Publications

Adler, P., Reimand, J., Jänes, J., Kolde, R., Peterson, H., & Vilo, J. (2008). KEGGanim: pathway animations for high-throughput data. Bioinformatics24(4), 588–90. doi:10.1093/bioinformatics/btm581

Reimand, J., Tooming, L., Peterson, H., Adler, P., & Vilo, J. (2008). GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. Nucleic Acids Research36(Web Server issue)

Adler, P., Peterson, H., Agius, P., Reimand, J., & Vilo, J. (2009). Ranking genes by their co-expression to subsets of pathway members. Annals of the New York Academy of Sciences1158, 1–13.

Adler, P., Kolde, R., Kull, M., Tkachenko, A., Peterson, H., Reimand, J., & Vilo, J. (2009). Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods. Genome Biology10(12), R139.

Schulz, H., Kolde, R., Adler, P., Aksoy, I., Anastassiadis, K., Bader, M., Billon, N., Boeuf, H., Bourillot, P.-Y., Buchholz, F., Dani, C., Doss, M. X., Forrester, L., Gitton, M., Henrique, D., Hescheler, J., Himmelbauer, H., Hübner, N., Karantzali, E., Kretsovali, A., Lubitz, S., Pradier, L., Rai, M., Reimand, J., Rolletschek, A., Sachinidis, A., Savatier, P., Stewart, F., Storm, M. P., Trouillas, M., Vilo, J., Welham, M. J., Winkler, J., Wobus, A. M., & Hatzopoulos, A. K. (2009). The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PLoS ONE4(9), e6804. doi:10.1371/journal.pone.0006804

Billon, N., Kolde, R., Reimand, J., Monteiro, M. C., Kull, M., Peterson, H., Tretyakov, K., Adler, P., Wdziekonski, B., Vilo, J., & Dani, C. (2010). Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development. Genome Biology11(8), R80.

Kolde, R., Laur, S., Adler, P., & Vilo, J. (2012). Robust rank aggregation for gene list integration and meta-analysis. Bioinformatics28(4), 573–580.

Hériché, J.-K., Lees, J. G., Morilla, I., Walter, T., Petrova, B., Roberti, M. J., Hossain, M. J., Adler, P., Fernández, J. M., Krallinger M., Haering C. H., Vilo, J., Valencia, A., Ranea, J. A., Orengo, C., & Ellenberg, J. (2014). Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation. Molecular Biology of the Cell25(16), 2522–2536.

Lees, J. G., Hériché, J.-K., Morilla, I., Fernández, J. M., Adler, P., Krallinger, M., Vilo, J., Valencia, A., Ellenberg, J., Ranea, J. A., & Orengo, C. (2015). FUN-L: Gene prioritization for RNAi screens. Bioinformatics, btv073.

Örd, T., Örd, D., Adler, P., Vilo, J., & Örd, T. (2015). TRIB3 enhances cell viability during glucose deprivation in HEK293-derived cells by upregulating IGFBP2, a novel nutrient deficiency survival factor. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research1853(10), 2492-2505

Reimand, J., Arak, T., Adler, P., Kolberg, L., Reisberg, S., Peterson, H., Vilo, J. (2016). g:Profiler-a web server for functional interpretation of gene lists (2016 update). Nucleic Acids Res. doi: 10.1093/nar/gkw199