Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 41

1.

An evaluation of different classification algorithms for protein sequence-based reverse vaccinology prediction.

Heinson AI, Ewing RM, Holloway JW, Woelk CH, Niranjan M.

PLoS One. 2019 Dec 13;14(12):e0226256. doi: 10.1371/journal.pone.0226256. eCollection 2019.

PMID:
31834914
2.

Deep proteomic analysis of Dnmt1 mutant/hypomorphic colorectal cancer cells reveals dysregulation of epithelial-mesenchymal transition and subcellular re-localization of Beta-Catenin.

Bowler EH, Smith-Vidal A, Lester A, Bell J, Wang Z, Bell CG, Wang Y, Divecha N, Skipp PJ, Ewing RM.

Epigenetics. 2019 Aug 26:1-15. doi: 10.1080/15592294.2019.1656154. [Epub ahead of print]

PMID:
31448663
3.

iOmicsPASS: network-based integration of multiomics data for predictive subnetwork discovery.

Koh HWL, Fermin D, Vogel C, Choi KP, Ewing RM, Choi H.

NPJ Syst Biol Appl. 2019 Jul 9;5:22. doi: 10.1038/s41540-019-0099-y. eCollection 2019.

4.

SGLT1 is required for the survival of triple-negative breast cancer cells via potentiation of EGFR activity.

Liu H, Ertay A, Peng P, Li J, Liu D, Xiong H, Zou Y, Qiu H, Hancock D, Yuan X, Huang WC, Ewing RM, Downward J, Wang Y.

Mol Oncol. 2019 Sep;13(9):1874-1886. doi: 10.1002/1878-0261.12530. Epub 2019 Jun 14.

5.

Proteomic Analysis of Azacitidine-Induced Degradation Profiles Identifies Multiple Chromatin and Epigenetic Regulators Including Uhrf1 and Dnmt1 as Sensitive to Azacitidine.

Bowler EH, Bell J, Divecha N, Skipp P, Ewing RM.

J Proteome Res. 2019 Mar 1;18(3):1032-1042. doi: 10.1021/acs.jproteome.8b00745. Epub 2019 Feb 7.

PMID:
30672294
6.

ELF3 is an antagonist of oncogenic-signalling-induced expression of EMT-TF ZEB1.

Liu D, Skomorovska Y, Song J, Bowler E, Harris R, Ravasz M, Bai S, Ayati M, Tamai K, Koyuturk M, Yuan X, Wang Z, Wang Y, Ewing RM.

Cancer Biol Ther. 2019;20(1):90-100. doi: 10.1080/15384047.2018.1507256. Epub 2018 Aug 27.

7.

Paracrine signalling during ZEB1-mediated epithelial-mesenchymal transition augments local myofibroblast differentiation in lung fibrosis.

Yao L, Conforti F, Hill C, Bell J, Drawater L, Li J, Liu D, Xiong H, Alzetani A, Chee SJ, Marshall BG, Fletcher SV, Hancock D, Coldwell M, Yuan X, Ottensmeier CH, Downward J, Collins JE, Ewing RM, Richeldi L, Skipp P, Jones MG, Davies DE, Wang Y.

Cell Death Differ. 2019 May;26(5):943-957. doi: 10.1038/s41418-018-0175-7. Epub 2018 Jul 26.

8.

Multiproteomic and Transcriptomic Analysis of Oncogenic β-Catenin Molecular Networks.

Ewing RM, Song J, Gokulrangan G, Bai S, Bowler EH, Bolton R, Skipp P, Wang Y, Wang Z.

J Proteome Res. 2018 Jun 1;17(6):2216-2225. doi: 10.1021/acs.jproteome.8b00180. Epub 2018 May 18.

PMID:
29747501
9.

Proteomics and Network Analyses Reveal Inhibition of Akt-mTOR Signaling in CD4+ T Cells by Mycobacterium tuberculosis Mannose-Capped Lipoarabinomannan.

Karim AF, Sande OJ, Tomechko SE, Ding X, Li M, Maxwell S, Ewing RM, Harding CV, Rojas RE, Chance MR, Boom WH.

Proteomics. 2017 Nov;17(22). doi: 10.1002/pmic.201700233.

10.

Noise-processing by signaling networks.

Kontogeorgaki S, Sánchez-García RJ, Ewing RM, Zygalakis KC, MacArthur BD.

Sci Rep. 2017 Apr 3;7(1):532. doi: 10.1038/s41598-017-00659-x.

