| Year |
Citation |
Score |
| 2020 |
Bolado-Carrancio A, Rukhlenko OS, Nikonova E, Tsyganov MA, Wheeler A, Garcia-Munoz A, Kolch W, von Kriegsheim A, Kholodenko BN. Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration. Elife. 9. PMID 32705984 DOI: 10.7554/Elife.58165 |
0.342 |
|
| 2020 |
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, ... ... Kholodenko BN, et al. Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRAS. Nature Communications. 11: 499. PMID 31980649 DOI: 10.1038/S41467-019-14224-9 |
0.398 |
|
| 2020 |
Bolado-Carrancio A, Rukhlenko OS, Nikonova E, Tsyganov MA, Wheeler A, Garcia-Munoz A, Kolch W, Kriegsheim Av, Kholodenko BN. Author response: Periodic propagating waves coordinate RhoGTPase network dynamics at the leading and trailing edges during cell migration Elife. DOI: 10.7554/Elife.58165.Sa2 |
0.307 |
|
| 2019 |
Erickson KE, Rukhlenko OS, Shahinuzzaman M, Slavkova KP, Lin YT, Suderman R, Stites EC, Anghel M, Posner RG, Barua D, Kholodenko BN, Hlavacek WS. Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor. Plos Computational Biology. 15: e1006706. PMID 30653502 DOI: 10.1371/Journal.Pcbi.1006706 |
0.39 |
|
| 2018 |
Thomaseth C, Fey D, Santra T, Rukhlenko OS, Radde NE, Kholodenko BN. Impact of measurement noise, experimental design, and estimation methods on Modular Response Analysis based network reconstruction. Scientific Reports. 8: 16217. PMID 30385767 DOI: 10.1038/S41598-018-34353-3 |
0.355 |
|
| 2018 |
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, et al. Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling. Cell Systems. PMID 30007540 DOI: 10.1016/J.Cels.2018.06.002 |
0.387 |
|
| 2018 |
Santra T, Rukhlenko OS, Zhernovkov V, Kholodenko BN. Reconstructing static and dynamic models of signaling pathways using Modular Response Analysis Current Opinion in Systems Biology. 9: 11-21. DOI: 10.1016/J.Coisb.2018.02.003 |
0.362 |
|
| 2017 |
Magi S, Iwamoto K, Yumoto N, Hiroshima M, Nagashima T, Ohki R, Garcia-Munoz A, Volinsky N, Kriegsheim AV, Sako Y, Takahashi K, Kimura S, Kholodenko BN, Okada-Hatakeyama M. Transcriptionally inducible Pleckstrin homology-like domain family A member 1 attenuates ErbB receptor activity by inhibiting receptor oligomerization. The Journal of Biological Chemistry. PMID 29233889 DOI: 10.1074/Jbc.M117.778399 |
0.408 |
|
| 2017 |
Fey D, Aksamitiene E, Kiyatkin A, Kholodenko BN. Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols. Methods in Molecular Biology (Clifton, N.J.). 1636: 417-453. PMID 28730495 DOI: 10.1007/978-1-4939-7154-1_27 |
0.467 |
|
| 2016 |
Halasz M, Kholodenko BN, Kolch W, Santra T. Integrating network reconstruction with mechanistic modeling to predict cancer therapies. Science Signaling. 9: ra114. PMID 27879396 DOI: 10.1126/Scisignal.Aae0535 |
0.374 |
|
| 2016 |
Zhang R, Fruhwirth GO, Coban O, Barrett JE, Burgoyne T, Lee SH, Simonson PD, Baday M, Kholodenko B, Futter CE, Ng T, Selvin PR. Probing the Heterogeneity of Protein Kinase Activation in Cells by Super-Resolution Microscopy. Acs Nano. PMID 27768850 DOI: 10.1021/Acsnano.6B05356 |
0.374 |
|
| 2016 |
Sánchez-Sanz G, Tywoniuk B, Matallanas D, Romano D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV. SARAH Domain-Mediated MST2-RASSF Dimeric Interactions. Plos Computational Biology. 12: e1005051. PMID 27716844 DOI: 10.1371/Journal.Pcbi.1005051 |
0.325 |
|
| 2016 |
Nguyen LK, Kholodenko BN, von Kriegsheim A. Rac1 and RhoA: networks, loops and bistability. Small Gtpases. 0. PMID 27533896 DOI: 10.1080/21541248.2016.1224399 |
0.382 |
|
| 2016 |
Rauch N, Rukhlenko OS, Kolch W, Kholodenko BN. MAPK kinase signalling dynamics regulate cell fate decisions and drug resistance. Current Opinion in Structural Biology. 41: 151-158. PMID 27521656 DOI: 10.1016/J.Sbi.2016.07.019 |
0.373 |
|
| 2016 |
Fey D, Matallanas D, Rauch J, Rukhlenko OS, Kholodenko BN. The complexities and versatility of the RAS-to-ERK signalling system in normal and cancer cells. Seminars in Cell & Developmental Biology. PMID 27350026 DOI: 10.1016/J.Semcdb.2016.06.011 |
0.445 |
|
| 2016 |
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, ... ... Kholodenko BN, et al. Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches. Cell Systems. 2: 38-48. PMID 27136688 DOI: 10.1016/J.Cels.2016.01.003 |
0.687 |
|
| 2016 |
