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Steven P. Gygi, Ph.D.

Co-Author

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This page shows the publications co-authored by Steven Gygi and Joao Paulo.
Steven Gygi
Connection Strength
18.417
Joao Paulo
  1. Paulo JA, Navarrete-Perea J, Gygi SP. Multiplexed proteome profiling of carbon source perturbations in two yeast species with SL-SP3-TMT. J Proteomics. 2020 01 06; 210:103531.
    View in: PubMed
    Score: 0.932
  2. Paulo JA, Gygi SP. mTMT: An Alternative, Nonisobaric, Tandem Mass Tag Allowing for Precursor-Based Quantification. Anal Chem. 2019 10 01; 91(19):12167-12172.
    View in: PubMed
    Score: 0.928
  3. Paulo JA, Navarrete-Perea J, Guha Thakurta S, Gygi SP. TKO6: A Peptide Standard To Assess Interference for Unit-Resolved Isobaric Labeling Platforms. J Proteome Res. 2019 01 04; 18(1):565-570.
    View in: PubMed
    Score: 0.878
  4. Paulo JA, Gygi SP. Isobaric Tag-Based Protein Profiling of a Nicotine-Treated Alpha7 Nicotinic Receptor-Null Human Haploid Cell Line. Proteomics. 2018 06; 18(11):e1700475.
    View in: PubMed
    Score: 0.845
  5. Paulo JA, Jedrychowski MP, Chouchani ET, Kazak L, Gygi SP. Multiplexed Isobaric Tag-Based Profiling of Seven Murine Tissues Following In Vivo Nicotine Treatment Using a Minimalistic Proteomics Strategy. Proteomics. 2018 05; 18(10):e1700326.
    View in: PubMed
    Score: 0.843
  6. Paulo JA, Navarrete-Perea J, Erickson AR, Knott J, Gygi SP. An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies. J Am Soc Mass Spectrom. 2018 07; 29(7):1505-1511.
    View in: PubMed
    Score: 0.841
  7. Paulo JA, Mancias JD, Gygi SP. Proteome-Wide Protein Expression Profiling Across Five Pancreatic Cell Lines. Pancreas. 2017 May/Jun; 46(5):690-698.
    View in: PubMed
    Score: 0.786
  8. Paulo JA, Gygi SP. Nicotine-induced protein expression profiling reveals mutually altered proteins across four human cell lines. Proteomics. 2017 01; 17(1-2).
    View in: PubMed
    Score: 0.767
  9. Paulo JA, O'Connell JD, Everley RA, O'Brien J, Gygi MA, Gygi SP. Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources. J Proteomics. 2016 10 04; 148:85-93.
    View in: PubMed
    Score: 0.744
  10. Paulo JA, O'Connell JD, Gygi SP. A Triple Knockout (TKO) Proteomics Standard for Diagnosing Ion Interference in Isobaric Labeling Experiments. J Am Soc Mass Spectrom. 2016 10; 27(10):1620-5.
    View in: PubMed
    Score: 0.744
  11. Paulo JA, O'Connell JD, Gaun A, Gygi SP. Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae. Mol Biol Cell. 2015 Nov 05; 26(22):4063-74.
    View in: PubMed
    Score: 0.704
  12. Paulo JA, Gaun A, Gygi SP. Global Analysis of Protein Expression and Phosphorylation Levels in Nicotine-Treated Pancreatic Stellate Cells. J Proteome Res. 2015 Oct 02; 14(10):4246-56.
    View in: PubMed
    Score: 0.700
  13. Paulo JA, Gygi SP. A comprehensive proteomic and phosphoproteomic analysis of yeast deletion mutants of 14-3-3 orthologs and associated effects of rapamycin. Proteomics. 2015 Jan; 15(2-3):474-86.
    View in: PubMed
    Score: 0.667
  14. Paulo JA, McAllister FE, Everley RA, Beausoleil SA, Banks AS, Gygi SP. Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10-plex quantitative proteomics and phosphoproteomics. Proteomics. 2015 Jan; 15(2-3):462-73.
    View in: PubMed
    Score: 0.660
  15. Liu X, Gygi SP, Paulo JA. Isobaric Tag-Based Protein Profiling Across Eight Human Cell lines Using High-Field Asymmetric Ion Mobility Spectrometry (FAIMS) and Real-Time Database Searching (RTS). Proteomics. 2020 Oct 04; e2000218.
    View in: PubMed
    Score: 0.249
  16. 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.
    View in: PubMed
    Score: 0.241
  17. 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.
    View in: PubMed
    Score: 0.241
  18. 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.
    View in: PubMed
    Score: 0.240
  19. 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.
    View in: PubMed
    Score: 0.240
  20. Schweppe DK, Rusin SF, Gygi SP, Paulo JA. Optimized Workflow for Multiplexed Phosphorylation Analysis of TMT-Labeled Peptides Using High-Field Asymmetric Waveform Ion Mobility Spectrometry. J Proteome Res. 2020 01 03; 19(1):554-560.
