Highlighted papers of the major research areas of the lab are listed below. See the full list of publications in the Google Scholar profile. Asterisk (*) indicates co-first and co-corresponding authorships. Current and former lab members are shown in bold.

cancer drivers and passengers

Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes.
Christian A Lee*, Diala Abd-Rabbo*, Jüri Reimand.
Genome Biology 22 (1), 133 (2021)
link.

Chromatin accessibility of primary human cancers ties regional mutational processes with tissues of origin.
Oliver Ocsenas, Jüri Reimand.
bioRxiv 10.1101/2021.05.14.444202 (2021)
link.

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, Minggao Liang, J Drew Thompson, Yao Li, Luyao Ruan, Michal Krassowski, Irakli Dzneladze, Jared T Simpson, Mathieu Lupien, Lincoln D Stein, Paul C Boutros, Michael D Wilson, Jüri Reimand.
Molecular Cell 77 (6) 1307-1321. e10 (2020)
link.

multi-omics data integration, pathways and networks

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.
Nature Communications 11, Article number: 735 (2020)
link.

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 Bader.
Nature Protocols 14, pages 482–517 (2019)
link.

Impact of outdated gene annotations on pathway enrichment analysis.
Lina Wadi, Mona Meyer, Joel Weiser, Lincoln D Stein, Jüri Reimand.
Nature Methods 13 (9), 705-706 (2016)
link.

cancer biomarker and drug target discovery

Comprehensive analysis of lncRNAs reveals candidate prognostic biomarkers in multiple cancer types.
Keren Isaev, Lingyan Jiang, Christian A Lee, Ricky Tsai, Fiona Coutinho, Peter B Dirks, Daniel Schramek, Jüri Reimand.
bioRxiv, 861039, doi.org/10.1101/861039 (2019)
link.