Harvard Catalyst Profiles

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Joao A Paulo, Ph.D.

Other Positions

The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. R01GM132129 (PAULO, JOAO A) Sep 15, 2019 - Aug 31, 2024
    Advancing Multiplexed Isobaric Tag-based Strategies for Proteome Profiling
    Role: Principal Investigator
  2. K01DK098285 (PAULO, JOAO A) Sep 16, 2013 - Nov 30, 2018
    Resolving the role of nicotine-mediated phosphorylation on pancreatic fibrosis
    Role: Principal Investigator
  3. F32DK085835 (PAULO, JOAO A) May 1, 2010 - Apr 30, 2013
    Proteomics of Pancreatic Fluid and Urine in Chronic Pancreatitis
    Role: Principal Investigator

Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Rossio V, Paulo JA, King RW. Identification of Deubiquitinase Substrates in Xenopus Egg Extract. Methods Mol Biol. 2023; 2591:219-236. PMID: 36350551; PMCID: PMC9662951.
    Citations:    Fields:    
  2. Agarwal R, Wakimoto H, Paulo JA, Zhang Q, Reichart D, Toepfer C, Sharma A, Tai AC, Lun M, Gorham J, DePalma SR, Gygi SP, Seidman JG, Seidman CE. Pathogenesis of Cardiomyopathy Caused by Variants in ALPK3, an Essential Pseudokinase in the Cardiomyocyte Nucleus and Sarcomere. Circulation. 2022 Nov 02. PMID: 36321451.
    Citations:    Fields:    
  3. Xiao H, Bozi LHM, Sun Y, Riley CL, Philip VM, Chen M, Li J, Zhang T, Mills EL, Emont MP, Sun W, Reddy A, Garrity R, Long J, Becher T, Vitas LP, Laznik-Bogoslavski D, Ordonez M, Liu X, Chen X, Wang Y, Liu W, Tran N, Liu Y, Zhang Y, Cypess AM, White AP, He Y, Deng R, Schöder H, Paulo JA, Jedrychowski MP, Banks AS, Tseng YH, Cohen P, Tsai LT, Rosen ED, Klein S, Chondronikola M, McAllister FE, Van Bruggen N, Huttlin EL, Spiegelman BM, Churchill GA, Gygi SP, Chouchani ET. Architecture of the outbred brown fat proteome defines regulators of metabolic physiology. Cell. 2022 Nov 02. PMID: 36334589.
    Citations:    Fields:    
  4. Gassaway BM, Li J, Rad R, Mintseris J, Mohler K, Levy T, Aguiar M, Beausoleil SA, Paulo JA, Rinehart J, Huttlin EL, Gygi SP. A multi-purpose, regenerable, proteome-scale, human phosphoserine resource for phosphoproteomics. Nat Methods. 2022 Nov; 19(11):1371-1375. PMID: 36280721.
    Citations:    Fields:    
  5. Park H, Hundley FV, Yu Q, Overmyer KA, Brademan DR, Serrano L, Paulo JA, Paoli JC, Swarup S, Coon JJ, Gygi SP, Wade Harper J. Spatial snapshots of amyloid precursor protein intramembrane processing via early endosome proteomics. Nat Commun. 2022 Oct 16; 13(1):6112. PMID: 36245040; PMCID: PMC9573879.
    Citations:    Fields:    
  6. McKenna MJ, Adams BM, Chu V, Paulo JA, Shao S. ATP13A1 prevents ERAD of folding-competent mislocalized and misoriented proteins. Mol Cell. 2022 Oct 15. PMID: 36283413.
    Citations:    Fields:    
  7. Boland S, Swarup S, Ambaw YA, Malia PC, Richards RC, Fischer AW, Singh S, Aggarwal G, Spina S, Nana AL, Grinberg LT, Seeley WW, Surma MA, Klose C, Paulo JA, Nguyen AD, Harper JW, Walther TC, Farese RV. Deficiency of the frontotemporal dementia gene GRN results in gangliosidosis. Nat Commun. 2022 Oct 07; 13(1):5924. PMID: 36207292; PMCID: PMC9546883.
    Citations:    Fields:    
  8. Prew MS, Adhikary U, Choi DW, Portero EP, Paulo JA, Gowda P, Budhraja A, Opferman JT, Gygi SP, Danial NN, Walensky LD. MCL-1 is a master regulator of cancer dependency on fatty acid oxidation. Cell Rep. 2022 10 04; 41(1):111445. PMID: 36198266.
    Citations:    Fields:    
  9. Schaefer IM, Hemming ML, Lundberg MZ, Serrata MP, Goldaracena I, Liu N, Yin P, Paulo JA, Gygi SP, George S, Morgan JA, Bertagnolli MM, Sicinska ET, Chu C, Zheng S, Mariño-Enríquez A, Hornick JL, Raut CP, Ou WB, Demetri GD, Saka SK, Fletcher JA. Concurrent inhibition of CDK2 adds to the anti-tumour activity of CDK4/6 inhibition in GIST. Br J Cancer. 2022 Sep 29. PMID: 36175617.
    Citations:    Fields:    
  10. Paulo JA. Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing. Proteomics. 2022 10; 22(19-20):e2200328. PMID: 36089831.
    Citations:    Fields:    
  11. Sultonova M, Blackmore B, Du R, Philips O, Paulo JA, Murphy JP. Integrated changes in thermal stability and proteome abundance during altered nutrient states in Escherichia coli and human cells. Proteomics. 2022 10; 22(19-20):e2100254. PMID: 36082775.
    Citations:    Fields:    
  12. Mirzaei M, Abyadeh M, Turner AJ, Wall RV, Chick JM, Paulo JA, Gupta VK, Basavarajappa D, Chitranshi N, Mirshahvaladi SSO, You Y, Fitzhenry MJ, Amirkhani A, Haynes PA, Klistorner A, Gupta V, Graham SL. Fingolimod effects on the brain are mediated through biochemical modulation of bioenergetics, autophagy, and neuroinflammatory networks. Proteomics. 2022 10; 22(19-20):e2100247. PMID: 35866514.
