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J. Göke · SciRah

Researcher profile · Semantic Scholar

J. Göke

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J. Göke — researcher profile on SciRah

h-index: 35
Works: 79
Citations: 6,381

Most-cited papers

Midbrain-like organoids from human pluripotent stem cells contain functional dopaminergic and neuromelanin producing neurons
J. Jo, Yixin Xiao, A. Sun, Engin Cukuroglu +19 more
2016Cell Stem Cell780 citations Open access
Semantic Scholar
The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity
Xin-Yi Lu, F. Sachs, L. Ramsay, P. Jacques +3 more
2014Nature Structural &Molecular Biology415 citations
Semantic Scholar
Induction of a human pluripotent state with distinct regulatory circuitry that resembles preimplantation epiblast.
Yun-Shen Chan, J. Göke, Jia-Hui Ng, Xin-Yi Lu +6 more
2013Cell Stem Cell407 citations Open access
Semantic Scholar
Genomic basis for RNA alterations in cancer
C. Calabrese, Natalie R. Davidson, Deniz C. Demircioglu, Nuno A. Fonseca +70 more
2020Nature357 citations Open access
Semantic Scholar
Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells.
J. Göke, Xin-Yi Lu, Yun-Shen Chan, H. Ng +3 more
2015Cell Stem Cell343 citations Open access
Semantic Scholar
X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes
H. Hu, S. Haas, J. Chelly, H. Van Esch +80 more
2015Molecular Psychiatry296 citations Open access
Semantic Scholar
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore
Ploy N. Pratanwanich, Fei Yao, Ying Chen, C. W. Koh +11 more
2021Nature Biotechnology264 citations Open access
Semantic Scholar
Detection of m6A from direct RNA sequencing using a multiple instance learning framework
Christopher Hendra, Ploy N. Pratanwanich, Yuk-Kei Wan, Sho W. S. Goh +2 more
2021bioRxiv254 citations Open access
Semantic Scholar
Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers
L. Wratten, A. Wilm, J. Göke
2021Nature Methods219 citations
Semantic Scholar
A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters.
Deniz C. Demircioglu, Engin Cukuroglu, M. Kindermans, T. Nandi +10 more
2019Cell211 citations Open access
Semantic Scholar
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Francisco J. Pardo-Palacios, Dingjie Wang, Fairlie Reese, M. Diekhans +83 more
2024Nature Methods207 citations Open access
Semantic Scholar
Reduced Oct4 Expression Directs a Robust Pluripotent State with Distinct Signaling Activity and Increased Enhancer Occupancy by Oct4 and Nanog
Violetta Karwacki-Neisius, J. Göke, Rodrigo Osorno, F. Halbritter +10 more
2013Cell Stem Cell204 citations Open access
Semantic Scholar
Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides
P. McMurdie, S. Behrens, Jochen A. Müller, J. Göke +7 more
2009PLoS Genetics179 citations Open access
Semantic Scholar
Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu
Ying Chen, Andre D. Sim, Yuk-Kei Wan, Keith Yeo +4 more
2022bioRxiv172 citations Open access
Semantic Scholar
Klf2 is an essential factor that sustains ground state pluripotency.
Jia-Chi Yeo, Jianming Jiang, Zi-Ying Tan, Guo-Rong Yim +11 more
2014Cell Stem Cell130 citations Open access
Semantic Scholar
Tumor-associated B cells and humoral immune response in head and neck squamous cell carcinoma
A. Lechner, H. Schlösser, M. Thelen, K. Wennhold +15 more
2019Oncoimmunology128 citations Open access
Semantic Scholar
A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines
Ying Chen, N. Davidson, Yuk-Kei Wan, H. Patel +41 more
2021bioRxiv121 citations Open access
Semantic Scholar
SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells
Xin-Yi Lu, J. Göke, F. Sachs, P. Jacques +5 more
2013Nature Cell Biology109 citations Open access
Semantic Scholar
Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data.
Yuk-Kei Wan, Christopher Hendra, Ploy N. Pratanwanich, J. Göke
2021Trends in Genetics104 citations Open access
Semantic Scholar
Genome-wide kinase-chromatin interactions reveal the regulatory network of ERK signaling in human embryonic stem cells.
J. Göke, Yun-Shen Chan, Jun-Li Yan, M. Vingron +1 more
2013Molecules and Cells103 citations Open access
Semantic Scholar
Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes
Wei-Yu Zhang, Fu-Quan Chen, Rui-Qing Chen, Dan Xie +8 more
2019Nucleic Acids Research101 citations Open access
Semantic Scholar
CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome
J. Göke, H. Ng
2016EMBO Reports87 citations Open access
Semantic Scholar
Molecular Features Underlying Neurodegeneration Identified through In Vitro Modeling of Genetically Diverse Parkinson's Disease Patients.
Lin Lin, J. Göke, Engin Cukuroglu, Mark R Dranias +2 more
2016Cell Reports84 citations Open access
Semantic Scholar
JAFFAL: detecting fusion genes with long-read transcriptome sequencing
N. Davidson, Ying Chen, T. Sadras, G. Ryland +4 more
2021Genome Biology81 citations Open access
Semantic Scholar
Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer
K. Huang, Jia-Wen Huang, J. Wu, Ming Lee +10 more
2021Genome Biology80 citations Open access
Semantic Scholar
A PRC2‐Dependent Repressive Role of PRDM14 in Human Embryonic Stem Cells and Induced Pluripotent Stem Cell Reprogramming
