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Publications
Lab members in bold; * co-first author; # co-corresponding author; ★ featured paper; collaborations are shown in lighter type. Also on Google Scholar.
101 papers
Lab publications (2015–present)
2026
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Aneuploidy selects for the acquisition of driver genes in breast cancerKhalid N Al-Zahrani, Ellen R Langille, Jocelyn Nurtanto, Andreea Obersterescu, Katie Teng, Christopher Lowden, Julien Dessapt, Cynthia H Chiu, Lauren V Caldwell, David P Cook, Miguel A Pérez-Castro, …, Alexander T Bahcheli, …, Jüri Reimand, Jeffrey L Wrana, Daniel SchramekNature 2026 doi
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Chromatin accessibility of primary cancers informs regional mutagenesis in metastases through multi-scale deep learningHanli Jiang, Alexander T Bahcheli, Kevin CL Cheng, Jüri Reimand
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Experimental assessment of AI-based interactome mappingLuke Lambourne, Anupama Yadav, Yang Wang, Alice Desbuleux, Dae-Kyum Kim, Florent Laval, Kerstin Spirohn-Fitzgerald, Tiziana Cafarelli, Carles Pons, István A Kovács, Noor Jailkhani, …, Jüri Reimand, …, Jean-Claude Twizere, Marc VidalNature Communications 2026
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Extracellular vesicles from aged individuals trigger mitochondrial dysfunction in haematopoietic progenitor cellsIsabelle J Grenier-Pleau, Jasleen Kaur, Christopher J Wells, Michael Vermeulen, Mykhaylo Slobodyanyuk, Samantha M Holmes, Éric Bonneil, Christine Hall, Jamie Beaulieu, Mohsen Hosseini, Steven M Chan, …, Jüri Reimand, Edmond YW Chan, Sheela A AbrahamHaematologica 2026
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Fluid shear stress activates a targetable mechano-metastatic cascade to promote medulloblastoma metastasisHyun-Kee Min, Hongyu Zhao, Alexander Bahcheli, Peng Pan, Jade Chan, Junsheng Chen, Esther Low, Yuxiao Zhou, Xian Wang, Savo Bajic, Ran Peng, …, Jüri Reimand, Xinyu Liu, Xi HuangNature Biomedical Engineering 2026 doi
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Functional identification of non-coding regulatory regions that drive breast and skin carcinogenesisRobin H Oh*, Kevin CL Cheng*, Evgenija Serafimova, Ellen Langille, Miguel Ángel Pérez-Castro, Christopher Lowden, Jocelyn Nurtanto, Julien Dessapt, Iosifina Fotiadou, Shahan Haider, Jacob Berman, …, Jüri Reimand#, Daniel Schramek#Cell Reports 2026 doi
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Genomic profiling implicates candidate genes and mutagenic pathways driving lung cancer recurrenceLaura Luhari*, Ann Valter*, Alexander T Bahcheli*, Kevin CL Cheng, Masroor Bayati, Anu Ustav, Agne Velthut-Meikas, Kersti Oselin#, Jüri Reimand#medRxiv 2026
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Integrated signatures define mutational processes in prostate cancer★Andreas J Gruber*, André V Olsen*, Barbara Hernando*, Kevin CL Cheng*, Clarissa Gerhäuser, Marina Torres, Francesco Favero, Daria Kiriy, Ángel Fernández-Sanromán, Juan Maria Roldan-Romero, Lucy Barton, Diogo Pellegrina, …, Geoff Macintyre#, Jüri Reimand#, Joachim Weischenfeldt#Nature 2026 doi
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Medulloblastoma Forms Symbiotic Metabolic Partnerships with Macrophages to Establish Leptomeningeal MetastasesVernon Fong, Michelle Ly, Anders W Erickson, Namal Abeysundara, Liam Hendrikse, Randy Van Ommeren, Polina Balin, Jigyansa Mishra, Bryn Livingston, Patryk Skowron, Olga Sirbu, …, Oliver Ocsenas, …, Jüri Reimand, …, Michael D Taylor, Xiaochong WubioRxiv 2026
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Multi-platform reassessment of human mitochondrial DNA methylation reveals signals consistent with technical artifactsSalman Basrai, Alexander T Bahcheli, Djarren Tan, Philip C Zuzarte, Andrea Bevan, Theodore Chan, Kristie Ng, Bernard Lam, Andrea Arruda, Sunit Das, Mark D Minden, Jared T Simpson, Jüri Reimand, Sagi AbelsonbioRxiv 2026
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Mutational signatures in cancer genomes alter protein sequence motifs in cellular signaling networksJigyansa Mishra*, Masroor Bayati*, Zoe P Klein, Kevin CL Cheng, Omar Wagih, Nina Adler, Maria Farina-Morillas, Alexander T Bahcheli, Jüri ReimandbioRxiv 2026
