Juri Reimand
Jüri Reimand PhD

I am now a principal investigator at Ontario Institute for Cancer Research (OICR) in Toronto. My lab focuses on network biology, bioinformatics, and cancer research. I recently obtained an assistant professor appointment at the University of Toronto with the Department of Medical Biophysics. While my lab website is under construction and this page is slowly going out of date, please have a look at my faculty profile and my publications in Google Scholar.

Email: juri.reimand[at]utoronto.ca, juri.reimand[at]oicr.on.ca


Previous post-doctoral positions:

Bader lab
The Donnelly Centre for Cellular+Biomolecular Research
University of Toronto
160 College Street, Toronto
M5S 3E1 Ontario, Canada

Taylor lab
The Arthur and Sonia Labatt Brain Tumour Research Centre
The Hospital for Sick Children
110 College Street, Toronto
M5G 1L7 Ontario, Canada


Current biomedical research often uses large-scale experimental techniques to rapidly accumulate data and study the molecular structure of life at an unprecedented resolution. It is now possible to explore the source code and transcriptional programs of cells using DNA and RNA sequencing and epigenomic techniques, and study the execution of these programs in cellular signaling circuits and protein-protein interaction networks. Furthermore, we are increasingly able to elucidate the mechanisms of human disease and cancer by highlighting features in molecular data profiles that are often subtle in nature.

My research in the team of Prof. Gary Bader is in the field of computational biology and currently focuses on several aspects of cancer genomics. I am interested in analyzing regulatory systems such as transcriptional programs and post-translational signal circuits, and discovering how these are altered and rewired in tumor cells. I often construct and apply statistical models and algorithms to integrate heterogeneous sources of biological data and molecular networks. An important aspect of my work is functional interpretation of genes, pathways, and systems, as well as clinical analysis of disease-related variants and alterations.

I recently also joined the lab of Prof. Michael D. Taylor to study the biology of brain cancer and gain some experimental experience. I am working on medulloblastoma, a pediatric brain tumor, and aim to use a mouse model of the disease to investigate the genetic and transcriptional properties of metastatic cells.

I have been involved in the development of several computational tools:
  • HyperModules, a network search algorithm that finds groups of interacting genes where mutations are correlated with clinical information such as patient survival;
  • ActiveDriver, a regression-based method to discover frequently mutated or variable protein sites - current application involves discovery of cancer driver genes and pathways with mutations in signalling and phosphorylation sites;
  • m:Explorer, a regression-based algorithm to discover process-specific transcription factors from heterogeneous high-throughput data;
  • g:Profiler, a web server for functional analysis of gene lists with Gene Ontology, pathways and DNA elements, gene ID conversion and gene orthology search;
  • GraphWeb, a module detection and functional analysis tool for biological networks;
  • KEGGanim, a visualisation and animation tool for linking biological pathways and microarray measurements;
  • VISHIC, a software for detecting functionally optimal gene clusters in microarray data;
  • MEM, a web server for studying gene coexpression across thousands of microarray datasets.

Previous affiliations:
BIIT Group at the University of Tartu, Estonia.
Luscombe Group at EMBL-EBI, United Kingdom.

