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Items: 1 to 50 of 65

1.

Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs.

van de Kooij B, Creixell P, van Vlimmeren A, Joughin BA, Miller CJ, Haider N, Simpson CD, Linding R, Stambolic V, Turk BE, Yaffe MB.

Elife. 2019 May 24;8. pii: e44635. doi: 10.7554/eLife.44635.

2.

Comprehensive profiling of the STE20 kinase family defines features essential for selective substrate targeting and signaling output.

Miller CJ, Lou HJ, Simpson C, van de Kooij B, Ha BH, Fisher OS, Pirman NL, Boggon TJ, Rinehart J, Yaffe MB, Linding R, Turk BE.

PLoS Biol. 2019 Mar 21;17(3):e2006540. doi: 10.1371/journal.pbio.2006540. eCollection 2019 Mar.

3.

Farnesylated heat shock protein 40 is a component of membrane-bound RISC in Arabidopsis.

Sjögren L, Floris M, Barghetti A, Völlmy F, Linding R, Brodersen P.

J Biol Chem. 2018 Oct 26;293(43):16608-16622. doi: 10.1074/jbc.RA118.003887. Epub 2018 Sep 7.

4.

Unravelling the GSK3β-related genotypic interaction network influencing hippocampal volume in recurrent major depressive disorder.

Inkster B, Simmons A, Cole JH, Schoof E, Linding R, Nichols T, Muglia P, Holsboer F, Sämann PG, McGuffin P, Fu CHY, Miskowiak K, Matthews PM, Zai G, Nicodemus K.

Psychiatr Genet. 2018 Oct;28(5):77-84. doi: 10.1097/YPG.0000000000000203.

5.

Bowhead: Bayesian modelling of cell velocity during concerted cell migration.

Engel M, Longden J, Ferkinghoff-Borg J, Robin X, Saginc G, Linding R.

PLoS Comput Biol. 2018 Jan 8;14(1):e1005900. doi: 10.1371/journal.pcbi.1005900. eCollection 2018 Jan.

6.

Cancer systems biology: Harnessing off-target effects.

Saginc G, Voellmy F, Linding R.

Nat Chem Biol. 2017 Nov 21;13(12):1204-1205. doi: 10.1038/nchembio.2519. No abstract available.

PMID:
29161245
7.

Dynamic Rearrangement of Cell States Detected by Systematic Screening of Sequential Anticancer Treatments.

Koplev S, Longden J, Ferkinghoff-Borg J, Blicher Bjerregård M, Cox TR, Erler JT, Pedersen JT, Voellmy F, Sommer MOA, Linding R.

Cell Rep. 2017 Sep 19;20(12):2784-2791. doi: 10.1016/j.celrep.2017.08.095.

8.

Dataset for the proteomic inventory and quantitative analysis of the breast cancer hypoxic secretome associated with osteotropism.

Cox TR, Schoof EM, Gartland A, Erler JT, Linding R.

Data Brief. 2015 Oct 23;5:621-5. doi: 10.1016/j.dib.2015.09.039. eCollection 2015 Dec.

9.

Unmasking determinants of specificity in the human kinome.

Creixell P, Palmeri A, Miller CJ, Lou HJ, Santini CC, Nielsen M, Turk BE, Linding R.

Cell. 2015 Sep 24;163(1):187-201. doi: 10.1016/j.cell.2015.08.057. Epub 2015 Sep 17.

10.

Kinome-wide decoding of network-attacking mutations rewiring cancer signaling.

Creixell P, Schoof EM, Simpson CD, Longden J, Miller CJ, Lou HJ, Perryman L, Cox TR, Zivanovic N, Palmeri A, Wesolowska-Andersen A, Helmer-Citterich M, Ferkinghoff-Borg J, Itamochi H, Bodenmiller B, Erler JT, Turk BE, Linding R.

Cell. 2015 Sep 24;163(1):202-17. doi: 10.1016/j.cell.2015.08.056. Epub 2015 Sep 17.

11.

Pathway and network analysis of cancer genomes.

Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael BJ, Marks DS, Ouellette BFF, Valencia A, Bader GD, Boutros PC, Stuart JM, Linding R, Lopez-Bigas N, Stein LD; Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consortium.

Nat Methods. 2015 Jul;12(7):615-621. doi: 10.1038/nmeth.3440.

12.

The hypoxic cancer secretome induces pre-metastatic bone lesions through lysyl oxidase.

Cox TR, Rumney RMH, Schoof EM, Perryman L, Høye AM, Agrawal A, Bird D, Latif NA, Forrest H, Evans HR, Huggins ID, Lang G, Linding R, Gartland A, Erler JT.