Frank TD, Kiyatkin A, Cheong A, Kholodenko BN. Three-factor models versus time series models: quantifying time-dependencies of interactions between stimuli in cell biology and psychobiology for short longitudinal data. Mathematical Medicine and Biology : a Journal of the Ima. PMID 27079221 DOI: 10.1093/Imammb/Dqw001 |
0.364 |
|
| 2016 |
Fey D, Kuehn A, Kholodenko BN. On the personalised modelling of cancer signalling Ifac-Papersonline. 49: 312-317. DOI: 10.1016/J.Ifacol.2016.12.145 |
0.301 |
|
| 2016 |
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, ... ... Kholodenko BN, et al. Bistability in the Rac1, PAK, and RhoA Signaling Network Drives Actin Cytoskeleton Dynamics and Cell Motility Switches Cell Systems. 2: 38-48. DOI: 10.1016/j.cels.2016.01.003 |
0.639 |
|
| 2015 |
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. Signaling pathway models as biomarkers: Patient-specific simulations of JNK activity predict the survival of neuroblastoma patients. Science Signaling. 8: ra130. PMID 26696630 DOI: 10.1126/Scisignal.Aab0990 |
0.429 |
|
| 2015 |
Jambrina PG, Rauch N, Pilkington R, Rybakova K, Nguyen LK, Kholodenko BN, Buchete NV, Kolch W, Rosta E. Phosphorylation of RAF Kinase Dimers Drives Conformational Changes that Facilitate Transactivation. Angewandte Chemie (International Ed. in English). PMID 26644280 DOI: 10.1002/Anie.201509272 |
0.376 |
|
| 2015 |
Ryu H, Chung M, Dobrzyński M, Fey D, Blum Y, Lee SS, Peter M, Kholodenko BN, Jeon NL, Pertz O. Frequency modulation of ERK activation dynamics rewires cell fate. Molecular Systems Biology. 11: 838. PMID 26613961 DOI: 10.15252/Msb.20156458 |
0.382 |
|
| 2015 |
Nguyen LK, Kholodenko BN. Feedback regulation in cell signalling: Lessons for cancer therapeutics. Seminars in Cell & Developmental Biology. PMID 26481970 DOI: 10.1016/J.Semcdb.2015.09.024 |
0.437 |
|
| 2015 |
Sánchez-Sanz G, Matallanas D, Nguyen LK, Kholodenko BN, Rosta E, Kolch W, Buchete NV. MST2-RASSF protein-protein interactions through SARAH domains. Briefings in Bioinformatics. PMID 26443615 DOI: 10.1093/Bib/Bbv070 |
0.435 |
|
| 2015 |
Kholodenko BN. Drug Resistance Resulting from Kinase Dimerization Is Rationalized by Thermodynamic Factors Describing Allosteric Inhibitor Effects. Cell Reports. 12: 1939-49. PMID 26344764 DOI: 10.1016/J.Celrep.2015.08.014 |
0.321 |
|
| 2015 |
Kolch W, Halasz M, Granovskaya M, Kholodenko BN. The dynamic control of signal transduction networks in cancer cells. Nature Reviews. Cancer. 15: 515-27. PMID 26289315 DOI: 10.1038/Nrc3983 |
0.407 |
|
| 2015 |
Varusai TM, Kolch W, Kholodenko BN, Nguyen LK. Protein-protein interactions generate hidden feedback and feed-forward loops to trigger bistable switches, oscillations and biphasic dose-responses. Molecular Biosystems. PMID 26266875 DOI: 10.1039/C5Mb00385G |
0.445 |
|
| 2015 |
Nguyen LK, Degasperi A, Cotter P, Kholodenko BN. DYVIPAC: an integrated analysis and visualisation framework to probe multi-dimensional biological networks. Scientific Reports. 5: 12569. PMID 26220783 DOI: 10.1038/Srep12569 |
0.354 |
|
| 2015 |
Roth S, Kholodenko BN, Smit MJ, Bruggeman FJ. G Protein-Coupled Receptor Signaling Networks from a Systems Perspective. Molecular Pharmacology. 88: 604-16. PMID 26162865 DOI: 10.1124/Mol.115.100057 |
0.452 |
|
| 2015 |
Milewska M, Romano D, Herrero A, Guerriero ML, Birtwistle M, Quehenberger F, Hatzl S, Kholodenko BN, Segatto O, Kolch W, Zebisch A. Mitogen-Inducible Gene-6 Mediates Feedback Inhibition from Mutated BRAF towards the Epidermal Growth Factor Receptor and Thereby Limits Malignant Transformation. Plos One. 10: e0129859. PMID 26065894 DOI: 10.1371/Journal.Pone.0129859 |
0.66 |
|
| 2015 |
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, ... ... Kholodenko BN, et al. Silence on the relevant literature and errors in implementation. Nature Biotechnology. 33: 336-9. PMID 25850052 DOI: 10.1038/Nbt.3185 |
0.555 |
|
| 2015 |
Kim TH, Monsefi N, Song JH, von Kriegsheim A, Vandamme D, Pertz O, Kholodenko BN, Kolch W, Cho KH. Network-based identification of feedback modules that control RhoA activity and cell migration. Journal of Molecular Cell Biology. 7: 242-52. PMID 25780058 DOI: 10.1093/Jmcb/Mjv017 |
0.403 |
|
| 2015 |
Nguyen LK, Cavadas MA, Kholodenko BN, Frank TD, Cheong A. Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate. Cellular and Molecular Life Sciences : Cmls. 72: 2431-43. PMID 25697863 DOI: 10.1007/S00018-015-1850-1 |