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Pairwise genomic alterations identify prognostic tumor states in multiple cancer typesMasroor Bayati, Jigyansa Mishra, Laura Luhari, Maria Farina-Morillas, Jüri ReimandbioRxiv 2026
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Recurrent mechanisms of biallelic epigenetic inactivation reveal new putative tumour suppressor genes in prostate cancerDaria Kiriy, Francesco Favero, Clarissa Gerhäuser, Jessica Heilmann, Pavlo Lutsik, Francisco German Rodriguez Gonzalez, Alessio Locallo, Jakob Schmidt Jespersen, Andreas J Gruber, Andre V Olsen, Barbara Hernando, Kevin CL Cheng, Diogo Pellegrina, …, Jüri Reimand, Joachim WeischenfeldtNature Communications 2026
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The molecular heterogeneity and clinical impact of genomic driver alterations in prostate cancer★Diogo Pellegrina*, Daria Kiriy*, Kevin CL Cheng*, Francesco Favero, Enrichetta Miletti, Zoe P Klein, Barbara Hernando, Andre V Olsen, Atef Sahli, Yunfan Fu, Pavlo Lutsik, …, Joachim Weischenfeldt#, Jüri Reimand#Nature Communications 2026 doi
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Therapy-associated mutagenesis at CTCF binding sites is shaped by chromatin context and DNA repair capacityKevin CL Cheng, Zoe P Klein, Jigyansa Mishra, Alexander T Bahcheli, Benjamin H Lok, Trevor J Pugh, Jüri ReimandbioRxiv 2026
2025
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Cancer genomic alterations and microenvironmental features encode synergistic interactions with disease outcomes★Masroor Bayati, Zoe P Klein, Alexander T Bahcheli, Mykhaylo Slobodyanyuk, Jeffrey To, Kevin CL Cheng, Jigyansa Mishra, Diogo Pellegrina, Kissy Guevara-Hoyer, Chris McIntosh, Mamatha Bhat, Jüri Reimand
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Carbonic Anhydrase Inhibition Sensitizes Group 3 Medulloblastoma to RadiotherapyCory M Richman, Alexandra Rasnitsyn, Borja L Holgado, Maria Vladoiu, Namal Abeysundara, Sandra Majo, Sara Chabi, Lucie J Taunay, Hiromichi Suzuki, Ichiyo Shibahara, Joonas Haapasalo, …, Oliver Ocsenas, …, Jüri Reimand, …, Michael D Taylor, Pasqualino De AntonellisCancer Research 2025 doi
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Causes of evolutionary divergence in prostate cancerEmre Esentürk, Atef Sahli, Valeriia Haberland, Aleksandra Ziuboniewicz, Christopher Wirth, G Steven Bova, Robert G Bristow, Mark N Brook, Benedikt Brors, Adam Butler, Géraldine Cancel-Tassin, Kevin CL Cheng, …, Diogo Pellegrina, …, Jüri Reimand, …, Daniel S Brewer, Dan J WoodcockarXiv 2025
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Extracellular Vesicles Define Discrete Nano-Based Niches Within the Human Haematopoietic SystemIsabelle J Grenier-Pleau, Christopher J Wells, Samantha M Holmes, Christine Hall, Michael Vermeulen, Camille A de Villiers, Jelle Penders, Simon Vilms Pedersen, Sarah A Dick, Eric Bonneil, Mykhaylo Slobodyanyuk, …, Jüri Reimand, …, Edmond YW Chan, Sheela A AbrahamJournal of Extracellular Vesicles 2025 doi
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Metastatic medulloblastoma remodels the local leptomeningeal microenvironment to promote further metastatic colonization and growthNamal Abeysundara, Alexandra Rasnitsyn, Vernon Fong, Alexander Bahcheli, Randy Van Ommeren, Kyle Juraschka, Maria Vladoiu, Winnie Ong, Bryn Livingston, Pasqualino de Antonellis, Michelle Ly, …, Jüri Reimand, …, Xi Huang, Michael D TaylorNature Cell Biology 2025
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Myelin–axon interface vulnerability in Alzheimer’s disease revealed by subcellular proteomics and imaging of human and mouse brainYifei Cai, Iguaracy Pinheiro-de-Sousa, Mykhaylo Slobodyanyuk, Fuyi Chen, Tram Huynh, Jean Kanyo, Peiyang Tang, Lukas A Fuentes, Amber Braker, Rachel Welch, Anita Huttner, …, Jüri Reimand, Angus C Nairn, Jaime GrutzendlerNature Neuroscience 2025 doi
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Pathogenic variants reveal candidate genes for prostate cancer germline testing for men of African ancestryKazzem Gheybi, Pamela XY Soh, Jue Jiang, Tumisang MN Mbeki, Melanie Louw, Daniel Burns, Piyushkumar Mundra, Daria Kiriy, Md Mehedi Hasan, Weerachai Jaratlerdsiri, Maphuti Tebogo Lebelo, …, Jüri Reimand, …, MS Riana Bornman, Vanessa M HayesNature Communications 2025 doi