Nature. 2015 Jun 4;522(7554):106-110. doi: 10.1038/nature14492. Epub 2015 May 27.

13.

Integrative analysis of kinase networks in TRAIL-induced apoptosis provides a source of potential targets for combination therapy.

So J, Pasculescu A, Dai AY, Williton K, James A, Nguyen V, Creixell P, Schoof EM, Sinclair J, Barrios-Rodiles M, Gu J, Krizus A, Williams R, Olhovsky M, Dennis JW, Wrana JL, Linding R, Jorgensen C, Pawson T, Colwill K.

Sci Signal. 2015 Apr 7;8(371):rs3. doi: 10.1126/scisignal.2005700.

PMID:
25852190
14.

KinomeXplorer: an integrated platform for kinome biology studies.

Horn H, Schoof EM, Kim J, Robin X, Miller ML, Diella F, Palma A, Cesareni G, Jensen LJ, Linding R.

Nat Methods. 2014 Jun;11(6):603-4. doi: 10.1038/nmeth.2968. No abstract available.

PMID:
24874572
15.

Modulation of the chromatin phosphoproteome by the Haspin protein kinase.

Maiolica A, de Medina-Redondo M, Schoof EM, Chaikuad A, Villa F, Gatti M, Jeganathan S, Lou HJ, Novy K, Hauri S, Toprak UH, Herzog F, Meraldi P, Penengo L, Turk BE, Knapp S, Linding R, Aebersold R.

Mol Cell Proteomics. 2014 Jul;13(7):1724-40. doi: 10.1074/mcp.M113.034819. Epub 2014 Apr 14.

16.

Identification of hypoxia-regulated proteins using MALDI-mass spectrometry imaging combined with quantitative proteomics.

Djidja MC, Chang J, Hadjiprocopis A, Schmich F, Sinclair J, Mršnik M, Schoof EM, Barker HE, Linding R, Jørgensen C, Erler JT.

J Proteome Res. 2014 May 2;13(5):2297-313. doi: 10.1021/pr401056c. Epub 2014 Apr 24.

PMID:
24702160
17.

Experimental and computational tools for analysis of signaling networks in primary cells.

Schoof EM, Linding R.

Curr Protoc Immunol. 2014 Feb 4;104:Unit 11.11.. doi: 10.1002/0471142735.im1111s104.

PMID:
24510617
18.

CoreFlow: a computational platform for integration, analysis and modeling of complex biological data.

Pasculescu A, Schoof EM, Creixell P, Zheng Y, Olhovsky M, Tian R, So J, Vanderlaan RD, Pawson T, Linding R, Colwill K.

J Proteomics. 2014 Apr 4;100:167-73. doi: 10.1016/j.jprot.2014.01.023. Epub 2014 Feb 3.

PMID:
24503186
19.

Personalized network-based treatments in oncology.

Robin X, Creixell P, Radetskaya O, Santini CC, Longden J, Linding R.

Clin Pharmacol Ther. 2013 Dec;94(6):646-50. doi: 10.1038/clpt.2013.171. Epub 2013 Aug 29. Review.

PMID:
23995267
20.

Computational approaches to identify functional genetic variants in cancer genomes.

Gonzalez-Perez A, Mustonen V, Reva B, Ritchie GR, Creixell P, Karchin R, Vazquez M, Fink JL, Kassahn KS, Pearson JV, Bader GD, Boutros PC, Muthuswamy L, Ouellette BF, Reimand J, Linding R, Shibata T, Valencia A, Butler A, Dronov S, Flicek P, Shannon NB, Carter H, Ding L, Sander C, Stuart JM, Stein LD, Lopez-Bigas N; International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group.

Nat Methods. 2013 Aug;10(8):723-9. doi: 10.1038/nmeth.2562.

21.

Global characterization of signalling networks associated with tamoxifen resistance in breast cancer.

Browne BC, Hochgräfe F, Wu J, Millar EK, Barraclough J, Stone A, McCloy RA, Lee CS, Roberts C, Ali NA, Boulghourjian A, Schmich F, Linding R, Farrow L, Gee JM, Nicholson RI, O'Toole SA, Sutherland RL, Musgrove EA, Butt AJ, Daly RJ.

FEBS J. 2013 Nov;280(21):5237-57. doi: 10.1111/febs.12441. Epub 2013 Aug 19.

22.

In vivo SILAC-based proteomics reveals phosphoproteome changes during mouse skin carcinogenesis.

Zanivan S, Meves A, Behrendt K, Schoof EM, Neilson LJ, Cox J, Tang HR, Kalna G, van Ree JH, van Deursen JM, Trempus CS, Machesky LM, Linding R, Wickström SA, Fässler R, Mann M.

