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

por Göke, Jonathan, Schulz, Marcel H., Lasserre, Julia, Vingron, Martin
Publicado 2012

An ontology-based method for assessing batch effect adjustment approaches in heterogeneous datasets

por Schmidt, Florian, List, Markus, Cukuroglu, Engin, Köhler, Sebastian, Göke, Jonathan, Schulz, Marcel H
Publicado 2018

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

por Hendra, Christopher, Pratanwanich, Ploy N., Wan, Yuk Kei, Goh, W. S. Sho, Thiery, Alexandre, Göke, Jonathan
Publicado 2022

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

por Göke, Jonathan, Jung, Marc, Behrens, Sarah, Chavez, Lukas, O'Keeffe, Sean, Timmermann, Bernd, Lehrach, Hans, Adjaye, James, Vingron, Martin
Publicado 2011

JAFFAL: detecting fusion genes with long-read transcriptome sequencing

por Davidson, Nadia M., Chen, Ying, Sadras, Teresa, Ryland, Georgina L., Blombery, Piers, Ekert, Paul G., Göke, Jonathan, Oshlack, Alicia
Publicado 2022

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

por Itahana, Yoko, Zhang, Jinqiu, Göke, Jonathan, Vardy, Leah A., Han, Rachel, Iwamoto, Kozue, Cukuroglu, Engin, Robson, Paul, Pouladi, Mahmoud A., Colman, Alan, Itahana, Koji
Publicado 2016

Zscan4c activates endogenous retrovirus MERVL and cleavage embryo genes

por Zhang, Weiyu, Chen, Fuquan, Chen, Ruiqing, Xie, Dan, Yang, Jiao, Zhao, Xin, Guo, Renpeng, Zhang, Yongwang, Shen, Yang, Göke, Jonathan, Liu, Lin, Lu, Xinyi
Publicado 2019

Integrative analysis of epigenetics data identifies gene-specific regulatory elements

por 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
Publicado 2021

Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides

por 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.
Publicado 2009

Antisense RNAs Influence Promoter Usage of Their Counterpart Sense Genes in Cancer

por Bellido Molias, Fernando, Sim, Andre, Leong, Ka Wai, An, Omer, Song, Yangyang, Ng, Vanessa Hui En, Lim, Max Wei Jie, Ying, Chen, Teo, Jasmin Xin Jia, Göke, Jonathan, Chen, Leilei
Publicado 2021

Long-read transcriptome sequencing reveals abundant promoter diversity in distinct molecular subtypes of gastric cancer

por 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
Publicado 2021

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

por Szczerbinska, Iwona, Gonzales, Kevin Andrew Uy, Cukuroglu, Engin, Ramli, Muhammad Nadzim Bin, Lee, Bertha Pei Ge, Tan, Cheng Peow, Wong, Cheng Kit, Rancati, Giulia Irene, Liang, Hongqing, Göke, Jonathan, Ng, Huck-Hui, Chan, Yun-Shen
Publicado 2019

Reduced Oct4 Expression Directs a Robust Pluripotent State with Distinct Signaling Activity and Increased Enhancer Occupancy by Oct4 and Nanog

por Karwacki-Neisius, Violetta, Göke, Jonathan, Osorno, Rodrigo, Halbritter, Florian, Ng, Jia Hui, Weiße, Andrea Y., Wong, Frederick C.K., Gagliardi, Alessia, Mullin, Nicholas P., Festuccia, Nicola, Colby, Douglas, Tomlinson, Simon R., Ng, Huck-Hui, Chambers, Ian
Publicado 2013

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

por Do, Dang Vinh, Strauss, Bernhard, Cukuroglu, Engin, Macaulay, Iain, Wee, Keng Boon, Hu, Tim Xiaoming, Igor, Ruiz De Los Mozos, Lee, Caroline, Harrison, Andrew, Butler, Richard, Dietmann, Sabine, Jernej, Ule, Marioni, John, Smith, Christopher W. J., Göke, Jonathan, Surani, M. Azim
Publicado 2018

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

por Lechner, Axel, Schlößer, Hans A., Thelen, Martin, Wennhold, Kerstin, Rothschild, Sacha I., Gilles, Ramona, Quaas, Alexander, Siefer, Oliver G., Huebbers, Christian U., Cukuroglu, Engin, Göke, Jonathan, Hillmer, Axel, Gathof, Birgit, Meyer, Moritz F., Klussmann, Jens P., Shimabukuro-Vornhagen, Alexander, Theurich, Sebastian, Beutner, Dirk, von Bergwelt-Baildon, Michael
Publicado 2019

Multiple Myeloma DREAM Challenge reveals epigenetic regulator PHF19 as marker of aggressive disease

por Mason, Mike J., Schinke, Carolina, Eng, Christine L. P., Towfic, Fadi, Gruber, Fred, Dervan, Andrew, White, Brian S., Pratapa, Aditya, Guan, Yuanfang, Chen, Hongjie, Cui, Yi, Li, Bailiang, Yu, Thomas, Chaibub Neto, Elias, Mavrommatis, Konstantinos, Ortiz, Maria, Lyzogubov, Valeriy, Bisht, Kamlesh, Dai, Hongyue Y., Schmitz, Frank, Flynt, Erin, Dan Rozelle, Danziger, Samuel A., Ratushny, Alexander, Dalton, William S., Goldschmidt, Hartmut, Avet-Loiseau, Herve, Samur, Mehmet, Hayete, Boris, Sonneveld, Pieter, Shain, Kenneth H., Munshi, Nikhil, Auclair, Daniel, Hose, Dirk, Morgan, Gareth, Trotter, Matthew, Bassett, Douglas, Goke, Jonathan, Walker, Brian A., Thakurta, Anjan, Guinney, Justin
Publicado 2020

