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Items: 1 to 50 of 193

1.

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.

2.

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.

3.

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.

4.

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.

PMID:
30007540
5.

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.

PMID:
29518522
6.

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.

7.

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.

8.

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
9.

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
10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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
16.

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.

17.

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.

18.

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
19.

Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients.

Fey D, Halasz M, Dreidax D, Kennedy SP, Hastings JF, Rauch N, Munoz AG, Pilkington R, Fischer M, Westermann F, Kolch W, Kholodenko BN, Croucher DR.

Sci Signal. 2015 Dec 22;8(408):ra130. doi: 10.1126/scisignal.aab0990.

PMID:
26696630
20.

Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation.

Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E.

Angew Chem Int Ed Engl. 2016 Jan 18;55(3):983-6. doi: 10.1002/anie.201509272. Epub 2015 Dec 8.

21.

Frequency modulation of ERK activation dynamics rewires cell fate.

Ryu H, Chung M, Dobrzyński M, Fey D, Blum Y, Lee SS, Peter M, Kholodenko BN, Jeon NL, Pertz O.

Mol Syst Biol. 2015 Nov 27;11(11):838. doi: 10.15252/msb.20156458. Erratum in: Mol Syst Biol. 2016 Apr;12(4):866.

22.

Feedback regulation in cell signalling: Lessons for cancer therapeutics.

Nguyen LK, Kholodenko BN.

Semin Cell Dev Biol. 2016 Feb;50:85-94. doi: 10.1016/j.semcdb.2015.09.024. Epub 2015 Oct 19. Review.

PMID:
26481970
23.

MST2-RASSF protein-protein interactions through SARAH domains.

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

Brief Bioinform. 2016 Jul;17(4):593-602. doi: 10.1093/bib/bbv070. Epub 2015 Oct 5.

24.

Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor Effects.

Kholodenko BN.

Cell Rep. 2015 Sep 22;12(11):1939-49. doi: 10.1016/j.celrep.2015.08.014. Epub 2015 Sep 3.

25.

The dynamic control of signal transduction networks in cancer cells.

Kolch W, Halasz M, Granovskaya M, Kholodenko BN.

Nat Rev Cancer. 2015 Sep;15(9):515-27. doi: 10.1038/nrc3983. Epub 2015 Aug 20. Review.

PMID:
26289315
26.

Protein-protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose-responses.

Varusai TM, Kolch W, Kholodenko BN, Nguyen LK.

Mol Biosyst. 2015 Oct;11(10):2750-62. doi: 10.1039/c5mb00385g.

PMID:
26266875
27.

DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks.

Nguyen LK, Degasperi A, Cotter P, Kholodenko BN.

Sci Rep. 2015 Jul 29;5:12569. doi: 10.1038/srep12569.

28.

G Protein-Coupled Receptor Signaling Networks from a Systems Perspective.

Roth S, Kholodenko BN, Smit MJ, Bruggeman FJ.

Mol Pharmacol. 2015 Sep;88(3):604-16. doi: 10.1124/mol.115.100057. Epub 2015 Jul 10. Review.

PMID:
26162865
29.

Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant Transformation.

Milewska M, Romano D, Herrero A, Guerriero ML, Birtwistle M, Quehenberger F, Hatzl S, Kholodenko BN, Segatto O, Kolch W, Zebisch A.

PLoS One. 2015 Jun 12;10(6):e0129859. doi: 10.1371/journal.pone.0129859. eCollection 2015.

30.

Silence on the relevant literature and errors in implementation.

Bastiaens P, Birtwistle MR, Blüthgen N, Bruggeman FJ, Cho KH, Cosentino C, de la Fuente A, Hoek JB, Kiyatkin A, Klamt S, Kolch W, Legewie S, Mendes P, Naka T, Santra T, Sontag E, Westerhoff HV, Kholodenko BN.

Nat Biotechnol. 2015 Apr;33(4):336-9. doi: 10.1038/nbt.3185. No abstract available.

PMID:
25850052
31.

Network-based identification of feedback modules that control RhoA activity and cell migration.

Kim TH, Monsefi N, Song JH, von Kriegsheim A, Vandamme D, Pertz O, Kholodenko BN, Kolch W, Cho KH.

J Mol Cell Biol. 2015 Jun;7(3):242-52. doi: 10.1093/jmcb/mjv017. Epub 2015 Mar 16.

PMID:
25780058
32.

Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate.

Nguyen LK, Cavadas MA, Kholodenko BN, Frank TD, Cheong A.

Cell Mol Life Sci. 2015 Jun;72(12):2431-43. doi: 10.1007/s00018-015-1850-1. Epub 2015 Feb 20.

33.

Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies.

Tortolina L, Duffy DJ, Maffei M, Castagnino N, Carmody AM, Kolch W, Kholodenko BN, De Ambrosi C, Barla A, Biganzoli EM, Nencioni A, Patrone F, Ballestrero A, Zoppoli G, Verri A, Parodi S.

Oncotarget. 2015 Mar 10;6(7):5041-58.

34.

Signalling mechanisms regulating phenotypic changes in breast cancer cells.

Volinsky N, McCarthy CJ, von Kriegsheim A, Saban N, Okada-Hatakeyama M, Kolch W, Kholodenko BN.

Biosci Rep. 2015 Mar 18;35(2). pii: e00178. doi: 10.1042/BSR20140172.

35.