0.338 |
|
| 2015 |
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, et al. Advances in dynamic modeling of colorectal cancer signaling-network regions, a path toward targeted therapies. Oncotarget. 6: 5041-58. PMID 25671297 DOI: 10.18632/Oncotarget.3238 |
0.43 |
|
| 2015 |
Volinsky N, McCarthy CJ, von Kriegsheim A, Saban N, Okada-Hatakeyama M, Kolch W, Kholodenko BN. Signalling mechanisms regulating phenotypic changes in breast cancer cells. Bioscience Reports. 35. PMID 25643809 DOI: 10.1042/Bsr20140172 |
0.434 |
|
| 2015 |
Nguyen LK, Matallanas DG, Romano D, Kholodenko BN, Kolch W. Competing to coordinate cell fate decisions: the MST2-Raf-1 signaling device. Cell Cycle (Georgetown, Tex.). 14: 189-99. PMID 25607644 DOI: 10.4161/15384101.2014.973743 |
0.428 |
|
| 2015 |
Nagashima T, Inoue N, Yumoto N, Saeki Y, Magi S, Volinsky N, Sorkin A, Kholodenko BN, Okada-Hatakeyama M. Feedforward regulation of mRNA stability by prolonged extracellular signal-regulated kinase activity. The Febs Journal. 282: 613-29. PMID 25491268 DOI: 10.1111/Febs.13172 |
0.403 |
|
| 2014 |
Nguyen LK, Zhao Q, Varusai TM, Kholodenko BN. Ubiquitin chain specific auto-ubiquitination triggers sustained oscillation, bistable switches and excitable firing. Iet Systems Biology. 8: 282-92. PMID 25478702 DOI: 10.1049/Iet-Syb.2014.0024 |
0.333 |
|
| 2014 |
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, ... ... Kholodenko BN, et al. The ErbB4 CYT2 variant protects EGFR from ligand-induced degradation to enhance cancer cell motility. Science Signaling. 7: ra78. PMID 25140053 DOI: 10.1126/Scisignal.2005157 |
0.322 |
|
| 2014 |
Dobrzyński M, Nguyen LK, Birtwistle MR, von Kriegsheim A, Blanco Fernández A, Cheong A, Kolch W, Kholodenko BN. Nonlinear signalling networks and cell-to-cell variability transform external signals into broadly distributed or bimodal responses. Journal of the Royal Society, Interface / the Royal Society. 11: 20140383. PMID 24966234 DOI: 10.1098/Rsif.2014.0383 |
0.656 |
|
| 2014 |
Romano D, Nguyen LK, Matallanas D, Halasz M, Doherty C, Kholodenko BN, Kolch W. Protein interaction switches coordinate Raf-1 and MST2/Hippo signalling. Nature Cell Biology. 16: 673-84. PMID 24929361 DOI: 10.1038/Ncb2986 |
0.467 |
|
| 2014 |
Song JH, Huels DJ, Ridgway RA, Sansom OJ, Kholodenko BN, Kolch W, Cho KH. The APC network regulates the removal of mutated cells from colonic crypts. Cell Reports. 7: 94-103. PMID 24685131 DOI: 10.1016/J.Celrep.2014.02.043 |
0.34 |
|
| 2014 |
Santra T, Kolch W, Kholodenko BN. Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. Plos Computational Biology. 10: e1003385. PMID 24550716 DOI: 10.1371/Journal.Pcbi.1003385 |
0.365 |
|
| 2014 |
Nguyen LK, Dobrzy?ski M, Fey D, Kholodenko BN. Polyubiquitin chain assembly and organization determine the dynamics of protein activation and degradation. Frontiers in Physiology. 5: 4. PMID 24478717 DOI: 10.3389/Fphys.2014.00004 |
0.343 |
|
| 2014 |
Degasperi A, Birtwistle MR, Volinsky N, Rauch J, Kolch W, Kholodenko BN. Evaluating strategies to normalise biological replicates of Western blot data. Plos One. 9: e87293. PMID 24475266 DOI: 10.1371/Journal.Pone.0087293 |
0.586 |
|
| 2013 |
Volinsky N, Kholodenko BN. Complexity of receptor tyrosine kinase signal processing. Cold Spring Harbor Perspectives in Biology. 5: a009043. PMID 23906711 DOI: 10.1101/Cshperspect.A009043 |
0.497 |
|
| 2013 |
Nguyen LK, Kolch W, Kholodenko BN. When ubiquitination meets phosphorylation: a systems biology perspective of EGFR/MAPK signalling. Cell Communication and Signaling : Ccs. 11: 52. PMID 23902637 DOI: 10.1186/1478-811X-11-52 |
0.474 |
|
| 2013 |
Nikonova E, Tsyganov MA, Kolch W, Fey D, Kholodenko BN. Control of the G-protein cascade dynamics by GDP dissociation inhibitors. Molecular Biosystems. 9: 2454-62. PMID 23872884 DOI: 10.1039/C3Mb70152B |
0.39 |
|
| 2013 |
Reiterer V, Fey D, Kolch W, Kholodenko BN, Farhan H. Pseudophosphatase STYX modulates cell-fate decisions and cell migration by spatiotemporal regulation of ERK1/2. Proceedings of the National Academy of Sciences of the United States of America. 110: E2934-43. PMID 23847209 DOI: 10.1073/Pnas.1301985110 |
0.433 |
|
| 2013 |
Santra T, Kolch W, Kholodenko BN. Integrating Bayesian variable selection with Modular Response Analysis to infer biochemical network topology. Bmc Systems Biology. 7: 57. PMID 23829771 DOI: 10.1186/1752-0509-7-57 |