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The Germline and Somatic Origins of Prostate Cancer HeterogeneityTakafumi N Yamaguchi*, Kathleen E Houlahan*, Helen Zhu*, Natalie Kurganovs*, Julie Livingstone*, Natalie S Fox*, Jiapei Yuan, Jocelyn Sietsma Penington, Chol-Hee Jung, Tommer Schwarz, Weerachai Jaratlerdsiri, …, Niall M Corcoran#, Jüri Reimand#, Christopher M Hovens#, Paul C Boutros#Cancer Discovery 2025 doi
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Therapeutic radiation drives leptomeningeal dissemination of medulloblastoma through an innate immune processCarolina Nör, Kaitlin Kharas, Alex Rasnitsyn, Maria C Vladoiu, Nam Woo Cho, Jacob S Young, Felipe Nör, Ncedile Mankahla, Joonas Haapasalo, Kristiina Nordfors, Sara Rapic, …, Alexander T Bahcheli, Oliver Ocsenas, …, Jüri Reimand, …, David R Raleigh, Michael D TaylorDevelopmental Cell 2025
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Topoisomerase IIb binding delineates localized mutational processes and driver mutations in cancer genomes★Liis Uusküla-Reimand*, Christian A Lee*, Robin H Oh, Zoe P Klein, Nina Adler, Sana Akhtar Alvi, Ellen Langille, Elisa Pasini, Kevin CL Cheng, Evgenija Serafimova, Diala Abd-Rabbo, …, Michael D Wilson, Jüri ReimandNature Communications 2025 doi
2024
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Acyl-CoA Thioesterase 1 Contributes to Transition of Steatosis to Metabolic-Associated SteatohepatitisElisa Pasini, Cristina Baciu, Marc Angeli, Bianca Arendt, Diogo Pellegrina, Jüri Reimand, Keyur Patel, George Tomlinson, Mohammad T Mazhab-Jafari, Lakshmi P Kotra, Sandra Fischer, Johane P Allard, Atul Humar, Mamatha BhatInternational Journal of Hepatology 2024
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Directional integration and pathway enrichment analysis for multi-omics data★Mykhaylo Slobodyanyuk*, Alexander T Bahcheli*, Zoe P Klein, Masroor Bayati, Lisa J Strug, Jüri Reimand
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Pan-cancer ion transport signature reveals functional regulators of glioblastoma aggression★Alexander T Bahcheli*, Hyun-Kee Min*, Masroor Bayati, Hongyu Zhao, Alexander Fortuna, Weifan Dong, Irakli Dzneladze, Jade Chan, Xin Chen, Kissy Guevara-Hoyer, Peter B Dirks, Xi Huang#, Jüri Reimand#The EMBO Journal 2024 doi
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Tobacco smoking and other exposures shut off cancer-fighting genesJüri Reimand, Nina AdlerTheScienceBreaker 2024
2023
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In vivo CRISPR screens reveal Serpinb9 and Adam2 as regulators of immune therapy response in lung cancerDzana Dervovic, Ahmad A Malik, Edward LY Chen, Masahiro Narimatsu, Nina Adler, Somaieh Afiuni-Zadeh, Dagmar Krenbek, Sebastien Martinez, Ricky Tsai, Jonathan Boucher, Jacob M Berman, …, Jüri Reimand, Hartland W Jackson, Daniel SchramekNature Communications 2023
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Mutational processes of tobacco smoking and APOBEC activity generate protein-truncating mutations in cancer genomesNina Adler, Alexander T Bahcheli, Kevin CL Cheng, Khalid N Al-Zahrani, Mykhaylo Slobodyanyuk, Diogo Pellegrina, Daniel Schramek, Jüri ReimandScience Advances 2023
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Transcriptomic changes in liver transplant recipients with non-alcoholic steatohepatitis indicate dysregulation of wound healingDiogo Pellegrina*, Khairunnadiya Prayitno*, Amirhossein Azhie, Elisa Pasini, Cristina Baciu, Sandra Fischer, Jüri Reimand#, Mamatha Bhat#Frontiers in Endocrinology 2023
2022
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Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastomaMichelle M Kameda-Smith, Helen Zhu, En-Ching Luo, Yujin Suk, Agata Xella, Brian Yee, Chirayu Chokshi, Sansi Xing, Frederick Tan, Raymond G Fox, Ashley A Adile, …, Jüri Reimand, …, Gene W Yeo, Sheila K SinghNature Communications 2022
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Chromatin accessibility of primary human cancers ties regional mutational processes and signatures with tissues of originOliver Ocsenas, Jüri ReimandPLOS Computational Biology 2022 doi
