Publications
Publications
Supporting the scientific spirit of transparency, the Stowers Institute for Medical Research makes the data underlying its scientific publications freely accessible to the scientific community. Access to original, unprocessed data allows other scientists to validate and extend findings made by Stowers researchers.
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Proteome-Wide Identification of RNA-Dependent Proteins: An Emerging Role of RNAs in Plasmodium falciparum Protein Complexes
Hollin T, Abel S, Banks C, Hristov B, Prudhomme J, Hales K, Florens L, Stafford Noble W, Le Roch KG. Nat Commun. 2024;15:1365 doi: 10.1038/s41467-024-45519-1.
Hypomyelination, hypodontia and craniofacial abnormalities in a Polr3b mouse model of leukodystrophy
Michell-Robinson MA, Watt KEN, Grouza V, Macintosh J, Pinard M, Tuznik M, Chen X, Darbelli L, Wu CL, Perrier S, Chitsaz D, Uccelli NA, Liu H, Cox TC, Muller CW, Kennedy TE, Coulombe B, Rudko DA, Trainor PA, Bernard G. [published ahead of print August 28 2023]. Brain. 2023:1-16.
Identifying dynamical persistent biomarker structures for rare events using modern integrative machine learning approach
Dutta S, Box AC, Li Y, Sardiu ME. Proteomics. 2023:e2200290.
Functional genomics of RAP proteins and their role in mitoribosome regulation in Plasmodium falciparum
Hollin T, Abel S, Falla A, Pasaje CFA, Bhatia A, Hur M, Kirkwood JS, Saraf A, Prudhomme J, de Souza A, Florens L, Niles JC, Le Roch KG. Nat Commun. 2022;13:1275. doi: 1210.1038/s41467-41022-28981-41467.
Perturbation of BRMS1 interactome reveals pathways that impact metastasis
Zimmermann RC, Sardiu ME, Manton CA, Miah MS, Banks CAS, Adams MK, Koestler DC, Hurst DR, Edmonds MD, Washburn MP, Welch DR. PloS One. 2021;16:e0259128. doi: 10.1371/journal.pone.0259128.
Decellularization enables functional analysis of ECM remodeling in planarian regeneration
Sonpho E, Mann FG, Jr., Levy M, Ross EJ, Guerrero-Hernandez C, Florens L, Saraf A, Doddihal V, Ounjai P, Sánchez Alvarado A. Mol Cell Proteomics. 2021:100137. doi: 100110.101016/j.mcpro.102021.100137.
Identification of Stem Cells from Large Cell Populations with Topological Scoring
Sardiu ME, Box AC, Haug JS, Washburn MP. Mol Omics. 2021;17:59-65.
Harnessing Ionic Selectivity In Acetyltransferase Chemoproteomic Probes
Jing Y, Montano JL, Levy M, Lopez JE, Kung PP, Richardson P, Krajewski K, Florens L, Washburn MP, Meier JL. ACS Chem Biol. 2021;16:27-34.
High-Throughput Identification of Nuclear Envelope Protein Interactions in Schizosaccharomyces pombe Using an Arrayed Membrane Yeast-Two Hybrid Library
Varberg JM, Gardner JM, McCroskey S, Saravanan S, Bradford WD, Jaspersen SL. G3 (Bethesda). 2020.
Differential complex formation via paralogs in the human Sin3 protein interaction network
Adams MK, Banks CAS, Thornton JL, Kempf CG, Zhang Y, Miah S, Hao Y, Sardiu ME, Killer M, Hattem GL, Murray A, Katt ML, Florens L, Washburn MP. Mol Cell Proteomics. 2020;19:1468-1484.
The Chromatin Bound Proteome of the Human Malaria Parasite
Batugedara G, Lu XM, Saraf A, Sardiu ME, Cort A, Abel S, Prudhomme J, Washburn MP, Florens L, Bunnik EM, Le Roch KG. Microb Genom. 2020;6:e000327. doi: 000310.001099/mgen.000320.000327.
Towards the molecular deciphering of Pomacea canaliculata immunity: first proteomic analysis of circulating hemocytes
Boraldi F, Lofaro FD, Accorsi A, Ross E, Malagoli D. Proteomics. 2019;19:e1800314. doi: 1800310.1801002/pmic.201800314.
Probing the Sensitivity of the Orbitrap Lumos Mass Spectrometer using a Standard Reference Protein in a Complex Background
Levy MJ, Washburn MP, Florens L. J Proteome Res. 2018;17:3586-3592.
DYRK1A interacts with histone acetyl transferase p300 and CBP and localizes to enhancers
Vitorino FNL, Montoni F, Moreno JN, de Souza BF, Lopes MC, Cordeiro B, Fonseca CS, Gilmore JM, Sardiu MI, Reis MS, Florens LA, Washburn MP, Armelin HA, da Cunha JPC. Proteomics. 2018;18:e1800203. doi: 1800210.1801002/pmic.201800203.
FGF-2 Antiproliferative Stimulation Induces Proteomic Dynamic Changes and High Expression of fosB and junB in K-Ras-Driven Mouse Tumor Cells
Vitorino FNL, Montoni F, Moreno JN, de Souza BF, Lopes MC, Cordeiro B, Fonseca CS, Gilmore JM, Sardiu MI, Reis MS, Florens LA, Washburn MP, Armelin HA, da Cunha JPC. Proteomics.2018:e1800203.
