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Items: 1 to 50 of 223

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.

The E3 ubiquitin ligase SPOP controls resolution of systemic inflammation by triggering MYD88 degradation.

Guillamot M, Ouazia D, Dolgalev I, Yeung ST, Kourtis N, Dai Y, Corrigan K, Zea-Redondo L, Saraf A, Florens L, Washburn MP, Tikhonova AN, Malumbres M, Gong Y, Tsirigos A, Park C, Barbieri C, Khanna KM, Busino L, Aifantis I.

Nat Immunol. 2019 Sep;20(9):1196-1207. doi: 10.1038/s41590-019-0454-6. Epub 2019 Aug 12.

PMID:
31406379
3.

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
4.

Ataxin-7 and Non-stop coordinate SCAR protein levels, subcellular localization, and actin cytoskeleton organization.

Cloud V, Thapa A, Morales-Sosa P, Miller TM, Miller SA, Holsapple D, Gerhart PM, Momtahan E, Jack JL, Leiva E, Rapp SR, Shelton LG, Pierce RA, Martin-Brown S, Florens L, Washburn MP, Mohan RD.

Elife. 2019 Jul 26;8. pii: e49677. doi: 10.7554/eLife.49677.

5.

Junctional tumor suppressors interact with 14-3-3 proteins to control planar spindle alignment.

Nakajima YI, Lee ZT, McKinney SA, Swanson SK, Florens L, Gibson MC.

J Cell Biol. 2019 Jun 3;218(6):1824-1838. doi: 10.1083/jcb.201803116. Epub 2019 May 14.

PMID:
31088859
6.

Evaluating Chromatographic Approaches for the Quantitative Analysis of a Human Proteome on Orbitrap-Based Mass Spectrometry Systems.

Zhang Y, Wen Z, Washburn MP, Florens L.

J Proteome Res. 2019 Apr 5;18(4):1857-1869. doi: 10.1021/acs.jproteome.9b00036. Epub 2019 Mar 27.

PMID:
30884231
7.

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.

8.

DYRK1A regulates the recruitment of 53BP1 to the sites of DNA damage in part through interaction with RNF169.

Menon VR, Ananthapadmanabhan V, Swanson S, Saini S, Sesay F, Yakovlev V, Florens L, DeCaprio JA, Washburn MP, Dozmorov M, Litovchick L.

Cell Cycle. 2019 Mar;18(5):531-551. doi: 10.1080/15384101.2019.1577525. Epub 2019 Feb 17.

9.

RUNX proteins desensitize multiple myeloma to lenalidomide via protecting IKZFs from degradation.

Zhou N, Gutierrez-Uzquiza A, Zheng XY, Chang R, Vogl DT, Garfall AL, Bernabei L, Saraf A, Florens L, Washburn MP, Illendula A, Bushweller JH, Busino L.

Leukemia. 2019 Aug;33(8):2006-2021. doi: 10.1038/s41375-019-0403-2. Epub 2019 Feb 13.

10.

A chemoproteomic portrait of the oncometabolite fumarate.

Kulkarni RA, Bak DW, Wei D, Bergholtz SE, Briney CA, Shrimp JH, Alpsoy A, Thorpe AL, Bavari AE, Crooks DR, Levy M, Florens L, Washburn MP, Frizzell N, Dykhuizen EC, Weerapana E, Linehan WM, Meier JL.

Nat Chem Biol. 2019 Apr;15(4):391-400. doi: 10.1038/s41589-018-0217-y. Epub 2019 Feb 4.

11.

Host Vesicle Fusion Protein VAPB Contributes to the Nuclear Egress Stage of Herpes Simplex Virus Type-1 (HSV-1) Replication.

Saiz-Ros N, Czapiewski R, Epifano I, Stevenson A, Swanson SK, Dixon CR, Zamora DB, McElwee M, Vijayakrishnan S, Richardson CA, Dong L, Kelly DA, Pytowski L, Goldberg MW, Florens L, Graham SV, Schirmer EC.

Cells. 2019 Feb 3;8(2). pii: E120. doi: 10.3390/cells8020120.

12.

Characterization of a metazoan ADA acetyltransferase complex.

Soffers JHM, Li X, Saraf A, Seidel CW, Florens L, Washburn MP, Abmayr SM, Workman JL.