Publications
[Google Scholar]
2014
  • Jüri Reimand*, Omar Wagih, Gary D. Bader: Evolutionary constraint and disease associations of post-translational modification sites in human genomes. (2014) PLOS Genetics, in press.
    [signalling][functional analysis][networks]
  • Mona Meyer*, Jüri Reimand*, Xiaoyang Lan, Renee Head, Xueming Zhu, Michelle Kushida, Jane Bayani, Jessica C. Pressey, Anath Lionel, Ian D. Clarke, Michael Cusimano, Jeremy Squire, Stephen Scherer, Mark Bernstein, Melanie A. Woodin, Gary D. Bader, and Peter B. Dirks: Single cell derived clonal analysis of human glioblastoma links functional and genomic heterogeneity. (2014) PNAS, in press.
    [cancer][functional analysis][networks]
  • Marcel Kool, David T.W. Jones, Natalie Jäger, Paul A. Northcott, Trevor J. Pugh, Volker Hovestadt, Rosario M. Piro, L. Adriana Esparza, Shirley L. Markant, Marc Remke, Till Milde, Franck Bourdeaut, Marina Ryzhova, Dominik Sturm, Elke Pfaff, Sebastian Stark, Sonja Hutter, Huriye Seker-Cin, Pascal Johann, Sebastian Bender, Christin Schmidt, Tobias Rausch, David Shih, Jüri Reimand, Laura Sieber, Andrea Wittmann, Linda Linke, Hendrik Witt, Ursula D. Weber, Marc Zapatka, Rainer König, Rameen Beroukhim, Guillaume Bergthold, Peter van Sluis, Richard Volckmann, Jan Koster, Rogier Versteeg, Sabine Schmidt, Stephan Wolf, Chris Lawerenz, Cynthia C. Bartholomae, Christof von Kalle, Andreas Unterberg, Christel Herold-Mende, Silvia Hofer, Andreas E. Kulozik, Andreas von Deimling, Wolfram Scheurlen, Jörg Felsberg, Guido Reifenberger, Martin Hasselblatt, John R. Crawford, Gerald A. Grant, Nada Jabado, Arie Perry, Cynthia Cowdrey, Sydney Croul, Gelareh Zadeh, Jan O. Korbel, Francois Doz, Olivier Delattre, Gary D. Bader, Martin G. McCabe, V. Peter Collins, Mark W. Kieran, Yoon-Jae Cho, Scott L. Pomeroy, Olaf Witt, Benedikt Brors, Michael D. Taylor, Ulrich Schüller, Andrey Korshunov, Roland Eils, Robert J. Wechsler-Reya, Peter Lichter, Stefan M. Pfister on behalf of the ICGC PedBrain Tumor Project: Genome sequencing of SHH medulloblastoma predicts genotype-related response to smoothened inhibition. (2014) Cancer Cell.2014 Mar 17;25(3):393-405. doi: 10.1016/j.ccr.2014.02.004
    [cancer][functional analysis][networks] [PDF]
  • Alvin Leung, Gary D. Bader*, Jüri Reimand*: HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery. (2014) Bioinformatics. 2014 Aug 1;30(15):2230-2. doi: 10.1093/bioinformatics/btu172
    [cancer][method][networks] [PDF][Cytoscape App Store][website]
2013
  • Jüri Reimand, Gary Bader, Adam Margolin, Abel Gonzalez-Perez, David Tamborero, Nuria Lopez-Bigas, John Weinstein, Joshua Stuart, Myles Axton: TCGA pan-cancer project, thread 2: Network models. (2013) Nature Genetics, ng.2787, doi:10.1038/ng.2787
    [cancer][networks] [website]
  • David 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-Bigas: Comprehensive identification of mutational cancer driver genes across 12 tumor types. (2013) Scientific Reports, 3, 2650; doi:10.1038/srep02650
    [cancer][dataset] [PDF]
  • Jüri Reimand, Omar Wagih, Gary D. Bader: The mutational landscape of phosphorylation signaling in cancer. (2013) Scientific Reports, 3, 2651; doi:10.1038/srep02651
    [cancer][signalling][networks][functional analysis][dataset] [PDF]
