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Items: 1 to 50 of 254

1.

Systems biology: old news or new stimulus for biochemistry.

Kolch W, Fey D, Ryan CJ.

Essays Biochem. 2018 Oct 26;62(4):483-486. doi: 10.1042/EBC20180002. Print 2018 Oct 26.

PMID:
30366987
2.

From oncogenic mutation to dynamic code.

Kolch W, Kiel C.

Science. 2018 Aug 31;361(6405):844-845. doi: 10.1126/science.aau8059. No abstract available.

PMID:
30166473
3.

ALIX Regulates Tumor-Mediated Immunosuppression by Controlling EGFR Activity and PD-L1 Presentation.

Monypenny J, Milewicz H, Flores-Borja F, Weitsman G, Cheung A, Chowdhury R, Burgoyne T, Arulappu A, Lawler K, Barber PR, Vicencio JM, Keppler M, Wulaningsih W, Davidson SM, Fraternali F, Woodman N, Turmaine M, Gillett C, Franz D, Quezada SA, Futter CE, Von Kriegsheim A, Kolch W, Vojnovic B, Carlton JG, Ng T.

Cell Rep. 2018 Jul 17;24(3):630-641. doi: 10.1016/j.celrep.2018.06.066.

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.

Metabolic stress regulates ERK activity by controlling KSR-RAF heterodimerization.

Verlande A, Krafčíková M, Potěšil D, Trantírek L, Zdráhal Z, Elkalaf M, Trnka J, Souček K, Rauch N, Rauch J, Kolch W, Uldrijan S.

EMBO Rep. 2018 Feb;19(2):320-336. doi: 10.15252/embr.201744524. Epub 2017 Dec 20.

PMID:
29263201
6.

Characterisation of HRas local signal transduction networks using engineered site-specific exchange factors.

Herrero A, Reis-Cardoso M, Jiménez-Gómez I, Doherty C, Agudo-Ibañez L, Pinto A, Calvo F, Kolch W, Crespo P, Matallanas D.

Small GTPases. 2017 Nov 26:1-13. doi: 10.1080/21541248.2017.1406434. [Epub ahead of print]

PMID:
29172991
7.

Proteomics analysis of bladder cancer invasion: Targeting EIF3D for therapeutic intervention.

Latosinska A, Mokou M, Makridakis M, Mullen W, Zoidakis J, Lygirou V, Frantzi M, Katafigiotis I, Stravodimos K, Hupe MC, Dobrzynski M, Kolch W, Merseburger AS, Mischak H, Roubelakis MG, Vlahou A.

Oncotarget. 2017 Apr 20;8(41):69435-69455. doi: 10.18632/oncotarget.17279. eCollection 2017 Sep 19.

8.

A Brain-Derived Neurotrophic Factor Mimetic Is Sufficient to Restore Cone Photoreceptor Visual Function in an Inherited Blindness Model.

Daly C, Shine L, Heffernan T, Deeti S, Reynolds AL, O'Connor JJ, Dillon ET, Duffy DJ, Kolch W, Cagney G, Kennedy BN.

Sci Rep. 2017 Sep 12;7(1):11320. doi: 10.1038/s41598-017-11513-5.

9.

Personalized Computational Models as Biomarkers.

Kolch W, Fey D.

J Pers Med. 2017 Sep 1;7(3). pii: E9. doi: 10.3390/jpm7030009.

10.

Lapatinib potentiates cytotoxicity of  YM155 in neuroblastoma via inhibition of the ABCB1 efflux transporter.

Radic-Sarikas B, Halasz M, Huber KVM, Winter GE, Tsafou KP, Papamarkou T, Brunak S, Kolch W, Superti-Furga G.

Sci Rep. 2017 Jun 8;7(1):3091. doi: 10.1038/s41598-017-03129-6.

11.

Identification of potential new treatment response markers and therapeutic targets using a Gaussian process-based method in lapatinib insensitive breast cancer models.

Santra T, Roche S, Conlon N, O'Donovan N, Crown J, O'Connor R, Kolch W.

PLoS One. 2017 May 8;12(5):e0177058. doi: 10.1371/journal.pone.0177058. eCollection 2017.

12.

