Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap
Reimand, Jüri, Isserlin, Ruth, Voisin, Veronique, Kucera, Mike, Tannus-Lopes, Christian, Rostamianfar, Asha, Wadi, Lina, Meyer, Mona, Wong, Jeff, Xu, Changjiang, Merico, Daniele, Bader, Gary D
Published in Nature protocols (01.02.2019)
Published in Nature protocols (01.02.2019)
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Journal Article
Impact of outdated gene annotations on pathway enrichment analysis
Wadi, Lina, Meyer, Mona, Weiser, Joel, Stein, Lincoln D, Reimand, Jüri
Published in Nature methods (30.08.2016)
Published in Nature methods (30.08.2016)
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Journal Article
Candidate Cancer Driver Mutations in Distal Regulatory Elements and Long-Range Chromatin Interaction Networks
Zhu, Helen, Uusküla-Reimand, Liis, Isaev, Keren, Wadi, Lina, Alizada, Azad, Shuai, Shimin, Huang, Vincent, Aduluso-Nwaobasi, Dike, Paczkowska, Marta, Abd-Rabbo, Diala, Ocsenas, Oliver, Liang, Minggao, Thompson, J. Drew, Li, Yao, Ruan, Luyao, Krassowski, Michal, Dzneladze, Irakli, Simpson, Jared T., Lupien, Mathieu, Stein, Lincoln D., Boutros, Paul C., Wilson, Michael D., Reimand, Jüri
Published in Molecular cell (19.03.2020)
Published in Molecular cell (19.03.2020)
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Journal Article
A comprehensive survey of C. elegans argonaute proteins reveals organism-wide gene regulatory networks and functions
Seroussi, Uri, Lugowski, Andrew, Wadi, Lina, Lao, Robert X, Willis, Alexandra R, Zhao, Winnie, Sundby, Adam E, Charlesworth, Amanda G, Reinke, Aaron W, Claycomb, Julie M
Published in eLife (15.02.2023)
Published in eLife (15.02.2023)
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Journal Article
Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma
Kahn, Suzana A, Wang, Xin, Nitta, Ryan T, Gholamin, Sharareh, Theruvath, Johanna, Hutter, Gregor, Azad, Tej D, Wadi, Lina, Bolin, Sara, Ramaswamy, Vijay, Esparza, Rogelio, Liu, Kun-Wei, Edwards, Michael, Swartling, Fredrik J, Sahoo, Debashis, Li, Gordon, Wechsler-Reya, Robert J, Reimand, Jüri, Cho, Yoon-Jae, Taylor, Michael D, Weissman, Irving L, Mitra, Siddhartha S, Cheshier, Samuel H
Published in Nature communications (08.10.2018)
Published in Nature communications (08.10.2018)
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Journal Article
Publisher Correction: Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastoma
Kahn, Suzana A, Wang, Xin, Nitta, Ryan T, Gholamin, Sharareh, Theruvath, Johanna, Hutter, Gregor, Azad, Tej D, Wadi, Lina, Bolin, Sara, Ramaswamy, Vijay, Esparza, Rogelio, Liu, Kun-Wei, Edwards, Michael, Swartling, Fredrik J, Sahoo, Debashis, Li, Gordon, Wechsler-Reya, Robert J, Reimand, Jüri, Cho, Yoon-Jae, Taylor, Michael D, Weissman, Irving L, Mitra, Siddhartha S, Cheshier, Samuel H
Published in Nature communications (02.11.2018)
Published in Nature communications (02.11.2018)
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Journal Article
Genomic and phenotypic evolution of nematode-infecting microsporidia
Wadi, Lina, El Jarkass, Hala Tamim, Tran, Tuan D, Islah, Nizar, Luallen, Robert J, Reinke, Aaron W
Published in PLoS pathogens (20.07.2023)
Published in PLoS pathogens (20.07.2023)
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Journal Article
Genomic and phenotypic evolution of nematode-infecting microsporidia
Wadi, Lina, Hala Tamim El Jarkass, Tran, Tuan D, Islah, Nizar, Luallen, Robert J, Reinke, Aaron W
Published in bioRxiv (12.02.2023)
Published in bioRxiv (12.02.2023)
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Paper
Impact of knowledge accumulation on pathway enrichment analysis
Wadi, Lina, Meyer, Mona, Weiser, Joel, Stein, Lincoln D, Reimand, Juri
Published in bioRxiv (19.04.2016)
Published in bioRxiv (19.04.2016)
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Paper
Candidate cancer driver mutations in super-enhancers and long-range chromatin interaction networks
Wadi, Lina, Uuskula-Reimand, Liis, Isaev, Keren, Shuai, Shimin, Huang, Vincent, Liang, Minggao, Thompson, Drew, Yao, Li, Ruan, Luyao, Paczkowska, Marta, Krassowski, Michal, Dzneladze, Irakli, Kron, Ken, Murison, Alexander, Mazrooei, Parisa, Bristow, Robert G, Simpson, Jared T, Lupien, Mathieu, Wilson, Michael D, Stein, Lincoln D, Boutros, Paul C, Reimand, Juri
Published in bioRxiv (19.12.2017)
Published in bioRxiv (19.12.2017)
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