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Development of diagnostic and prognostic molecular biomarkers in hepatocellular carcinoma using machine learning: A systematic reviewAmanpreet Brar, Alice Zhu, Cristina Baciu, Divya Sharma, Wei Xu, Ani Orchanian-Cheff, Bo Wang, Jüri Reimand, Robert Grant, Mamatha BhatLiver Cancer International 2022
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Failure of human rhombic lip differentiation underlies medulloblastoma formationLiam D Hendrikse, Parthiv Haldipur, Olivier Saulnier, Jake Millman, Alexandria H Sjoboen, Anders W Erickson, Winnie Ong, Victor Gordon, Ludivine Coudière-Morrison, Audrey L Mercier, Mohammad Shokouhian, …, Alec Bahcheli, …, Jüri Reimand, …, Kathleen J Millen, Michael D TaylorNature 2022
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Human phospho-signaling networks of SARS-CoV-2 infection are rewired by population genetic variantsDiogo Pellegrina*, Alexander T Bahcheli*, Michal Krassowski, Jüri ReimandMolecular Systems Biology 2022 doi
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Mutations in Noncoding Cis-Regulatory Elements Reveal Cancer Driver Cistromes in Luminal Breast CancerSamah El Ghamrasni, Rene Quevedo, James Hawley, Parisa Mazrooei, Youstina Hanna, Iulia Cirlan, Helen Zhu, Jeff P Bruce, Leslie E Oldfield, SY Cindy Yang, Paul Guilhamon, Jüri Reimand, …, Mathieu Lupien, Trevor J PughMolecular Cancer Research 2022
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Rare Germline Variants Are Associated with Rapid Biochemical Recurrence After Radical Prostate Cancer Treatment: A Pan Prostate Cancer Group StudyDaniel Burns, Ezequiel Anokian, Edward J Saunders, Robert G Bristow, Michael Fraser, Jüri Reimand, Thorsten Schlomm, Guido Sauter, Benedikt Brors, Jan Korbel, Joachim Weischenfeldt, …, Zsofia Kote-Jarai, Rosalind A EelesEuropean Urology 2022
2021
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ActiveDriverDB: interpreting genetic variation in human and cancer genomes using post-translational modification sites and signaling networks (2021 Update)Michal Krassowski, Diogo Pellegrina, Miles W Mee, Amelie Fradet-Turcotte, Mamatha Bhat, Jüri ReimandFrontiers in Cell and Developmental Biology 2021
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Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes★Christian A Lee*, Diala Abd-Rabbo*, Jüri Reimand
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Pan-cancer analysis of non-coding transcripts reveals the prognostic onco-lncRNA HOXA10-AS in gliomas★Keren Isaev*, Lingyan Jiang*, Shuai Wu*, Christian A Lee, Valerie Watters, Victoire Fort, Ricky Tsai, Fiona Coutinho, Samer M I Hussein, Jie Zhang, Jinsong Wu, Peter B Dirks, Daniel Schramek#, Jüri Reimand#Cell Reports 2021
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Single allele loss-of-function mutations select and sculpt conditional cooperative networks in breast cancerNathan F Schachter, Jessica R Adams, Patryk Skowron, Katelyn J Kozma, Christian A Lee, Nandini Raghuram, Joanna Yang, Amanda J Loch, Wei Wang, Aaron Kucharczuk, Katherine L Wright, …, Jüri Reimand, Michael D Taylor, Sean E EganNature Communications 2021
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The transcriptional landscape of Shh medulloblastomaPatryk Skowron, Hamza Farooq, Florence MG Cavalli, A Sorana Morrissy, Michelle Ly, Liam D Hendrikse, Evan Y Wang, Haig Djambazian, Helen Zhu, Karen L Mungall, Quang M Trinh, …, Diala Abd-Rabbo, …, Jüri Reimand, …, Hiromichi Suzuki, Michael D TaylorNature Communications 2021
2020
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Analyses of non-coding somatic drivers in 2,658 cancer whole genomesEsther Rheinbay, Morten Muhlig Nielsen, Federico Abascal, Jeremiah A Wala, Ofer Shapira, Grace Tiao, Henrik Hornshøj, Julian M Hess, Randi Istrup Juul, Ziao Lin, Lars Feuerbach, …, Keren Isaev, …, Lina Wadi, …, Jüri Reimand, …, Jakob Skou Pedersen, Gad GetzNature 2020
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Candidate cancer driver mutations in distal regulatory elements and long-range chromatin interaction networks★Helen Zhu*, Liis Uusküla-Reimand*, Keren Isaev*, Lina Wadi, Azad Alizada, Shimin Shuai, Vincent Huang, Dike Aduluso-Nwaobasi, Marta Paczkowska, Diala Abd-Rabbo, Oliver Ocsenas, …, J Drew Thompson, Yao Li, Luyao Ruan, Michal Krassowski, Irakli Dzneladze, …, Michael D Wilson, Jüri Reimand