0.326 |
|
| 2013 |
Nguyen LK, Cavadas MA, Scholz CC, Fitzpatrick SF, Bruning U, Cummins EP, Tambuwala MM, Manresa MC, Kholodenko BN, Taylor CT, Cheong A. A dynamic model of the hypoxia-inducible factor 1α (HIF-1α) network. Journal of Cell Science. 126: 1454-63. PMID 23390316 DOI: 10.1242/Jcs.119974 |
0.322 |
|
| 2013 |
Baljuls A, Kholodenko BN, Kolch W. It takes two to tango--signalling by dimeric Raf kinases. Molecular Biosystems. 9: 551-8. PMID 23212737 DOI: 10.1039/C2Mb25393C |
0.384 |
|
| 2013 |
Nguyen LK, Matallanas D, Croucher DR, von Kriegsheim A, Kholodenko BN. Signalling by protein phosphatases and drug development: a systems-centred view. The Febs Journal. 280: 751-65. PMID 22340367 DOI: 10.1111/J.1742-4658.2012.08522.X |
0.476 |
|
| 2012 |
Fey D, Croucher DR, Kolch W, Kholodenko BN. Crosstalk and signaling switches in mitogen-activated protein kinase cascades. Frontiers in Physiology. 3: 355. PMID 23060802 DOI: 10.3389/Fphys.2012.00355 |
0.467 |
|
| 2012 |
Birtwistle MR, von Kriegsheim A, Dobrzyński M, Kholodenko BN, Kolch W. Mammalian protein expression noise: scaling principles and the implications for knockdown experiments. Molecular Biosystems. 8: 3068-76. PMID 22990612 DOI: 10.1039/C2Mb25168J |
0.628 |
|
| 2012 |
Birtwistle MR, Rauch J, Kiyatkin A, Aksamitiene E, Dobrzyński M, Hoek JB, Kolch W, Ogunnaike BA, Kholodenko BN. Emergence of bimodal cell population responses from the interplay between analog single-cell signaling and protein expression noise. Bmc Systems Biology. 6: 109. PMID 22920937 DOI: 10.1186/1752-0509-6-109 |
0.747 |
|
| 2012 |
Frank TD, Cheong A, Okada-Hatakeyama M, Kholodenko BN. Catching transcriptional regulation by thermostatistical modeling. Physical Biology. 9: 045007. PMID 22871947 DOI: 10.1088/1478-3975/9/4/045007 |
0.318 |
|
| 2012 |
Kholodenko B, Yaffe MB, Kolch W. Computational approaches for analyzing information flow in biological networks Science Signaling. 5. PMID 22510471 DOI: 10.1126/Scisignal.2002961 |
0.376 |
|
| 2012 |
Aksamitiene E, Kiyatkin A, Kholodenko BN. Cross-talk between mitogenic Ras/MAPK and survival PI3K/Akt pathways: a fine balance. Biochemical Society Transactions. 40: 139-46. PMID 22260680 DOI: 10.1042/Bst20110609 |
0.411 |
|
| 2012 |
Tsyganov MA, Kolch W, Kholodenko BN. The topology design principles that determine the spatiotemporal dynamics of G-protein cascades. Molecular Biosystems. 8: 730-43. PMID 22218529 DOI: 10.1039/C2Mb05375F |
0.345 |
|
| 2012 |
Santra T, Kholodenko B, Kolch W. An integrated Bayesian framework for identifying phosphorylation networks in stimulated cells. Advances in Experimental Medicine and Biology. 736: 59-80. PMID 22161322 DOI: 10.1007/978-1-4419-7210-1_3 |
0.392 |
|
| 2011 |
Nguyen LK, Muñoz-García J, Maccario H, Ciechanover A, Kolch W, Kholodenko BN. Switches, excitable responses and oscillations in the Ring1B/Bmi1 ubiquitination system. Plos Computational Biology. 7: e1002317. PMID 22194680 DOI: 10.1371/Journal.Pcbi.1002317 |
0.303 |
|
| 2011 |
Aksamitiene E, Achanta S, Kolch W, Kholodenko BN, Hoek JB, Kiyatkin A. Prolactin-stimulated activation of ERK1/2 mitogen-activated protein kinases is controlled by PI3-kinase/Rac/PAK signaling pathway in breast cancer cells. Cellular Signalling. 23: 1794-805. PMID 21726627 DOI: 10.1016/J.Cellsig.2011.06.014 |
0.446 |
|
| 2010 |
Sturm OE, Orton R, Grindlay J, Birtwistle M, Vyshemirsky V, Gilbert D, Calder M, Pitt A, Kholodenko B, Kolch W. The mammalian MAPK/ERK pathway exhibits properties of a negative feedback amplifier. Science Signaling. 3: ra90. PMID 21177493 DOI: 10.1126/Scisignal.2001212 |
0.684 |
|
| 2010 |
Muñoz-García J, Kholodenko BN. Signalling over a distance: gradient patterns and phosphorylation waves within single cells. Biochemical Society Transactions. 38: 1235-41. PMID 20863291 DOI: 10.1042/Bst0381235 |
0.343 |
|
| 2010 |
Muñoz-García J, Kholodenko BN, Neufeld Z. Formation of intracellular concentration landscapes by multisite protein modification. Biophysical Journal. 99: 59-66. PMID 20655833 DOI: 10.1016/J.Bpj.2010.04.014 |
0.37 |
|
| 2010 |
Kholodenko BN, Hancock JF, Kolch W. Signalling ballet in space and time. Nature Reviews. Molecular Cell Biology. 11: 414-26. PMID 20495582 DOI: 10.1038/Nrm2901 |
0.415 |
|
| 2010 |