11.

Corrigendum: Alternate wiring of a KNOXI genetic network underlies differences in leaf development of A. thaliana and C. hirsuta.

Rast-Somssich MI, Broholm S, Jenkins H, Canales C, Vlad D, Kwantes M, Bilsborough G, Dello Ioio R, Ewing RM, Laufs P, Huijser P, Ohno C, Heisler MG, Hay A, Tsiantis M.

Genes Dev. 2016 Jan 1;30(1):132. No abstract available.

12.

Alternate wiring of a KNOXI genetic network underlies differences in leaf development of A. thaliana and C. hirsuta.

Rast-Somssich MI, Broholm S, Jenkins H, Canales C, Vlad D, Kwantes M, Bilsborough G, Dello Ioio R, Ewing RM, Laufs P, Huijser P, Ohno C, Heisler MG, Hay A, Tsiantis M.

Genes Dev. 2015 Nov 15;29(22):2391-404. doi: 10.1101/gad.269050.115. Erratum in: Genes Dev. 2016 Jan 1;30(1):132.

13.

Proteomic and bioinformatics profile of paired human alveolar macrophages and peripheral blood monocytes.

Tomechko SE, Lundberg KC, Jarvela J, Bebek G, Chesnokov NG, Schlatzer D, Ewing RM, Boom WH, Chance MR, Silver RF.

Proteomics. 2015 Nov;15(22):3797-805. doi: 10.1002/pmic.201400496.

14.

How do oncoprotein mutations rewire protein-protein interaction networks?

Bowler EH, Wang Z, Ewing RM.

Expert Rev Proteomics. 2015;12(5):449-55. doi: 10.1586/14789450.2015.1084875. Epub 2015 Sep 1. Review.

15.

A Protein Interaction between β-Catenin and Dnmt1 Regulates Wnt Signaling and DNA Methylation in Colorectal Cancer Cells.

Song J, Du Z, Ravasz M, Dong B, Wang Z, Ewing RM.

Mol Cancer Res. 2015 Jun;13(6):969-81. doi: 10.1158/1541-7786.MCR-13-0644. Epub 2015 Mar 9.

16.

Integrated analysis of the Wnt responsive proteome in human cells reveals diverse and cell-type specific networks.

Song J, Wang Z, Ewing RM.

Mol Biosyst. 2014 Jan;10(1):45-53. doi: 10.1039/c3mb70417c.

17.

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data.

Mellacheruvu D, Wright Z, Couzens AL, Lambert JP, St-Denis NA, Li T, Miteva YV, Hauri S, Sardiu ME, Low TY, Halim VA, Bagshaw RD, Hubner NC, Al-Hakim A, Bouchard A, Faubert D, Fermin D, Dunham WH, Goudreault M, Lin ZY, Badillo BG, Pawson T, Durocher D, Coulombe B, Aebersold R, Superti-Furga G, Colinge J, Heck AJ, Choi H, Gstaiger M, Mohammed S, Cristea IM, Bennett KL, Washburn MP, Raught B, Ewing RM, Gingras AC, Nesvizhskii AI.

Nat Methods. 2013 Aug;10(8):730-6. doi: 10.1038/nmeth.2557. Epub 2013 Jul 7.

18.

Gain of interaction with IRS1 by p110α-helical domain mutants is crucial for their oncogenic functions.

Hao Y, Wang C, Cao B, Hirsch BM, Song J, Markowitz SD, Ewing RM, Sedwick D, Liu L, Zheng W, Wang Z.

Cancer Cell. 2013 May 13;23(5):583-93. doi: 10.1016/j.ccr.2013.03.021. Epub 2013 May 2.

19.

A semantic proteomics dashboard (SemPoD) for data management in translational research.

Jayapandian CP, Zhao M, Ewing RM, Zhang GQ, Sahoo SS.

BMC Syst Biol. 2012;6 Suppl 3:S20. doi: 10.1186/1752-0509-6-S3-S20. Epub 2012 Dec 17.

20.

Identifying novel protein complexes in cancer cells using epitope-tagging of endogenous human genes and affinity-purification mass spectrometry.

Song J, Hao Y, Du Z, Wang Z, Ewing RM.

J Proteome Res. 2012 Dec 7;11(12):5630-41. doi: 10.1021/pr300598t. Epub 2012 Nov 7.

21.