    Citations:    Fields:    
  13. Wang P, Karakose E, Argmann C, Wang H, Balev M, Brody RI, Rivas HG, Liu X, Wood O, Liu H, Choleva L, Hasson D, Bernstein E, Paulo JA, Scott DK, Lambertini L, DeCaprio JA, Stewart AF. Disrupting the DREAM complex enables proliferation of adult human pancreatic ß cells. J Clin Invest. 2022 08 01; 132(15). PMID: 35700053; PMCID: PMC9337832.
    Citations: 1     Fields:    
  14. Senabouth A, Daniszewski M, Lidgerwood GE, Liang HH, Hernández D, Mirzaei M, Keenan SN, Zhang R, Han X, Neavin D, Rooney L, Lopez Sanchez MIG, Gulluyan L, Paulo JA, Clarke L, Kearns LS, Gnanasambandapillai V, Chan CL, Nguyen U, Steinmann AM, McCloy RA, Farbehi N, Gupta VK, Mackey DA, Bylsma G, Verma N, MacGregor S, Watt MJ, Guymer RH, Powell JE, Hewitt AW, Pébay A. Transcriptomic and proteomic retinal pigment epithelium signatures of age-related macular degeneration. Nat Commun. 2022 07 26; 13(1):4233. PMID: 35882847; PMCID: PMC9325891.
    Citations: 1     Fields:    Translation:HumansCells
  15. Feng P, Wu X, Erramilli SK, Paulo JA, Knejski P, Gygi SP, Kossiakoff AA, Rapoport TA. A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel. Nature. 2022 07; 607(7918):374-380. PMID: 35768507; PMCID: PMC9279156.
    Citations: 2     Fields:    Translation:HumansCells
  16. Nehme R, Pietiläinen O, Artomov M, Tegtmeyer M, Valakh V, Lehtonen L, Bell C, Singh T, Trehan A, Sherwood J, Manning D, Peirent E, Malik R, Guss EJ, Hawes D, Beccard A, Bara AM, Hazelbaker DZ, Zuccaro E, Genovese G, Loboda AA, Neumann A, Lilliehook C, Kuismin O, Hamalainen E, Kurki M, Hultman CM, Kähler AK, Paulo JA, Ganna A, Madison J, Cohen B, McPhie D, Adolfsson R, Perlis R, Dolmetsch R, Farhi S, McCarroll S, Hyman S, Neale B, Barrett LE, Harper W, Palotie A, Daly M, Eggan K. The 22q11.2 region regulates presynaptic gene-products linked to schizophrenia. Nat Commun. 2022 06 27; 13(1):3690. PMID: 35760976; PMCID: PMC9237031.
    Citations: 1     Fields:    Translation:HumansCells
  17. Dou Q, Turanov AA, Mariotti M, Hwang JY, Wang H, Lee SG, Paulo JA, Yim SH, Gygi SP, Chung JJ, Gladyshev VN. Selenoprotein TXNRD3 supports male fertility via the redox regulation of spermatogenesis. J Biol Chem. 2022 08; 298(8):102183. PMID: 35753352; PMCID: PMC9352919.
    Citations: 2     Fields:    
  18. Perez Verdaguer M, Zhang T, Surve S, Paulo JA, Wallace C, Watkins SC, Gygi SP, Sorkin A. Time-resolved proximity labeling of protein networks associated with ligand-activated EGFR. Cell Rep. 2022 06 14; 39(11):110950. PMID: 35705039; PMCID: PMC9248364.
    Citations: 2     Fields:    Translation:Cells
  19. Emfinger CH, de Klerk E, Schueler KL, Rabaglia ME, Stapleton DS, Simonett SP, Mitok KA, Wang Z, Liu X, Paulo JA, Yu Q, Cardone RL, Foster HR, Lewandowski SL, Perales JC, Kendziorski CM, Gygi SP, Kibbey RG, Keller MP, Hebrok M, Merrins MJ, Attie AD. ß Cell-specific deletion of Zfp148 improves nutrient-stimulated ß cell Ca2+ responses. JCI Insight. 2022 05 23; 7(10). PMID: 35603790; PMCID: PMC9220824.
    Citations: 1     Fields:    Translation:AnimalsCells
  20. Liu X, Li J, Gygi SP, Paulo JA. Profiling Yeast Deletion Strains Using Sample Multiplexing and Network-Based Analyses. J Proteome Res. 2022 06 03; 21(6):1525-1536. PMID: 35544774; PMCID: PMC9614305.
    Citations:    Fields:    Translation:Animals
  21. Carrasco M, Wang C, Søviknes AM, Bjørlykke Y, Abadpour S, Paulo JA, Tjora E, Njølstad P, Ghabayen J, Nermoen I, Lyssenko V, Chera S, Ghila LM, Vaudel M, Scholz H, Ræder H. Spatial Environment Affects HNF4A Mutation-Specific Proteome Signatures and Cellular Morphology in hiPSC-Derived ß-Like Cells. Diabetes. 2022 04 01; 71(4):862-869. PMID: 35043148; PMCID: PMC8965667.
    Citations:    Fields:    Translation:HumansCells
  22. Zhou H, Stein CB, Shafiq TA, Shipkovenska G, Kalocsay M, Paulo JA, Zhang J, Luo Z, Gygi SP, Adelman K, Moazed D. Rixosomal RNA degradation contributes to silencing of Polycomb target genes. Nature. 2022 04; 604(7904):167-174. PMID: 35355014; PMCID: PMC8986528.
    Citations: 1     Fields:    Translation:HumansAnimalsCells
  23. Jiang H, Chiang CY, Chen Z, Nathan S, D'Agostino G, Paulo JA, Song G, Zhu H, Gabelli SB, Cole PA. Enzymatic analysis of WWP2 E3 ubiquitin ligase using protein microarrays identifies autophagy-related substrates. J Biol Chem. 2022 05; 298(5):101854. PMID: 35331737; PMCID: PMC9034101.