Nakakuki T, Birtwistle MR, Saeki Y, Yumoto N, Ide K, Nagashima T, Brusch L, Ogunnaike BA, Okada-Hatakeyama M, Kholodenko BN. Ligand-specific c-Fos expression emerges from the spatiotemporal control of ErbB network dynamics. Cell. 141: 884-96. PMID 20493519 DOI: 10.1016/J.Cell.2010.03.054 |
0.727 |
|
| 2010 |
Aksamitiene E, Kholodenko BN, Kolch W, Hoek JB, Kiyatkin A. PI3K/Akt-sensitive MEK-independent compensatory circuit of ERK activation in ER-positive PI3K-mutant T47D breast cancer cells. Cellular Signalling. 22: 1369-78. PMID 20471474 DOI: 10.1016/J.Cellsig.2010.05.006 |
0.418 |
|
| 2010 |
Kolch W, Birtwistle M, Kholodenko B, Grindlay J, Sturm O, Orton R, Gilbert D, von Kriegsheim A. 11 From benchside to byteside: what we can learn from computational modelling European Journal of Cancer Supplements. 8: 3. DOI: 10.1016/S1359-6349(10)70820-X |
0.663 |
|
| 2009 |
Kholodenko BN, Birtwistle MR. Four-dimensional dynamics of MAPK information processing systems. Wiley Interdisciplinary Reviews. Systems Biology and Medicine. 1: 28-44. PMID 20182652 DOI: 10.1002/Wsbm.16 |
0.697 |
|
| 2009 |
Kholodenko BN. Spatially distributed cell signalling. Febs Letters. 583: 4006-12. PMID 19800332 DOI: 10.1016/J.Febslet.2009.09.045 |
0.438 |
|
| 2009 |
Kaimachnikov NP, Kholodenko BN. Toggle switches, pulses and oscillations are intrinsic properties of the Src activation/deactivation cycle. The Febs Journal. 276: 4102-18. PMID 19627364 DOI: 10.1111/J.1742-4658.2009.07117.X |
0.431 |
|
| 2009 |
Birtwistle MR, Kholodenko BN. Endocytosis and signalling: a meeting with mathematics. Molecular Oncology. 3: 308-20. PMID 19596615 DOI: 10.1016/J.Molonc.2009.05.009 |
0.671 |
|
| 2009 |
Borisov N, Aksamitiene E, Kiyatkin A, Legewie S, Berkhout J, Maiwald T, Kaimachnikov NP, Timmer J, Hoek JB, Kholodenko BN. Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Molecular Systems Biology. 5: 256. PMID 19357636 DOI: 10.1038/Msb.2009.19 |
0.42 |
|
| 2009 |
Muñoz-García J, Neufeld Z, Kholodenko BN. Positional information generated by spatially distributed signaling cascades. Plos Computational Biology. 5: e1000330. PMID 19300504 DOI: 10.1371/Journal.Pcbi.1000330 |
0.401 |
|
| 2009 |
Suenaga A, Hatakeyama M, Kiyatkin AB, Radhakrishnan R, Taiji M, Kholodenko BN. Molecular dynamics simulations reveal that Tyr-317 phosphorylation reduces Shc binding affinity for phosphotyrosyl residues of epidermal growth factor receptor. Biophysical Journal. 96: 2278-88. PMID 19289054 DOI: 10.1016/J.Bpj.2008.11.018 |
0.365 |
|
| 2009 |
Stelling J, Kholodenko BN. Signaling cascades as cellular devices for spatial computations. Journal of Mathematical Biology. 58: 35-55. PMID 18283462 DOI: 10.1007/S00285-008-0162-6 |
0.393 |
|
| 2008 |
Borisov NM, Chistopolsky AS, Faeder JR, Kholodenko BN. Domain-oriented reduction of rule-based network models Iet Systems Biology. 2: 342-351. PMID 19045829 DOI: 10.1049/Iet-Syb:20070081 |
0.378 |
|
| 2008 |
Kholodenko BN, Kolch W. Giving space to cell signaling. Cell. 133: 566-7. PMID 18485861 DOI: 10.1016/J.Cell.2008.04.033 |
0.374 |
|
| 2007 |
Birtwistle MR, Hatakeyama M, Yumoto N, Ogunnaike BA, Hoek JB, Kholodenko BN. Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses. Molecular Systems Biology. 3: 144. PMID 18004277 DOI: 10.1038/Msb4100188 |
0.755 |
|
| 2007 |
Aksamitiene E, Hoek JB, Kholodenko B, Kiyatkin A. Multistrip Western blotting to increase quantitative data output. Electrophoresis. 28: 3163-73. PMID 17722184 DOI: 10.1002/Elps.200700002 |
0.317 |
|
| 2007 |
Kholodenko BN. Untangling the signalling wires. Nature Cell Biology. 9: 247-9. PMID 17330115 DOI: 10.1038/Ncb0307-247 |
0.461 |
|
| 2007 |
Chickarmane V, Kholodenko BN, Sauro HM. Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation. Journal of Theoretical Biology. 244: 68-76. PMID 16949102 DOI: 10.1016/J.Jtbi.2006.05.013 |
0.384 |
|
| 2007 |
Kholodenko BN. Employing systems biology to quantify receptor tyrosine kinase signaling in time and space Introduction to Systems Biology. 300-318. DOI: 10.1007/978-1-59745-531-2_16 |
0.383 |
|
| 2007 |
Birtwistle MR, Kholodenko BN, Kiyatkin A, Hoek JB, Ogunnaike BA. Experimental investigation and probabilistic modeling of switch-like signal transduction systems Aiche Annual Meeting, Conference Proceedings. |
0.696 |
|
| 2006 |
Markevich NI, Tsyganov MA, Hoek JB, Kholodenko BN. Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades. Molecular Systems Biology. 2: 61. PMID 17102806 DOI: 10.1038/Msb4100108 |