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

por Sundar, Raghav, Huang, Kie-Kyon, Kumar, Vikrant, Ramnarayanan, Kalpana, Demircioglu, Deniz, Her, Zhisheng, Ong, Xuewen, Bin Adam Isa, Zul Fazreen, Xing, Manjie, Tan, Angie Lay-Keng, Tai, David Wai Meng, Choo, Su Pin, Zhai, Weiwei, Lim, Jia Qi, Das Thakur, Meghna, Molinero, Luciana, Cha, Edward, Fasso, Marcella, Niger, Monica, Pietrantonio, Filippo, Lee, Jeeyun, Jeyasekharan, Anand D, Qamra, Aditi, Patnala, Radhika, Fabritius, Arne, De Simone, Mark, Yeong, Joe, Ng, Cedric Chuan Young, Rha, Sun Young, Narita, Yukiya, Muro, Kei, Guo, Yu Amanda, Skanderup, Anders Jacobsen, So, Jimmy Bok Yan, Yong, Wei Peng, Chen, Qingfeng, Göke, Jonathan, Tan, Patrick
Publicado 2022

Genomic basis for RNA alterations in cancer

por Calabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G., Su, Hong, Tan, Patrick, Waszak, Sebastian M., Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Meyerson, Matthew, Ouellette, B. F. Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N., Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F., Stegle, Oliver, Zhang, Zemin
Publicado 2020

Author Correction: Genomic basis for RNA alterations in cancer

por Calabrese, Claudia, Davidson, Natalie R., Demircioğlu, Deniz, Fonseca, Nuno A., He, Yao, Kahles, André, Lehmann, Kjong-Van, Liu, Fenglin, Shiraishi, Yuichi, Soulette, Cameron M., Urban, Lara, Greger, Liliana, Li, Siliang, Liu, Dongbing, Perry, Marc D., Xiang, Qian, Zhang, Fan, Zhang, Junjun, Bailey, Peter, Erkek, Serap, Hoadley, Katherine A., Hou, Yong, Huska, Matthew R., Kilpinen, Helena, Korbel, Jan O., Marin, Maximillian G., Markowski, Julia, Nandi, Tannistha, Pan-Hammarström, Qiang, Pedamallu, Chandra Sekhar, Siebert, Reiner, Stark, Stefan G., Su, Hong, Tan, Patrick, Waszak, Sebastian M., Yung, Christina, Zhu, Shida, Awadalla, Philip, Creighton, Chad J., Meyerson, Matthew, Ouellette, B. F. Francis, Wu, Kui, Yang, Huanming, Brazma, Alvis, Brooks, Angela N., Göke, Jonathan, Rätsch, Gunnar, Schwarz, Roland F., Stegle, Oliver, Zhang, Zemin
Publicado 2023

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

por Pardo-Palacios, Francisco J., Wang, Dingjie, Reese, Fairlie, Diekhans, Mark, Carbonell-Sala, Sílvia, Williams, Brian, Loveland, Jane E., De María, Maite, Adams, Matthew S., Balderrama-Gutierrez, Gabriela, Behera, Amit K., Gonzalez, Jose M., Hunt, Toby, Lagarde, Julien, Liang, Cindy E., Li, Haoran, Jerryd Meade, Marcus, Moraga Amador, David A., Prjibelski, Andrey D., Birol, Inanc, Bostan, Hamed, Brooks, Ashley M., Hasan Çelik, Muhammed, Chen, Ying, Du, Mei R,M., Felton, Colette, Göke, Jonathan, Hafezqorani, Saber, Herwig, Ralf, Kawaji, Hideya, Lee, Joseph, Liang Li, Jian, Lienhard, Matthias, Mikheenko, Alla, Mulligan, Dennis, Ming Nip, Ka, Pertea, Mihaela, Ritchie, Matthew E., Sim, Andre D., Tang, Alison D., Kei Wan, Yuk, Wang, Changqing, Wong, Brandon Y., Yang, Chen, Barnes, If, Berry, Andrew, Capella, Salvador, Dhillon, Namrita, Fernandez-Gonzalez, Jose M., Ferrández-Peral, Luis, Garcia-Reyero, Natàlia, Goetz, Stefan, Hernández-Ferrer, Carles, Kondratova, Liudmyla, Liu, Tianyuan, Martinez-Martin, Alessandra, Menor, Carlos, Mestre-Tomás, Jorge, Mudge, Jonathan M., Panayotova, Nedka G., Paniagua, Alejandro, Repchevsky, Dmitry, Rouchka, Eric, Saint-John, Brandon, Sapena, Enrique, Sheynkman, Leon, Laird Smith, Melissa, Suner, Marie-Marthe, Takahashi, Hazuki, Youngworth, Ingrid Ashley., Carninci, Piero, Denslow, Nancy D., Guigó, Roderic, Hunter, Margaret E., Tilgner, Hagen U., Wold, Barbara J., Vollmers, Christopher, Frankish, Adam, Fai Au, Kin, Sheynkman, Gloria M., Mortazavi, Ali, Conesa, Ana, Brooks, Angela N.
Publicado 2023