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Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore.
Published in:
Nature Biotechnology, 2021, v. 39, n. 11, p. 1394, doi. 10.1038/s41587-021-00949-w
By:
- Pratanwanich, Ploy N.;
- Yao, Fei;
- Chen, Ying;
- Koh, Casslynn W. Q.;
- Wan, Yuk Kei;
- Hendra, Christopher;
- Poon, Polly;
- Goh, Yeek Teck;
- Yap, Phoebe M. L.;
- Chooi, Jing Yuan;
- Chng, Wee Joo;
- Ng, Sarah B.;
- Thiery, Alexandre;
- Goh, W. S. Sho;
- Göke, Jonathan
Publication type:
Article
A PRC2-Dependent Repressive Role of PRDM14 in Human Embryonic Stem Cells and Induced Pluripotent Stem Cell Reprogramming.
Published in:
Stem Cells, 2013, v. 31, n. 4, p. 682, doi. 10.1002/stem.1307
By:
- YUN-SHEN CHAN;
- GöKE, JONATHAN;
- XINYI LU;
- VENKATESAN, NANDINI;
- BO FENG;
- I-HSIN SU;
- HUCK-HUI NG
Publication type:
Article
The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity.
Published in:
Nature Structural & Molecular Biology, 2014, v. 21, n. 4, p. 423, doi. 10.1038/nsmb.2799
By:
- Lu, Xinyi;
- Sachs, Friedrich;
- Ramsay, LeeAnn;
- Jacques, Pierre-Étienne;
- Göke, Jonathan;
- Bourque, Guillaume;
- Ng, Huck-Hui
Publication type:
Article
Flexiplex: a versatile demultiplexer and search tool for omics data.
Published in:
Bioinformatics, 2024, v. 40, n. 3, p. 1, doi. 10.1093/bioinformatics/btae102
By:
- Cheng, Oliver;
- Ling, Min Hao;
- Wang, Changqing;
- Wu, Shuyi;
- Ritchie, Matthew E;
- Göke, Jonathan;
- Amin, Noorul;
- Davidson, Nadia M
Publication type:
Article
Histone modifications and p53 binding poise the p21 promoter for activation in human embryonic stem cells.
Published in:
Scientific Reports, 2016, p. 28112, doi. 10.1038/srep28112
By:
- Itahana, Yoko;
- Zhang, Jinqiu;
- Göke, Jonathan;
- Vardy, Leah A.;
- Han, Rachel;
- Iwamoto, Kozue;
- Cukuroglu, Engin;
- Robson, Paul;
- Pouladi, Mahmoud A.;
- Colman, Alan;
- Itahana, Koji
Publication type:
Article
JAFFAL: detecting fusion genes with long-read transcriptome sequencing.
Published in:
Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-021-02588-5
By:
- Davidson, Nadia M.;
- Chen, Ying;
- Sadras, Teresa;
- Ryland, Georgina L.;
- Blombery, Piers;
- Ekert, Paul G.;
- Göke, Jonathan;
- Oshlack, Alicia
Publication type:
Article
Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02261-x
By:
- Kie Kyon Huang;
- Jiawen Huang;
- Jeanie Kar Leng Wu;
- Minghui Lee;
- Su Ting Tay;
- Kumar, Vikrant;
- Ramnarayanan, Kalpana;
- Padmanabhan, Nisha;
- Chang Xu;
- Angie Lay Keng Tan;
- Charlene Chan;
- Kappei, Dennis;
- Göke, Jonathan;
- Tan, Patrick
Publication type:
Article
Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer.
Published in:
Genome Biology, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s13059-021-02261-x
By:
- Huang, Kie Kyon;
- Huang, Jiawen;
- Wu, Jeanie Kar Leng;
- Lee, Minghui;
- Tay, Su Ting;
- Kumar, Vikrant;
- Ramnarayanan, Kalpana;
- Padmanabhan, Nisha;
- Xu, Chang;
- Tan, Angie Lay Keng;
- Chan, Charlene;
- Kappei, Dennis;
- Göke, Jonathan;
- Tan, Patrick
Publication type:
Article
CTRL+ INSERT: retrotransposons and their contribution to regulation and innovation of the transcriptome.
