Search Results - "Rukhlenko, Oleksii"

MAPK kinase signalling dynamics regulate cell fate decisions and drug resistance by Rauch, Nora, Rukhlenko, Oleksii S, Kolch, Walter, Kholodenko, Boris N

“…•Distinct cell fates result from different spatiotemporal MAPK dynamics.•Versatile MAPK dynamics include adaptive/sustained activity, switches and…”
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Reversing pathological cell states: the road less travelled can extend the therapeutic horizon by Kholodenko, Boris N., Kolch, Walter, Rukhlenko, Oleksii S.

“…•The ability to determine cell states is essential for understanding cell fate decisions•Recent methods, such as pseudotime and RNA velocity, allow mapping…”
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A systematic analysis of signaling reactivation and drug resistance by Kholodenko, Boris N., Rauch, Nora, Kolch, Walter, Rukhlenko, Oleksii S.

“…Increasing evidence suggests that the reactivation of initially inhibited signaling pathways causes drug resistance. Here, we analyze how network topologies…”
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Control of cell state transitions by Rukhlenko, Oleksii S., Halasz, Melinda, Rauch, Nora, Zhernovkov, Vadim, Prince, Thomas, Wynne, Kieran, Maher, Stephanie, Kashdan, Eugene, MacLeod, Kenneth, Carragher, Neil O., Kolch, Walter, Kholodenko, Boris N.

“…Understanding cell state transitions and purposefully controlling them is a longstanding challenge in biology. Here we present cell state transition assessment…”
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The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells by Fey, Dirk, Matallanas, David, Rauch, Jens, Rukhlenko, Oleksii S., Kholodenko, Boris N.

“…The intricate dynamic control and plasticity of RAS to ERK mitogenic, survival and apoptotic signalling has mystified researches for more than 30 years…”
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Mathematical Modeling of Intravascular Blood Coagulation under Wall Shear Stress by Rukhlenko, Oleksii S, Dudchenko, Olga A, Zlobina, Ksenia E, Guria, Georgy Th

“…Increased shear stress such as observed at local stenosis may cause drastic changes in the permeability of the vessel wall to procoagulants and thus initiate…”
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Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration by Bolado-Carrancio, Alfonso, Rukhlenko, Oleksii S, Nikonova, Elena, Tsyganov, Mikhail A, Wheeler, Anne, Garcia-Munoz, Amaya, Kolch, Walter, von Kriegsheim, Alex, Kholodenko, Boris N

“…Migrating cells need to coordinate distinct leading and trailing edge dynamics but the underlying mechanisms are unclear. Here, we combine experiments and…”
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Modeling the Nonlinear Dynamics of Intracellular Signaling Networks by Rukhlenko, Oleksii S, Kholodenko, Boris N

“…This protocol illustrates a pipeline for modeling the nonlinear behavior of intracellular signaling pathways. At fixed spatial points, nonlinear signaling…”
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Cell-specific models reveal conformation-specific RAF inhibitor combinations that synergistically inhibit ERK signaling in pancreatic cancer cells by Sevrin, Thomas, Imoto, Hiroaki, Robertson, Sarah, Rauch, Nora, Dyn’ko, Uscinnia, Koubova, Katerina, Wynne, Kieran, Kolch, Walter, Rukhlenko, Oleksii S., Kholodenko, Boris N.

“…Pancreatic ductal adenocarcinoma (PDAC) presents significant challenges for targeted clinical interventions due to prevalent KRAS mutations, rendering PDAC…”
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Cell State Transition Models Stratify Breast Cancer Cell Phenotypes and Reveal New Therapeutic Targets by Rukhlenko, Oleksii S, Imoto, Hiroaki, Tambde, Ayush, McGillycuddy, Amy, Junk, Philipp, Tuliakova, Anna, Kolch, Walter, Kholodenko, Boris N

“…Understanding signaling patterns of transformation and controlling cell phenotypes is a challenge of current biology. Here we applied a cell State Transition…”
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Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor by Erickson, Keesha E, Rukhlenko, Oleksii S, Shahinuzzaman, Md, Slavkova, Kalina P, Lin, Yen Ting, Suderman, Ryan, Stites, Edward C, Anghel, Marian, Posner, Richard G, Barua, Dipak, Kholodenko, Boris N, Hlavacek, William S