Yun-Shen Chan, J. Göke, Xin-Kai Lu, N. Venkatesan +3 more
2013Stem Cells70 citations
Semantic Scholar
B cells in esophago-gastric adenocarcinoma are highly differentiated, organize in tertiary lymphoid structures and produce tumor-specific antibodies
H. Schlösser, M. Thelen, A. Lechner, K. Wennhold +15 more
2018Oncoimmunology66 citations Open access
Semantic Scholar
Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development
J. Göke, Marc Jung, S. Behrens, L. Chavez +5 more
2011PLoS Comput. Biol.66 citations Open access
Semantic Scholar
An atlas of transcription initiation reveals regulatory principles of gene and transposable element expression in early mammalian development.
Marlies E. Oomen, Diego Rodriguez-Terrones, M. Kurome, V. Zakhartchenko +11 more
2025Cell59 citations Open access
Semantic Scholar
SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements
Dang Vinh Do, Bernhard Strauss, Engin Cukuroglu, I. Macaulay +12 more
2018Cell Discovery59 citations Open access
Semantic Scholar
A systematic benchmark of Nanopore long-read RNA sequencing for transcript-level analysis in human cell lines
Ying Chen, Nadia M. Davidson, Yuk-Kei Wan, Fei Yao +45 more
2025Nature Methods52 citations Open access
Semantic Scholar
Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease
M. Mason, C. Schinke, Christine L. P. Eng, F. Towfic +38 more
2019bioRxiv52 citations Open access
Semantic Scholar
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts
J. Göke, Marcel H. Schulz, Julia A. Lasserre, M. Vingron
2012Bioinform.50 citations Open access
Semantic Scholar
PREDICTING GENE EXPRESSION IN MASSIVELY PARALLEL REPORTER ASSAYS: A COMPARATIVE STUDY
Anat Kreimer, Haoyang Zeng, M. Edwards, Yuchun Guo +19 more
2017Human Mutation46 citations Open access
Semantic Scholar
Epigenetic promoter alterations in GI tumour immune-editing and resistance to immune checkpoint inhibition
R. Sundar, K. Huang, Vikrant Kumar, Kalpana Ramnarayanan +34 more
2021Gut35 citations Open access
Semantic Scholar
Simulation of different applicator positions for treatment of a presacral tumour
J. Gellermann, J. Göke, Robert Figiel, Mirko Weihrauch +4 more
2007International Journal of Hyperthermia34 citations Open access
Semantic Scholar
WNT signalling control by KDM5C during development affects cognition
Violetta Karwacki-Neisius, Ahram Jang, Engin Cukuroglu, Albert Tai +16 more
2024Nature31 citations Open access
Semantic Scholar
A Chemically Defined Feeder-free System for the Establishment and Maintenance of the Human Naive Pluripotent State
Iwona Szczerbinska, Kevin Andrew Uy Gonzales, Engin Cukuroglu, Muhammad Nadzim Bin Ramli +8 more
2019Stem Cell Reports31 citations Open access
Semantic Scholar
Flexiplex: a versatile demultiplexer and search tool for omics data
Oliver Y. Cheng, Min-Hao Ling, Changqing Wang, Shu-Yi Wu +4 more
2024bioRxiv29 citations Open access
Semantic Scholar
Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells
Yoko Itahana, Jinqiu Zhang, J. Göke, L. Vardy +7 more
2016Scientific Reports28 citations Open access
Semantic Scholar
Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types
C. Calabrese, Natalie R. Davidson, Nuno A. Fonseca, Y. He +45 more
201727 citations Open access
Semantic Scholar
EZH2 promotes neoplastic transformation through VAV interaction-dependent extranuclear mechanisms
N. Venkatesan, J. Wong, K. Tan, H. H. Chung +9 more
2018Oncogene24 citations Open access
Semantic Scholar
Reduced Oct 4 expression directs a robust pluripotent state with distinct signaling activity and increased enhancer occupancy by Oct 4 and Nanog
Violetta Karwacki-Neisius, J. Göke, Rodrigo Osorno, F. Halbritter +10 more
201324 citations
Semantic Scholar
Integrative analysis of epigenetics data identifies gene-specific regulatory elements
Florian Schmidt, Alexander Marx, N. Baumgarten, Marie Hebel +7 more
2019bioRxiv23 citations Open access
Semantic Scholar
The RMaP challenge of predicting RNA modifications by nanopore sequencing
Jannes Spangenberg, Stefan Mündnich, Anne Busch, S. Pastore +20 more
2025Communications Chemistry18 citations Open access
Semantic Scholar
Detection of differential RNA modifications from direct RNA sequencing of human cell lines
Ploy N. Pratanwanich, Fei Yao, Ying Chen, C. W. Koh +10 more
2020bioRxiv17 citations Open access
Semantic Scholar
A Bayesian approach to copy-number-polymorphism analysis in nuclear pedigrees.
K. Kosta, I. Sabroe, J. Göke, R. Nibbs +3 more
2007American Journal of Human Genetics17 citations Open access
Semantic Scholar
Pan-cancer study of heterogeneous RNA aberrations
Nuno A. Fonseca, A. Kahles, K. Lehmann, C. Calabrese +65 more
2017bioRxiv15 citations Open access
Semantic Scholar
Antisense RNAs Influence Promoter Usage of Their Counterpart Sense Genes in Cancer
Fernando Bellido Molias, Andre D. Sim, K. Leong, Omer An +7 more
2021Cancer Research11 citations Open access
Semantic Scholar
AERON: Transcript quantification and gene-fusion detection using long reads
Mikko Rautiainen, Dilip A. Durai, Ying Chen, Lixia Xin +4 more
2020bioRxiv11 citations Open access
Semantic Scholar

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