Published in:
EMBO Reports, 2016, v. 17, n. 8, p. 1131, doi. 10.15252/embr.201642743
By:
- Göke, Jonathan;
- Ng, Huck Hui
Publication type:
Article
Disrupting Interactions Between β-Catenin and Activating TCFs Reconstitutes Ground State Pluripotency in Mouse Embryonic Stem Cells.
Published in:
Stem Cells, 2017, v. 35, n. 8, p. 1924, doi. 10.1002/stem.2647
By:
- Saj, Abil;
- Chatterjee, Sujash S.;
- Zhu, Bowen;
- Cukuroglu, Engin;
- Gocha, Tenzin;
- Zhang, Xiaoqian;
- Göke, Jonathan;
- DasGupta, Ramanuj
Publication type:
Article
SON connects the splicing-regulatory network with pluripotency in human embryonic stem cells.
Published in:
Nature Cell Biology, 2013, v. 15, n. 10, p. 1141, doi. 10.1038/ncb2839
By:
- Lu, Xinyi;
- Göke, Jonathan;
- Sachs, Friedrich;
- Jacques, Pierre-Étienne;
- Liang, Hongqing;
- Feng, Bo;
- Bourque, Guillaume;
- Bubulya, Paula A.;
- Ng, Huck-Hui
Publication type:
Article
Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development.
Published in:
PLoS Computational Biology, 2011, v. 7, n. 12, p. 1, doi. 10.1371/journal.pcbi.1002304
By:
- Göke, Jonathan;
- Jung, Marc;
- Behrens, Sarah;
- Chavez, Lukas;
- O'Keeffe, Sean;
- Timmermann, Bernd;
- Lehrach, Hans;
- Adjaye, James;
- Vingron, Martin
Publication type:
Article
JAFFAL: detecting fusion genes with long-read transcriptome sequencing.
Published in:
Genome Biology, 2022, v. 23, n. 1, p. 1, doi. 10.1186/s13059-021-02588-5
By:
- Davidson, Nadia M.;
- Chen, Ying;
- Sadras, Teresa;
- Ryland, Georgina L.;
- Blombery, Piers;
- Ekert, Paul G.;
- Göke, Jonathan;
- Oshlack, Alicia
Publication type:
Article
Integrative analysis of epigenetics data identifies gene-specific regulatory elements.
Published in:
Nucleic Acids Research, 2021, v. 49, n. 18, p. 10397, doi. 10.1093/nar/gkab798
By:
- Schmidt, Florian;
- Marx, Alexander;
- Baumgarten, Nina;
- Hebel, Marie;
- Wegner, Martin;
- Kaulich, Manuel;
- Leisegang, Matthias S;
- Brandes, Ralf P;
- Göke, Jonathan;
- Vreeken, Jilles;
- Schulz, Marcel H
Publication type:
Article
Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes.
Published in:
Nucleic Acids Research, 2019, v. 47, n. 16, p. 8485, doi. 10.1093/nar/gkz594
By:
- Zhang, Weiyu;
- Chen, Fuquan;
- Chen, Ruiqing;
- Xie, Dan;
- Yang, Jiao;
- Zhao, Xin;
- Guo, Renpeng;
- Zhang, Yongwang;
- Shen, Yang;
- Göke, Jonathan;
- Liu, Lin;
- Lu, Xinyi
Publication type:
Article
Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides.
Published in:
PLoS Genetics, 2009, v. 5, n. 11, p. 1, doi. 10.1371/journal.pgen.1000714
By:
- McMurdie, Paul J.;
- Behrens, Sebastian F.;
- Müller, Jochen A.;
- Göke, Jonathan;
- Ritalahti, Kirsti M.;
- Wagner, Ryan;
- Goltsman, Eugene;
- Lapidus, Alla;
- Holmes, Susan;
- Löffler, Frank E.;
- Spormann, Alfred M.
Publication type:
Article
An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets.
Published in:
Bioinformatics, 2018, v. 34, n. 17, p. i908, doi. 10.1093/bioinformatics/bty553
By:
- Schmidt, Florian;
- List, Markus;
- Cukuroglu, Engin;
- Köhler, Sebastian;
- Göke, Jonathan;
- Schulz, Marcel H
Publication type:
Article
Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.
Published in:
Bioinformatics, 2012, v. 28, n. 5, p. 656, doi. 10.1093/bioinformatics/bts028
By:
- Göke, Jonathan;
- Schulz, Marcel H.;
- Lasserre, Julia;
- Vingron, Martin
Publication type:
Article

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