  • Abel Gonzalez-Perez, Ville Mustonen, Boris Reva, Graham R. S. Ritchie, Pau Creixell, Rachel Karchin, Miguel Vazquez, J. Lynn Fink, Karin S. Kassahn, John V. Pearson, Gary D. Bader, Paul C. Boutros, Lakshmi Muthuswamy, B. F. Francis Ouellette, Jüri Reimand, Rune Linding, Tatsuhiro Shibata, Alfonso Valencia, Adam Butler, Serge Dronov, Paul Flicek, Nick B. Shannon, Hannah Carter, Li Ding, Chris Sander, Josh M. Stuart, Lincoln D. Stein and Nuria Lopez-Bigas: Computational approaches to identify functional genetic variants in cancer genomes. (2013) Nature Methods, 10, 723-729; doi:10.1038/nmeth.2562
    [cancer][signalling][method] [PDF]
  • Jüri Reimand and Gary D. Bader: Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers. (2013) Molecular Systems Biology, 9:637, doi:10.1038/msb.2012.68
    [cancer][signalling][method][networks][functional analysis][dataset] [PDF][website]
2012
  • Liis Uusküla, Jaana Männik, Kristiina Rull, Ave Minajeva, Sulev Kõks, Pille Vaas, Pille Teesalu, Jüri Reimand* and Maris Laan*: Mid-gestational gene expression profile in placenta and link to pregnancy complications. (2012) PLoS ONE, 7(11): e49248; doi:10.1371/journal.pone.0049248
    [functional analysis][fertility][dataset][experimental] [PDF]
  • Xiaoling Xiong*, Anna Chorzalska*, Patrycja M. Dubielecka, Julie R. White, Yogindra Vedvyas, Cyrus V. Hedvat, Adriana Haimovitz-Friedman, Jason A. Koutcher, Jüri Reimand, Gary D. Bader, Janet A. Sawicki and Leszek Kotula: Disruption of Abi1/Hssh3bp1 expression induces prostatic intraepithelial neoplasia in the conditional Abi1/Hssh3bp1 KO mice. (2012) Oncogenesis, 1:e26; doi: 10.1038/oncsis.2012.28
    [functional analysis][cancer] [PDF]
  • Paul A. Northcott*, David J. H. Shih*, John Peacock, Livia Garzia, A. Sorana Morrissy, Thomas Zichner, Adrian M. Stütz, Andrey Korshunov, Jüri Reimand, Steven E. Schumacher, Rameen Beroukhim, David W. Ellison, Christian R. Marshall, Anath C. Lionel, Stephen Mack, Adrian Dubuc, Yuan Yao, Vijay Ramaswamy, Betty Luu, Adi Rolider, Florence M. G. Cavalli, Xin Wang, Marc Remke, Xiaochong Wu, Readman Y. B. Chiu, Andy Chu, Eric Chuah, Richard D. Corbett, Gemma R. Hoad, Shaun D. Jackman, Yisu Li, Allan Lo, Karen L. Mungall, Ka Ming Nip, Jenny Q. Qian, Anthony G. J. Raymond, Nina Thiessen, Richard J. Varhol, Inanc Birol, Richard A. Moore, Andrew J. Mungall, Robert Holt, Daisuke Kawauchi, Martine F. Roussel, Marcel Kool, David T. W. Jones, Hendrick Witt, Africa Fernandez-L, Anna M. Kenney, Robert J. Wechsler-Reya, Peter Dirks, Tzvi Aviv, Wieslawa A. Grajkowska, Marta Perek-Polnik, Christine C. Haberler, Olivier Delattre, Stephanie S. Reynaud, Francois F. Doz, Sarah S. Pernet-Fattet, Byung-Kyu Cho, Seung-Ki Kim, Kyu-Chang Wang, Wolfram Scheurlen, Charles G. Eberhart, Michelle Fevre-Montange, Anne Jouvet, Ian F. Pollack, Xing Fan, Karin M. Muraszko, G. Yancey Gillespie, Concezio Di Rocco, Luca Massimi, Erna M. C. Michiels, Nanne K. Kloosterhof, Pim J. French, Johan M. Kros, James M. Olson, Richard G. Ellenbogen, Karel Zitterbart, Leos Kren, Reid C. Thompson, Michael K. Cooper, Boleslaw Lach, Roger E. McLendon, Darell D. Bigner, Adam Fontebasso, Steffen Albrecht, Nada Jabado, Janet C. Lindsey, Simon Bailey, Nalin Gupta, William A. Weiss, Laszlo Bognar, Almos Klekner, Timothy E. Van Meter, Toshihiro Kumabe, Teiji Tominaga, Samer K. Elbabaa, Jeffrey R. Leonard, Joshua B. Rubin, Linda M. Liau, Erwin G. Van Meir, Maryam Fouladi, Hideo Nakamura, Giuseppe Cinalli, Miklos Garami, Peter Hauser, Ali G. Saad, Achille Iolascon, Shin Jung, Carlos G. Carlotti, Rajeev Vibhakar, Young Shin Ra, Shenandoah Robinson, Massimo Zollo, Claudia C. Faria, Jennifer A. Chan, Michael L. Levy, Poul H. B. Sorensen, Matthew Meyerson, Scott L. Pomeroy, Yoon-Jae Cho, Gary D. Bader, Uri Tabori, Cynthia E. Hawkins, Eric Bouffet, Stephen W. Scherer, James T. Rutka, David Malkin, Steven C. Clifford, Steven J. M. Jones, Jan O. Korbel, Stefan M. Pfister, Marco A. Marra and Michael D. Taylor: Subgroup-specific structural variation across 1,000 medulloblastoma genomes. (2012) Nature Aug 2;488(7409):49-56; doi: 10.1038/nature11327.
