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Items: 26

1.

Generating topological protein interaction scores and data visualization with TopS.

Sardiu ME, Florens L, Washburn MP.

Methods. 2019 Aug 30. pii: S1046-2023(19)30138-0. doi: 10.1016/j.ymeth.2019.08.010. [Epub ahead of print]

PMID:
31476375
2.

Biochemical Reduction of the Topology of the Diverse WDR76 Protein Interactome.

Dayebgadoh G, Sardiu ME, Florens L, Washburn MP.

J Proteome Res. 2019 Sep 6;18(9):3479-3491. doi: 10.1021/acs.jproteome.9b00373. Epub 2019 Aug 9.

PMID:
31353912
3.

Topological scoring of protein interaction networks.

Sardiu ME, Gilmore JM, Groppe BD, Dutta A, Florens L, Washburn MP.

Nat Commun. 2019 Mar 8;10(1):1118. doi: 10.1038/s41467-019-09123-y.

4.

The WHHERE coactivator complex is required for retinoic acid-dependent regulation of embryonic symmetry.

Vilhais-Neto GC, Fournier M, Plassat JL, Sardiu ME, Saraf A, Garnier JM, Maruhashi M, Florens L, Washburn MP, Pourquié O.

Nat Commun. 2017 Sep 28;8(1):728. doi: 10.1038/s41467-017-00593-6.

5.

Identification of Topological Network Modules in Perturbed Protein Interaction Networks.

Sardiu ME, Gilmore JM, Groppe B, Florens L, Washburn MP.

Sci Rep. 2017 Mar 8;7:43845. doi: 10.1038/srep43845.

6.

Dynamic and Combinatorial Landscape of Histone Modifications during the Intraerythrocytic Developmental Cycle of the Malaria Parasite.

Saraf A, Cervantes S, Bunnik EM, Ponts N, Sardiu ME, Chung DW, Prudhomme J, Varberg JM, Wen Z, Washburn MP, Florens L, Le Roch KG.

J Proteome Res. 2016 Aug 5;15(8):2787-801. doi: 10.1021/acs.jproteome.6b00366. Epub 2016 Jun 24.

7.

WDR76 Co-Localizes with Heterochromatin Related Proteins and Rapidly Responds to DNA Damage.

Gilmore JM, Sardiu ME, Groppe BD, Thornton JL, Liu X, Dayebgadoh G, Banks CA, Slaughter BD, Unruh JR, Workman JL, Florens L, Washburn MP.

PLoS One. 2016 Jun 1;11(6):e0155492. doi: 10.1371/journal.pone.0155492. eCollection 2016.

8.

Conserved abundance and topological features in chromatin-remodeling protein interaction networks.

Sardiu ME, Gilmore JM, Groppe BD, Herman D, Ramisetty SR, Cai Y, Jin J, Conaway RC, Conaway JW, Florens L, Washburn MP.

EMBO Rep. 2015 Jan;16(1):116-26. doi: 10.15252/embr.201439403. Epub 2014 Nov 26.

9.

Suberoylanilide hydroxamic acid (SAHA)-induced dynamics of a human histone deacetylase protein interaction network.

Sardiu ME, Smith KT, Groppe BD, Gilmore JM, Saraf A, Egidy R, Peak A, Seidel CW, Florens L, Workman JL, Washburn MP.

Mol Cell Proteomics. 2014 Nov;13(11):3114-25. doi: 10.1074/mcp.M113.037127. Epub 2014 Jul 29.

10.

The multifunctional autophagy pathway in the human malaria parasite, Plasmodium falciparum.

Cervantes S, Bunnik EM, Saraf A, Conner CM, Escalante A, Sardiu ME, Ponts N, Prudhomme J, Florens L, Le Roch KG.

Autophagy. 2014 Jan;10(1):80-92. doi: 10.4161/auto.26743. Epub 2013 Nov 11.

11.

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.

12.

Quantitative proteomics demonstrates that the RNA polymerase II subunits Rpb4 and Rpb7 dissociate during transcriptional elongation.

Mosley AL, Hunter GO, Sardiu ME, Smolle M, Workman JL, Florens L, Washburn MP.

Mol Cell Proteomics. 2013 Jun;12(6):1530-8. doi: 10.1074/mcp.M112.024034. Epub 2013 Feb 15.

13.