0.413 |
|
| 2006 |
Yalamanchili N, Zak DE, Ogunnaike BA, Schwaber JS, Kriete A, Kholodenko BN. Quantifying gene network connectivity in silico: scalability and accuracy of a modular approach. Systems Biology. 153: 236-46. PMID 16986625 DOI: 10.1049/ip-syb:20050090 |
0.519 |
|
| 2006 |
Ortega F, Garcés JL, Mas F, Kholodenko BN, Cascante M. Bistability from double phosphorylation in signal transduction. Kinetic and structural requirements. The Febs Journal. 273: 3915-26. PMID 16934033 DOI: 10.1111/J.1742-4658.2006.05394.X |
0.372 |
|
| 2006 |
Kiyatkin A, Aksamitiene E, Markevich NI, Borisov NM, Hoek JB, Kholodenko BN. Scaffolding protein Grb2-associated binder 1 sustains epidermal growth factor-induced mitogenic and survival signaling by multiple positive feedback loops. The Journal of Biological Chemistry. 281: 19925-38. PMID 16687399 DOI: 10.1074/Jbc.M600482200 |
0.446 |
|
| 2006 |
Kholodenko BN. Cell-signalling dynamics in time and space. Nature Reviews. Molecular Cell Biology. 7: 165-76. PMID 16482094 DOI: 10.1038/Nrm1838 |
0.433 |
|
| 2006 |
Blüthgen N, Bruggeman FJ, Legewie S, Herzel H, Westerhoff HV, Kholodenko BN. Effects of sequestration on signal transduction cascades. The Febs Journal. 273: 895-906. PMID 16478465 DOI: 10.1111/J.1742-4658.2006.05105.X |
0.443 |
|
| 2006 |
Conzelmann H, Saez-Rodriguez J, Sauter T, Kholodenko BN, Gilles ED. A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. Bmc Bioinformatics. 7: 34. PMID 16430778 DOI: 10.1186/1471-2105-7-34 |
0.357 |
|
| 2006 |
Borisov NM, Markevich NI, Hoek JB, Kholodenko BN. Trading the micro-world of combinatorial complexity for the macro-world of protein interaction domains. Bio Systems. 83: 152-66. PMID 16242235 DOI: 10.1016/J.Biosystems.2005.03.006 |
0.423 |
|
| 2006 |
Birtwistle MR, Hatakeyama M, Yumoto N, Hoek JB, Kholodenko BN, Ogunnaike BA. Modeling the ErbB signaling network in MCF-7 breast cancer cells and analysis of ligand-dependent responses Aiche Annual Meeting, Conference Proceedings. |
0.738 |
|
| 2005 |
Borisov NM, Markevich NI, Hoek JB, Kholodenko BN. Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity. Biophysical Journal. 89: 951-66. PMID 15923229 DOI: 10.1529/Biophysj.105.060533 |
0.416 |
|
| 2005 |
Andrec M, Kholodenko BN, Levy RM, Sontag E. Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. Journal of Theoretical Biology. 232: 427-41. PMID 15572066 DOI: 10.1016/J.Jtbi.2004.08.022 |
0.37 |
|
| 2004 |
Sauro HM, Kholodenko BN. Quantitative analysis of signaling networks. Progress in Biophysics and Molecular Biology. 86: 5-43. PMID 15261524 DOI: 10.1016/J.Pbiomolbio.2004.03.002 |
0.427 |
|
| 2004 |
Sontag E, Kiyatkin A, Kholodenko BN. Inferring dynamic architecture of cellular networks using time series of gene expression, protein and metabolite data. Bioinformatics (Oxford, England). 20: 1877-86. PMID 15037511 DOI: 10.1093/Bioinformatics/Bth173 |
0.336 |
|
| 2004 |
Markevich NI, Hoek JB, Kholodenko BN. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. The Journal of Cell Biology. 164: 353-9. PMID 14744999 DOI: 10.1083/Jcb.200308060 |
0.416 |
|
| 2004 |
Suenaga A, Kiyatkin AB, Hatakeyama M, Futatsugi N, Okimoto N, Hirano Y, Narumi T, Kawai A, Susukita R, Koishi T, Furusawa H, Yasuoka K, Takada N, Ohno Y, Taiji M, ... ... Kholodenko BN, et al. Tyr-317 phosphorylation increases Shc structural rigidity and reduces coupling of domain motions remote from the phosphorylation site as revealed by molecular dynamics simulations. The Journal of Biological Chemistry. 279: 4657-62. PMID 14613932 DOI: 10.1074/Jbc.M310598200 |
0.323 |
|
| 2003 |
Peletier MA, Westerhoff HV, Kholodenko BN. Control of spatially heterogeneous and time-varying cellular reaction networks: A new summation law Journal of Theoretical Biology. 225: 477-487. PMID 14615206 DOI: 10.1016/S0022-5193(03)00289-3 |
0.364 |
|
| 2003 |
Kholodenko BN. Four-dimensional organization of protein kinase signaling cascades: the roles of diffusion, endocytosis and molecular motors. The Journal of Experimental Biology. 206: 2073-82. PMID 12756289 DOI: 10.1242/Jeb.00298 |
0.449 |
|
| 2002 |
Bruggeman FJ, Westerhoff HV, Hoek JB, Kholodenko BN. Modular response analysis of cellular regulatory networks Journal of Theoretical Biology. 218: 507-520. PMID 12384053 DOI: 10.1006/Jtbi.2002.3096 |