    Citations:    Fields:    Translation:HumansCells
  24. Liu X, Rossio V, Thakurta SG, Flora A, Foster L, Bomgarden RD, Gygi SP, Paulo JA. Fe3+-NTA magnetic beads as an alternative to spin column-based phosphopeptide enrichment. J Proteomics. 2022 05 30; 260:104561. PMID: 35331916; PMCID: PMC9195054.
    Citations: 1     Fields:    Translation:Cells
  25. Berle M, Hestetun KE, Vethe H, Chera S, Paulo JA, Dahl O, Myklebust MP. Mapping Proteome Changes in Microsatellite Stable, Recurrent Colon Cancer Reveals a Significant Immune System Signature. Cancer Genomics Proteomics. 2022 Mar-Apr; 19(2):130-144. PMID: 35181583; PMCID: PMC8865039.
    Citations:    Fields:    Translation:HumansCells
  26. Johnson CW, Seo HS, Terrell EM, Yang MH, KleinJan F, Gebregiworgis T, Gasmi-Seabrook GMC, Geffken EA, Lakhani J, Song K, Bashyal P, Popow O, Paulo JA, Liu A, Mattos C, Marshall CB, Ikura M, Morrison DK, Dhe-Paganon S, Haigis KM. Regulation of GTPase function by autophosphorylation. Mol Cell. 2022 03 03; 82(5):950-968.e14. PMID: 35202574; PMCID: PMC8986090.
    Citations: 1     Fields:    Translation:AnimalsCells
  27. Gupta V, Chitranshi N, Gupta V, You Y, Rajput R, Paulo JA, Mirzaei M, van den Buuse M, Graham SL. TrkB Receptor Agonist 7,8 Dihydroxyflavone is Protective Against the Inner Retinal Deficits Induced by Experimental Glaucoma. Neuroscience. 2022 05 10; 490:36-48. PMID: 35217121; PMCID: PMC9142859.
    Citations: 1     Fields:    Translation:Animals
  28. Kennedy BE, Giacomantonio M, Murphy JP, Cutler S, Sadek M, Konda P, Paulo JA, Pathak GP, Renkens SHJ, Grieve S, Pol J, Gygi SP, Richardson C, Gaston D, Reiman A, Kroemer G, Elnenaei MO, Gujar SA. NAD+ depletion enhances reovirus-induced oncolysis in multiple myeloma. Mol Ther Oncolytics. 2022 Mar 17; 24:695-706. PMID: 35284625; PMCID: PMC8904403.
  29. Pfeiffer CT, Paulo JA, Gygi SP, Rockman HA. Proximity labeling for investigating protein-protein interactions. Methods Cell Biol. 2022; 169:237-266. PMID: 35623704.
    Citations: 1     Fields:    
  30. Zhang T, Fassl A, Vaites LP, Fu S, Sicinski P, Paulo JA, Gygi SP. Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment. J Proteome Res. 2022 02 04; 21(2):494-506. PMID: 35044772; PMCID: PMC9142857.
    Citations: 1     Fields:    Translation:HumansCells
  31. Navarrete-Perea J, Liu X, Rad R, Gygi JP, Gygi SP, Paulo JA. Assessing interference in isobaric tag-based sample multiplexing using an 18-plex interference standard. Proteomics. 2022 04; 22(7):e2100317. PMID: 34918453; PMCID: PMC9231818.
    Citations:    Fields:    Translation:Animals
  32. Ji Z, Li H, Peterle D, Paulo JA, Ficarro SB, Wales TE, Marto JA, Gygi SP, Engen JR, Rapoport TA. Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase. Mol Cell. 2022 02 03; 82(3):570-584.e8. PMID: 34951965; PMCID: PMC8818041.
    Citations: 8     Fields:    Translation:AnimalsCells
  33. Kim Y, Konda P, Murphy JP, Paulo JA, Gygi SP, Gujar S. Immune Checkpoint Blockade Augments Changes Within Oncolytic Virus-induced Cancer MHC-I Peptidome, Creating Novel Antitumor CD8 T Cell Reactivities. Mol Cell Proteomics. 2022 02; 21(2):100182. PMID: 34922008; PMCID: PMC8864471.
    Citations: 1     Fields:    Translation:AnimalsCells
  34. Iuchi S, Paulo JA. RNAmetasome network for macromolecule biogenesis in human cells. Commun Biol. 2021 12 15; 4(1):1399. PMID: 34912035.
    Citations: 1     Translation:HumansCells
  35. Liu X, Fields R, Schweppe DK, Paulo JA. Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging. Expert Rev Proteomics. 2021 09; 18(9):795-807. PMID: 34652972; PMCID: PMC8595857.
    Citations: 1     Fields:    Translation:HumansCells
  36. Ordureau A, Kraus F, Zhang J, An H, Park S, Ahfeldt T, Paulo JA, Harper JW. Temporal proteomics during neurogenesis reveals large-scale proteome and organelle remodeling via selective autophagy. Mol Cell. 2021 12 16; 81(24):5082-5098.e11. PMID: 34699746; PMCID: PMC8688335.
    Citations: 6     Fields:    Translation:HumansCells
  37. Calvo IA, Sharma S, Paulo JA, Gulka AOD, Boeszoermenyi A, Zhang J, Lombana JM, Palmieri CM, Laviolette LA, Arthanari H, Iliopoulos O, Gygi SP, Motamedi M. The fission yeast FLCN/FNIP complex augments TORC1 repression or activation in response to amino acid (AA) availability. iScience. 2021 Nov 19; 24(11):103338. PMID: 34805795; PMCID: PMC8590082.
  38. Li J, Cai Z, Vaites LP, Shen N, Mitchell DC, Huttlin EL, Paulo JA, Harry BL, Gygi SP. Proteome-wide mapping of short-lived proteins in human cells. Mol Cell. 2021 11 18; 81(22):4722-4735.e5. PMID: 34626566; PMCID: PMC8892350.