    View in: PubMed
    Score: 0.236
  21. Li J, Paulo JA, Nusinow DP, Huttlin EL, Gygi SP. Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast. Cell Rep. 2019 11 12; 29(7):2092-2104.e4.
    View in: PubMed
    Score: 0.234
  22. Lim MY, Paulo JA, Gygi SP. Evaluating False Transfer Rates from the Match-between-Runs Algorithm with a Two-Proteome Model. J Proteome Res. 2019 11 01; 18(11):4020-4026.
    View in: PubMed
    Score: 0.232
  23. Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey DJ, Huguet R, Jedrychowski MP, Rad R, McAlister G, Abbatiello SE, Woulters ER, Zabrouskov V, Dunyach JJ, Paulo JA, Gygi SP. Characterization and Optimization of Multiplexed Quantitative Analyses Using High-Field Asymmetric-Waveform Ion Mobility Mass Spectrometry. Anal Chem. 2019 03 19; 91(6):4010-4016.
    View in: PubMed
    Score: 0.223
  24. Erickson BK, Mintseris J, Schweppe DK, Navarrete-Perea J, Erickson AR, Nusinow DP, Paulo JA, Gygi SP. Active Instrument Engagement Combined with a Real-Time Database Search for Improved Performance of Sample Multiplexing Workflows. J Proteome Res. 2019 03 01; 18(3):1299-1306.
    View in: PubMed
    Score: 0.222
  25. Gygi JP, Yu Q, Navarrete-Perea J, Rad R, Gygi SP, Paulo JA. Web-Based Search Tool for Visualizing Instrument Performance Using the Triple Knockout (TKO) Proteome Standard. J Proteome Res. 2019 02 01; 18(2):687-693.
    View in: PubMed
    Score: 0.219
  26. Navarrete-Perea J, Yu Q, Gygi SP, Paulo JA. Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3. J Proteome Res. 2018 06 01; 17(6):2226-2236.
    View in: PubMed
    Score: 0.211
  27. O'Connell JD, Paulo JA, O'Brien JJ, Gygi SP. Proteome-Wide Evaluation of Two Common Protein Quantification Methods. J Proteome Res. 2018 05 04; 17(5):1934-1942.
    View in: PubMed
    Score: 0.210
  28. Stepanova E, Gygi SP, Paulo JA. Filter-Based Protein Digestion (FPD): A Detergent-Free and Scaffold-Based Strategy for TMT Workflows. J Proteome Res. 2018 03 02; 17(3):1227-1234.
    View in: PubMed
    Score: 0.208
  29. O'Brien JJ, O'Connell JD, Paulo JA, Thakurta S, Rose CM, Weekes MP, Huttlin EL, Gygi SP. Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags. J Proteome Res. 2018 01 05; 17(1):590-599.
    View in: PubMed
    Score: 0.205
  30. Lim MY, O'Brien J, Paulo JA, Gygi SP. Improved Method for Determining Absolute Phosphorylation Stoichiometry Using Bayesian Statistics and Isobaric Labeling. J Proteome Res. 2017 11 03; 16(11):4217-4226.
    View in: PubMed
    Score: 0.204
  31. Erickson BK, Rose CM, Braun CR, Erickson AR, Knott J, McAlister GC, Wühr M, Paulo JA, Everley RA, Gygi SP. A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization. Mol Cell. 2017 Jan 19; 65(2):361-370.
    View in: PubMed
    Score: 0.192
  32. Isasa M, Rose CM, Elsasser S, Navarrete-Perea J, Paulo JA, Finley DJ, Gygi SP. Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains. J Proteome Res. 2015 Dec 04; 14(12):5306-17.
    View in: PubMed
    Score: 0.177
  33. Huttlin EL, Ting L, Bruckner RJ, Gebreab F, Gygi MP, Szpyt J, Tam S, Zarraga G, Colby G, Baltier K, Dong R, Guarani V, Vaites LP, Ordureau A, Rad R, Erickson BK, Wühr M, Chick J, Zhai B, Kolippakkam D, Mintseris J, Obar RA, Harris T, Artavanis-Tsakonas S, Sowa ME, De Camilli P, Paulo JA, Harper JW, Gygi SP. The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell. 2015 Jul 16; 162(2):425-440.
    View in: PubMed
    Score: 0.174
  34. Murphy JP, Stepanova E, Everley RA, Paulo JA, Gygi SP. Comprehensive Temporal Protein Dynamics during the Diauxic Shift in Saccharomyces cerevisiae. Mol Cell Proteomics. 2015 Sep; 14(9):2454-65.
    View in: PubMed
    Score: 0.173
  35. 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 Sep 24; 37:101735.
    View in: PubMed
    Score: 0.062
  36. 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 Sep 23; 10(1):15473.
    View in: PubMed
    Score: 0.062
  37. 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 Oct 01; 183(1):62-75.e17.