Nucleic Acids Res. 2019 Apr 23;47(7):3383-3394. doi: 10.1093/nar/gkz042.

13.

The ULK1-FBXW5-SEC23B nexus controls autophagy.

Jeong YT, Simoneschi D, Keegan S, Melville D, Adler NS, Saraf A, Florens L, Washburn MP, Cavasotto CN, Fenyö D, Cuervo AM, Rossi M, Pagano M.

Elife. 2018 Dec 31;7. pii: e42253. doi: 10.7554/eLife.42253.

14.

The Drosophila Dbf4 ortholog Chiffon forms a complex with Gcn5 that is necessary for histone acetylation and viability.

Torres-Zelada EF, Stephenson RE, Alpsoy A, Anderson BD, Swanson SK, Florens L, Dykhuizen EC, Washburn MP, Weake VM.

J Cell Sci. 2019 Jan 16;132(2). pii: jcs214072. doi: 10.1242/jcs.214072.

15.

PTPN14 regulates Roquin2 stability by tyrosine dephosphorylation.

Choi J, Saraf A, Florens L, Washburn MP, Busino L.

Cell Cycle. 2018;17(18):2243-2255. doi: 10.1080/15384101.2018.1522912. Epub 2018 Sep 25.

PMID:
30209976
16.

Differential HDAC1/2 network analysis reveals a role for prefoldin/CCT in HDAC1/2 complex assembly.

Banks CAS, Miah S, Adams MK, Eubanks CG, Thornton JL, Florens L, Washburn MP.

Sci Rep. 2018 Sep 12;8(1):13712. doi: 10.1038/s41598-018-32009-w.

17.

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 Oct 5;17(10):3586-3592. doi: 10.1021/acs.jproteome.8b00269. Epub 2018 Sep 13.

PMID:
30180573
18.

DYRK1A interacts with histone acetyl transferase p300 and CBP and localizes to enhancers.

Li S, Xu C, Fu Y, Lei PJ, Yao Y, Yang W, Zhang Y, Washburn MP, Florens L, Jaiswal M, Wu M, Mohan M.

Nucleic Acids Res. 2018 Nov 30;46(21):11202-11213. doi: 10.1093/nar/gky754.

19.

Schizosaccharomyces pombe Pol II transcription elongation factor ELL functions as part of a rudimentary super elongation complex.

Gopalan S, Gibbon DM, Banks CA, Zhang Y, Florens LA, Washburn MP, Dabas P, Sharma N, Seidel CW, Conaway RC, Conaway JW.

Nucleic Acids Res. 2018 Nov 2;46(19):10095-10105. doi: 10.1093/nar/gky713.

20.

MPTAC Determines APP Fragmentation via Sensing Sulfur Amino Acid Catabolism.

Suganuma T, Swanson SK, Gogol M, Garrett TJ, Conkright-Fincham J, Florens L, Washburn MP, Workman JL.

Cell Rep. 2018 Aug 7;24(6):1585-1596. doi: 10.1016/j.celrep.2018.07.013.

21.

FGF2 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 Sep;18(17):e1800203. doi: 10.1002/pmic.201800203. Epub 2018 Aug 14.

PMID:
30035358
22.

Analysis of RNA-Seq datasets reveals enrichment of tissue-specific splice variants for nuclear envelope proteins.

Capitanchik C, Dixon CR, Swanson SK, Florens L, Kerr ARW, Schirmer EC.

Nucleus. 2018;9(1):410-430. doi: 10.1080/19491034.2018.1469351.

PMID:
29912636
23.

Loss of KLHL6 promotes diffuse large B-cell lymphoma growth and survival by stabilizing the mRNA decay factor roquin2.

Choi J, Lee K, Ingvarsdottir K, Bonasio R, Saraf A, Florens L, Washburn MP, Tadros S, Green MR, Busino L.

Nat Cell Biol. 2018 May;20(5):586-596. doi: 10.1038/s41556-018-0084-5. Epub 2018 Apr 25.

24.

A Structured Workflow for Mapping Human Sin3 Histone Deacetylase Complex Interactions Using Halo-MudPIT Affinity-Purification Mass Spectrometry.

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 Jul;17(7):1432-1447. doi: 10.1074/mcp.TIR118.000661. Epub 2018 Mar 29.

