publications

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