    Citations: 4     Fields:    Translation:HumansCells
  39. Eapen VV, Swarup S, Hoyer MJ, Paulo JA, Harper JW. Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy. Elife. 2021 09 29; 10. PMID: 34585663; PMCID: PMC8523161.
    Citations: 12     Fields:    Translation:HumansCells
  40. Abyadeh M, Gupta V, Paulo JA, Gupta V, Chitranshi N, Godinez A, Saks D, Hasan M, Amirkhani A, McKay M, Salekdeh GH, Haynes PA, Graham SL, Mirzaei M. A Proteomic View of Cellular and Molecular Effects of Cannabis. Biomolecules. 2021 09 27; 11(10). PMID: 34680044; PMCID: PMC8533448.
    Citations: 2     Fields:    Translation:HumansAnimals
  41. Keele GR, Zhang T, Pham DT, Vincent M, Bell TA, Hock P, Shaw GD, Paulo JA, Munger SC, de Villena FP, Ferris MT, Gygi SP, Churchill GA. Regulation of protein abundance in genetically diverse mouse populations. Cell Genom. 2021 Oct 13; 1(1). PMID: 36212994; PMCID: PMC9536773.
    Citations: 1     
  42. Mulcahy MJ, Huard SM, Paulo JA, Wang JH, McKinney S, Marks MJ, Henderson BJ, Lester HA. Protein profiling in the habenula after chronic (-)-menthol exposure in mice. J Neurochem. 2021 09; 158(6):1345-1358. PMID: 34407206; PMCID: PMC8577691.
    Citations:    Fields:    Translation:Animals
  43. Agarwal R, Paulo JA, Toepfer CN, Ewoldt JK, Sundaram S, Chopra A, Zhang Q, Gorham J, DePalma SR, Chen CS, Gygi SP, Seidman CE, Seidman JG. Filamin C Cardiomyopathy Variants Cause Protein and Lysosome Accumulation. Circ Res. 2021 09 17; 129(7):751-766. PMID: 34405687; PMCID: PMC9053646.
    Citations: 4     Fields:    Translation:HumansCells
  44. Wang X, Paulo JA, Li X, Zhou H, Yu J, Gygi SP, Moazed D. A composite DNA element that functions as a maintainer required for epigenetic inheritance of heterochromatin. Mol Cell. 2021 10 07; 81(19):3979-3991.e4. PMID: 34375584; PMCID: PMC8500937.
    Citations: 3     Fields:    Translation:AnimalsCells
  45. Fuchs RP, Isogawa A, Paulo JA, Onizuka K, Takahashi T, Amunugama R, Duxin JP, Fujii S. Crosstalk between repair pathways elicits double-strand breaks in alkylated DNA and implications for the action of temozolomide. Elife. 2021 07 08; 10. PMID: 34236314.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  46. Popow O, Liu X, Haigis KM, Gygi SP, Paulo JA. A Compendium of Murine (Phospho)Peptides Encompassing Different Isobaric Labeling and Data Acquisition Strategies. J Proteome Res. 2021 07 02; 20(7):3678-3688. PMID: 34043369; PMCID: PMC8254770.
    Citations: 4     Fields:    Translation:AnimalsCells
  47. Perez Verdaguer M, Zhang T, Paulo JA, Gygi S, Watkins SC, Sakurai H, Sorkin A. Mechanism of p38 MAPK-induced EGFR endocytosis and its crosstalk with ligand-induced pathways. J Cell Biol. 2021 07 05; 220(7). PMID: 34032851.
    Citations: 3     Fields:    Translation:HumansCells
  48. Cao C, Prado MA, Sun L, Rockowitz S, Sliz P, Paulo JA, Finley D, Fleming MD. Maternal Iron Deficiency Modulates Placental Transcriptome and Proteome in Mid-Gestation of Mouse Pregnancy. J Nutr. 2021 05 11; 151(5):1073-1083. PMID: 33693820; PMCID: PMC8112763.
    Citations: 2     Fields:    Translation:AnimalsCells
  49. Huttlin EL, Bruckner RJ, Navarrete-Perea J, Cannon JR, Baltier K, Gebreab F, Gygi MP, Thornock A, Zarraga G, Tam S, Szpyt J, Gassaway BM, Panov A, Parzen H, Fu S, Golbazi A, Maenpaa E, Stricker K, Guha Thakurta S, Zhang T, Rad R, Pan J, Nusinow DP, Paulo JA, Schweppe DK, Vaites LP, Harper JW, Gygi SP. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell. 2021 05 27; 184(11):3022-3040.e28. PMID: 33961781; PMCID: PMC8165030.
    Citations: 93     Fields:    Translation:HumansCells
  50. Liu X, Gygi SP, Paulo JA. A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation. J Am Soc Mass Spectrom. 2021 Jun 02; 32(6):1519-1529. PMID: 33950666; PMCID: PMC8210952.
    Citations: 3     Fields:    
  51. Pfeiffer CT, Wang J, Paulo JA, Jiang X, Gygi SP, Rockman HA. Mapping Angiotensin II Type 1 Receptor-Biased Signaling Using Proximity Labeling and Proteomics Identifies Diverse Actions of Biased Agonists. J Proteome Res. 2021 06 04; 20(6):3256-3267. PMID: 33950683.
    Citations: 3     Fields:    Translation:Cells
  52. Mena EL, Donahue CJ, Vaites LP, Li J, Rona G, O'Leary C, Lignitto L, Miwatani-Minter B, Paulo JA, Dhabaria A, Ueberheide B, Gygi SP, Pagano M, Harper JW, Davey RA, Elledge SJ. ORF10-Cullin-2-ZYG11B complex is not required for SARS-CoV-2 infection. Proc Natl Acad Sci U S A. 2021 04 27; 118(17). PMID: 33827988; PMCID: PMC8092598.
    Citations: 13     Fields:    Translation:HumansCells
  53. Li J, Cai Z, Bomgarden RD, Pike I, Kuhn K, Rogers JC, Roberts TM, Gygi SP, Paulo JA. TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing. J Proteome Res. 2021 05 07; 20(5):2964-2972. PMID: 33900084; PMCID: PMC8210943.