25.

dCas9-targeted locus-specific protein isolation method identifies histone gene regulators.

Tsui C, Inouye C, Levy M, Lu A, Florens L, Washburn MP, Tjian R.

Proc Natl Acad Sci U S A. 2018 Mar 20;115(12):E2734-E2741. doi: 10.1073/pnas.1718844115. Epub 2018 Mar 5.

26.

Merkel cell polyomavirus recruits MYCL to the EP400 complex to promote oncogenesis.

Cheng J, Park DE, Berrios C, White EA, Arora R, Yoon R, Branigan T, Xiao T, Westerling T, Federation A, Zeid R, Strober B, Swanson SK, Florens L, Bradner JE, Brown M, Howley PM, Padi M, Washburn MP, DeCaprio JA.

PLoS Pathog. 2017 Oct 13;13(10):e1006668. doi: 10.1371/journal.ppat.1006668. eCollection 2017 Oct.

27.

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.

28.

HOXA1 and TALE proteins display cross-regulatory interactions and form a combinatorial binding code on HOXA1 targets.

De Kumar B, Parker HJ, Paulson A, Parrish ME, Pushel I, Singh NP, Zhang Y, Slaughter BD, Unruh JR, Florens L, Zeitlinger J, Krumlauf R.

Genome Res. 2017 Sep;27(9):1501-1512. doi: 10.1101/gr.219386.116. Epub 2017 Aug 7.

29.

The human cytoplasmic dynein interactome reveals novel activators of motility.

Redwine WB, DeSantis ME, Hollyer I, Htet ZM, Tran PT, Swanson SK, Florens L, Washburn MP, Reck-Peterson SL.

Elife. 2017 Jul 18;6. pii: e28257. doi: 10.7554/eLife.28257.

30.

PTEN counteracts FBXL2 to promote IP3R3- and Ca2+-mediated apoptosis limiting tumour growth.

Kuchay S, Giorgi C, Simoneschi D, Pagan J, Missiroli S, Saraf A, Florens L, Washburn MP, Collazo-Lorduy A, Castillo-Martin M, Cordon-Cardo C, Sebti SM, Pinton P, Pagano M.

Nature. 2017 Jun 22;546(7659):554-558. doi: 10.1038/nature22965. Epub 2017 Jun 14.

31.

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 May 16;114(20):E3944-E3953. doi: 10.1073/pnas.1700128114. Epub 2017 May 2.

32.

The TDH-GCN5L1-Fbxo15-KBP axis limits mitochondrial biogenesis in mouse embryonic stem cells.

Donato V, Bonora M, Simoneschi D, Sartini D, Kudo Y, Saraf A, Florens L, Washburn MP, Stadtfeld M, Pinton P, Pagano M.

Nat Cell Biol. 2017 Apr;19(4):341-351. doi: 10.1038/ncb3491. Epub 2017 Mar 20.

33.

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.

34.

Composition and Function of Mutant Swi/Snf Complexes.

Dutta A, Sardiu M, Gogol M, Gilmore J, Zhang D, Florens L, Abmayr SM, Washburn MP, Workman JL.

Cell Rep. 2017 Feb 28;18(9):2124-2134. doi: 10.1016/j.celrep.2017.01.058.

35.

Cytosolic proteostasis through importing of misfolded proteins into mitochondria.

Ruan L, Zhou C, Jin E, Kucharavy A, Zhang Y, Wen Z, Florens L, Li R.

Nature. 2017 Mar 16;543(7645):443-446. doi: 10.1038/nature21695. Epub 2017 Mar 1.

36.

Mediator structure and rearrangements required for holoenzyme formation.

Tsai KL, Yu X, Gopalan S, Chao TC, Zhang Y, Florens L, Washburn MP, Murakami K, Conaway RC, Conaway JW, Asturias FJ.

Nature. 2017 Apr 13;544(7649):196-201. doi: 10.1038/nature21393. Epub 2017 Mar 1.

37.

Chromatin remodeller Fun30Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation.

Lee J, Choi ES, Seo HD, Kang K, Gilmore JM, Florens L, Washburn MP, Choe J, Workman JL, Lee D.

Nat Commun. 2017 Feb 20;8:14527. doi: 10.1038/ncomms14527.

38.