Cell Rep. 2013 Feb 21;3(2):552-66. doi: 10.1016/j.celrep.2013.01.003. Epub 2013 Jan 31.

23.

PROTEINCHALLENGE: crowd sourcing in proteomics analysis and software development.

Martin SF, Falkenberg H, Dyrlund TF, Khoudoli GA, Mageean CJ, Linding R.

J Proteomics. 2013 Aug 2;88:41-6. doi: 10.1016/j.jprot.2012.11.014. Epub 2012 Dec 7. Review.

24.

Navigating cancer network attractors for tumor-specific therapy.

Creixell P, Schoof EM, Erler JT, Linding R.

Nat Biotechnol. 2012 Sep;30(9):842-8. doi: 10.1038/nbt.2345.

PMID:
22965061
25.

Mutational properties of amino acid residues: implications for evolvability of phosphorylatable residues.

Creixell P, Schoof EM, Tan CS, Linding R.

Philos Trans R Soc Lond B Biol Sci. 2012 Sep 19;367(1602):2584-93. doi: 10.1098/rstb.2012.0076. Erratum in: Philos Trans R Soc Lond B Biol Sci. 2012 Nov 5;367(1602):3058.

26.

Cells, shared memory and breaking the PTM code.

Creixell P, Linding R.

Mol Syst Biol. 2012;8:598. doi: 10.1038/msb.2012.33. No abstract available.

27.

Network medicine strikes a blow against breast cancer.

Erler JT, Linding R.

Cell. 2012 May 11;149(4):731-3. doi: 10.1016/j.cell.2012.04.014.

28.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H.

Proteomics Clin Appl. 2011 Dec;5(11-12):580-9. doi: 10.1002/prca.201100097.

PMID:
22213554
29.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

Proteomics. 2012 Jan;12(1):11-20. doi: 10.1002/pmic.201100562. Epub 2011 Dec 14.

PMID:
22069307
30.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR, Rodriguez H.

J Proteome Res. 2012 Feb 3;11(2):1412-9. doi: 10.1021/pr201071t. Epub 2011 Dec 8.

31.

Recommendations for mass spectrometry data quality metrics for open access data (corollary to the Amsterdam Principles).

Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B, Gorman J, Grimm R, Hancock W, Hermjakob H, Horn D, Hunter C, Kolar P, Kraus HJ, Langen H, Linding R, Moritz RL, Omenn GS, Orlando R, Pandey A, Ping P, Rahbar A, Rivers R, Seymour SL, Simpson RJ, Slotta D, Smith RD, Stein SE, Tabb DL, Tagle D, Yates JR 3rd, Rodriguez H.

Mol Cell Proteomics. 2011 Dec;10(12):O111.015446. doi: 10.1074/mcp.O111.015446. Epub 2011 Nov 3.

32.

Verification of systems biology research in the age of collaborative competition.

Meyer P, Alexopoulos LG, Bonk T, Califano A, Cho CR, de la Fuente A, de Graaf D, Hartemink AJ, Hoeng J, Ivanov NV, Koeppl H, Linding R, Marbach D, Norel R, Peitsch MC, Rice JJ, Royyuru A, Schacherer F, Sprengel J, Stolle K, Vitkup D, Stolovitzky G.

Nat Biotechnol. 2011 Sep 8;29(9):811-5. doi: 10.1038/nbt.1968. No abstract available.

PMID:
21904331
33.

OpenFreezer: a reagent information management software system.

Olhovsky M, Williton K, Dai AY, Pasculescu A, Lee JP, Goudreault M, Wells CD, Park JG, Gingras AC, Linding R, Pawson T, Colwill K.

Nat Methods. 2011 Jul 28;8(8):612-3. doi: 10.1038/nmeth.1658. No abstract available.

PMID:
21799493
34.

DNA damage activates a spatially distinct late cytoplasmic cell-cycle checkpoint network controlled by MK2-mediated RNA stabilization.

Reinhardt HC, Hasskamp P, Schmedding I, Morandell S, van Vugt MA, Wang X, Linding R, Ong SE, Weaver D, Carr SA, Yaffe MB.

Mol Cell. 2010 Oct 8;40(1):34-49. doi: 10.1016/j.molcel.2010.09.018.

35.

(R)evolution of complex regulatory systems.

Linding R.

Sci Signal. 2010 Jun 22;3(127):eg4. doi: 10.1126/scisignal.3127eg4.

36.

Multivariate signal integration.

Linding R.

Nat Rev Mol Cell Biol. 2010 Jun;11(6):391. doi: 10.1038/nrm2906. Epub 2010 May 6. No abstract available.