A structured workflow for mapping human Sin3 histone deacetylase complex interactions using Halo-MudPIT AP-MS
Banks CAS, Thornton JL, Eubanks CG, Adams MK, Miah S, Boanca G, Liu X, Katt ML, Parmely TJ, Florens L, Washburn MP. Mol Cell Proteomics.2018;17:1432-1447.
Myeloid Leukemia Factor acts in a chaperone complex to regulate transcription factor stability and gene
Dyer JO, Dutta A, Gogol M, Weake VM, Dialynas G, Wu X, Seidel C, Zhang Y, Florens L, Washburn MP, Abmayr SM, Workman JL. J Mol Biol.2017;429:2093-2107.
Different phosphoisoforms of RNA polymerase II engage the Rtt103 termination factor in a structurally analogous manner
Nemec CM, Yang F, Gilmore JM, Hintermair C, Ho YH, Tseng SC, Heidemann M, Zhang Y, Florens L, Gasch AP, Eick D, Washburn MP, Varani G, Ansari AZ. Proc Natl Acad Sci U S A.2017;114:E3944-E39.
TNIP2 is a hub protein in the NF-&(kappa)B network with both protein and RNA mediated interactions.
Banks CA, Boanca G, Lee ZT, Eubanks CG, Hattem GL, Peak A, Weems LE, Conkright JJ, Florens L, Washburn MP. Mol Cell Proteomics. 2016;15:3435-3449.
Proteomic and genomic analyses of the Rvb1 and Rvb2 interaction network upon deletion of R2TP complex components
Lakshminarasimhan M, Boanca G, Banks CA, Hattem GL, Gabriel AE, Groppe BD, Smoyer C, Malanowski KE, Peak A, Florens L, Washburn MP. Mol Cell Proteomics. 2016;15:960-974.
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Multiplexed Quantitative Proteomics Analysis of Developing Human Brain Organoids
Florens L, Saraf A, Hao Y, Zhang Y, Wang Y, Parmely TJ, Zhao C, Washburn MP. In: W Wang, Y Wang, and N Rohner, eds. Emerging Model Organisms; 2023;194:325-355.
Regulation of kinetochore configuration during mitosis
Dhatchinamoorthy K, Mattingly M, Gerton JL. Curr Genet. 2018;64:1197-1203.
Unravelling the biology of chromatin in health and cancer using proteomic approaches
Eubanks CG, Dayebgadoh G, Liu X, Washburn MP. Expert Rev Proteomics.2017;14:905-915.
Advancement of mass spectrometry-based proteomics technologies to explore triple negative breast cancer
Miah S, Banks CA, Adams MK, Florens L, Lukong KE, Washburn MP. Mol Biosyst.2016;13:42-55.
Reshaping the Chromatin and Epigenetic Landscapes with Quantitative Mass Spectrometry
Washburn MP, Zhao Y, Garcia BA. Mol Cell Proteomics.2016;15:753-754.
The H-Index of 'An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database'.
Washburn MP. J Am Soc Mass Spectrom. 2015;26:1799-803.
Shotgun Proteomics.
Banks CAS, Lakshminarasimhan M, Washburn MP. In: eLS Chichester, England: John Wiley & Sons, Ltd; 2014. DOI: 10.1002/9780470015902.a0006197.pub2
Quantitative Proteomics Characterization of Chromatin-Remodeling Complexes in Health and Disease.
Lakshminarasimhan M, Washburn MP. In: Emili A, Greenblatt J, Wodak S, eds. Systems Analysis of Chromatin-Related Protein Complexes in Cancer. SpringerLink; 2014:177-196.
Quantitative proteomics.
Yates JR, 3rd, Washburn MP. Anal Chem. 2013;85:8881.
Construction of protein interaction networks based on the label-free quantitative proteomics.
Sardiu ME, Washburn MP. Methods Mol Biol. 2011;781:71-85.
Building protein-protein interaction networks with proteomics and informatics tools.
Sardiu ME, Washburn MP. J Biol Chem. 2011;286:23645-23651.
Driving biochemical discovery with quantitative proteomics.
Washburn MP. Trends Biochem Sci. 2011;36:170-177.
Advances in shotgun proteomics and the analysis of membrane proteomes.
Gilmore JM, Washburn MP. J Proteomics. 2010;73:2078-2091.
Enriching quantitative proteomics with SI(N).
Sardiu ME, Washburn MP. Nat Biotechnol. 2010;28:40-42.
Use of sequential chemical extractions to purify nuclear membrane proteins for proteomics identification.
Korfali N, Fairley EA, Swanson SK, Florens L, Schirmer EC. Methods Mol Biol. 2009;528:201-225.
Generation and analysis of multidimensional protein identification technology datasets
Swanson SK, Florens L, Washburn MP. Methods Mol Biol. 2009;492:1-20.
Subcellular Fractionation and Proteomics of Nuclear Envelopes
Florens L, Korfali N, Schirmer EC. Methods Mol Biol. 2008;432:117-137.
Sample preparation and in-solution protease digestion of proteins for chromatography-based proteomic analysis
Washburn MP. Curr Protoc Protein Sci. 2008;Chapter 23:Unit 23 26 21-23 26 11.
Application of Shotgun Proteomics to Transcriptional Regulatory Pathways
Mosley AL, Washburn M. In: DS Sem, ed. Spectral Techniques in Proteomics. Boca Raton: CRC Press; 2007:207-222.
Quantitative shotgun proteomics using a protease with broad specificity and normalized spectral abundance factors
Zybailov BL, Florens L, Washburn MP. Mol Biosyst.2007;3:354-360.
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