0.423 |
|
| 2002 |
Kholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV, Hoek JB. Untangling the wires: A strategy to trace functional interactions in signaling and gene networks Proceedings of the National Academy of Sciences of the United States of America. 99: 12841-12846. PMID 12242336 DOI: 10.1073/Pnas.192442699 |
0.393 |
|
| 2002 |
Bruggeman FJ, Kholodenko BN. Modular interaction strengths in regulatory networks; an example. Molecular Biology Reports. 29: 57-61. PMID 12241075 DOI: 10.1023/A:1020354302260 |
0.349 |
|
| 2002 |
Kholodenko BN. MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience? Trends in Cell Biology. 12: 173-7. PMID 11978536 DOI: 10.1016/S0962-8924(02)02251-1 |
0.443 |
|
| 2002 |
Moehren G, Markevich N, Demin O, Kiyatkin A, Goryanin I, Hoek JB, Kholodenko BN. Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model. Biochemistry. 41: 306-20. PMID 11772030 DOI: 10.1021/Bi011506C |
0.394 |
|
| 2002 |
Reijenga KA, Westerhoff HV, Kholodenko BN, Snoep JL. Control analysis for autonomously oscillating biochemical networks Biophysical Journal. 82: 99-108. PMID 11751299 DOI: 10.1016/S0006-3495(02)75377-0 |
0.327 |
|
| 2001 |
De Atauri P, Acerenza L, Kholodenko BN, De La Iglesia N, Guinovart JJ, Agius L, Cascante M. Occurrence of paradoxical or sustained control by an enzyme when overexpressed: Necessary conditions and experimental evidence with regard to hepatic glucokinase Biochemical Journal. 355: 787-793. PMID 11311143 DOI: 10.1042/Bj3550787 |
0.317 |
|
| 2000 |
Kholodenko BN, Brown GC, Hoek JB. Diffusion control of protein phosphorylation in signal transduction pathways Biochemical Journal. 350: 901-907. PMID 10970807 DOI: 10.1042/Bj3500901 |
0.378 |
|
| 2000 |
Kholodenko BN, Hoek JB, Westerhoff HV. Why cytoplasmic signalling proteins should be recruited to cell membranes Trends in Cell Biology. 10: 173-178. PMID 10754559 DOI: 10.1016/S0962-8924(00)01741-4 |
0.383 |
|
| 2000 |
Schuster S, Kholodenko BN, Westerhoff HV. Cellular information transfer regarded from a stoichiometry and control analysis perspective Biosystems. 55: 73-81. PMID 10745111 DOI: 10.1016/S0303-2647(99)00085-4 |
0.402 |
|
| 2000 |
Kholodenko BN. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades European Journal of Biochemistry. 267: 1583-1588. PMID 10712587 DOI: 10.1046/J.1432-1327.2000.01197.X |
0.41 |
|
| 1999 |
Kholodenko BN, Demin OV, Moehren G, Hoek JB. Quantification of short term signaling by the epidermal growth factor receptor Journal of Biological Chemistry. 274: 30169-30181. PMID 10514507 DOI: 10.1074/Jbc.274.42.30169 |
0.447 |
|
| 1999 |
Brown GC, Kholodenko BN. Spatial gradients of cellular phospho-proteins Febs Letters. 457: 452-454. PMID 10471827 DOI: 10.1016/S0014-5793(99)01058-3 |
0.363 |
|
| 1999 |
Demin OV, Westerhoff HV, Kholodenko BN. Control analysis of stationary forced oscillations. Journal of Physical Chemistry B. 103: 10695-10710. DOI: 10.1021/Jp991597B |
0.307 |
|
| 1998 |
Hoek JB, Kholodenko BN. The intracellular signaling network as a target for ethanol Alcoholism: Clinical and Experimental Research. 22. PMID 9727641 DOI: 10.1111/J.1530-0277.1998.Tb04007.X |
0.378 |
|
| 1998 |
Rohwer JM, Postma PW, Kholodenko BN, Westerhoff HV. Implications of macromolecular crowding for signal transduction and metabolite channeling Proceedings of the National Academy of Sciences of the United States of America. 95: 10547-10552. PMID 9724740 DOI: 10.1073/Pnas.95.18.10547 |
0.335 |
|
| 1998 |
Westerhoff H, Jensen P, Snoep J, Kholodenko B. Thermodynamics of complexity. The live cell Thermochimica Acta. 309: 111-120. DOI: 10.1016/S0040-6031(97)00353-5 |
0.316 |
|
| 1998 |
Kholodenko BN, Rohwer JM, Cascante M, Westerhoff HV. Subtleties in control by metabolic channelling and enzyme organization Molecular and Cellular Biochemistry. 184: 311-320. DOI: 10.1007/978-1-4615-5653-4_20 |
0.339 |
|
| 1997 |
Kholodenko BN, Hoek JB, Westerhoff HV, Brown GC. Quantification of information transfer via cellular signal transduction pathways Febs Letters. 414: 430-434. PMID 9315734 DOI: 10.1016/S0014-5793(97)01018-1 |
0.436 |
|
| 1997 |
Brown GC, Hoek JB, Kholodenko BN. Why do protein kinase cascades have more than one level? Trends in Biochemical Sciences. 22: 288. PMID 9270298 DOI: 10.1016/S0968-0004(97)82216-5 |
0.33 |
|
| 1996 |