Human family with sequence similarity 60 member A (FAM60A) protein: a new subunit of the Sin3 deacetylase complex.

Smith KT, Sardiu ME, Martin-Brown SA, Seidel C, Mushegian A, Egidy R, Florens L, Washburn MP, Workman JL.

Mol Cell Proteomics. 2012 Dec;11(12):1815-28. doi: 10.1074/mcp.M112.020255. Epub 2012 Sep 14.

14.

Characterization of a highly conserved histone related protein, Ydl156w, and its functional associations using quantitative proteomic analyses.

Gilmore JM, Sardiu ME, Venkatesh S, Stutzman B, Peak A, Seidel CW, Workman JL, Florens L, Washburn MP.

Mol Cell Proteomics. 2012 Apr;11(4):M111.011544. doi: 10.1074/mcp.M111.011544. Epub 2011 Dec 22.

15.

Construction of protein interaction networks based on the label-free quantitative proteomics.

Sardiu ME, Washburn MP.

Methods Mol Biol. 2011;781:71-85. doi: 10.1007/978-1-61779-276-2_5.

PMID:
21877278
16.

Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes.

Lee KK, Sardiu ME, Swanson SK, Gilmore JM, Torok M, Grant PA, Florens L, Workman JL, Washburn MP.

Mol Syst Biol. 2011 Jul 5;7:503. doi: 10.1038/msb.2011.40.

17.

Building protein-protein interaction networks with proteomics and informatics tools.

Sardiu ME, Washburn MP.

J Biol Chem. 2011 Jul 8;286(27):23645-51. doi: 10.1074/jbc.R110.174052. Epub 2011 May 12. Review.

18.

Highly reproducible label free quantitative proteomic analysis of RNA polymerase complexes.

Mosley AL, Sardiu ME, Pattenden SG, Workman JL, Florens L, Washburn MP.

Mol Cell Proteomics. 2011 Feb;10(2):M110.000687. doi: 10.1074/mcp.M110.000687. Epub 2010 Nov 3.

19.

Enriching quantitative proteomics with SI(N).

Sardiu ME, Washburn MP.

Nat Biotechnol. 2010 Jan;28(1):40-2. doi: 10.1038/nbt0110-40. No abstract available.

PMID:
20062039
20.

Delayed correlation of mRNA and protein expression in rapamycin-treated cells and a role for Ggc1 in cellular sensitivity to rapamycin.

Fournier ML, Paulson A, Pavelka N, Mosley AL, Gaudenz K, Bradford WD, Glynn E, Li H, Sardiu ME, Fleharty B, Seidel C, Florens L, Washburn MP.

Mol Cell Proteomics. 2010 Feb;9(2):271-84. doi: 10.1074/mcp.M900415-MCP200. Epub 2009 Nov 10.

21.

Determining protein complex connectivity using a probabilistic deletion network derived from quantitative proteomics.

Sardiu ME, Gilmore JM, Carrozza MJ, Li B, Workman JL, Florens L, Washburn MP.

PLoS One. 2009 Oct 6;4(10):e7310. doi: 10.1371/journal.pone.0007310.

22.

Evaluation of clustering algorithms for protein complex and protein interaction network assembly.

Sardiu ME, Florens L, Washburn MP.

J Proteome Res. 2009 Jun;8(6):2944-52. doi: 10.1021/pr900073d.

PMID:
19317493
23.

Probabilistic assembly of human protein interaction networks from label-free quantitative proteomics.

Sardiu ME, Cai Y, Jin J, Swanson SK, Conaway RC, Conaway JW, Florens L, Washburn MP.

Proc Natl Acad Sci U S A. 2008 Feb 5;105(5):1454-9. doi: 10.1073/pnas.0706983105. Epub 2008 Jan 24.

24.

Cysteine-cysteine contact preference leads to target-focusing in protein folding.

Sardiu ME, Cheung MS, Yu YK.

Biophys J. 2007 Aug 1;93(3):938-51.

25.

Statistical analysis of membrane proteome expression changes in Saccharomyces cerevisiae.

Zybailov B, Mosley AL, Sardiu ME, Coleman MK, Florens L, Washburn MP.

J Proteome Res. 2006 Sep;5(9):2339-47.

PMID:
16944946
26.

Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem.

Sardiu ME, Alves G, Yu YK.

Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Dec;72(6 Pt 1):061917. Epub 2005 Dec 23.

PMID:
16485984

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