Jonathan Göke, Ph.D.
Senior Research Scientist
gokej@gis.a-star.edu.sg
RESEARCH FOCUS
 


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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.

 

EDUCATION

2007-2012 PhD, Max Planck Institute for Molecular Genetics (IMPRS-CBSC), Freie Universität Berlin

2007 B.Sc. thesis, Stanford University

2004-2007 B.Sc. Bioinformatics, Freie Universität Berlin

 

PROFESSIONAL APPOINTMENTS

since 2016 Senior Research Scientist, Genome Institute of Singapore

since 2017 Principal Investigator, National Cancer Center Singapore

2014-2016 GIS Fellow (Junior PI)

2012-2014 Postdoctoral Fellow, Genome Institute of Singapore

 

HONORS AND AWARDS

2012-2014 Postdoctoral Fellowship, German Academic Exchange Service (DAAD)

2007-2012 Ph.D Fellowship, International Max Planck Research School for Computational Biology and Scientific Computing

2007 Exchange scholarship (Stanford University), DAAD

 

EXTERNAL GRANT
 

2017-2020 (NMRC) Engineering of novel and synthetic cellular states for applications in regenerative medicine
2017-2020 (NMRC) Open Fund - Individual Research Grant: ERVs in Cancer
2017-2018 (BMBF) Using EPIgenomes to model non-Coding gene REGulation
2015-2018 (NRF) SynBioLogics: A Platform for Rational Design of Human Cells for Synthesis of Biologics

 

COMPLETE PUBLICATION LIST

Calabrese C, Davidson NR, Demircioğlu D, Fonseca NA, He Y, Kahles A, Lehmann KV, Liu F, Shiraishi Y, Soulette CM, Urban L, Greger L, Li S, Liu D, Perry MD, Xiang Q, Zhang F, Zhang J, Bailey P, Erkek S, Hoadley KA, Hou Y, Huska MR, Kilpinen H, Korbel JO, Marin MG, Markowski J, Nandi T, Pan-Hammarström Q, Pedamallu CS, Siebert R, Stark SG, Su H, Tan P, Waszak SM, Yung C, Zhu S, Awadalla P, Creighton CJ, Meyerson M, Ouellette BFF, Wu K, Yang H, Brazma A*, Brooks AN*, Göke J*, Rätsch G*, Schwarz RF*, Stegle O*, Zhang Z* "Genomic basis for RNA alterations in cancer." Nature 2020 02 ; 578(7793) : 129-136
Abstract
 
ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. "Pan-cancer analysis of whole genomes." Nature 2020 02 ; 578(7793) : 82-93
Abstract
 
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
 
Szczerbinska I, Gonzales KAU, Cukuroglu E, Ramli MNB, Lee BPG, Tan CP, Wong CK, Rancati GI, Liang H, Göke J, Ng HH, Chan YS "A Chemically Defined Feeder-free System for the Establishment and Maintenance of the Human Naive Pluripotent State." Stem Cell Reports 2019 10 08 ; 13(4) : 612-626
Abstract
 
Ohka F, Shinjo K, Deguchi S, Matsui Y, Okuno Y, Katsushima K, Suzuki M, Kato A, Ogiso N, Yamamichi A, Aoki K, Suzuki H, Sato S, Arul Rayan N, Prabhakar S, Göke J, Shimamura T, Maruyama R, Takahashi S, Suzumura A, Kimura H, Wakabayashi T, Zong H, Natsume A, Kondo Y "Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas." Cancer Res 2019 Oct 01 ; 79(19) : 4814-4827
Abstract
 
Zhang W, Chen F, Chen R, Xie D, Yang J, Zhao X, Guo R, Zhang Y, Shen Y, Göke J, Liu L, Lu X "Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes." Nucleic Acids Res 2019 09 19 ; 47(16) : 8485-8501
Abstract
 
Lechner A, Schlößer HA, Thelen M, Wennhold K, Rothschild SI, Gilles R, Quaas A, Siefer OG, Huebbers CU, Cukuroglu E, Göke J, Hillmer A, Gathof B, Meyer MF, Klussmann JP, Shimabukuro-Vornhagen A, Theurich S, Beutner D, von Bergwelt-Baildon M "Tumor-associated B cells and humoral immune response in head and neck squamous cell carcinoma." Oncoimmunology 2019 ; 8(3) : 1535293
Abstract
 
Schlößer HA, Thelen M, Lechner A, Wennhold K, Garcia-Marquez MA, Rothschild SI, Staib E, Zander T, Beutner D, Gathof B, Gilles R, Cukuroglu E, Göke J, Shimabukuro-Vornhagen A, Drebber U, Quaas A, Bruns CJ, Hölscher AH, Von Bergwelt-Baildon MS "B cells in esophago-gastric adenocarcinoma are highly differentiated, organize in tertiary lymphoid structures and produce tumor-specific antibodies." Oncoimmunology 2019 ; 8(1) : e1512458
Abstract
 
Schmidt F, List M, Cukuroglu E, Köhler S, Göke J, Schulz MH "An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets." Bioinformatics 2018 09 01 ; 34(17) : i908-i916
Abstract
 
Do DV, Strauss B, Cukuroglu E, Macaulay I, Wee KB, Hu TX, Igor RLM, Lee C, Harrison A, Butler R, Dietmann S, Jernej U, Marioni J, Smith CWJ, Göke J, Surani MA "SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements." Cell Discov 2018 ; 4 : 33
Abstract
 
Venkatesan, N. et al. (2018) "EZH2 promotes neoplastic transformation through VAV interaction-dependent extranuclear mechanisms." Oncogene (2017):10.1038/onc.2017.309
 
 
Saj A, Chatterjee SS, Zhu B, Cukuroglu E, Gocha T, Zhang X, Göke J, DasGupta R (2017) "Disrupting Interactions Between β-Catenin and Activating TCFs Reconstitutes Ground State Pluripotency in Mouse Embryonic Stem Cells." Stem Cells;35(8):1924-1933. doi: 10.1002/stem.264
Abstract
 
Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N (2017) "Predicting gene expression in massively parallel reporter assays: A comparative study." Hum Mutat Sep ; 38(9) : 1240-1250
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)
 
 
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., ... & 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.
 
 
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.
 
 
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.
 
 
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.
 
 
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., Schulz, MH., Lasserre, J., & Vingron, M. (2012). Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. Bioinformatics, 28(5), 656-663.
 
 
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.