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Integrative pathway enrichment analysis of multivariate omics data★Marta Paczkowska*, Jonathan Barenboim*, Nardnisa Sintupisut, Natalie S Fox, Helen Zhu, Diala Abd-Rabbo, Miles W Mee, Paul C Boutros, PCAWG Drivers and Functional Interpretation Working Group, Jüri Reimand, PCAWG Consortium
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Pan-cancer analysis of whole genomesThe ICGC/TCGA Pan-Cancer Analysis of Whole Genomes ConsortiumNature 2020
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Pathway and network analysis of more than 2500 whole cancer genomesMatthew A Reyna, David Haan, Marta Paczkowska, Lieven PC Verbeke, Miguel Vazquez, Abdullah Kahraman, Sergio Pulido-Tamayo, Jonathan Barenboim, Lina Wadi, Priyanka Dhingra, Raunak Shrestha, …, Jüri Reimand#, Joshua M Stuart#, Benjamin J Raphael#Nature Communications 2020
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Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1Otto Kauko, Susumu Y Imanishi, Evgeny Kulesskiy, Laxman Yetukuri, Teemu Daniel Laajala, Mukund Sharma, Karolina Pavic, Anna Aakula, Christian Rupp, Mikael Jumppanen, Pekka Haapaniemi, Luyao Ruan, …, Jüri Reimand, …, Tero Aittokallio, Jukka WestermarckJournal of Biological Chemistry 2020
2019
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A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survivalRodrigo Guarischi-Sousa, Jhonatas S Monteiro, Lilian C Alecrim, Jussara S Michaloski, Laura B Cardeal, Elisa N Ferreira, Dirce M Carraro, Diana N Nunes, Emmanuel Dias-Neto, Jüri Reimand, Paul C Boutros, João C Setubal, Ricardo J GiordanoPLOS Genetics 2019
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BEHST: genomic set enrichment analysis enhanced through integration of chromatin long-range interactionsDavide Chicco, Haixin Sarah Bi, Jüri Reimand, Michael M HoffmanbioRxiv 2019
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ID1 is critical for tumorigenesis and regulates chemoresistance in glioblastomaRohit Sachdeva, Megan Wu, Sandra Smiljanic, Oleksandra Kaskun, Kimia Ghannad-Zadeh, Angela Celebre, Keren Isaev, A Sorana Morrissy, Jennifer Guan, Jiefei Tong, Jeffrey Chan, …, Jüri Reimand, Sunit DasCancer Research 2019
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Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap★Jüri Reimand*, Ruth Isserlin*, Veronique Voisin, Mike Kucera, Christian Tannus-Lopes, Asha Rostamianfar, Lina Wadi, Mona Meyer, Jeff Wong, Changjiang Xu, Daniele Merico, Gary D BaderNature Protocols 2019 doi
2018
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ActiveDriverDB: human disease mutations and genome variation in post-translational modification sites of proteinsMichal Krassowski, Marta Paczkowska, Kim Cullion, Tina Huang, Irakli Dzneladze, BF Francis Ouellette, Joseph T Yamada, Amelie Fradet-Turcotte, Jüri ReimandNucleic Acids Research 2018 doi
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Global phosphoproteomic analysis identifies SRMS-regulated secondary signaling intermediatesRaghuveera Kumar Goel, Mona Meyer, Marta Paczkowska, Jüri Reimand, Frederick Vizeacoumar, Franco Vizeacoumar, TuKiet T Lam, Kiven Erique LukongProteome Science 2018
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Notch1 regulates the initiation of metastasis and self-renewal of Group 3 medulloblastomaSuzana A Kahn, Xin Wang, Ryan T Nitta, Sharareh Gholamin, Johanna Theruvath, Gregor Hutter, Tej D Azad, Lina Wadi, Sara Bolin, Vijay Ramaswamy, Rogelio Esparza, …, Jüri Reimand, …, Siddhartha S Mitra, Samuel H CheshierNature Communications 2018
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Pathogenic germline variants in 10,389 adult cancersKuan-Lin Huang, R Jay Mashl, Yige Wu, Deborah I Ritter, Jiayin Wang, Clara Oh, Marta Paczkowska, Sheila Reynolds, Matthew A Wyczalkowski, Ninad Oak, Adam D Scott, Michal Krassowski, …, Jüri Reimand, …, Feng Chen, Li DingCell 2018
