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Items: 1 to 20 of 184

1.

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D.

Kennedy SA, Jarboui MA, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn MA, Fasterius E, Al-Khalili Szigyarto C, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko BN, Iglesias-Martinez LF, Ryan CJ, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn DJ, Kolch W.

Nat Commun. 2020 Jan 24;11(1):499. doi: 10.1038/s41467-019-14224-9.

2.

An integrative computational approach for a prioritization of key transcription regulators associated with nanomaterial-induced toxicity.

Zhernovkov V, Santra T, Cassidy H, Rukhlenko O, Matallanas D, Krstic A, Kolch W, Lobaskin V, Kholodenko BN.

Toxicol Sci. 2019 Jul 4. pii: kfz151. doi: 10.1093/toxsci/kfz151. [Epub ahead of print]

PMID:
31271423
3.

Mapping connections in signaling networks with ambiguous modularity.

Lill D, Rukhlenko OS, Mc Elwee AJ, Kashdan E, Timmer J, Kholodenko BN.

NPJ Syst Biol Appl. 2019 May 23;5:19. doi: 10.1038/s41540-019-0096-1. eCollection 2019.

4.

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

Erickson KE, Rukhlenko OS, Shahinuzzaman M, Slavkova KP, Lin YT, Suderman R, Stites EC, Anghel M, Posner RG, Barua D, Kholodenko BN, Hlavacek WS.

PLoS Comput Biol. 2019 Jan 17;15(1):e1006706. doi: 10.1371/journal.pcbi.1006706. eCollection 2019 Jan.

5.

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

Thomaseth C, Fey D, Santra T, Rukhlenko OS, Radde NE, Kholodenko BN.

Sci Rep. 2018 Nov 1;8(1):16217. doi: 10.1038/s41598-018-34353-3.

6.

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

Rukhlenko OS, Khorsand F, Krstic A, Rozanc J, Alexopoulos LG, Rauch N, Erickson KE, Hlavacek WS, Posner RG, Gómez-Coca S, Rosta E, Fitzgibbon C, Matallanas D, Rauch J, Kolch W, Kholodenko BN.

Cell Syst. 2018 Aug 22;7(2):161-179.e14. doi: 10.1016/j.cels.2018.06.002. Epub 2018 Jul 11.

7.

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

Erickson KE, Rukhlenko OS, Posner RG, Hlavacek WS, Kholodenko BN.

Semin Cancer Biol. 2019 Feb;54:162-173. doi: 10.1016/j.semcancer.2018.02.008. Epub 2018 Mar 5. Review.

8.

Transcriptionally inducible Pleckstrin homology-like domain, family A, member 1, attenuates ErbB receptor activity by inhibiting receptor oligomerization.

Magi S, Iwamoto K, Yumoto N, Hiroshima M, Nagashima T, Ohki R, Garcia-Munoz A, Volinsky N, Von Kriegsheim A, Sako Y, Takahashi K, Kimura S, Kholodenko BN, Okada-Hatakeyama M.

J Biol Chem. 2018 Feb 9;293(6):2206-2218. doi: 10.1074/jbc.M117.778399. Epub 2017 Dec 12.

9.

Performance of objective functions and optimisation procedures for parameter estimation in system biology models.

Degasperi A, Fey D, Kholodenko BN.

NPJ Syst Biol Appl. 2017 Aug 8;3:20. doi: 10.1038/s41540-017-0023-2. eCollection 2017.

10.

Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols.

Fey D, Aksamitiene E, Kiyatkin A, Kholodenko BN.

Methods Mol Biol. 2017;1636:417-453. doi: 10.1007/978-1-4939-7154-1_27.

PMID:
28730495
11.

Integrating network reconstruction with mechanistic modeling to predict cancer therapies.

Halasz M, Kholodenko BN, Kolch W, Santra T.

Sci Signal. 2016 Nov 22;9(455):ra114.

PMID:
27879396
12.

Probing the Heterogeneity of Protein Kinase Activation in Cells by Super-resolution Microscopy.

Zhang R, Fruhwirth GO, Coban O, Barrett JE, Burgoyne T, Lee SH, Simonson PD, Baday M, Kholodenko BN, Futter CE, Ng T, Selvin PR.

ACS Nano. 2017 Jan 24;11(1):249-257. doi: 10.1021/acsnano.6b05356. Epub 2016 Nov 3.

13.

SARAH Domain-Mediated MST2-RASSF Dimeric Interactions.

Sánchez-Sanz G, Tywoniuk B, Matallanas D, Romano D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV.

PLoS Comput Biol. 2016 Oct 7;12(10):e1005051. doi: 10.1371/journal.pcbi.1005051. eCollection 2016 Oct.

14.

HER2-HER3 dimer quantification by FLIM-FRET predicts breast cancer metastatic relapse independently of HER2 IHC status.

Weitsman G, Barber PR, Nguyen LK, Lawler K, Patel G, Woodman N, Kelleher MT, Pinder SE, Rowley M, Ellis PA, Purushotham AD, Coolen AC, Kholodenko BN, Vojnovic B, Gillett C, Ng T.

Oncotarget. 2016 Aug 9;7(32):51012-51026. doi: 10.18632/oncotarget.9963.

15.

Rac1 and RhoA: Networks, loops and bistability.

Nguyen LK, Kholodenko BN, von Kriegsheim A.

Small GTPases. 2018 Jul 4;9(4):316-321. doi: 10.1080/21541248.2016.1224399. Epub 2016 Sep 10. Review.

16.

MAPK kinase signalling dynamics regulate cell fate decisions and drug resistance.

Rauch N, Rukhlenko OS, Kolch W, Kholodenko BN.

Curr Opin Struct Biol. 2016 Dec;41:151-158. doi: 10.1016/j.sbi.2016.07.019. Epub 2016 Aug 10. Review.

17.

The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells.

Fey D, Matallanas D, Rauch J, Rukhlenko OS, Kholodenko BN.

Semin Cell Dev Biol. 2016 Oct;58:96-107. doi: 10.1016/j.semcdb.2016.06.011. Epub 2016 Jun 24. Review.

PMID:
27350026
18.

Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches.

Byrne KM, Monsefi N, Dawson JC, Degasperi A, Bukowski-Wills JC, Volinsky N, Dobrzyński M, Birtwistle MR, Tsyganov MA, Kiyatkin A, Kida K, Finch AJ, Carragher NO, Kolch W, Nguyen LK, von Kriegsheim A, Kholodenko BN.

Cell Syst. 2016 Jan 27;2(1):38-48. doi: 10.1016/j.cels.2016.01.003. Epub 2016 Jan 27.

19.

Frequency modulation of ERK activation dynamics rewires cell fate.

Ryu H, Chung M, Dobrzyński M, Fey D, Blum Y, Sik Lee S, Peter M, Kholodenko BN, Li Jeon N, Pertz O.

Mol Syst Biol. 2016 Apr 22;12(4):866. doi: 10.15252/msb.20166982. No abstract available.

20.

Three-factor models versus time series models: quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data.

Frank TD, Kiyatkin A, Cheong A, Kholodenko BN.

Math Med Biol. 2017 Jun 1;34(2):177-191. doi: 10.1093/imammb/dqw001.

PMID:
27079221

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