“…Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation…”
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Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D by Kennedy, Susan A., Jarboui, Mohamed-Ali, Srihari, Sriganesh, Raso, Cinzia, Bryan, Kenneth, Dernayka, Layal, Charitou, Theodosia, Bernal-Llinares, Manuel, Herrera-Montavez, Carlos, Krstic, Aleksandar, Matallanas, David, Kotlyar, Max, Jurisica, Igor, Curak, Jasna, Wong, Victoria, Stagljar, Igor, LeBihan, Thierry, Imrie, Lisa, Pillai, Priyanka, Lynn, Miriam A., Fasterius, Erik, Al-Khalili Szigyarto, Cristina, Breen, James, Kiel, Christina, Serrano, Luis, Rauch, Nora, Rukhlenko, Oleksii, Kholodenko, Boris N., Iglesias-Martinez, Luis F., Ryan, Colm J., Pilkington, Ruth, Cammareri, Patrizia, Sansom, Owen, Shave, Steven, Auer, Manfred, Horn, Nicola, Klose, Franziska, Ueffing, Marius, Boldt, Karsten, Lynn, David J., Kolch, Walter

“…Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their…”
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Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction by Thomaseth, Caterina, Fey, Dirk, Santra, Tapesh, Rukhlenko, Oleksii S., Radde, Nicole E., Kholodenko, Boris N.

“…Modular Response Analysis (MRA) is a method to reconstruct signalling networks from steady-state perturbation data which has frequently been used in different…”
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New insights into RAS biology reinvigorate interest in mathematical modeling of RAS signaling by Erickson, Keesha E., Rukhlenko, Oleksii S., Posner, Richard G., Hlavacek, William S., Kholodenko, Boris N.

“…RAS is the most frequently mutated gene across human cancers, but developing inhibitors of mutant RAS has proven to be challenging. Given the difficulties of…”
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Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling by Rukhlenko, Oleksii S, Khorsand, Fahimeh, Krstic, Aleksandar, Rozanc, Jan, Alexopoulos, Leonidas G, Rauch, Nora, Erickson, Keesha E, Hlavacek, William S, Posner, Richard G, Gómez-Coca, Silvia, Rosta, Edina, Fitzgibbon, Cheree, Matallanas, David, Rauch, Jens, Kolch, Walter, Kholodenko, Boris N

“…Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical…”
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A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression by Imoto, Hiroaki, Rauch, Nora, Neve, Ashish J, Khorsand, Fahimeh, Kreileder, Martina, Alexopoulos, Leonidas G, Rauch, Jens, Okada, Mariko, Kholodenko, Boris N, Rukhlenko, Oleksii S

“…Cancer cells often adapt to targeted therapies, yet the molecular mechanisms underlying adaptive resistance remain only partially understood. Here, we explore…”
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On the chemotherapeutic agents localization in tissue by means of snake venoms by Rukhlenko, Oleksii S, Guria, Georgy Th, Vorobiev, Andrey I

“…Abstract The efficiency of anti-tumour drug strongly depends on its dose. Higher drug doses and exposure times usually result in better treatment. It is why…”
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Cell state transition analysis identifies interventions that improve control of Mycobacterium tuberculosis infection by susceptible macrophages by Yabaji, Shivraj M., Rukhlenko, Oleksii S., Chatterjee, Sujoy, Bhattacharya, Bidisha, Wood, Emily, Kasaikina, Marina, Kholodenko, Boris N., Gimelbrant, Alexander A., Kramnik, Igor

“…Understanding cell state transitions and purposefully controlling them to improve therapies is a longstanding challenge in biological research and medicine…”
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Reconstructing static and dynamic models of signaling pathways using Modular Response Analysis by Santra, Tapesh, Rukhlenko, Oleksii, Zhernovkov, Vadim, Kholodenko, Boris N.

“…In this review we discuss the origination and evolution of Modular Response Analysis (MRA), which is a physics-based method for reconstructing quantitative…”
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Channeling macrophage polarization by rocaglates increases macrophage resistance to Mycobacterium tuberculosis by Chatterjee, Sujoy, Yabaji, Shivraj M., Rukhlenko, Oleksii S., Bhattacharya, Bidisha, Waligurski, Emily, Vallavoju, Nandini, Ray, Somak, Kholodenko, Boris N., Brown, Lauren E., Beeler, Aaron B., Ivanov, Alexander R., Kobzik, Lester, Porco, John A., Kramnik, Igor

“…Macrophages contribute to host immunity and tissue homeostasis via alternative activation programs. M1-like macrophages control intracellular bacterial…”
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