 1465-1477.e17 Abstract
- Göke, Jonathan+, and Huck Hui Ng. (2016) "CTRL+ INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome." EMBO Reports (2016): e201642743.(+ corresponding author) Abstract
- Jo, J., Xiao, Y., Sun, A. X., Cukuroglu, E., Tran, H. D., Göke, J., ... & Ng HH. (2016). Midbrain-like Organoids from Human Pluripotent Stem Cells Contain Functional Dopaminergic and Neuromelanin-Producing Neurons. Cell Stem Cell.19(2):248-57 Abstract
- Lin, L., Göke, J., Cukuroglu, E., Dranias, M. R., VanDongen, A. M., & Stanton, L. W. (2016). Molecular Features Underlying Neurodegeneration Identified through In Vitro Modeling of Genetically Diverse Parkinson's Disease Patients. Cell Reports, 15(11), 2411-2426. Abstract
- Göke, J+., Lu, X., Chan, Y. S., Ng, H. H., Ly, L. H., Sachs, F., & Szczerbinska, I. (2015). Dynamic Transcription of Distinct Classes of Endogenous Retroviral Elements Marks Specific Populations of Early Human Embryonic Cells. Cell Stem Cell, 16(2), 135-141. (+corresponding author) Abstract
- Lu, X., Sachs, F., Ramsay, L., Jacques, P. É., Göke, J., Bourque, G., & Ng, H. H. (2014). The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nature Structural & Molecular Biology. 21 (4), 423-425. Abstract
- Chan, YS.*, Göke, J.*, Ng JH.*, Lu X., Gonzales K., Tan CP., ... & Ng HH. (2013) Induction of a Human Pluripotent State with Distinct Regulatory Circuitry that Resembles Preimplantation Epiblast. Cell Stem Cell, 13(6), 663-675. (*equal contribution) Abstract
- Lu X*, Göke J*, Sachs F, Jacques PÉ, Liang H, Feng B, Bourque G, Bubulya PA, Ng HH (2013) SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells. Nat Cell Biol 15(10) : 1141-52 (*equal contribution) Abstract
- Göke, J., Chan, YS., Yan, J., Vingron, M., & Ng, HH. (2013). Genome-wide Kinase-Chromatin Interactions Reveal the Regulatory Network of ERK Signaling in Human Embryonic Stem Cells. Molecular Cell, 50(6), 844-855. Abstract
- Göke, J., Schulz, MH., Lasserre, J., & Vingron, M. (2012). Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics, 28(5), 656-663. Abstract