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Phosphoproteomics analysis identifies novel candidate substrates of the nonreceptor tyrosine kinase, src-related kinase lacking C-terminal regulatory tyrosine and N-terminal myristoylation sites (SRMS)Raghuveera Kumar Goel, Marta Paczkowska, Jüri Reimand, Scott Napper, Kiven Erique LukongMolecular & Cellular Proteomics 2018
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SubID, a non-median dichotomization tool for heterogeneous populations, reveals the pan-cancer significance of INPP4B and its regulation by EVI1 in AMLIrakli Dzneladze, John F Woolley, Carla Rossell, Youqi Han, Ayesha Rashid, Michael Jain, Jüri Reimand, Mark D Minden, Leonardo SalmenaPLOS One 2018
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Therapeutic targeting of ependymoma as informed by oncogenic enhancer profilingStephen C Mack, Kristian W Pajtler, Lukas Chavez, Konstantin Okonechnikov, Kelsey C Bertrand, Xiuxing Wang, Serap Erkek, Alexander Federation, Anne Song, Christine Lee, Xin Wang, …, Jüri Reimand, …, Michael D Taylor, Jeremy N RichNature 2018
2017
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Intertumoral heterogeneity within medulloblastoma subgroupsFlorence MG Cavalli, Marc Remke, Ladislav Rampasek, John Peacock, David JH Shih, Betty Luu, Livia Garzia, Jonathon Torchia, Carolina Nor, A Sorana Morrissy, Sameer Agnihotri, …, Keren Isaev, …, Jüri Reimand, …, Vijay Ramaswamy, Michael D TaylorCancer Cell 2017
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Spatial heterogeneity in medulloblastomaA Sorana Morrissy, Florence MG Cavalli, Marc Remke, Vijay Ramaswamy, David JH Shih, Borja L Holgado, Hamza Farooq, Laura K Donovan, Livia Garzia, Sameer Agnihotri, Erin N Kiehna, …, Jüri Reimand, …, Marco A Marra, Michael D TaylorNature Genetics 2017
2016
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Divergent clonal selection dominates medulloblastoma at recurrenceA Sorana Morrissy, Livia Garzia, David JH Shih, Scott Zuyderduyn, Xi Huang, Patryk Skowron, Marc Remke, Florence MG Cavalli, Vijay Ramaswamy, Patricia E Lindsay, Salomeh Jelveh, …, Jüri Reimand, …, Marco A Marra, Michael D TaylorNature 2016
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Frequent mutations in acetylation and ubiquitination sites suggest novel driver mechanisms of cancerSoumil Narayan, Gary D Bader#, Jüri Reimand#Genome Medicine 2016
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Functional genomic landscape of human breast cancer drivers, vulnerabilities, and resistanceRichard Marcotte, Azin Sayad, Kevin R Brown, Felix Sanchez-Garcia, Jüri Reimand, Maliha Haider, Carl Virtanen, James E Bradner, Gary D Bader, Gordon B Mills, Dana Pe'er, Jason Moffat, Benjamin G NeelCell 2016
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Impact of outdated gene annotations on pathway enrichment analysisLina Wadi, Mona Meyer, Joel Weiser, Lincoln D Stein, Jüri ReimandNature Methods 2016 doi
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New brain tumor entities emerge from molecular classification of CNS-PNETsDominik Sturm, Brent A Orr, Umut H Toprak, Volker Hovestadt, David TW Jones, David Capper, Martin Sill, Ivo Buchhalter, Paul A Northcott, Irina Leis, Marina Ryzhova, …, Jüri Reimand, …, Andrey Korshunov, Marcel KoolCell 2016
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Topoisomerase II beta interacts with cohesin and CTCF at topological domain bordersLiis Uusküla-Reimand, Huayun Hou, Payman Samavarchi-Tehrani, Matteo Vietri Rudan, Minggao Liang, Alejandra Medina-Rivera, Hisham Mohammed, Dominic Schmidt, Petra Schwalie, Edwin J Young, Jüri Reimand, Suzana Hadjur, Anne-Claude Gingras, Michael D WilsonGenome Biology 2016
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g:Profiler—a web server for functional interpretation of gene lists (2016 update)Jüri Reimand, Tambet Arak, Priit Adler, Liis Kolberg, Sulev Reisberg, Hedi Peterson, Jaak ViloNucleic Acids Research 2016
2015
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EAG2 potassium channel with evolutionarily conserved function as a brain tumor targetXi Huang, Ye He, Adrian M Dubuc, Rintaro Hashizume, Wei Zhang, Jüri Reimand, Huanghe Yang, Tongfei A Wang, Samantha J Stehbens, Susan Younger, Suzanne Barshow, …, Yuh Nung Jan, Lily Yeh JanNature Neuroscience 2015
