Papers

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.
PLOS Computational Biology Aug 10;18(8):e1010393 (2022)
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

Human phospho‐signaling networks of SARS‐CoV‐2 infection are rewired by population genetic variants.
Diogo Pellegrina*, Alexander T Bahcheli*, Michal Krassowski, Jüri Reimand.
Molecular Systems Biology 18 (5), Article number: e10823 (2022)
link.

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Impact of outdated gene annotations on pathway enrichment analysis.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

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, Vol 37, Issue 3, 109873, (2021) link.