Jonathan Göke

发表

The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

G. Bourque, H. Ng, P. Jacques, 2014, Nature Structural &Molecular Biology.

Tumor-associated B cells and humoral immune response in head and neck squamous cell carcinoma

A. Quaas, A. Hillmer, E. Cukuroglu, 2019, Oncoimmunology.

Context-aware transcript quantification from long-read RNA-seq data with Bambu

M. Love, J. Göke, Ying Chen, 2022, bioRxiv.

Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers

A. Wilm, J. Göke, L. Wratten, 2021, Nature Methods.

Induction of a human pluripotent state with distinct regulatory circuitry that resembles preimplantation epiblast.

H. Ng, J. Göke, Yun-Shen Chan, 2013, Cell stem cell.

X-exome sequencing of 405 unresolved families identifies seven novel intellectual disability genes

K. Friend, M. Shaw, E. Haan, 2015, Molecular Psychiatry.

Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells.

H. Ng, Lam-Ha Ly, Yun-Shen Chan, 2015, Cell stem cell.

B cells in esophago-gastric adenocarcinoma are highly differentiated, organize in tertiary lymphoid structures and produce tumor-specific antibodies

T. Zander, A. Quaas, A. Hölscher, 2018, Oncoimmunology.

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

Gunnar Rätsch, Nuno A. Fonseca, André Kahles, 2019, Cell.

A pan cancer analysis of promoter activity highlights the regulatory role of alternative transcription start sites and their association with noncoding mutations

Nuno A. Fonseca, Angela N. Brooks, G. Rätsch, 2017, bioRxiv.

A Pan-Cancer Transcriptome Analysis Reveals Pervasive Regulation through Tumor-Associated Alternative Promoters

Nuno A. Fonseca, G. Rätsch, A. Brazma, 2018 .

A pan cancer analysis of promoter activity highlights the regulatory role of alternative transcription start sites and their association with noncoding mutations

Angela N. Brooks, G. Rätsch, A. Brazma, 2017 .

Patterns of somatic structural variation in human cancer genomes

Nuno A. Fonseca, Gary D Bader, Benjamin J. Raphael, 2020, Nature.

Epigenetic promoter alterations in GI tumour immune-editing and resistance to immune checkpoint inhibition

Jia Qi Lim, A. Jeyasekharan, L. Molinero, 2021, Gut.

High-coverage whole-genome analysis of 1220 cancers reveals hundreds of genes deregulated by rearrangement-mediated cis-regulatory alterations

Nuno A. Fonseca, Angela N. Brooks, David T. W. Jones, 2020, Nature Communications.

Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes

J. Göke, Xinyi Lu, Lin Liu, 2019, Nucleic acids research.

Detection of m6A from direct RNA sequencing using a multiple instance learning framework

Ploy N. Pratanwanich, J. Göke, W. Goh, 2021, bioRxiv.

Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

Ploy N. Pratanwanich, J. Göke, W. Chng, 2021, Nature Biotechnology.

Genomic basis for RNA alterations in cancer

Mary Goldman, Nuno A. Fonseca, Brian Craft, 2020, Nature.

CTRL+INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome

Jonathan Göke, H. Ng, J. Göke, 2016, EMBO reports.

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts

Marcel H. Schulz, Julia A. Lasserre, M. Vingron, 2012, Bioinform..

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

Paul J. McMurdie, A. Lapidus, A. Spormann, 2009, PLoS genetics.

Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells

P. Robson, Jinqiu Zhang, E. Cukuroglu, 2016, Scientific Reports.

WNT signalling control by KDM5C during development affects cognition

Shannan J. Ho Sui, K. Õunap, Jiekai Chen, 2024, Nature.

Genomic basis for RNA alterations revealed by whole-genome analyses of 27 cancer types

Gunnar Rätsch, Junjun Zhang, Nuno A. Fonseca, 2017 .

Pan-cancer study of heterogeneous RNA aberrations

Nuno A. Fonseca, Angela N. Brooks, Stefan G. Stark, 2017, bioRxiv.

Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data.

Ploy N. Pratanwanich, J. Göke, Christopher Hendra, 2021, Trends in genetics : TIG.

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines

Philip A. Ewels, Ploy N. Pratanwanich, H. Ng, 2021, bioRxiv.

Detection of differential RNA modifications from direct RNA sequencing of human cell lines

Ploy N. Pratanwanich, J. Göke, W. Chng, 2020, bioRxiv.

Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-wild-type Diffuse Astrocytic Gliomas.

T. Shimamura, Hiromichi Suzuki, S. Prabhakar, 2019, Cancer research.

A Chemically Defined Feeder-free System for the Establishment and Maintenance of the Human Naive Pluripotent State

H. Ng, E. Cukuroglu, J. Göke, 2019, Stem cell reports.

SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements

J. Marioni, I. Macaulay, M. Surani, 2018, Cell Discovery.

Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development

Martin Vingron, Hans Lehrach, Sean O'Keeffe, 2011, PLoS Comput. Biol..

Klf2 is an essential factor that sustains ground state pluripotency.

Jianming Jiang, H. Ng, P. Kraus, 2014, Cell stem cell.