Publications

Publication Highlights

2025

  • Chen Y, Davidson N, Wan YK, Yao F, Su Y, Gamaarachchi H, Sim A, Patel H, Low HM, Hendra C, Wratten L, […], Lezhava A, Pratanwanich PN, Love MI, Goh WSS, Ng SB, Oshlack A, SG-NEx consortium, Göke J+,. A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. Nature Methods (2025) 22: 801–812
    • The Singapore Nanopore Expression Project (SG-NEx) describes one of the largest long read RNA-Seq data sets, hosten on the AWS Open Data Registry
  • Oomen E, Rodriguez-Terrones, Rodriguez-Terrones D, Simmet K, […], Göke J, Wolf E , Kaessmann H and Torres-Padilla ME. Mapping transcription initiation across mammalian species using Smart-seq+5’ reveals regulatory principles of embryonic genome activation. Cell (2025)
  • Sim AD, Ling MH, Chen Y, Lu H, See YX, Perrin A, Leng Agnes OB, Cao EY, Chia B, Liu J, Wüstefeld T., Shin J+,  Göke J+, Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump, bioRxiv. 2025:2024-12
    • The manuscripts describes the single cell and spatial long read RNA-Seq module for Bambu
  • Sarashetti P, Lipovac J, Jia Q, Wang L, Li Z, Vrček L, Chen Y, Yao F, Sia YY, […], Chambers JC, Hwang WYK, Tan P, Göke J, Sikic M, Liu J, A complete telomere-to-telomere diploid reference genome for Indian population. bioRxiv (2025), p. 2025.07.12.664550, , doi:10.1101/2025.07.12.664550.

2024

  • Karwacki-Neisius V, Jang A, Cukuroglu E, […], Göke J, He X, Lehtinen M, Pomeroy S, Shi Y. WNT signalling control by KDM5C during development affects cognition. Nature (2024): 1-10.
  • Pardo-Palacios, Francisco J., et al. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature Methods (2024): 1-15.
  • Davidson NM, Amin N, Min Hao L, Wang C, Cheng O, Göke J, Ritchie ME and Wu S,. Flexiplex: A versatile demultiplexer and search tool for omics data. Bioinformatics 40.3 (2024): btae102.

2023

  • Chen Y*, Sim AD*, Wan YK, Yeo K, Lee JJX, Ling MH, Love MI and Göke J+,. Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu. Nature Methods (2023)

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.
  • Wan YK, Hendra C, Pratanwanich PN, Göke J+. Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. (2022) Trends in Genetics.

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.

2020

  • PCAWG Transcriptome Core Group, et al. (2020). Genomic basis for RNA alterations 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.

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.

 

 

Complete Publication List

2025

  • Oomen E, Rodriguez-Terrones, Rodriguez-Terrones D, Simmet K, […], Göke J, Wolf E , Kaessmann H and Torres-Padilla ME. Mapping transcription initiation across mammalian species using Smart-seq+5’ reveals regulatory principles of embryonic genome activation. Cell (2025)
  • Chen Y, Davidson N, Wan YK, Yao F, Su Y, Gamaarachchi H, Sim A, Patel H, Low HM, Hendra C, Wratten L, […], Lezhava A, Pratanwanich PN, Love MI, Goh WSS, Ng SB, Oshlack A, SG-NEx consortium, Göke J+,. A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. Nature Methods (2025).
  • Sim AD, Ling MH, Chen Y, Lu H, See YX, Perrin A, Leng Agnes OB, Cao EY, Chia B, Liu J, Wüstefeld T., Shin J+,  Göke J+, Isoform-level discovery, quantification and fusion analysis from single-cell and spatial long-read RNA-seq data with Bambu-Clump, bioRxiv. 2025:2024-12
  • Spangenberg, J, et al. “The RMaP challenge of predicting RNA modifications by nanopore sequencing.” Communications Chemistry 8.1 (2025): 115.
  • Samarakoon, H., Kei Wan, Y., Parameswaran, S., Göke, J., Gamaarachchi, H., & Deveson, I. W . “Leveraging basecaller’s move table to generate a lightweight k-mer model for nanopore sequencing analysis.” Bioinformatics 41.4 (2025): btaf111.

2024

  • Karwacki-Neisius V, Jang A, Cukuroglu E, […], Göke J, He X, Lehtinen M, Pomeroy S, Shi Y. WNT signalling control by KDM5C during development affects cognition. Nature (2024): 1-10.
  • Pardo-Palacios, Francisco J., et al. Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. Nature Methods (2024): 1-15.
  • Davidson NM, Amin N, Min Hao L, Wang C, Cheng O, Göke J, Ritchie ME and Wu S,. Flexiplex: A versatile demultiplexer and search tool for omics data. Bioinformatics 40.3 (2024): btae102.
  • The Critical Assessment of Genome Interpretation Consortium. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biology 25, 53 (2024). https://doi.org/10.1186/s13059-023-03113-6
  • Yip, Chi Wai, et al. “CFC-seq: identification of full-length capped RNAs unveil enhancer-derived transcription.” bioRxiv (2024): 2024-10.
  • Alagna, Nicolò, et al. “Predicting RNA modifications by nanopore sequencing: The RMaP challenge.”Research Square Pre-Print; (2024).
  • Samarakoon, H., Kei Wan, Y., Parameswaran, S., Göke, J., Gamaarachchi, H., & Deveson, I. W. “Leveraging Basecaller’s Move Table to Generate a Lightweight k-mer Model.” bioRxiv (2024): 2024-06.

2023

  • Chen Y*, Sim AD*, Wan YK, Yeo K, Lee JJX, Ling MH, Love MI and Göke J+,. Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu. Nature Methods (2023)

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.
  • 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., […] 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 alterations 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
  • 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.

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.
  • 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.
  • 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)

  • Chen Y*, Sim AD*, Wan YK, Yeo K, Lee JJX, Ling MH, Love MI and Göke J+,. Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu. bioRxiv. 2022
  • Chen Y, Davidson N, Wan YK, Yao F, Su Y, Gamaarachchi H, Sim A, Patel H, Low HM, Hendra C, Wratten L, Hakkaart C, Sawyer C, Iakovleva V, Lee PL,  Xin L, Ng H, Loo JM, Ong X, Ng HQA, Wang J, Koh WQC, Poon SKP, Stanojevic D, Tran HD, Lim KHE, Toh SY, Ewels PA, Ng HH, Iyer NG, Thiery A,  Chng WJ, Chen L, DasGupta R, Sikic M, Chan YS, Tan P, Wan Y, Tam WL, Yu Q, Khor CC, Wüstefeld T, Lezhava A, Pratanwanich PN, Love MI, Goh WSS, Ng SB, Oshlack A, SG-NEx consortium, Göke J+, SG-NEx consortium. A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. bioRxiv (2021)
  • 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.