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.
Distinct states of nucleolar stress induced by anti-cancer drugs
Potapova T, Unruh J, Conkright-Fincham J, Banks CAS, Florens L, Schneider DHG, Gerton JL. eLife. 2023.
Metabolic reprogramming underlies cavefish muscular endurance despite loss of muscle mass and contractility
Olsen L, Levy M, Medley JK, Hassan H, Miller B, Alexander R, Wilcock E, Yi K, Florens L, Weaver K, McKinney SA, Peuss R, Persons J, Kenzior A, Maldonado E, Delventhal K, Gluesenkamp A, Mager E, Coughlin D, Rohner N. Proc Natl Acad Sci U S A. 2023;120:e2204427120.
FGF2 antiproliferative effect in K-ras-driven tumor cells involves modulation of rRNA and nucleolus
de Luna Vitorino FN, Levy MJ, Mansano Wailemann RA, Lopes M, Silva ML, Sardiu ME, Garcia BA, Motta MCM, Oliveira CC, Armelin HA, Florens LA, Washburn MP, da Cunha JPC. [published ahead of print Novermber 3 2023]. J Cell Sci. 2023.
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.
Extravillous trophoblast cell lineage development is associated with active remodeling of the chromatin landscape
Varberg KM, Dominguez EM, Koseva B, Varberg JM, McNally RP, Moreno-Irusta A, Wesley ER, Iqbal K, Cheung WA, Schwendinger-Schreck C, Smail C, Okae H, Arima T, Lydic M, Holoch K, Marsh C, Soares MJ, Grundberg E. Nat Commun. 2023;14:4826 doi: 10.1038/s41467-023-40424-5.
A Borrelia burgdorferi LptD homolog is required for flipping of surface lipoproteins through the spirochetal outer membrane
He H, Pramanik AS, Swanson SK, Johnson DK, Florens L, Zuckert WR. Mol Microbiol. 2023;119:752-767.
Circadian rhythm disruption linked to skeletal muscle dysfunction in the Mexican Cavefish
Olsen L, Krishnan J, Banks C, Hassan H, Rohner N. Curr Biol. 2023;33:R255-R256.
Paraspeckles interact with SWI/SNF subunit ARID1B to regulate transcription and splicing
Reddy D, Bhattacharya S, Levy M, Zhang Y, Gogol M, Li H, Florens L, Workman JL. EMBO Rep 2023;24:e55345 doi: 10.15252/embr.202255345.
The Caenorhabditis elegans ASPP homolog APE-1 is a junctional protein phosphatase 1 modulator
Beacham GM, Wei DT, Beyrent E, Zhang Y, Zheng J, Camacho MMK, Florens L, Hollopeter G. Genetics. 2022;222 doi: 10.1093/genetics/iyac102.
An apical protein, Pcr2, is required for persistent movement by the human parasite Toxoplasma gondii
Munera Lopez J, Tengganu IF, Liu J, Murray JM, Arias Padilla LF, Zhang Y, Brown PT, Florens L, Hu K. PLoS Pathog. 2022;18:e1010776 doi: 10.1371/journal.ppat.1010776.
Dynamic regulation and requirement for ribosomal RNA transcription during mammalian development
Falcon KT, Watt KEN, Dash S, Zhao R, Sakai D, Moore EL, Fitriasari S, Childers M, Sardiu ME, Swanson S, Tsuchiya D, Unruh J, Bugarinovic G, Li L, Shiang R, Achilleos A, Dixon J, Dixon MJ, Trainor PA. Proc Natl Acad Sci U S A. 2022;119:e2116974119 doi: 10.1073/pnas.2116974119.
Mediator recruits the cohesin loader Scc2 to RNA Pol II transcribed genes and promotes sister chromatid cohesion
Mattingly M, Seidel C, Munoz S, Hao Y, Zhang Y, Wen Z, Florens L, Uhlmann F, Gerton JL. [published ahead of print June 3 2022]. Curr Biol. 2022;32.
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.
A putative cap binding protein and the methyl phosphate capping enzyme Bin3/MePCE function in telomerase biogenesis
Paez-Moscoso DJ, Ho DV, Pan L, Hildebrand K, Jensen KL, Levy MJ, Florens L, Baumann P. Nat Commun. 2022;13:1067. doi: 1010.1038/s41467-41022-28545-41469.
Cytidine acetylation yields a hypoinflammatory synthetic messenger RNA
Nance KD, Gamage ST, Alam MM, Yang A, Levy MJ, Link CN, Florens L, Washburn MP, Gu S, Oppenheim JJ, Meier JL. Cell Chem Biol. 2022;29:312-320 e317.
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.
Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing
Bhattacharya S, Wang S, Reddy D, Shen S, Zhang Y, Zhang N, Li H, Washburn MP, Florens L, Shi Y, Workman JL, Li F. Nat Commun. 2021;12:6452. doi: 6410.1038/s41467-41021-26799-41463.
Multiple roles for PARP1 in ALC1-dependent nucleosome remodeling
Ooi SK, Sato S, Tomomori-Sato C, Zhang Y, Wen Z, Banks CAS, Washburn MP, Unruh JR, Florens L, Conaway RC, Conaway JW. Proc Natl Acad Sci U S A. 2021;118:e2107277118. doi: 2107277110.2107271073/pnas.2107277118.
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.
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Second Special Issue on Methods for Omics Research: Proteome Research and Beyond
Florens L, Dong MQ, LaBaer J. J Proteome Res. 2023;22:1381-1384.
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.
To Bead or not to Bead? That is the question with cross-linking mass spectrometry.
Florens L, Hao Y, Zhang Y, Wen Z, Banks CAS, Washburn MP. J Biomol Tech : JBT. 2020;31:S24.
New and Improved Tools for the Omics Crew
Florens, L., Dong, M.-Q., LaBaer, J. J Proteome Res 2020;19:2525-2528. doi:10.1021/acs.jproteome.0c00328.
Generation and isolation of recombinant retinoid oxidoreductase complex
Adams MK, Belyaeva OV, Kedishvili NY. Methods Enzymol. 2020;637:77-93.
Purification and enzymatic assay of class I histone deacetylase enzymes
Adams MK, Banks CAS, Miah S, Killer M, Washburn MP. Methods Enzymol. 2019;626:23-40.
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.
Isolation, Proteomic Analysis, and Microscopy Confirmation of the Liver Nuclear Envelope Proteome
Korfali N, Florens L, Schirmer EC. Methods Mol Biol. 2016;1411:3-44.
There is no human interactome
Washburn MP. Genome Biol. 2016;17:48.
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.
Affinity purification of protein complexes for analysis by multidimensional protein identification technology.
Banks CA, Kong SE, Washburn MP. Protein Expr Purif. 2012;86:105-119.
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.
Unraveling the dynamics of protein interactions with quantitative mass spectrometry.
Ramisetty SR, Washburn MP. Crit Rev Biochem Mol Biol. 2011;46:216-228.
Driving biochemical discovery with quantitative proteomics.
Washburn MP. Trends Biochem Sci. 2011;36:170-177.
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