    [functional analysis][dataset][cancer] [link]
  • Jüri Reimand, Anu Aun, Jaak Vilo, Juan M. Vaquerizas, Juhan Sedman and Nicholas M. Luscombe: m:Explorer - multinomial regression models reveal positive and negative regulators of longevity in yeast quiescence. (2012) Genome Biol 13:R55; doi: 10.1186/gb-2012-13-6-r55.
    [gene regulation][method][functional analysis][dataset][networks][experimental] [PDF]
  • Jüri Reimand, Shirley Hui, Shobhit Jain, Brian Law and Gary D. Bader: Domain-mediated protein interaction prediction: From genome to network. (2012) FEBS letters (review). Aug 14;586(17):2751-63. doi: 10.1016/j.febslet.2012.04.027
    [networks][functional analysis] [PDF]
    * - equal contribution First/Last Authors.
2011
  • Signe Altmäe*, Jüri Reimand*, Outi Hovatta, Pu Zhang, Juha Kere, Triin Laisk, Merli Saare, Maire Peters, Jaak Vilo, Anneli Stavreus-Evers and Andres Salumets: Research Resource: Interactome of Human Embryo Implantation: Identification of Gene Expression Pathways, Regulation, and Integrated Regulatory Networks. (2011) Mol. Endocrinon. 26 (1): 203. doi: 10.1210/me.2011-1196
    [gene regulation][fertility][networks][dataset][experimental][PDF]
  • Jüri Reimand, Tambet Arak and Jaak Vilo: g:Profiler - a web server for functional interpretation of gene lists (2011 update). (2011) Nucl. Acids. Res. 39 (suppl 2): W307-W315. doi: 10.1093/nar/gkr378
    [method][functional analysis][PDF]
    * - equal contribution First Authors.
2010
  • Marko Lõoke, Jüri Reimand, Tiina Sedman, Juhan Sedman, Lari Järvinen, Signe Värv, Kadri Peil, Kersti Kristjuhan, Jaak Vilo and Arnold Kristjuhan: Relicensing of transcriptionally inactivated replication origins in budding yeast. (2010) J. Biol. Chem. 285(51):40004-11; doi:10.1074/jbc.M110.148924
    [gene regulation][experimental][PDF]
  • Nathalie Billon, Raivo Kolde*, Jüri Reimand*, Miguel C. Monteiro*, Meelis Kull, Hedi Peterson, Konstantin Tretjakov, Priit Adler, Brigitte Wdziekonski, Jaak Vilo, Christian Dani: Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development. (2010) Genome Biol. 11:R80; doi:10.1186/gb-2010-11-8-r80
    [gene regulation][dataset][experimental][PDF]
  • Jüri Reimand, Juan M. Vaquerizas, Annabel E. Todd, Jaak Vilo, Nicholas M. Luscombe: Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. (2010) Nucl. Acids Res. 38 (14): 4768-4777; doi:10.1093/nar/gkq232
    [gene regulation][networks][dataset][PDF]
    * - equal contribution First Authors.
2009
  • Priit Adler*, Raivo Kolde*, Meelis Kull, Aleksandr Tkachenko, Hedi Peterson, Jüri Reimand, Jaak Vilo: Mining for co-expression across hundreds of datasets using novel rank aggregation and visualisation methods. (2009) Genome Biol. 10:R139; doi:10.1186/gb-2009-10-12-r139
    [gene regulation][method][dataset][PDF]
  • Darya Krushevskaya, Hedi Peterson, Jüri Reimand, Meelis Kull, Jaak Vilo: VisHiC -- hierarchical functional enrichment analysis of microarray data. (2009) Nucl. Acids Res. 37:W587-W592; doi:10.1093/nar/gkp435
    [method][gene regulation][functional analysis] [PDF]
