Publications

Preprints

  • Chen, Y., Davidson, N. M., Wan, Y. K., Patel, H., Yao, F., Low, H. M., Hendra, C., Watten, L., Sim, A., Sawyer, C., Iakovleva, V., Lee, P. L., Xin, L., Ng, H. E. V., Loo, J. M., Ong, X., Ng, H. Q. A., Wang, J., Koh, W. Q. C., … SG-NEx consortium. (2021). A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. In bioRxiv (p. 2021.04.21.440736). https://doi.org/10.1101/2021.04.21.440736
  • Rautiainen, M., Durai, D. A., Chen, Y., Xin, L., Low, H. M., Göke, J., Marschall, T., Schulz, M. H. (2020). AERON: Transcript quantification and gene-fusion detection using long reads. BioRxiv. (2020)

Publications

2022

  • Hendra, C., Pratanwanich, P. N., Wan, Y. K., Goh, W. S., Thiery, A., & Göke, J. (2022). Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. Nature Methods, 1-9.
  • Davidson, N. M., Chen, Y., Ryland, G. L., Blombery, P., Göke, J., & Oshlack, A. (2022). JAFFAL: Detecting fusion genes with long read transcriptome sequencing. Genome Biology 23.1: 1-20.cover_TIG_2022
  • Wan YK, Hendra C, Pratanwanich PN, Göke J+. Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. (2022) Trends in Genetics.
  • Sundar, Raghav, et al. (2022) “Epigenetic promoter alterations in GI tumour immune-editing and resistance to immune checkpoint inhibition.” Gut.

2021

  • Pratanwanich, P. N.+, Yao, F., Chen, Y., Koh, C. W. Q., Wan, Y. K., Hendra, C., Poon, P., Goh, Y. T., Yap, P. M. L., Chooi, J. Y., Chng, W. J., Ng, S. B., Thiery, A., Goh, W. S. S.+, & Göke, J.+ (2021). Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. Nature Biotechnology. https://doi.org/10.1038/s41587-021-00949-w
  • Wratten L, Wilm A, Göke J. Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers. Nature Methods. 2021 Sep 23:1-8.xPore_socialGithub_v4
  • Huang, K. K., Huang, J., Wu, J. K. L., Lee, M., Tay, S. T., Kumar, V., Ramnarayanan, K., Padmanabhan, N., Xu, C., Tan, A. L. K., Chan, C., Kappei, D., Göke, J., & Tan, P. (2021). Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer. Genome Biology, 22(1), 44.
  • Molias FB, Sim A, Leong KW, An O, Song Y, Ng VH, Lim MW, Ying C, Teo JX, Göke J+, Chen L. Antisense RNAs influence promoter usage of their counterpart sense genes in cancer. Cancer Research. 2021 Jan 1.
  • Schmidt F, Marx A, Baumgarten N, Hebel M, Wegner M, Kaulich M, Leisegang MS, Brandes RP, Göke J, Vreeken J, Schulz MH. Integrative analysis of epigenetics data identifies gene-specific regulatory elements. Nucleic Acids Research. 2021 Oct 11;49(18):10397-418.

2020

  • PCAWG Transcriptome Core Group, et al. (2020). Genomic basis for RNA Nature_PCAWGalterations in cancer. Nature, 578(7793), 129-136.
  • The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium.  “Pan-cancer analysis of whole genomes.” Nature 578.7793 (2020): 82.
  • Mason, M. J.*, Schinke, C.*, Eng, C. L.*, Towfic, F.*, Gruber, F.*, Dervan, A.*,[…],Bassett, D.+, Göke, J.+, Walker, B.+, Thakurta, A.+, Guinney, J+. (2020). Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease. Leukemia, 1-9.
  • Trott, J., Alpagu, Y., Tan, E. K, et al.(2020). Mitchell-Riley syndrome iPSCs exhibit reduced pancreatic endoderm differentiation due to a mutation in RFX6. Development , 147(21). https://doi.org/10.1242/dev.194878

2019

Cell Cover 2019

  • Demircioğlu, D., Cukuroglu, E., Kindermans, M., Nandi, T., Calabrese, C., Fonseca, N. A., Kahles, A., Lehmann, K., Stegle, O., Brazma, A., Brooks, A.N., Rätsch, G., Tan, P., Göke, J.(2019). A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters. Cell, 178(6) 1465-1477. (On the Cell cover September 5th 2019)
  • Zhang, W., Chen, F., Chen, R., Xie, D., Yang, J., Zhao, X., et al.(2019). Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes. Nucleic acids research, 1.
  • Ohka, F., Shinjo, K., Deguchi, S., Matsui, Y., Okuno, Y., Katsushima, K.,et al. (2019). Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-wild-type Diffuse Astrocytic Gliomas. Cancer Research, 1272.
  • Schlößer, H. A., Thelen, M., Lechner, A., Wennhold, K., Garcia-Marquez, M. A., Rothschild, S. I., et al. (2019). B cells in esophago-gastric adenocarcinoma are highly differentiated, organize in tertiary lymphoid structures and produce tumor-specific antibodies. OncoImmunology, 8(1), e1512458.
  • Lechner, A., Schlößer, H. A., Thelen, M., Wennhold, K., Rothschild, S. I., Gilles, R., et al.  (2019). Tumor-associated B cells and humoral immune response in head and neck squamous cell carcinoma. Oncoimmunology, 8(3), 1535293.
  • Szczerbinska, I., Gonzales, K.A.U., Cukuroglu, E., Ramli, M.N.B., Lee, B.P.G., Tan, C.P., Wong, C.K., Rancati, G.I., Liang, H., Göke, J., Ng, H.H., Chan WS, 2019. A Chemically Defined Feeder-free System for the Establishment and Maintenance of the Human Naive Pluripotent State. Stem Cell Reports, 13(4), pp.612-626.

2018

  • 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

2017

  • 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.

2016

  • 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.

2015

  • 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.

2014

  • 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.

2013

Molecular Cell Cover

  • 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. (On the cover of Molecular Cell June 27th 2013)
  • 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)
  • 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.

Preprints (Now published)

  • Hendra C, Pratanwanich PN, Wan YK, Goh WS, Thiery A, Göke J+. Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. bioRxiv. 2021 Jan 1.
  • Davidson, N. M., Chen, Y., Ryland, G. L., Blombery, P., Göke, J., & Oshlack, A. (2021). JAFFAL: Detecting fusion genes with long read transcriptome sequencing. In bioRxiv (p. 2021.04.26.441398). https://doi.org/10.1101/2021.04.26.441398
  • Pratanwanich, P.N., Yao, F., Chen, Y., Koh, C.W., Hendra, C., Poon, P., Goh, Y.T., Yap, P.M., Yuan, C.J., Chng, W.J. and Ng, S., Thiery, A., Goh, S*. Göke, J*. 2020. Detection of differential RNA modifications from direct RNA sequencing of human cell lines. BioRxiv.
  • 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. bioRxiv 176487; doi: https://doi.org/10.1101/176487
  • Mason, M. J.*, Schinke, C.*, Eng, C. L.*, Towfic, F.*, Gruber, F.*, Dervan, A.*, … & Bassett, D.+, Göke, J.+, Walker, B.+, Thakurta, A.+, Guinney J.+, Multiple Myeloma DREAM Consortium. (2019). Multiple Myeloma DREAM Challenge Reveals Epigenetic Regulator PHF19 As Marker of Aggressive Disease. bioRxiv, 737122.
  • 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; doi: https://doi.org/10.1101/183889
  • 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.