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Evolutionary constraint and disease associations of post-translational modification sites in human genomesJüri Reimand, Omar Wagih, Gary D BaderPLOS Genetics 2015
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MIMP: predicting the impact of mutations on kinase-substrate phosphorylationOmar Wagih#, Jüri Reimand#, Gary D Bader#Nature Methods 2015
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Molecular classification of ependymal tumors across all CNS compartments, histopathological grades, and age groupsKristian W Pajtler, Hendrik Witt, Martin Sill, David TW Jones, Volker Hovestadt, Fabian Kratochwil, Khalida Wani, Ruth Tatevossian, Chandanamali Punchihewa, Pascal Johann, Jüri Reimand, …, Marcel Kool, Stefan M PfisterCancer Cell 2015
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Pathway and network analysis of cancer genomesPau Creixell*, Jüri Reimand*, Syed Haider, Guanming Wu, Tatsuhiro Shibata, Miguel Vazquez, Ville Mustonen, Abel Gonzalez-Perez, John Pearson, Chris Sander, Benjamin J Raphael, …, Nuria Lopez-Bigas, Lincoln D SteinNature Methods 2015
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Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneityMona Meyer*, Jüri Reimand*, Xiaoyang Lan, Renee Head, Xueming Zhu, Michelle Kushida, Jane Bayani, Jessica C Pressey, Anath C Lionel, Ian D Clarke, Michael Cusimano, …, Gary D Bader, Peter B DirksProceedings of the National Academy of Sciences 2015
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Systematic analysis of somatic mutations impacting gene expression in 12 tumour typesJiarui Ding, Melissa K McConechy, Hugo M Horlings, Gavin Ha, Fong Chun Chan, Tyler Funnell, Sarah C Mullaly, Jüri Reimand, Ali Bashashati, Gary D Bader, David Huntsman, Samuel Aparicio, Anne Condon, Sohrab P ShahNature Communications 2015
Earlier work (before 2015)
Doctoral and postdoctoral research before the lab was founded.
2014
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Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibitionMarcel Kool, David TW Jones, Natalie Jäger, Paul A Northcott, Trevor J Pugh, Volker Hovestadt, Rosario M Piro, L Adriana Esparza, Shirley L Markant, Marc Remke, Till Milde, …, Jüri Reimand, …, Stefan M Pfister, ICGC PedBrain Tumor ProjectCancer Cell 2014
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HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discoveryAlvin Leung, Gary D Bader, Jüri ReimandBioinformatics 2014
2013
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Comprehensive identification of mutational cancer driver genes across 12 tumor typesDavid Tamborero, Abel Gonzalez-Perez, Christian Perez-Llamas, Jordi Deu-Pons, Cyriac Kandoth, Jüri Reimand, Michael S Lawrence, Gad Getz, Gary D Bader, Li Ding, Nuria Lopez-BigasScientific Reports 2013
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Computational approaches to identify functional genetic variants in cancer genomesAbel Gonzalez-Perez, Ville Mustonen, Boris Reva, Graham RS Ritchie, Pau Creixell, Rachel Karchin, Miguel Vazquez, J Lynn Fink, Karin S Kassahn, John V Pearson, Gary D Bader, …, Jüri Reimand, …, Nuria Lopez-Bigas, International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working GroupNature Methods 2013
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Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer driversJüri Reimand, Gary D BaderMolecular Systems Biology 2013
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The mutational landscape of phosphorylation signaling in cancerJüri Reimand, Omar Wagih, Gary D BaderScientific Reports 2013
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Thread 2: Network modelsJüri Reimand, Gary Bader, Adam Margolin, Abel Gonzalez-Perez, David Tamborero, Nuria Lopez-Bigas, John Weinstein, Joshua Stuart, Myles AxtonNature Genetics 2013
2012
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Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO miceX Xiong, A Chorzalska, PM Dubielecka, JR White, Y Vedvyas, CV Hedvat, A Haimovitz-Friedman, JA Koutcher, J Reimand, GD Bader, JA Sawicki, L KotulaOncogenesis 2012
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Domain-mediated protein interaction prediction: From genome to networkJüri Reimand, Shirley Hui, Shobhit Jain, Brian Law, Gary D BaderFEBS Letters 2012