    Citations: 33     Fields:    Translation:Cells
  54. Navarrete-Perea J, Gygi SP, Paulo JA. Temporal proteomic changes induced by nicotine in human cells: A quantitative proteomics approach. J Proteomics. 2021 06 15; 241:104244. PMID: 33895337; PMCID: PMC8199844.
    Citations: 1     Fields:    Translation:HumansCells
  55. Schnell HM, Walsh RM, Rawson S, Kaur M, Bhanu MK, Tian G, Prado MA, Guerra-Moreno A, Paulo JA, Gygi SP, Roelofs J, Finley D, Hanna J. Structures of chaperone-associated assembly intermediates reveal coordinated mechanisms of proteasome biogenesis. Nat Struct Mol Biol. 2021 05; 28(5):418-425. PMID: 33846632.
    Citations: 6     Fields:    Translation:AnimalsCells
  56. Ghila L, Legøy TA, Mathisen AF, Abadpour S, Paulo JA, Scholz H, Ræder H, Chera S. Chronically Elevated Exogenous Glucose Elicits Antipodal Effects on the Proteome Signature of Differentiating Human iPSC-Derived Pancreatic Progenitors. Int J Mol Sci. 2021 Apr 02; 22(7). PMID: 33918250.
    Citations: 1     Fields:    Translation:HumansCells
  57. Navarrete-Perea J, Guerra-Moreno A, Van Vranken J, Isasa M, Paulo JA, Gygi SP. Iron Deficiency and Recovery in Yeast: A Quantitative Proteomics Approach. J Proteome Res. 2021 05 07; 20(5):2751-2761. PMID: 33797912; PMCID: PMC8210944.
    Citations:    Fields:    Translation:HumansAnimals
  58. Paulo JA, Schweppe DK. Advances in quantitative high-throughput phosphoproteomics with sample multiplexing. Proteomics. 2021 05; 21(9):e2000140. PMID: 33455035; PMCID: PMC8209658.
    Citations: 6     Fields:    Translation:Cells
  59. Zhang T, Keele GR, Churchill GA, Gygi SP, Paulo JA. Strain-Specific Peptide (SSP) Interference Reference Sample: A Genetically Encoded Quality Control for Isobaric Tagging Strategies. Anal Chem. 2021 03 30; 93(12):5241-5247. PMID: 33735571; PMCID: PMC8210951.
    Citations: 3     Fields:    Translation:Animals
  60. Hollingsworth LR, Sharif H, Griswold AR, Fontana P, Mintseris J, Dagbay KB, Paulo JA, Gygi SP, Bachovchin DA, Wu H. DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation. Nature. 2021 04; 592(7856):778-783. PMID: 33731932; PMCID: PMC8299537.
    Citations: 32     Fields:    Translation:HumansCells
  61. Ordureau A, Yu Q, Bomgarden RD, Rogers JC, Harper JW, Gygi SP, Paulo JA. Super Heavy TMTpro Labeling Reagent: An Alternative and Higher-Charge-State-Amenable Stable-Isotope-Labeled TMTpro Variant. J Proteome Res. 2021 05 07; 20(5):3009-3013. PMID: 33689365; PMCID: PMC8210946.
    Citations:    Fields:    
  62. Lee JD, Paulo JA, Posey RR, Mugoni V, Kong NR, Cheloni G, Lee YR, Slack FJ, Tenen DG, Clohessy JG, Gygi SP, Pandolfi PP. Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. Nat Methods. 2021 03; 18(3):293-302. PMID: 33649590.
    Citations:    Fields:    Translation:HumansCells
  63. Gassaway BM, Paulo JA, Gygi SP. Categorization of Phosphorylation Site Behavior during the Diauxic Shift in Saccharomyces cerevisiae. J Proteome Res. 2021 05 07; 20(5):2487-2496. PMID: 33630598; PMCID: PMC8210948.
    Citations: 1     Fields:    Translation:AnimalsCells
  64. Mukhopadhyay S, Biancur DE, Parker SJ, Yamamoto K, Banh RS, Paulo JA, Mancias JD, Kimmelman AC. Autophagy is required for proper cysteine homeostasis in pancreatic cancer through regulation of SLC7A11. Proc Natl Acad Sci U S A. 2021 02 09; 118(6). PMID: 33531365.
    Citations: 15     Fields:    Translation:HumansAnimalsCells
  65. O'Connell LA, O'Connell JD, Paulo JA, Trauger SA, Gygi SP, Murray AW. Rapid toxin sequestration modifies poison frog physiology. J Exp Biol. 2021 02 09; 224(Pt 3). PMID: 33408255; PMCID: PMC7888741.
    Citations: 6     Fields:    Translation:Animals
  66. Wong SJ, Ringel AE, Yuan W, Paulo JA, Yoon H, Currie MA, Haigis MC. Development of a colorimetric a-ketoglutarate detection assay for prolyl hydroxylase domain (PHD) proteins. J Biol Chem. 2021 Jan-Jun; 296:100397. PMID: 33571527; PMCID: PMC7961094.
    Citations: 1     Fields:    Translation:HumansCells
  67. Koduri V, Duplaquet L, Lampson BL, Wang AC, Sabet AH, Ishoey M, Paulk J, Teng M, Harris IS, Endress JE, Liu X, Dasilva E, Paulo JA, Briggs KJ, Doench JG, Ott CJ, Zhang T, Donovan KA, Fischer ES, Gygi SP, Gray NS, Bradner J, Medin JA, Buhrlage SJ, Oser MG, Kaelin WG. Targeting oncoproteins with a positive selection assay for protein degraders. Sci Adv. 2021 02; 7(6). PMID: 33547076; PMCID: PMC7864573.
