• Demircioğlu, Deniz, Kindermans, M., Nandi, T., Cukuroglu, E., Calabrese, C., Fonseca, N., Kahles, A., Lehmann, K., Stegle, O., PCAWG-3, PCAWG-Network, Brazma, A., Brooks, A., Rätsch, G., Tan, P., Göke, J., (2018). A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters. 176487; doi:
  • PCAWG Transcriptome Core Group (Demircioğlu, D), […], Brazma A, Brooks A, Göke, J, Ratsch G, Schwarz R, Stegle O, Zhang Z. Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types. bioRxiv (2018): 183889; 
  • Schmidt, Florian, Marx A, Hebel M, Wegner M, Baumgarten N, Kaulich M,Göke J, Vreeken J, and Schulz M. “Integrative analysis of epigenetics data identifies gene-specific regulatory elements.” bioRxiv (2019): 585125.



  • Schmidt, F., List, M., Cukuroglu, E., Köhler, S., Göke, J., & Schulz, M. H. (2018). An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets. Bioinformatics, 34(17), i908-i916.
  • Do, D.V., Strauss, B., Cukuroglu, E., Macaulay, I., Wee, K.B., Hu, T.X., Igor, R.D.L.M., Lee, C., Harrison, A., Butler, R., Dietmann, S., Jernej U., Marioni J., Smith, C. W. J., Göke, J.,  & Surani, M.A., 2018. SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements. Cell Discovery, 4(1), p.33.
  • Venkatesan, N. et al. (2017) “EZH2 promotes neoplastic transformation through VAV interaction-dependent extranuclear mechanisms.” Oncogene. 10.1038/onc.2017.309


  • Saj, A., Chatterjee, S.S., Zhu, B., Cukuroglu, E., Gocha, T., Zhang, X., Göke, J. and DasGupta, R., (2017). Disrupting Interactions Between β‐Catenin and Activating TCFs Reconstitutes Ground State pluripotency In Mouse Embryonic Stem Cells. Stem Cells.
  • Kreimer, A., Zeng, H., Edwards, M. D., Guo, Y., Tian, K., Shin, S. et al. (2017). Predicting gene expression in massively parallel reporter assays: A comparative study. Human Mutation.


  • Göke, Jonathan, and Huck Hui Ng. (2016) “CTRL+ INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome.” EMBO Reports (2016): e201642743.
  • 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
  • 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.
  • Itahana, Y., Zhang, J., Göke, J., Vardy, L. A., Han, R., Iwamoto, K.,Cukuroglu, E., Robson, P., Pouladi, M.A., Colman, A. and Itahana, K. (2016). Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells. Scientific Reports , 6.


  • 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)
  • Hu, H., Haas, S. A., Chelly, J., Van Esch, H., Raynaud, M., de Brouwer, A. P. M., … & Nelson, J. (2015). X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes. Molecular Psychiatry.


  • 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.
  • Yeo, JC, Jiang, J, Tan, ZY, Yim, GR, Ng, JH, Göke, J, … & Ng, HH (2014). Klf2 Is an Essential Factor that Sustains Ground State Pluripotency. Cell Stem Cell, 14(6), 864-872.


  • 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)
  • 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)
  • 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.
  • Karwacki-Neisius, V., Göke, J., Osorno, R., Halbritter, F., Ng, JH., Weiße, AY., … & Chambers, I. (2013). Reduced Oct4 Expression Directs a Robust Pluripotent State with Distinct Signaling Activity and Increased Enhancer Occupancy by Oct4 and Nanog. Cell Stem Cell, 12(5), 531-545.

2012 and older

  • 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.
  • Chan, YS., Göke, J., Lu, X., Venkatesan, N., Feng, B., Su, IH., & Ng, HH. (2012). A PRC2‐Dependent Repressive Role of PRDM14 in Human Embryonic Stem Cells and Induced Pluripotent Stem Cell Reprogramming. Stem Cells, 31(4), 682-692.
  • Göke, J., Jung, M., Behrens, S., Chavez, L., O’Keeffe, S., Timmermann, B., … & Vingron, M. (2011). Combinatorial binding in human and mouse embryonic stem cells identifies conserved enhancers active in early embryonic development. PLoS Computational Biology, 7(12), e1002304.
  • McMurdie, P. J., Behrens, S. F., Müller, J. A., Göke, J., Ritalahti, K. M., Wagner, R., … & Spormann, A. M. (2009). Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PLoS genetics, 5(11), e1000714.
  • Gellermann, J., Göke, J., Figiel, R., Weihrauch, M., Cho, C. H., Budach, V., … & Wust, P. (2007). Simulation of different applicator positions for treatment of a presacral tumour. International journal of hyperthermia, 23(1), 37-47.
  • Kosta, K., Sabroe, I., Göke, J., Nibbs, R. J., Tsanakas, J., Whyte, M. K., & Teare, M. D. (2007). A Bayesian Approach to Copy-Number–Polymorphism Analysis in Nuclear Pedigrees. The American Journal of Human Genetics, 81(4), 808-812.