PMID:
20445545
37.

Roles of “junk phosphorylation” in modulating biomolecular association of phosphorylated proteins?

Tan CS, Jørgensen C, Linding R.

Cell Cycle. 2010 Apr 1;9(7):1276-80.

PMID:
20234177
38.

A mitotic phosphorylation feedback network connects Cdk1, Plk1, 53BP1, and Chk2 to inactivate the G(2)/M DNA damage checkpoint.

van Vugt MA, Gardino AK, Linding R, Ostheimer GJ, Reinhardt HC, Ong SE, Tan CS, Miao H, Keezer SM, Li J, Pawson T, Lewis TA, Carr SA, Smerdon SJ, Brummelkamp TR, Yaffe MB.

PLoS Biol. 2010 Jan 26;8(1):e1000287. doi: 10.1371/journal.pbio.1000287.

39.

Simplistic pathways or complex networks?

Jørgensen C, Linding R.

Curr Opin Genet Dev. 2010 Feb;20(1):15-22. doi: 10.1016/j.gde.2009.12.003. Epub 2010 Jan 22. Review.

PMID:
20096559
40.

Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells.

Jørgensen C, Sherman A, Chen GI, Pasculescu A, Poliakov A, Hsiung M, Larsen B, Wilkinson DG, Linding R, Pawson T.

Science. 2009 Dec 11;326(5959):1502-9. doi: 10.1126/science.1176615.

41.

Eukaryotic protein domains as functional units of cellular evolution.

Jin J, Xie X, Chen C, Park JG, Stark C, James DA, Olhovsky M, Linding R, Mao Y, Pawson T.

Sci Signal. 2009 Nov 24;2(98):ra76. doi: 10.1126/scisignal.2000546.

42.

Network-based drugs and biomarkers.

Erler JT, Linding R.

J Pathol. 2010 Jan;220(2):290-6. doi: 10.1002/path.2646. Review.

PMID:
19921715
43.

ELM: the status of the 2010 eukaryotic linear motif resource.

Gould CM, Diella F, Via A, Puntervoll P, Gemünd C, Chabanis-Davidson S, Michael S, Sayadi A, Bryne JC, Chica C, Seiler M, Davey NE, Haslam N, Weatheritt RJ, Budd A, Hughes T, Pas J, Rychlewski L, Travé G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ.

Nucleic Acids Res. 2010 Jan;38(Database issue):D167-80. doi: 10.1093/nar/gkp1016. Epub 2009 Nov 17.

44.

Experimental and computational tools useful for (re)construction of dynamic kinase-substrate networks.

Tan CS, Linding R.

Proteomics. 2009 Dec;9(23):5233-42. doi: 10.1002/pmic.200900266. Review.

PMID:
19834900
45.

Phosphorylation dynamics during early differentiation of human embryonic stem cells.

Van Hoof D, Muñoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J.

Cell Stem Cell. 2009 Aug 7;5(2):214-26. doi: 10.1016/j.stem.2009.05.021.

46.

Comparative analysis reveals conserved protein phosphorylation networks implicated in multiple diseases.

Tan CS, Bodenmiller B, Pasculescu A, Jovanovic M, Hengartner MO, Jørgensen C, Bader GD, Aebersold R, Pawson T, Linding R.

Sci Signal. 2009 Jul 28;2(81):ra39. doi: 10.1126/scisignal.2000316.

47.

Positive selection of tyrosine loss in metazoan evolution.

Tan CS, Pasculescu A, Lim WA, Pawson T, Bader GD, Linding R.

Science. 2009 Sep 25;325(5948):1686-8. doi: 10.1126/science.1174301. Epub 2009 Jul 9.

48.

Dissecting the interface between signaling and transcriptional regulation in human B cells.

Wang K, Alvarez MJ, Bisikirska BC, Linding R, Basso K, Dalla Favera R, Califano A.

Pac Symp Biocomput. 2009:264-75.

49.

Dynamic modularity in protein interaction networks predicts breast cancer outcome.

Taylor IW, Linding R, Warde-Farley D, Liu Y, Pesquita C, Faria D, Bull S, Pawson T, Morris Q, Wrana JL.

Nat Biotechnol. 2009 Feb;27(2):199-204. doi: 10.1038/nbt.1522. Epub 2009 Feb 1.

PMID:
19182785
50.

Phosphorylation networks regulating JNK activity in diverse genetic backgrounds.

Bakal C, Linding R, Llense F, Heffern E, Martin-Blanco E, Pawson T, Perrimon N.

Science. 2008 Oct 17;322(5900):453-6. doi: 10.1126/science.1158739.

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