Network-based approaches for extending the Wnt signalling pathway and identifying context-specific sub-networks.

Saha S, Roman T, Galante A, Koyutürk M, Ewing RM.

Int J Comput Biol Drug Des. 2012;5(3-4):185-205. doi: 10.1504/IJCBDD.2012.049203. Epub 2012 Sep 24.

PMID:
23013649
22.

Computational framework for analysis of prey-prey associations in interaction proteomics identifies novel human protein-protein interactions and networks.

Saha S, Dazard JE, Xu H, Ewing RM.

J Proteome Res. 2012 Sep 7;11(9):4476-87. doi: 10.1021/pr300227y. Epub 2012 Aug 21.

23.

DNA and chromatin modification networks distinguish stem cell pluripotent ground states.

Song J, Saha S, Gokulrangan G, Tesar PJ, Ewing RM.

Mol Cell Proteomics. 2012 Oct;11(10):1036-47. Epub 2012 Jul 22.

24.

ROCS: a reproducibility index and confidence score for interaction proteomics studies.

Dazard JE, Saha S, Ewing RM.

BMC Bioinformatics. 2012 Jun 8;13:128. doi: 10.1186/1471-2105-13-128.

25.

Human biomarker discovery and predictive models for disease progression for idiopathic pneumonia syndrome following allogeneic stem cell transplantation.

Schlatzer DM, Dazard JE, Ewing RM, Ilchenko S, Tomcheko SE, Eid S, Ho V, Yanik G, Chance MR, Cooke KR.

Mol Cell Proteomics. 2012 Jun;11(6):M111.015479. doi: 10.1074/mcp.M111.015479. Epub 2012 Feb 15.

26.

DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization.

Erten S, Bebek G, Ewing RM, Koyutürk M.

BioData Min. 2011 Jun 24;4:19. doi: 10.1186/1756-0381-4-19.

27.

DNMT1 stability is regulated by proteins coordinating deubiquitination and acetylation-driven ubiquitination.

Du Z, Song J, Wang Y, Zhao Y, Guda K, Yang S, Kao HY, Xu Y, Willis J, Markowitz SD, Sedwick D, Ewing RM, Wang Z.

Sci Signal. 2010 Nov 2;3(146):ra80. doi: 10.1126/scisignal.2001462.

28.

The bait compatibility index: computational bait selection for interaction proteomics experiments.

Saha S, Kaur P, Ewing RM.

J Proteome Res. 2010 Oct 1;9(10):4972-81. doi: 10.1021/pr100267t.

PMID:
20731387
29.

Multiple myeloma phosphotyrosine proteomic profile associated with FGFR3 expression, ligand activation, and drug inhibition.

St-Germain JR, Taylor P, Tong J, Jin LL, Nikolic A, Stewart II, Ewing RM, Dharsee M, Li Z, Trudel S, Moran MF.

Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):20127-32. doi: 10.1073/pnas.0910957106. Epub 2009 Nov 9.

30.

Urinary protein profiles in a rat model for diabetic complications.

Schlatzer DM, Dazard JE, Dharsee M, Ewing RM, Ilchenko S, Stewart I, Christ G, Chance MR.

Mol Cell Proteomics. 2009 Sep;8(9):2145-58. doi: 10.1074/mcp.M800558-MCP200. Epub 2009 Jun 4.

31.

Human Proteinpedia enables sharing of human protein data.