  • Herbert Schulz*, Raivo Kolde*, Priit Adler, Irene Aksoy, Konstantinos Anastassiadis, Michael Bader, Nathalie Billon, Helene Boeuf, Pierre-Yves Bourillot, Frank Buchholz, Christian Dani, Michael Xavier Doss, Lesley Forrester, Murielle Gitton, Domingos Henrique, Jürgen Hescheler, Heinz Himmelbauer, Norbert Hübner, Efthimia Karantzali, Androniki Kretsovali, Sandra Lubitz, Laurent Pradier, Meena Rai, Jüri Reimand, Alexandra Rolletschek, Agapios Sachinidis, Pierre Savatier, Francis Stewart, Mike P. Storm, Marina Trouillas, Jaak Vilo, Melanie J. Welham, Johannes Winkler, Anna M. Wobus, Antonis K. Hatzopoulos: The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. (2009) PLoS One. 4(9):e6804; doi:10.1371/journal.pone.0006804
    [gene regulation][dataset][experimental] [PDF]
  • Priit Adler*, Hedi Peterson*, Phaedra Agius, Jüri Reimand, Jaak Vilo: Ranking genes by their co-expression to subsets of pathway members. (2009) Ann NY Acad Sci. Mar 1158:1-13; doi:10.1111/j.1749-6632.2008.03747.x
    [gene regulation][functional analysis] [PDF]
    * - equal contribution First Authors.
2008
  • Jüri Reimand*, Laur Tooming*, Hedi Peterson, Priit Adler, Jaak Vilo: GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. (2008) Nucl. Acids Res. 36:W452-W459; doi:10.1093/nar/gkn230
    [networks][functional analysis][method] [PDF]
  • Priit Adler*, Jüri Reimand*, Jürgen Jänes, Raivo Kolde, Hedi Peterson, Jaak Vilo: KEGGanim: pathway animations for high-throughput data. (2008) Bioinformatics 24(4):588-590. doi:10.1093/bioinformatics/btm581
    [gene regulation][functional analysis][method] [PDF]
    * - equal contribution First Authors.
2007
  • Jüri Reimand, Meelis Kull, Hedi Peterson, Jaanus Hansen, Jaak Vilo: g:Profiler - a web-based toolset for functional profiling of gene lists from large-scale experiments. (2007) Nucleic Acids Res. 35:W193-W200. doi:10.1093/nar/gkm226
    [functional analysis][method] [PDF]
    * - equal contribution First Authors.
Education
  • 2006-10 - University of Tartu, Institute of Computer Science, Doctor of Philosophy (PhD) in computer science
  • 2005-06 - University of Tartu, Institute of Computer Science, Master of Science (MSc) in computer science
  • 2004-05 - Johannes Kepler University (Linz, Austria), exchange student
  • 2001-05 - University of Tartu,Institute of Computer Science, Bachelor of Science (BSc) in computer science
  • 1989-2000 - Tallinn English College, secondary education
Work experience
  • Since 2012 - Hospital for Sick Children, SickKids Research Institute, Department of Developmental and Stem Cell Biology, The Arthur and Sonia Labatt Brain Tumour Research Centre, postdoctoral fellow at the Taylor Lab
  • Since 2011 - University of Toronto, Terrence Donnelly Centre for Cellular and Biomolecular Research, postdoctoral fellow at the Bader Lab
  • 2008-2010 - University of Tartu, Institute of Computer Science, research fellow
  • 2007-08 - EMBL European Bioinformatics Institute (EMBL-EBI, Hinxton Genome Campus, Cambridge, UK), Marie Curie Biostar fellow
  • 2005-07 - University of Tartu, Institute of Computer Science, scientific programmer
  • 2004 - Aprote LTD, software developer
  • 2003-04 - Inspiral.net LTD, software developer
Awards and fellowships
  • Estonian Ministry of Education Grand Prix for Student Research (2010, for my PhD thesis)
  • Ustus Agur Fellowship of the Association of Information Technology and Telecommunications (2009)
  • Artur Lind Fellowship of the Estonian Gene Centre (2009)
  • BioSapiens ISMB/ECCB Travel Fellowship (2009)
  • PhD fellowship of Estonian Information Technology Foundation (2007)
  • European Commission's Marie Curie Host Fellowship for Early Stage Training (EMBL-EBI) (2007-2008)