Competing to coordinate cell fate decisions: the MST2-Raf-1 signaling device.

Nguyen LK, Matallanas DG, Romano D, Kholodenko BN, Kolch W.

Cell Cycle. 2015;14(2):189-99. doi: 10.4161/15384101.2014.973743.

36.

A dynamic model of the hypoxia-inducible factor 1a (HIF-1a) network.

Nguyen LK, Cavadas MA, Scholz CC, Fitzpatrick SF, Bruning U, Cummins EP, Tambuwala MM, Manresa MC, Kholodenko BN, Taylor CT, Cheong A.

J Cell Sci. 2015 Jan 15;128(2):422. doi: 10.1242/jcs.167304. No abstract available.

37.

Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity.

Nagashima T, Inoue N, Yumoto N, Saeki Y, Magi S, Volinsky N, Sorkin A, Kholodenko BN, Okada-Hatakeyama M.

FEBS J. 2015 Feb;282(4):613-29. doi: 10.1111/febs.13172. Epub 2015 Jan 8.

38.

Ubiquitin chain specific auto-ubiquitination triggers sustained oscillation, bistable switches and excitable firing.

Nguyen LK, Zhao Q, Varusai TM, Kholodenko BN.

IET Syst Biol. 2014 Dec;8(6):282-92. doi: 10.1049/iet-syb.2014.0024.

PMID:
25478702
39.

The ErbB4 CYT2 variant protects EGFR from ligand-induced degradation to enhance cancer cell motility.

Kiuchi T, Ortiz-Zapater E, Monypenny J, Matthews DR, Nguyen LK, Barbeau J, Coban O, Lawler K, Burford B, Rolfe DJ, de Rinaldis E, Dafou D, Simpson MA, Woodman N, Pinder S, Gillett CE, Devauges V, Poland SP, Fruhwirth G, Marra P, Boersma YL, Plückthun A, Gullick WJ, Yarden Y, Santis G, Winn M, Kholodenko BN, Martin-Fernandez ML, Parker P, Tutt A, Ameer-Beg SM, Ng T.

Sci Signal. 2014 Aug 19;7(339):ra78. doi: 10.1126/scisignal.2005157.

PMID:
25140053
40.

Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses.

Dobrzyński M, Nguyen LK, Birtwistle MR, von Kriegsheim A, Blanco Fernández A, Cheong A, Kolch W, Kholodenko BN.

J R Soc Interface. 2014 Sep 6;11(98):20140383. doi: 10.1098/rsif.2014.0383.

41.

Protein interaction switches coordinate Raf-1 and MST2/Hippo signalling.

Romano D, Nguyen LK, Matallanas D, Halasz M, Doherty C, Kholodenko BN, Kolch W.

Nat Cell Biol. 2014 Jul;16(7):673-84. doi: 10.1038/ncb2986. Epub 2014 Jun 15.

PMID:
24929361
42.

The APC network regulates the removal of mutated cells from colonic crypts.

Song JH, Huels DJ, Ridgway RA, Sansom OJ, Kholodenko BN, Kolch W, Cho KH.

Cell Rep. 2014 Apr 10;7(1):94-103. doi: 10.1016/j.celrep.2014.02.043. Epub 2014 Mar 27.

43.

Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration.

Santra T, Kolch W, Kholodenko BN.

PLoS Comput Biol. 2014 Feb 13;10(2):e1003385. doi: 10.1371/journal.pcbi.1003385. eCollection 2014 Feb. Review.

44.

Polyubiquitin chain assembly and organization determine the dynamics of protein activation and degradation.

Nguyen LK, Dobrzyński M, Fey D, Kholodenko BN.

Front Physiol. 2014 Jan 24;5:4. doi: 10.3389/fphys.2014.00004. eCollection 2014.

45.

Evaluating strategies to normalise biological replicates of Western blot data.

Degasperi A, Birtwistle MR, Volinsky N, Rauch J, Kolch W, Kholodenko BN.

PLoS One. 2014 Jan 27;9(1):e87293. doi: 10.1371/journal.pone.0087293. eCollection 2014.

46.

Systems biology-embedded target validation: improving efficacy in drug discovery.

Vandamme D, Minke BA, Fitzmaurice W, Kholodenko BN, Kolch W.

Wiley Interdiscip Rev Syst Biol Med. 2014 Jan-Feb;6(1):1-11. doi: 10.1002/wsbm.1253. Epub 2013 Nov 8.

PMID:
24214316
47.

Systems medicine: opportunities and challenges for systems biology approaches.

Kolch W, Kholodenko BN.

FEBS J. 2013 Dec;280(23):5937. doi: 10.1111/febs.12560. Epub 2013 Oct 30.

48.

Complexity of receptor tyrosine kinase signal processing.

Volinsky N, Kholodenko BN.

Cold Spring Harb Perspect Biol. 2013 Aug 1;5(8):a009043. doi: 10.1101/cshperspect.a009043. Review.

49.

Systems medicine: helping us understand the complexity of disease.

Vandamme D, Fitzmaurice W, Kholodenko B, Kolch W.

QJM. 2013 Oct;106(10):891-5. doi: 10.1093/qjmed/hct163. Epub 2013 Jul 30. Review.

PMID:
23904523
50.

When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling.

Nguyen LK, Kolch W, Kholodenko BN.

Cell Commun Signal. 2013 Jul 31;11:52. doi: 10.1186/1478-811X-11-52. Review.

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