Department of Bioinformatics – BiGCaT

Publications


Recent Papers

  1. Using the semantic web for rapid integration of WikiPathways with other biological online data resources.
    A. Waagmeester, M. Kutmon, A. Riutta, R. Miller, EL. Willighagen, CT. Evelo, AR. Pico
    Jun 2016. PLoS Comput Biol 12 (6), e1004989+. 10.1371/journal.pcbi.1004989
  2. Reactome from a WikiPathways perspective.
    A. Bohler, G. Wu, M. Kutmon, LA. Pradhana, SL. Coort, K. Hanspers, R. Haw, AR. Pico, CT. Evelo
    May 2016. PLoS Comput Biol, 12 (5), e1004941+. 10.1371/journal.pcbi.1004941
  3. Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: Knowing the knowns.
    D. Digles, B. Zdrazil, JM. Neefs, H. Van Vlijmen, C. Herhaus, A. Caracoti,  J. Brea, B. Roibas, MI. Loza, N. Queralt Rosinach, LI. Furlong, A. Gaulton, L. Bartek, S. Senger, C. Chichester, O. Engkvist, CT. Evelo, NI. Franklin, D. Marren, GF. Ecker, E. Jacoby
    May 2016. Med. Chem. Commun. 10.1039/c6md00065g
  4. Gene promoter DNA methylation patterns have a limited role in orchestrating transcriptional changes in the fetal liver in response to maternal folate depletion during pregnancy.
    JA. McKay, M. Adriaens, CT. Evelo, D. Ford, JC. Mathers
    May 2016. Mol. Nutr. Food Res., 10.1002/mnfr.201600079
  5. The systems biology format converter.
    N. Rodriguez, JB. Pettit, P. Dalle Pezze, L. Li, A. Henry, MP van Iersel, G. Jalowicki, M. Kutmon, KN. Natarajan, D. Tolnay, MI. Stefan, CT. Evelo, N. Le Novère
    Apr 2016. BMC Bioinformatics 17 (1). 10.1186/s12859-016-1000-2
  6. The FAIR Guiding Principles for scientific data management and stewardship.
    MD. Wilkinson, M. Dumontier, IJ. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, JW. Boiten, LB. da Silva Santos, PE. Bourne, J. Bouwman, AJ. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, CT. Evelo, R. Finkers, A. Gonzalez-Beltran, AJ. Gray, P. Groth, C. Goble, JS. Grethe, J. Heringa, PA. ‘t Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, SJ. Lusher, ME. Martone, A. Mons, AL. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, SA. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, MA. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, B. Mons
    Mar 2016. Scientific Data, 3:160018. 10.1038/sdata.2016.18
  7. Inferring causal molecular networks: empirical assessment through a community-based effort.
    SM. Hill, LM. Heiser, T. Cokelaer, M. Unger, NK. Nesser, DE. Carlin, Y. Zhang, A. Sokolov, EO. Paull, CK. Wong, K. Graim, A. Bivol, H. Wang, F. Zhu, B. Afsari, LV. Danilova, AV. Favorov, W. Shing Lee, D. Taylor, CW. Hu, BL. Long, DP. Noren, AJ. Bisberg, The HPN-DREAM Consortium (BiGCaT members listed alphabetically : A. BohlerG. Budak , C. EveloM. Kutmon), GB. Mills, JW. Gray, M. Kellen, T. Norman, S. Friend, AA. Qutub, EJ. Fertig, Y. Guan, M. Song, JM. Stuart, PT. Spellman, H. Koeppl, G. Stolovitzky, J. Saez-Rodriguez, S. Mukherjee
    Feb 2016. Nature Methods10.1038/nmeth.3773
  8. The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands.
    L. Eijssen, C. Evelo, R. Kok, B. Mons, R. Hooft, et. al.
    Feb 2016. F1000Research, 4:33. 10.12688/f1000research.6009.2
  9. WikiPathways: capturing the full diversity of pathway knowledge.
    M. Kutmon, A. Riutta, N. Nunes, K. Hanspers, EL. Willighagen, A. Bohler, J. Mélius, A. Waagmeester, SR. Sinha, R. Miller, SL. Coort, E. Cirillo, B. Smeets, CT. Evelo, AR. Pico
    Jan 2016. Nucleic Acids Research. 44 (D1): D488-D494. 10.1093/nar/gkv1024

A full list can be found on this page.