    Citations: 7     Fields:    Translation:HumansCells
  68. Levine ZG, Potter SC, Joiner CM, Fei GQ, Nabet B, Sonnett M, Zachara NE, Gray NS, Paulo JA, Walker S. Mammalian cell proliferation requires noncatalytic functions of O-GlcNAc transferase. Proc Natl Acad Sci U S A. 2021 01 26; 118(4). PMID: 33419956; PMCID: PMC7848692.
    Citations: 11     Fields:    Translation:HumansAnimalsCells
  69. Liu Y, Mei Y, Han X, Korobova FV, Prado MA, Yang J, Peng Z, Paulo JA, Gygi SP, Finley D, Ji P. Membrane skeleton modulates erythroid proteome remodeling and organelle clearance. Blood. 2021 01 21; 137(3):398-409. PMID: 33036023; PMCID: PMC7819763.
    Citations: 2     Fields:    Translation:AnimalsCells
  70. Rossio V, Paulo JA, Chick J, Brasher B, Gygi SP, King RW. Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates and assess enzyme specificity. Cell Chem Biol. 2021 04 15; 28(4):487-502.e5. PMID: 33417828.
    Citations: 3     Fields:    Translation:HumansCells
  71. Whiteley AM, Prado MA, de Poot SAH, Paulo JA, Ashton M, Dominguez S, Weber M, Ngu H, Szpyt J, Jedrychowski MP, Easton A, Gygi SP, Kurz T, Monteiro MJ, Brown EJ, Finley D. Global proteomics of Ubqln2-based murine models of ALS. J Biol Chem. 2021 Jan-Jun; 296:100153. PMID: 33277362.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  72. Navarrete-Perea J, Gygi SP, Paulo JA. HYpro16: A Two-Proteome Mixture to Assess Interference in Isobaric Tag-Based Sample Multiplexing Experiments. J Am Soc Mass Spectrom. 2021 Jan 06; 32(1):247-254. PMID: 33175540.
    Citations: 5     Fields:    Translation:HumansCells
  73. Liu X, Gygi SP, Paulo JA. Isobaric Tag-Based Protein Profiling across Eight Human Cell Lines Using High-Field Asymmetric Ion Mobility Spectrometry and Real-Time Database Searching. Proteomics. 2021 01; 21(1):e2000218. PMID: 33015980.
    Citations: 1     Fields:    Translation:HumansCells
  74. Zhang T, Gygi SP, Paulo JA. Temporal Proteomic Profiling of SH-SY5Y Differentiation with Retinoic Acid Using FAIMS and Real-Time Searching. J Proteome Res. 2021 01 01; 20(1):704-714. PMID: 33054241.
    Citations: 7     Fields:    Translation:HumansCells
  75. Navarrete-Perea J, Gygi SP, Paulo JA. Growth media selection alters the proteome profiles of three model microorganisms. J Proteomics. 2021 01 16; 231:104006. PMID: 33038513; PMCID: PMC7719068.
    Citations: 3     Fields:    Translation:AnimalsCells
  76. E Costa RAP, Granato DC, Trino LD, Yokoo S, Carnielli CM, Kawahara R, Domingues RR, Pauletti BA, Neves LX, Santana AG, Paulo JA, Aragão AZB, Heleno Batista FA, Migliorini Figueira AC, Laurindo FRM, Fernandes D, Hansen HP, Squina F, Gygi SP, Paes Leme AF. ADAM17 cytoplasmic domain modulates Thioredoxin-1 conformation and activity. Redox Biol. 2020 10; 37:101735. PMID: 33011677; PMCID: PMC7513893.
    Citations:    Fields:    Translation:HumansCells
  77. Gerashchenko MV, Nesterchuk MV, Smekalova EM, Paulo JA, Kowalski PS, Akulich KA, Bogorad R, Dmitriev SE, Gygi S, Zatsepin T, Anderson DG, Gladyshev VN, Koteliansky VE. Translation elongation factor 2 depletion by siRNA in mouse liver leads to mTOR-independent translational upregulation of ribosomal protein genes. Sci Rep. 2020 09 23; 10(1):15473. PMID: 32968084; PMCID: PMC7511953.
    Citations: 4     Fields:    Translation:AnimalsCells
  78. Reddy A, Bozi LHM, Yaghi OK, Mills EL, Xiao H, Nicholson HE, Paschini M, Paulo JA, Garrity R, Laznik-Bogoslavski D, Ferreira JCB, Carl CS, Sjøberg KA, Wojtaszewski JFP, Jeppesen JF, Kiens B, Gygi SP, Richter EA, Mathis D, Chouchani ET. pH-Gated Succinate Secretion Regulates Muscle Remodeling in Response to Exercise. Cell. 2020 10 01; 183(1):62-75.e17. PMID: 32946811; PMCID: PMC7778787.
    Citations: 36     Fields:    Translation:HumansAnimalsCells
  79. Nowinski SM, Solmonson A, Rusin SF, Maschek JA, Bensard CL, Fogarty S, Jeong MY, Lettlova S, Berg JA, Morgan JT, Ouyang Y, Naylor BC, Paulo JA, Funai K, Cox JE, Gygi SP, Winge DR, DeBerardinis RJ, Rutter J. Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria. Elife. 2020 08 17; 9. PMID: 32804083.
    Citations: 17     Fields:    Translation:HumansAnimalsCells
  80. Sinha NK, Ordureau A, Best K, Saba JA, Zinshteyn B, Sundaramoorthy E, Fulzele A, Garshott DM, Denk T, Thoms M, Paulo JA, Harper JW, Bennett EJ, Beckmann R, Green R. EDF1 coordinates cellular responses to ribosome collisions. Elife. 2020 08 03; 9. PMID: 32744497; PMCID: PMC7486125.
    Citations: 33     Fields:    Translation:HumansCells
  81. Paul AS, Miliu A, Paulo JA, Goldberg JM, Bonilla AM, Berry L, Seveno M, Braun-Breton C, Kosber AL, Elsworth B, Arriola JSN, Lebrun M, Gygi SP, Lamarque MH, Duraisingh MT. Co-option of Plasmodium falciparum PP1 for egress from host erythrocytes. Nat Commun. 2020 07 15; 11(1):3532. PMID: 32669539; PMCID: PMC7363832.
