publications

  • SyBValS: a validation and error resolution service for biological pathway maps
    Y. Z. Ozgul, U. Dogrusoz, H. Balci
    BMC Genomics, 2025. DOI: 10.1186/s12864-025-12454-4
  • CMGV: Algorithms and a unified framework for complexity management in graph visualization
    O. Zafar, U. Dogrusoz, H. Balci, A. F. Halac
    Information Visualization, 2025. DOI: 10.1177/14738716251383173
  • Building Immune Digital Twins: An International and Transdisciplinary Community Effort
    A. Niarakis, G. An, L. Ladeira, …, H. Balci, …, and R. Laubenbacher
    ImmunoInformatics, 2025. DOI: 10.1016/j.immuno.2025.100060
  • Immune digital twins for complex human pathologies: applications, limitations, and challenges
    A. Niarakis, R. Laubenbacher, G. An, Y. Ilan, …, H. Balci, …, and J. A. Glazier
    NPJ Systems Biology and Applications, 10(01), 141, 2024. DOI: 10.1038/s41540-024-00450-5
  • WikiPathways 2024: next generation pathway database
    A. Agrawal, H. Balcı, K. Hanspers, S. L. Coort, M. Martens, D. N. Slenter, …, and A. R. Pico
    Nucleic Acids Research, 52(D1), D679-D689, 2024. DOI: 10.1093/nar/gkad960
  • SyBLaRS: A web service for laying out, rendering and mining biological maps in SBGN, SBML and more
    H. Balci, U. Dogrusoz, Y. Z. Ozgul, and P. Atayev
    PLOS Computational Biology, 18(11), pp. 1-12, 2022. DOI: 10.1371/journal.pcbi.1010635
  • fCoSE: a fast compound graph layout algorithm with constraint support
    H. Balci and U. Dogrusoz
    IEEE Transactions on Visualization and Computer Graphics, 28(12), pp. 4582-4593, 2022. DOI: 10.1109/TVCG.2021.3095303
  • CoSEP: a compound spring embedder layout algorithm with support for ports
    A. Okka, U. Dogrusoz, and H. Balci
    Information Visualization, 20(2-3), pp. 151-169, 2021. DOI: 10.1177/14738716211028136
  • Newt: a comprehensive web-based tool for viewing, constructing, and analyzing biological maps
    H. Balci, M. C. Siper, N. Saleh, I. Safarli, L. Roy, M. Kilicarslan, R. Ozaydin, A. Mazein, C. Auffray, O. Babur, E. Demir, and U. Dogrusoz
    Bioinformatics, 37(10), pp. 1475-1477, 2021. DOI: 10.1093/bioinformatics/btaa850
  • Efficient methods and readily customizable libraries for managing complexity of large networks
    U. Dogrusoz, A. Karacelik, I. Safarli, H. Balci, L. Dervishi, and M. C. Siper
    PLOS ONE, 13(5): e0197238, 2018. DOI: 10.1371/journal.pone.0197238
  • Sun position estimation and tracking for virtual object placement in time-lapse videos
    H. Balci and U. Gudukbay
    Signal, Image and Video Processing, 11(5), pp. 817-824, 2017. DOI: 10.1007/s11760-016-1027-x