Brown GC, Westerhoff HV, Kholodenko BN. Molecular control analysis: Control within proteins and molecular processes Journal of Theoretical Biology. 182: 389-396. PMID 8944172 DOI: 10.1006/Jtbi.1996.0178 |
0.338 |
|
| 1996 |
Kholodenko BN, Brown GC. Paradoxical control properties of enzymes within pathways: Can activation cause an enzyme to have increased control? Biochemical Journal. 314: 753-760. PMID 8615766 DOI: 10.1042/Bj3140753 |
0.32 |
|
| 1995 |
Kholodenko BN, Westerhoff HV. The macroworld versus the microworld of biochemical regulation and control Trends in Biochemical Sciences. 20: 52-54. PMID 7701560 DOI: 10.1016/S0968-0004(00)88955-0 |
0.334 |
|
| 1995 |
Kholodenko BN, Schuster S, Rohwer JM, Cascante M, Westerhoff HV. Composite control of cell function: metabolic pathways behaving as single control units Febs Letters. 368: 1-4. PMID 7615057 DOI: 10.1016/0014-5793(95)00562-N |
0.373 |
|
| 1995 |
MOLENAAR D, KHOLODENKO BN, VAN HEESWIJK WC, WESTERHOFF HV. DYNAMIC ASPECTS OF CASCADE-TYPE METABOLIC REGULATION Journal of Biological Systems. 3: 187-196. DOI: 10.1142/S0218339095000186 |
0.347 |
|
| 1995 |
KHOLODENKO B, CASCANTE M, MOLENAAR D, DEMIN O, VAN DER GUGTEN A, WESTERHOFF H. CONTROL THEORY OF CELL METABOLISM: TOWARDS MORE REALISTIC “NON-IDEAL” SYSTEMS Journal of Biological Systems. 3: 145-154. DOI: 10.1142/S0218339095000149 |
0.315 |
|
| 1995 |
JENSEN P, VAN DER GUGTEN A, BIER M, VAN HEESWIJK W, ROHWER J, MOLENAAR D, VAN WORKUM M, RICHARD P, TEUSINK B, BAKKER B, KHOLODENKO B, WESTERHOFF H. HIERARCHIES IN CONTROL Journal of Biological Systems. 3: 139-144. DOI: 10.1142/S0218339095000137 |
0.342 |
|
| 1995 |
Kholodenko BN, Molenaar D, Schuster S, Heinrich R, Westerhoff HV. Defining control coefficients in non-ideal metabolic pathways Biophysical Chemistry. 56: 215-226. DOI: 10.1016/0301-4622(95)00039-Z |
0.338 |
|
| 1995 |
Kholodenko BN, Westerhoff HV, Puigjaner J, Cascante M. Control in channelled pathways. A matrix method calculating the enzyme control coefficients Biophysical Chemistry. 53: 247-258. DOI: 10.1016/0301-4622(94)00104-R |
0.337 |
|
| 1995 |
Kholodenko BN, Westerhoff HV. Control theory of group transfer pathways Bba - Bioenergetics. 1229: 256-274. DOI: 10.1016/0005-2728(95)00014-A |
0.35 |
|
| 1995 |
Kholodenko BN, Westerhoff HV. How to reveal various aspects of regulation in group-transfer pathways Bba - Bioenergetics. 1229: 275-289. DOI: 10.1016/0005-2728(95)00013-9 |
0.321 |
|
| 1994 |
Westerhoff HV, Hofmeyr JHS, Kholodenko BN. Getting to the inside of cells using metabolic control analysis Biophysical Chemistry. 50: 273-283. PMID 8011948 DOI: 10.1016/0301-4622(93)E0095-M |
0.318 |
|
| 1994 |
Kholodenko BN, Sauro HM, Westerhoff HV. Control by enzymes, coenzymes and conserved moieties. A generalisation of the connectivity theorem of metabolic control analysis. European Journal of Biochemistry / Febs. 225: 179-86. PMID 7925436 DOI: 10.1111/J.1432-1033.1994.00179.X |
0.317 |
|
| 1993 |
Kholodenko BN, Demin OV, Westerhoff HV. 'Channelled' pathways can be more sensitive to specific regulatory signals Febs Letters. 320: 75-78. PMID 8462681 DOI: 10.1016/0014-5793(93)81661-I |
0.378 |
|
| 1993 |
van Dam K, van der Vlag J, Kholodenko BN, Westerhoff HV. The sum of the control coefficients of all enzymes on the flux through a group-transfer pathway can be as high as two. European Journal of Biochemistry / Febs. 212: 791-9. PMID 8462550 DOI: 10.1111/J.1432-1033.1993.Tb17720.X |
0.321 |
|
| 1993 |
Kholodenko BN, Cascante M, Westerhoff HV. Dramatic changes in control properties that accompany channelling and metabolite sequestration Febs Letters. 336: 381-384. PMID 8282097 DOI: 10.1016/0014-5793(93)80841-H |
0.304 |
|
| 1988 |
Kholodenko BN. How do external parameters control fluxes and concentrations of metabolites? An additional relationship in the theory of metabolic control Febs Letters. 232: 383-386. PMID 3378629 DOI: 10.1016/0014-5793(88)80775-0 |
0.326 |
|
| 1984 |
Kholodenko BN. Control of mitochondrial oxidative phosphorylation Journal of Theoretical Biology. 107: 179-188. PMID 6717037 DOI: 10.1016/S0022-5193(84)80020-X |
0.303 |
|
| 1982 |
Dibrov BF, Zhabotinsky AM, Kholodenko BN. Dynamic stability of steady states and static stabilization in unbranched metabolic pathways Journal of Mathematical Biology. 15: 51-63. PMID 7142835 DOI: 10.1007/Bf00275788 |
0.311 |
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