Spatial regulation of ARAF controls the MST2-Hippo pathway.

Rauch J, Kolch W.

Small GTPases. 2017 Mar 10:1-6. doi: 10.1080/21541248.2017.1288686. [Epub ahead of print]

PMID:
28281933
13.

A novel RNA sequencing data analysis method for cell line authentication.

Fasterius E, Raso C, Kennedy S, Rauch N, Lundin P, Kolch W, Uhlén M, Al-Khalili Szigyarto C.

PLoS One. 2017 Feb 13;12(2):e0171435. doi: 10.1371/journal.pone.0171435. eCollection 2017.

14.

Retinoic acid and TGF-β signalling cooperate to overcome MYCN-induced retinoid resistance.

Duffy DJ, Krstic A, Halasz M, Schwarzl T, Konietzny A, Iljin K, Higgins DG, Kolch W.

Genome Med. 2017 Feb 10;9(1):15. doi: 10.1186/s13073-017-0407-3.

15.

Vascular Endothelial Growth Factor (VEGF) Promotes Assembly of the p130Cas Interactome to Drive Endothelial Chemotactic Signaling and Angiogenesis.

Evans IM, Kennedy SA, Paliashvili K, Santra T, Yamaji M, Lovering RC, Britton G, Frankel P, Kolch W, Zachary IC.

Mol Cell Proteomics. 2017 Feb;16(2):168-180. doi: 10.1074/mcp.M116.064428. Epub 2016 Dec 22.

16.

Comparison of different statistical approaches for urinary peptide biomarker detection in the context of coronary artery disease.

Stanley E, Delatola EI, Nkuipou-Kenfack E, Spooner W, Kolch W, Schanstra JP, Mischak H, Koeck T.

BMC Bioinformatics. 2016 Dec 6;17(1):496.

17.

The spatiotemporal regulation of RAS signalling.

Herrero A, Matallanas D, Kolch W.

Biochem Soc Trans. 2016 Oct 15;44(5):1517-1522. Review.

PMID:
27911734
18.

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
19.
20.

Next Generation RNA Sequencing Analysis Reveals Expression of a Transient EMT Profile During Early Organization of MCF10A Cells in 3D.

Minke B, Vandamme D, Schwarzl T, Kolch W, Martin F.

Methods Mol Biol. 2017;1501:233-243.

PMID:
27796956
21.

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.

22.

Wnt signalling is a bi-directional vulnerability of cancer cells.

Duffy DJ, Krstic A, Schwarzl T, Halasz M, Iljin K, Fey D, Haley B, Whilde J, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W.

Oncotarget. 2016 Sep 13;7(37):60310-60331. doi: 10.18632/oncotarget.11203.

23.

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.

24.

Mesenchymal Stromal Cells Protect Endothelial Cells from Cytotoxic T Lymphocyte-Induced Lysis.

Cahill EF, Sax T, Hartmann I, Haffner S, Holler E, Holler B, Huss R, Günther C, Parolini O, Kolch W, Eissner G.

Scand J Immunol. 2016 Sep;84(3):158-64. doi: 10.1111/sji.12459.

25.

Stabilization of C-RAF:KSR1 complex by DiRas3 reduces availability of C-RAF for dimerization with B-RAF.

Baljuls A, Dobrzyński M, Rauch J, Rauch N, Kolch W.

Cell Signal. 2016 Oct;28(10):1451-62. doi: 10.1016/j.cellsig.2016.06.019. Epub 2016 Jun 29.

PMID:
27368419
26.

Autophosphorylation on S614 inhibits the activity and the transforming potential of BRAF.

Dernayka L, Rauch N, Jarboui MA, Zebisch A, Texier Y, Horn N, Romano D, Gloeckner CJ, Kriegsheim Av, Ueffing M, Kolch W, Boldt K.

Cell Signal. 2016 Sep;28(9):1432-9. doi: 10.1016/j.cellsig.2016.06.016. Epub 2016 Jun 21.

PMID:
27345148
27.

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.

28.

Differential localization of A-Raf regulates MST2-mediated apoptosis during epithelial differentiation.

Rauch J, Vandamme D, Mack B, McCann B, Volinsky N, Blanco A, Gires O, Kolch W.

