Inflammatory Bowel Disease (IBD) Database

Professor M Kaur

Professor Takashi Gojobori

  1. Belinky, F., Nativ, N., Stelzer, G., Zimmerman, S., Iny Stein, T., Safran, M., and Lancet, D. (2015). PathCards: multi-source consolidation of human biological pathways. Database 2015.
  2. Ben-Ari Fuchs, S., Lieder, I., Stelzer, G., Mazor, Y., Buzhor, E., Kaplan, S., Bogoch, Y., Plaschkes, I., Shitrit, A., and Rappaport, N. (2016). GeneAnalytics: an integrative gene set analysis tool for next generation sequencing, RNAseq and microarray data. Omics: a journal of integrative biology 20, 139-151.
  3. Braschi, B., Denny, P., Gray, K., Jones, T., Seal, R., Tweedie, S., Yates, B., and Bruford, E. (2019). Genenames. org: the HGNC and VGNC resources in 2019. Nucleic acids research 47, D786-D792.
  4. Chen, E.Y., Tan, C.M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G.V., Clark, N.R., and Ma’ayan, A. (2013). Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC bioinformatics 14, 128.
  5. Cotto, K.C., Wagner, A.H., Feng, Y.-Y., Kiwala, S., Coffman, A.C., Spies, G., Wollam, A., Spies, N.C., Griffith, O.L., and Griffith, M. (2018). DGIdb 3.0: a redesign and expansion of the drug–gene interaction database. Nucleic acids research 46, D1068-D1073.
  6. Ho Sui, S.J., Mortimer, J.R., Arenillas, D.J., Brumm, J., Walsh, C.J., Kennedy, B.P., and Wasserman, W.W. (2005). oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic acids research 33, 3154-3164.
  7. Huang da, W., Sherman, B.T., and Lempicki, R.A. (2009). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37, 1-13.
  8. Hunt, S.E., McLaren, W., Gil, L., Thormann, A., Schuilenburg, H., Sheppard, D., Parton, A., Armean, I.M., Trevanion, S.J., and Flicek, P. (2018). Ensembl variation resources. Database 2018.
  9. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, D. (2002). The human genome browser at UCSC. Genome research 12, 996-1006.
  10. Kheradpour, P., and Kellis, M. (2014). Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic acids research 42, 2976-2987.
  11. Kuleshov, M.V., Jones, M.R., Rouillard, A.D., Fernandez, N.F., Duan, Q., Wang, Z., Koplev, S., Jenkins, S.L., Jagodnik, K.M., and Lachmann, A. (2016). Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic acids research 44, W90-W97.
  12. Lachmann, A., Xu, H., Krishnan, J., Berger, S.I., Mazloom, A.R., and Ma'ayan, A. (2010). ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments. Bioinformatics 26, 2438-2444.
  13. Lu, Z. (2011). PubMed and beyond: a survey of web tools for searching biomedical literature. Database 2011.
  14. Maglott, D., Ostell, J., Pruitt, K.D., and Tatusova, T. (2007). Entrez Gene: gene-centered information at NCBI. Nucleic acids research 35, D26-D31.
  15. Roberts, R.J. (2001). PubMed Central: The GenBank of the published literature (National Acad Sciences).
  16. Rosen, N., Chalifa-Caspi, V., Shmueli, O., Adato, A., Lapidot, M., Stampnitzky, J., Safran, M., and Lancet, D. (2003). GeneLoc: exon-based integration of human genome maps. Bioinformatics 19, i222-i224.
  17. Stelzer, G., Plaschkes, I., Oz-Levi, D., Alkelai, A., Olender, T., Zimmerman, S., Twik, M., Belinky, F., Fishilevich, S., and Nudel, R. (2016). VarElect: the phenotype-based variation prioritizer of the GeneCards Suite. BMC genomics 17, 444.
  18. Yoo, M., Shin, J., Kim, J., Ryall, K.A., Lee, K., Lee, S., Jeon, M., Kang, J., and Tan, A.C. (2015). DSigDB: drug signatures database for gene set analysis. Bioinformatics 31, 3069-3071.