    Citations: 15     Fields:    Translation:HumansAnimalsCells
  82. Yoon H, Spinelli JB, Zaganjor E, Wong SJ, German NJ, Randall EC, Dean A, Clermont A, Paulo JA, Garcia D, Li H, Rombold O, Agar NYR, Goodyear LJ, Shaw RJ, Gygi SP, Auwerx J, Haigis MC. PHD3 Loss Promotes Exercise Capacity and Fat Oxidation in Skeletal Muscle. Cell Metab. 2020 08 04; 32(2):215-228.e7. PMID: 32663458; PMCID: PMC8065255.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  83. An H, Ordureau A, Körner M, Paulo JA, Harper JW. Systematic quantitative analysis of ribosome inventory during nutrient stress. Nature. 2020 07; 583(7815):303-309. PMID: 32612236.
    Citations: 26     Fields:    Translation:HumansCells
  84. Tan ZW, Fei G, Paulo JA, Bellaousov S, Martin SES, Duveau DY, Thomas CJ, Gygi SP, Boutz PL, Walker S. O-GlcNAc regulates gene expression by controlling detained intron splicing. Nucleic Acids Res. 2020 06 04; 48(10):5656-5669. PMID: 32329777.
    Citations: 25     Fields:    Translation:HumansCells
  85. Li X, Pritykin Y, Concepcion CP, Lu Y, La Rocca G, Zhang M, King B, Cook PJ, Au YW, Popow O, Paulo JA, Otis HG, Mastroleo C, Ogrodowski P, Schreiner R, Haigis KM, Betel D, Leslie CS, Ventura A. High-Resolution In Vivo Identification of miRNA Targets by Halo-Enhanced Ago2 Pull-Down. Mol Cell. 2020 07 02; 79(1):167-179.e11. PMID: 32497496.
    Citations: 10     Fields:    Translation:AnimalsCells
  86. Park DE, Cheng J, McGrath JP, Lim MY, Cushman C, Swanson SK, Tillgren ML, Paulo JA, Gokhale PC, Florens L, Washburn MP, Trojer P, DeCaprio JA. Author Correction: Merkel cell polyomavirus activates LSD1-mediated blockade of non-canonical BAF to regulate transformation and tumorigenesis. Nat Cell Biol. 2020 06; 22(6):752. PMID: 32415271.
    Citations: 1     Fields:    
  87. Jedrychowski MP, Lu GZ, Szpyt J, Mariotti M, Garrity R, Paulo JA, Schweppe DK, Laznik-Bogoslavski D, Kazak L, Murphy MP, Gladyshev VN, Gygi SP, Chouchani ET, Spiegelman BM. Facultative protein selenation regulates redox sensitivity, adipose tissue thermogenesis, and obesity. Proc Natl Acad Sci U S A. 2020 05 19; 117(20):10789-10796. PMID: 32358195.
    Citations: 12     Fields:    Translation:AnimalsCells
  88. Sun Y, Ning X, Fan J, Hu J, Jiang Y, Hu Z, Paulo JA, Liu J, Qiu X, Xu H, Fu S, Gygi SP, Zhang J, Zhou C. Loss of tumor suppressor inositol polyphosphate 4-phosphatase type B impairs DNA double-strand break repair by destabilization of DNA tethering protein Rad50. Cell Death Dis. 2020 04 27; 11(4):292. PMID: 32341333.
    Citations: 1     Fields:    Translation:HumansCells
  89. Parker SJ, Amendola CR, Hollinshead KER, Yu Q, Yamamoto K, Encarnación-Rosado J, Rose RE, LaRue MM, Sohn ASW, Biancur DE, Paulo JA, Gygi SP, Jones DR, Wang H, Philips MR, Bar-Sagi D, Mancias JD, Kimmelman AC. Selective Alanine Transporter Utilization Creates a Targetable Metabolic Niche in Pancreatic Cancer. Cancer Discov. 2020 07; 10(7):1018-1037. PMID: 32341021; PMCID: PMC7334074.
    Citations: 44     Fields:    Translation:HumansCells
  90. Yamamoto K, Venida A, Yano J, Biancur DE, Kakiuchi M, Gupta S, Sohn ASW, Mukhopadhyay S, Lin EY, Parker SJ, Banh RS, Paulo JA, Wen KW, Debnath J, Kim GE, Mancias JD, Fearon DT, Perera RM, Kimmelman AC. Autophagy promotes immune evasion of pancreatic cancer by degrading MHC-I. Nature. 2020 05; 581(7806):100-105. PMID: 32376951; PMCID: PMC7296553.
    Citations: 250     Fields:    Translation:HumansAnimalsCells
  91. Yu Q, Paulo JA, Naverrete-Perea J, McAlister GC, Canterbury JD, Bailey DJ, Robitaille AM, Huguet R, Zabrouskov V, Gygi SP, Schweppe DK. Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics. Anal Chem. 2020 05 05; 92(9):6478-6485. PMID: 32250601.
    Citations: 10     Fields:    
  92. Park DE, Cheng J, McGrath JP, Lim MY, Cushman C, Swanson SK, Tillgren ML, Paulo JA, Gokhale PC, Florens L, Washburn MP, Trojer P, DeCaprio JA. Merkel cell polyomavirus activates LSD1-mediated blockade of non-canonical BAF to regulate transformation and tumorigenesis. Nat Cell Biol. 2020 05; 22(5):603-615. PMID: 32284543; PMCID: PMC7336275.
    Citations: 26     Fields:    
  93. Li J, Van Vranken JG, Paulo JA, Huttlin EL, Gygi SP. Selection of Heating Temperatures Improves the Sensitivity of the Proteome Integral Solubility Alteration Assay. J Proteome Res. 2020 05 01; 19(5):2159-2166. PMID: 32243163; PMCID: PMC7294736.