Cell Death Differ. 2016 Aug;23(8):1283-95. doi: 10.1038/cdd.2016.2. Epub 2016 Feb 19.

29.

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
30.

Integrative omics reveals MYCN as a global suppressor of cellular signalling and enables network-based therapeutic target discovery in neuroblastoma.

Duffy DJ, Krstic A, Halasz M, Schwarzl T, Fey D, Iljin K, Mehta JP, Killick K, Whilde J, Turriziani B, Haapa-Paananen S, Fey V, Fischer M, Westermann F, Henrich KO, Bannert S, Higgins DG, Kolch W.

Oncotarget. 2015 Dec 22;6(41):43182-201. doi: 10.18632/oncotarget.6568.

31.

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.

32.

A microfluidic dual gradient generator for conducting cell-based drug combination assays.

Kilinc D, Schwab J, Rampini S, Ikpekha OW, Thampi A, Blasiak A, Li P, Schwamborn R, Kolch W, Matallanas D, Lee GU.

Integr Biol (Camb). 2016 Jan;8(1):39-49. doi: 10.1039/c5ib00209e. Epub 2015 Nov 16.

PMID:
26569638
33.

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.

34.

Measuring Transcription Rate Changes via Time-Course 4-Thiouridine Pulse-Labelling Improves Transcriptional Target Identification.

Schwarzl T, Higgins DG, Kolch W, Duffy DJ.

J Mol Biol. 2015 Oct 23;427(21):3368-74. doi: 10.1016/j.jmb.2015.09.006. Epub 2015 Sep 9.

PMID:
26362006
35.

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
36.

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
37.

ROCK activity and the Gβγ complex mediate chemotactic migration of mouse bone marrow-derived stromal cells.

Ryan CM, Brown JA, Bourke E, Prendergast ÁM, Kavanagh C, Liu Z, Owens P, Shaw G, Kolch W, O'Brien T, Barry FP.

Stem Cell Res Ther. 2015 Jul 24;6:136. doi: 10.1186/s13287-015-0125-y.

38.

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.

39.

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
40.

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
41.

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.

42.

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.

43.

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.

44.

Regulation of the MAPK pathway by raf kinase inhibitory protein.

Vandamme D, Herrero A, Al-Mulla F, Kolch W.

Crit Rev Oncog. 2014;19(6):405-15. Review.

PMID:
25597351
45.

Mechanochemical stimulation of MCF7 cells with rod-shaped Fe-Au Janus particles induces cell death through paradoxical hyperactivation of ERK.

Kilinc D, Lesniak A, Rashdan SA, Gandhi D, Blasiak A, Fannin PC, von Kriegsheim A, Kolch W, Lee GU.

Adv Healthc Mater. 2015 Feb 18;4(3):395-404. doi: 10.1002/adhm.201400391. Epub 2014 Oct 9.

PMID:
25296863
46.

In vitro study of the interaction of heregulin-functionalized magnetic-optical nanorods with MCF7 and MDA-MB-231 cells.

Lesniak A, Kilinc D, Rashdan SA, von Kriegsheim A, Ashall B, Zerulla D, Kolch W, Lee GU.

Faraday Discuss. 2014;175:189-201. doi: 10.1039/c4fd00115j.

PMID:
25266763
47.

One Hippo and many masters: differential regulation of the Hippo pathway in cancer.

Romano D, Matallanas D, Frederick DT, Flaherty KT, Kolch W.

Biochem Soc Trans. 2014 Aug;42(4):816-21. doi: 10.1042/BST20140030. Review.

PMID:
25109963
48.

Molecular mechanisms of asymmetric RAF dimer activation.

Jambrina PG, Bohuszewicz O, Buchete NV, Kolch W, Rosta E.

Biochem Soc Trans. 2014 Aug;42(4):784-90. doi: 10.1042/BST20140025. Review.

PMID:
25109958
49.

Robustness and evolvability of the human signaling network.

Kim J, Vandamme D, Kim JR, Munoz AG, Kolch W, Cho KH.

PLoS Comput Biol. 2014 Jul 31;10(7):e1003763. doi: 10.1371/journal.pcbi.1003763. eCollection 2014 Jul.

50.

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.

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