Publications by authors named "Boris Kholodenko"

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Lipid peroxidation and type I interferon coupling fuels pathogenic macrophage activation causing tuberculosis susceptibility.
Shivraj M Yabaji, Vadim Zhernovkov, Prasanna Babu Araveti, Suruchi Lata, Oleksii S Rukhlenko, Boris N Kholodenko

Elife· October 2025

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VEGF counteracts shear stress-determined arterial fate specification during capillary remodeling.
Dongying Chen, Oleksii S Rukhlenko, Divyesh Joshi, Martina Rudnicki, Brian G Coon, Boris N Kholodenko

bioRxiv· May 2025

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Lipid Peroxidation and Type I Interferon Coupling Fuels Pathogenic Macrophage Activation Causing Tuberculosis Susceptibility.
Shivraj M Yabaji, Vadim Zhernovkov, Prasanna Babu Araveti, Suruchi Lata, Oleksii S Rukhlenko, Boris N Kholodenko

bioRxiv· May 2025

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A structure-based modelling approach identifies effective drug combinations for RAS-mutant acute myeloid leukemia.
Luke Jones, Oleksii Rukhlenko, Tânia Dias, Hiroaki Imoto, Ciardha Carmody, Boris N Kholodenko

bioRxiv· May 2025

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cSTAR analysis identifies endothelial cell cycle as a key regulator of flow-dependent artery remodeling.
Hanqiang Deng, Oleksii S Rukhlenko, Divyesh Joshi, Xiaoyue Hu, Philipp Junk, Boris N Kholodenko

Sci Adv· January 2025

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Cell-specific models reveal conformation-specific RAF inhibitor combinations that synergistically inhibit ERK signaling in pancreatic cancer cells.
Thomas Sevrin, Hiroaki Imoto, Sarah Robertson, Nora Rauch, Uscinnia Dyn'ko, Boris N Kholodenko

Cell Rep· September 2024

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Cell State Transition Models Stratify Breast Cancer Cell Phenotypes and Reveal New Therapeutic Targets.
Oleksii S Rukhlenko, Hiroaki Imoto, Ayush Tambde, Amy McGillycuddy, Philipp Junk, Boris N Kholodenko

Cancers (Basel)· June 2024

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Reversing pathological cell states: the road less travelled can extend the therapeutic horizon.
Boris N Kholodenko, Walter Kolch, Oleksii S Rukhlenko

Trends Cell Biol· November 2023

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cSTAR analysis identifies endothelial cell cycle as a key regulator of flow-dependent artery remodeling.
Hanqiang Deng, Oleksii S Rukhlendo, Divyesh Joshi, Xiaoyue Hu, Philpp Junk, Boris N Kholodenko

bioRxiv· October 2023

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Cell state transition analysis identifies interventions that improve control of infection by susceptible macrophages.
Shivraj M Yabaji, Oleksii S Rukhlenko, Sujoy Chatterjee, Bidisha Bhattacharya, Emily Wood, Boris N Kholodenko

Sci Adv· September 2023

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A Combination of Conformation-Specific RAF Inhibitors Overcome Drug Resistance Brought about by RAF Overexpression.
Hiroaki Imoto, Nora Rauch, Ashish J Neve, Fahimeh Khorsand, Martina Kreileder, Boris N Kholodenko

Biomolecules· August 2023

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Cell state transition analysis identifies interventions that improve control of infection by susceptible macrophages.
Shivraj M Yabaji, Oleksii S Rukhlenko, Sujoy Chatterjee, Bidisha Bhattacharya, Emily Wood, Boris Kholodenko

bioRxiv· February 2023

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Control of cell state transitions.
Oleksii S Rukhlenko, Melinda Halasz, Nora Rauch, Vadim Zhernovkov, Thomas Prince, Boris N Kholodenko

Nature· September 2022

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Relationship Between Dimensionality and Convergence of Optimization Algorithms: A Comparison Between Data-Driven Normalization and Scaling Factor-Based Methods Using PEPSSBI.
Andrea Degasperi, Lan K Nguyen, Dirk Fey, Boris N Kholodenko

Methods Mol Biol· January 2022

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Can Systems Biology Advance Clinical Precision Oncology?
Andrea Rocca, Boris N Kholodenko

Cancers (Basel)· December 2021

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Channeling macrophage polarization by rocaglates increases macrophage resistance to .
Sujoy Chatterjee, Shivraj M Yabaji, Oleksii S Rukhlenko, Bidisha Bhattacharya, Emily Waligurski, Boris N Kholodenko

iScience· August 2021

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Reengineering protein-phosphorylation switches.
Boris N Kholodenko, Mariko Okada

Science· July 2021

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Modeling the Nonlinear Dynamics of Intracellular Signaling Networks.
Oleksii S Rukhlenko, Boris N Kholodenko

Bio Protoc· July 2021

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A systematic analysis of signaling reactivation and drug resistance.
Boris N Kholodenko, Nora Rauch, Walter Kolch, Oleksii S Rukhlenko

Cell Rep· May 2021

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Systems biology approaches to macromolecules: the role of dynamic protein assemblies in information processing.
Oleksii Rukhlenko, Boris N Kholodenko, Walter Kolch

Curr Opin Struct Biol· April 2021

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Inhaled multi-walled carbon nanotubes differently modulate global gene and protein expression in rat lungs.
Carole Seidel, Vadim Zhernovkov, Hilary Cassidy, Boris Kholodenko, David Matallanas

Nanotoxicology· March 2021

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Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration.
Alfonso Bolado-Carrancio, Oleksii S Rukhlenko, Elena Nikonova, Mikhail A Tsyganov, Anne Wheeler, Boris N Kholodenko

Elife· July 2020

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Acute Phase Response as a Biological Mechanism-of-Action of (Nano)particle-Induced Cardiovascular Disease.
Niels Hadrup, Vadim Zhernovkov, Nicklas Raun Jacobsen, Carola Voss, Maximilian Strunz, Boris Kholodenko

Small· May 2020

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Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS.
Susan A Kennedy, Mohamed-Ali Jarboui, Sriganesh Srihari, Cinzia Raso, Kenneth Bryan, Boris N Kholodenko

Nat Commun· January 2020

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An Integrative Computational Approach for a Prioritization of Key Transcription Regulators Associated With Nanomaterial-Induced Toxicity.
Vadim Zhernovkov, Tapesh Santra, Hilary Cassidy, Oleksii Rukhlenko, David Matallanas, Boris N Kholodenko

Toxicol Sci· October 2019

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