    Citations: 6     Fields:    
  94. Schweppe DK, Eng JK, Yu Q, Bailey D, Rad R, Navarrete-Perea J, Huttlin EL, Erickson BK, Paulo JA, Gygi SP. Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics. J Proteome Res. 2020 05 01; 19(5):2026-2034. PMID: 32126768; PMCID: PMC7295121.
    Citations: 49     Fields:    
  95. Gygi JP, Navarrete-Perea J, Younesi S, Gygi SP, Paulo JA. A Triple Knockout Isobaric-Labeling Quality Control Platform with an Integrated Online Database Search. J Am Soc Mass Spectrom. 2020 Jul 01; 31(7):1344-1349. PMID: 32202424.
    Citations: 8     Fields:    Translation:Animals
  96. Sharma S, Zhang T, Michowski W, Rebecca VW, Xiao M, Ferretti R, Suski JM, Bronson RT, Paulo JA, Frederick D, Fassl A, Boland GM, Geng Y, Lees JA, Medema RH, Herlyn M, Gygi SP, Sicinski P. Targeting the cyclin-dependent kinase 5 in metastatic melanoma. Proc Natl Acad Sci U S A. 2020 04 07; 117(14):8001-8012. PMID: 32193336.
    Citations: 9     Fields:    Translation:HumansAnimalsCells
  97. Li J, Van Vranken JG, Pontano Vaites L, Schweppe DK, Huttlin EL, Etienne C, Nandhikonda P, Viner R, Robitaille AM, Thompson AH, Kuhn K, Pike I, Bomgarden RD, Rogers JC, Gygi SP, Paulo JA. TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples. Nat Methods. 2020 04; 17(4):399-404. PMID: 32203386.
    Citations: 90     Fields:    Translation:HumansCells
  98. Cabal-Hierro L, van Galen P, Prado MA, Higby KJ, Togami K, Mowery CT, Paulo JA, Xie Y, Cejas P, Furusawa T, Bustin M, Long HW, Sykes DB, Gygi SP, Finley D, Bernstein BE, Lane AA. Chromatin accessibility promotes hematopoietic and leukemia stem cell activity. Nat Commun. 2020 03 16; 11(1):1406. PMID: 32179749.
    Citations: 11     Fields:    Translation:HumansAnimalsCells
  99. Richeson KV, Bodrug T, Sackton KL, Yamaguchi M, Paulo JA, Gygi SP, Schulman BA, Brown NG, King RW. Paradoxical mitotic exit induced by a small molecule inhibitor of APC/CCdc20. Nat Chem Biol. 2020 05; 16(5):546-555. PMID: 32152539; PMCID: PMC7289404.
    Citations: 8     Fields:    Translation:HumansCells
  100. Ordureau A, Paulo JA, Zhang J, An H, Swatek KN, Cannon JR, Wan Q, Komander D, Harper JW. Global Landscape and Dynamics of Parkin and USP30-Dependent Ubiquitylomes in iNeurons during Mitophagic Signaling. Mol Cell. 2020 03 05; 77(5):1124-1142.e10. PMID: 32142685.
    Citations: 50     Fields:    Translation:HumansCells
  101. Xiao H, Jedrychowski MP, Schweppe DK, Huttlin EL, Yu Q, Heppner DE, Li J, Long J, Mills EL, Szpyt J, He Z, Du G, Garrity R, Reddy A, Vaites LP, Paulo JA, Zhang T, Gray NS, Gygi SP, Chouchani ET. A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging. Cell. 2020 03 05; 180(5):968-983.e24. PMID: 32109415.
    Citations: 71     Fields:    Translation:HumansAnimalsCells
  102. Legøy TA, Mathisen AF, Salim Z, Vethe H, Bjørlykke Y, Abadpour S, Paulo JA, Scholz H, Ræder H, Ghila L, Chera S. In vivo Environment Swiftly Restricts Human Pancreatic Progenitors Toward Mono-Hormonal Identity via a HNF1A/HNF4A Mechanism. Front Cell Dev Biol. 2020; 8:109. PMID: 32161757; PMCID: PMC7052484.
    Citations: 9     
  103. Loo LSW, Vethe H, Soetedjo AAP, Paulo JA, Jasmen J, Jackson N, Bjørlykke Y, Valdez IA, Vaudel M, Barsnes H, Gygi SP, Raeder H, Teo AKK, Kulkarni RN. Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors. Stem Cells. 2020 04; 38(4):542-555. PMID: 31828876.
    Citations: 3     Fields:    Translation:HumansCells
  104. Giacomantonio MA, Sterea AM, Kim Y, Paulo JA, Clements DR, Kennedy BE, Bydoun MJ, Shi G, Waisman DM, Gygi SP, Giacomantonio CA, Murphy JP, Gujar S. Quantitative Proteome Responses to Oncolytic Reovirus in GM-CSF- and M-CSF-Differentiated Bone Marrow-Derived Cells. J Proteome Res. 2020 02 07; 19(2):708-718. PMID: 31884793; PMCID: PMC7294930.
    Citations: 2     Fields:    Translation:AnimalsCells
  105. Legøy TA, Vethe H, Abadpour S, Strand BL, Scholz H, Paulo JA, Ræder H, Ghila L, Chera S. Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signalling. Sci Rep. 2020 01 15; 10(1):414. PMID: 31942009.
    Citations: 18     Fields:    Translation:HumansCells
  106. Legøy TA, Ghila L, Vethe H, Abadpour S, Mathisen AF, Paulo JA, Scholz H, Raeder H, Chera S. In vivo hyperglycaemia exposure elicits distinct period-dependent effects on human pancreatic progenitor differentiation, conveyed by oxidative stress. Acta Physiol (Oxf). 2020 04; 228(4):e13433. PMID: 31872528.
    Citations: 3     Fields:    Translation:HumansAnimalsCells
  107. Ahfeldt T, Ordureau A, Bell C, Sarrafha L, Sun C, Piccinotti S, Grass T, Parfitt GM, Paulo JA, Yanagawa F, Uozumi T, Kiyota Y,