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Mid-gestational gene expression profile in placenta and link to pregnancy complicationsLiis Uusküla, Jaana Männik, Kristiina Rull, Ave Minajeva, Sulev Kõks, Pille Vaas, Pille Teesalu, Jüri Reimand#, Maris Laan#PLOS One 2012
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Research resource: interactome of human embryo implantation: identification of gene expression pathways, regulation, and integrated regulatory networksSigne Altmäe*, Jüri Reimand*, Outi Hovatta, Pu Zhang, Juha Kere, Triin Laisk, Merli Saare, Maire Peters, Jaak Vilo, Anneli Stavreus-Evers, Andres SalumetsMolecular Endocrinology 2012
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Subgroup-specific structural variation across 1,000 medulloblastoma genomesPaul A Northcott, David JH Shih, John Peacock, Livia Garzia, A Sorana Morrissy, Thomas Zichner, Adrian M Stütz, Andrey Korshunov, Jüri Reimand, Steven E Schumacher, Rameen Beroukhim, …, Marco A Marra, Michael D TaylorNature 2012
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m:Explorer: multinomial regression models reveal positive and negative regulators of longevity in yeast quiescenceJüri Reimand, Anu Aun, Jaak Vilo, Juan M Vaquerizas, Juhan Sedman, Nicholas M LuscombeGenome Biology 2012
2011
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g:Profiler—a web server for functional interpretation of gene lists (2011 update)Jüri Reimand, Tambet Arak, Jaak ViloNucleic Acids Research 2011
2010
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Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targetsJüri Reimand, Juan M Vaquerizas, Annabel E Todd, Jaak Vilo, Nicholas M LuscombeNucleic Acids Research 2010
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Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte developmentNathalie Billon, Raivo Kolde, Jüri Reimand, Miguel C Monteiro, Meelis Kull, Hedi Peterson, Konstantin Tretyakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo, Christian DaniGenome Biology 2010
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Relicensing of transcriptionally inactivated replication origins in budding yeastMarko Lõoke, Jüri Reimand, Tiina Sedman, Juhan Sedman, Lari Järvinen, Signe Värv, Kadri Peil, Kersti Kristjuhan, Jaak Vilo, Arnold KristjuhanJournal of Biological Chemistry 2010
2009
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Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methodsPriit Adler, Raivo Kolde, Meelis Kull, Aleksandr Tkachenko, Hedi Peterson, Jüri Reimand, Jaak ViloGenome Biology 2009
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Ranking genes by their co-expression to subsets of pathway membersPriit Adler, Hedi Peterson, Phaedra Agius, Jüri Reimand, Jaak ViloAnnals of the New York Academy of Sciences 2009
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The FunGenES database: a genomics resource for mouse embryonic stem cell differentiationHerbert Schulz, Raivo Kolde, Priit Adler, Irène Aksoy, Konstantinos Anastassiadis, Michael Bader, Nathalie Billon, Hélène Boeuf, Pierre-Yves Bourillot, Frank Buchholz, Christian Dani, …, Jüri Reimand, …, Antonis K Hatzopoulos, Functional Genomics in Embryonic Stem Cells ConsortiumPLOS One 2009
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VisHiC—hierarchical functional enrichment analysis of microarray dataDarya Krushevskaya, Hedi Peterson, Jüri Reimand, Meelis Kull, Jaak ViloNucleic Acids Research 2009
2008
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GraphWeb: mining heterogeneous biological networks for gene modules with functional significanceJüri Reimand, Laur Tooming, Hedi Peterson, Priit Adler, Jaak ViloNucleic Acids Research 2008
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KEGGanim: pathway animations for high-throughput dataPriit Adler, Jüri Reimand, Jürgen Jänes, Raivo Kolde, Hedi Peterson, Jaak ViloBioinformatics 2008
2007
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g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experimentsJüri Reimand, Meelis Kull, Hedi Peterson, Jaanus Hansen, Jaak ViloNucleic Acids Research 2007
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