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Investigation of adaptive design and rewiring of Survival-Apoptosis-Mitogenic (SAM) signalling transduction network

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Mapping connections in signaling networks with ambiguous modularity

Author(s): Daniel Lill, Oleksii S. Rukhlenko, Anthony James Mc Elwee, Eugene Kashdan, Jens Timmer, Boris N. Kholodenko
Published in: npj Systems Biology and Applications, Issue 5/1, 2019, ISSN 2056-7189
DOI: 10.1038/s41540-019-0096-1

Reconstructing static and dynamic models of signaling pathways using Modular Response Analysis

Author(s): Tapesh Santra, Oleksii Rukhlenko, Vadim Zhernovkov, Boris N. Kholodenko
Published in: Current Opinion in Systems Biology, Issue 9, 2018, Page(s) 11-21, ISSN 2452-3100
DOI: 10.1016/j.coisb.2018.02.003

New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling

Author(s): Keesha E. Erickson, Oleksii S. Rukhlenko, Richard G. Posner, William S. Hlavacek, Boris N. Kholodenko
Published in: Seminars in Cancer Biology, Issue 54, 2019, Page(s) 162-173, ISSN 1044-579X
DOI: 10.1016/j.semcancer.2018.02.008

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling

Author(s): Oleksii S. Rukhlenko, Fahimeh Khorsand, Aleksandar Krstic, Jan Rozanc, Leonidas G. Alexopoulos, Nora Rauch, Keesha E. Erickson, William S. Hlavacek, Richard G. Posner, Silvia Gómez-Coca, Edina Rosta, Cheree Fitzgibbon, David Matallanas, Jens Rauch, Walter Kolch, Boris N. Kholodenko
Published in: Cell Systems, Issue 7/2, 2018, Page(s) 161-179.e14, ISSN 2405-4712
DOI: 10.1016/j.cels.2018.06.002

Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction

Author(s): Caterina Thomaseth, Dirk Fey, Tapesh Santra, Oleksii S. Rukhlenko, Nicole E. Radde, Boris N. Kholodenko
Published in: Scientific Reports, Issue 8/1, 2018, ISSN 2045-2322
DOI: 10.1038/s41598-018-34353-3

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor

Author(s): Keesha E. Erickson, Oleksii S. Rukhlenko, Md Shahinuzzaman, Kalina P. Slavkova, Yen Ting Lin, Ryan Suderman, Edward C. Stites, Marian Anghel, Richard G. Posner, Dipak Barua, Boris N. Kholodenko, William S. Hlavacek
Published in: PLOS Computational Biology, Issue 15/1, 2019, Page(s) e1006706, ISSN 1553-7358
DOI: 10.1371/journal.pcbi.1006706