Comprehensive Spatial Analysis of the Borrelia burgdorferi Lipoproteome Reveals a Compartmentalization Bias toward the Bacterial Surface.

Dowdell AS, Murphy MD, Azodi C, Swanson SK, Florens L, Chen S, Zückert WR.

J Bacteriol. 2017 Feb 28;199(6). pii: e00658-16. doi: 10.1128/JB.00658-16. Print 2017 Mar 15.

39.

Therapeutic Targeting of MLL Degradation Pathways in MLL-Rearranged Leukemia.

Liang K, Volk AG, Haug JS, Marshall SA, Woodfin AR, Bartom ET, Gilmore JM, Florens L, Washburn MP, Sullivan KD, Espinosa JM, Cannova J, Zhang J, Smith ER, Crispino JD, Shilatifard A.

Cell. 2017 Jan 12;168(1-2):59-72.e13. doi: 10.1016/j.cell.2016.12.011. Epub 2017 Jan 5.

40.

Myeloid Leukemia Factor Acts in a Chaperone Complex to Regulate Transcription Factor Stability and Gene Expression.

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 Jun 30;429(13):2093-2107. doi: 10.1016/j.jmb.2016.10.026. Epub 2016 Oct 27.

41.

Trio, a Rho Family GEF, Interacts with the Presynaptic Active Zone Proteins Piccolo and Bassoon.

Terry-Lorenzo RT, Torres VI, Wagh D, Galaz J, Swanson SK, Florens L, Washburn MP, Waites CL, Gundelfinger ED, Reimer RJ, Garner CC.

PLoS One. 2016 Dec 1;11(12):e0167535. doi: 10.1371/journal.pone.0167535. eCollection 2016.

42.

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 Dec 20;13(1):42-55. Review.

43.

USP44 Is an Integral Component of N-CoR that Contributes to Gene Repression by Deubiquitinating Histone H2B.

Lan X, Atanassov BS, Li W, Zhang Y, Florens L, Mohan RD, Galardy PJ, Washburn MP, Workman JL, Dent SYR.

Cell Rep. 2016 Nov 22;17(9):2382-2393. doi: 10.1016/j.celrep.2016.10.076.

44.

Role for the MED21-MED7 Hinge in Assembly of the Mediator-RNA Polymerase II Holoenzyme.

Sato S, Tomomori-Sato C, Tsai KL, Yu X, Sardiu M, Saraf A, Washburn MP, Florens L, Asturias FJ, Conaway RC, Conaway JW.

J Biol Chem. 2016 Dec 23;291(52):26886-26898. doi: 10.1074/jbc.M116.756098. Epub 2016 Nov 7.

45.

TNIP2 is a Hub Protein in the NF-κB 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 Nov;15(11):3435-3449. Epub 2016 Sep 8.

46.

Cytoplasmic ATXN7L3B Interferes with Nuclear Functions of the SAGA Deubiquitinase Module.

Li W, Atanassov BS, Lan X, Mohan RD, Swanson SK, Farria AT, Florens L, Washburn MP, Workman JL, Dent SYR.

Mol Cell Biol. 2016 Oct 28;36(22):2855-2866. doi: 10.1128/MCB.00193-16. Print 2016 Nov 15.

47.

SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes.

Brannan KW, Jin W, Huelga SC, Banks CA, Gilmore JM, Florens L, Washburn MP, Van Nostrand EL, Pratt GA, Schwinn MK, Daniels DL, Yeo GW.

Mol Cell. 2016 Oct 20;64(2):282-293. doi: 10.1016/j.molcel.2016.09.003. Epub 2016 Oct 6.

48.

The mRNA-bound proteome of the human malaria parasite Plasmodium falciparum.

Bunnik EM, Batugedara G, Saraf A, Prudhomme J, Florens L, Le Roch KG.

Genome Biol. 2016 Jul 5;17(1):147. doi: 10.1186/s13059-016-1014-0.

49.

HIV-1 and HIV-2 exhibit divergent interactions with HLTF and UNG2 DNA repair proteins.

Hrecka K, Hao C, Shun MC, Kaur S, Swanson SK, Florens L, Washburn MP, Skowronski J.

Proc Natl Acad Sci U S A. 2016 Jul 5;113(27):E3921-30. doi: 10.1073/pnas.1605023113. Epub 2016 Jun 22.

50.

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.

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