Mathivanan S, Ahmed M, Ahn NG, Alexandre H, Amanchy R, Andrews PC, Bader JS, Balgley BM, Bantscheff M, Bennett KL, Björling E, Blagoev B, Bose R, Brahmachari SK, Burlingame AS, Bustelo XR, Cagney G, Cantin GT, Cardasis HL, Celis JE, Chaerkady R, Chu F, Cole PA, Costello CE, Cotter RJ, Crockett D, DeLany JP, De Marzo AM, DeSouza LV, Deutsch EW, Dransfield E, Drewes G, Droit A, Dunn MJ, Elenitoba-Johnson K, Ewing RM, Van Eyk J, Faca V, Falkner J, Fang X, Fenselau C, Figeys D, Gagné P, Gelfi C, Gevaert K, Gimble JM, Gnad F, Goel R, Gromov P, Hanash SM, Hancock WS, Harsha HC, Hart G, Hays F, He F, Hebbar P, Helsens K, Hermeking H, Hide W, Hjernø K, Hochstrasser DF, Hofmann O, Horn DM, Hruban RH, Ibarrola N, James P, Jensen ON, Jensen PH, Jung P, Kandasamy K, Kheterpal I, Kikuno RF, Korf U, Körner R, Kuster B, Kwon MS, Lee HJ, Lee YJ, Lefevre M, Lehvaslaiho M, Lescuyer P, Levander F, Lim MS, Löbke C, Loo JA, Mann M, Martens L, Martinez-Heredia J, McComb M, McRedmond J, Mehrle A, Menon R, Miller CA, Mischak H, Mohan SS, Mohmood R, Molina H, Moran MF, Morgan JD, Moritz R, Morzel M, Muddiman DC, Nalli A, Navarro JD, Neubert TA, Ohara O, Oliva R, Omenn GS, Oyama M, Paik YK, Pennington K, Pepperkok R, Periaswamy B, Petricoin EF, Poirier GG, Prasad TS, Purvine SO, Rahiman BA, Ramachandran P, Ramachandra YL, Rice RH, Rick J, Ronnholm RH, Salonen J, Sanchez JC, Sayd T, Seshi B, Shankari K, Sheng SJ, Shetty V, Shivakumar K, Simpson RJ, Sirdeshmukh R, Siu KW, Smith JC, Smith RD, States DJ, Sugano S, Sullivan M, Superti-Furga G, Takatalo M, Thongboonkerd V, Trinidad JC, Uhlen M, Vandekerckhove J, Vasilescu J, Veenstra TD, Vidal-Taboada JM, Vihinen M, Wait R, Wang X, Wiemann S, Wu B, Xu T, Yates JR, Zhong J, Zhou M, Zhu Y, Zurbig P, Pandey A.

Nat Biotechnol. 2008 Feb;26(2):164-7. doi: 10.1038/nbt0208-164. No abstract available.

32.

Large-scale mapping of human protein-protein interactions by mass spectrometry.

Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, Taylor R, Dharsee M, Ho Y, Heilbut A, Moore L, Zhang S, Ornatsky O, Bukhman YV, Ethier M, Sheng Y, Vasilescu J, Abu-Farha M, Lambert JP, Duewel HS, Stewart II, Kuehl B, Hogue K, Colwill K, Gladwish K, Muskat B, Kinach R, Adams SL, Moran MF, Morin GB, Topaloglou T, Figeys D.

Mol Syst Biol. 2007;3:89. Epub 2007 Mar 13.

33.

Emerging applications for phospho-proteomics in cancer molecular therapeutics.

Moran MF, Tong J, Taylor P, Ewing RM.

Biochim Biophys Acta. 2006 Dec;1766(2):230-41. Epub 2006 Jun 23. Review.

PMID:
16889898
34.

Expression profile analysis of the low-oxygen response in Arabidopsis root cultures.

Klok EJ, Wilson IW, Wilson D, Chapman SC, Ewing RM, Somerville SC, Peacock WJ, Dolferus R, Dennis ES.

Plant Cell. 2002 Oct;14(10):2481-94.

35.

Microarray analysis of chitin elicitation in Arabidopsis thaliana.

Ramonell KM, Zhang B, Ewing RM, Chen Y, Xu D, Stacey G, Somerville S.

Mol Plant Pathol. 2002 Sep 1;3(5):301-11. doi: 10.1046/j.1364-3703.2002.00123.x.

PMID:
20569338
36.
37.

Visualization of expression clusters using Sammon's non-linear mapping.

Ewing RM, Cherry JM.

Bioinformatics. 2001 Jul;17(7):658-9.

PMID:
11448886
38.

EST databases as multi-conditional gene expression datasets.

Ewing RM, Claverie JM.

Pac Symp Biocomput. 2000:430-42.

39.

Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression.

Ewing RM, Ben Kahla A, Poirot O, Lopez F, Audic S, Claverie JM.

Genome Res. 1999 Oct;9(10):950-9.

40.

An 85-kb tandem triplication in the slow Wallerian degeneration (Wlds) mouse.

Coleman MP, Conforti L, Buckmaster EA, Tarlton A, Ewing RM, Brown MC, Lyon MF, Perry VH.

Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):9985-90.

41.

Transcripts of maize RbcS genes accumulate differentially in C3 and C4 tissues.

Ewing RM, Jenkins GI, Langdale JA.

Plant Mol Biol. 1998 Mar;36(4):593-9.

PMID:
9484454

Supplemental Content

Loading ...
Support Center