    View in: PubMed
    Score: 0.062
  38. 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.
    View in: PubMed
    Score: 0.062
  39. 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.
    View in: PubMed
    Score: 0.061
  40. 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 Aug 04; 32(2):215-228.e7.
    View in: PubMed
    Score: 0.061
  41. 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.
    View in: PubMed
    Score: 0.061
  42. 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.
    View in: PubMed
    Score: 0.061
  43. 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 Jul; 10(7):1018-1037.
    View in: PubMed
    Score: 0.060
  44. 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 Apr 27; 11(4):292.
    View in: PubMed
    Score: 0.060
  45. 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.
    View in: PubMed
    Score: 0.060
  46. 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.
    View in: PubMed
    Score: 0.060
  47. 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.
    View in: PubMed
    Score: 0.060
  48. 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.
    View in: PubMed
    Score: 0.060
  49. 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.
    View in: PubMed
    Score: 0.060
  50. 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.
    View in: PubMed
    Score: 0.059
  51. 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.
    View in: PubMed
    Score: 0.059
  52. Guerra-Moreno A, Prado MA, Ang J, Schnell HM, Micoogullari Y, Paulo JA, Finley D, Gygi SP, Hanna J. Thiol-based direct threat sensing by the stress-activated protein kinase Hog1. Sci Signal. 2019 11 26; 12(609).
    View in: PubMed
    Score: 0.059
  53. Iglesias N, Paulo JA, Tatarakis A, Wang X, Edwards AL, Bhanu NV, Garcia BA, Haas W, Gygi SP, Moazed D. Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance. Mol Cell. 2020 01 02; 77(1):51-66.e8.
    View in: PubMed
    Score: 0.059
  54. Brubaker DK, Paulo JA, Sheth S, Poulin EJ, Popow O, Joughin BA, Strasser SD, Starchenko A, Gygi SP, Lauffenburger DA, Haigis KM. Proteogenomic Network Analysis of Context-Specific KRAS Signaling in Mouse-to-Human Cross-Species Translation. Cell Syst. 2019 09 25; 9(3):258-270.e6.
    View in: PubMed
    Score: 0.058
  55. Wang LW, Shen H, Nobre L, Ersing I, Paulo JA, Trudeau S, Wang Z, Smith NA, Ma Y, Reinstadler B, Nomburg J, Sommermann T, Cahir-McFarland E, Gygi SP, Mootha VK, Weekes MP, Gewurz BE. Epstein-Barr-Virus-Induced One-Carbon Metabolism Drives B Cell Transformation. Cell Metab. 2019 09 03; 30(3):539-555.e11.
    View in: PubMed
    Score: 0.057
  56. Murphy JP, Kim Y, Clements DR, Konda P, Schuster H, Kowalewski DJ, Paulo JA, Cohen AM, Stevanovic S, Gygi SP, Gujar S. Therapy-Induced MHC I Ligands Shape Neo-Antitumor CD8 T Cell Responses during Oncolytic Virus-Based Cancer Immunotherapy. J Proteome Res. 2019 06 07; 18(6):2666-2675.
    View in: PubMed
    Score: 0.057
  57. Poulin EJ, Bera AK, Lu J, Lin YJ, Strasser SD, Paulo JA, Huang TQ, Morales C, Yan W, Cook J, Nowak JA, Brubaker DK, Joughin BA, Johnson CW, DeStefanis RA, Ghazi PC, Gondi S, Wales TE, Iacob RE, Bogdanova L, Gierut JJ, Li Y, Engen JR, Perez-Mancera PA, Braun BS, Gygi SP, Lauffenburger DA, Westover KD, Haigis KM. Tissue-Specific Oncogenic Activity of KRASA146T. Cancer Discov. 2019 06; 9(6):738-755.
    View in: PubMed
    Score: 0.056
  58. Murphy JP, Yu Q, Konda P, Paulo JA, Jedrychowski MP, Kowalewski DJ, Schuster H, Kim Y, Clements D, Jain A, Stevanovic S, Gygi SP, Mancias JD, Gujar S. Multiplexed Relative Quantitation with Isobaric Tagging Mass Spectrometry Reveals Class I Major Histocompatibility Complex Ligand Dynamics in Response to Doxorubicin. Anal Chem. 2019 04 16; 91(8):5106-5115.
    View in: PubMed
    Score: 0.056
  59. Ron-Harel N, Notarangelo G, Ghergurovich JM, Paulo JA, Sage PT, Santos D, Satterstrom FK, Gygi SP, Rabinowitz JD, Sharpe AH, Haigis MC. Defective respiration and one-carbon metabolism contribute to impaired naïve T cell activation in aged mice. Proc Natl Acad Sci U S A. 2018 12 26; 115(52):13347-13352.
    View in: PubMed
    Score: 0.055
  60. O'Brien JJ, Gunawardena HP, Paulo JA, Chen X, Ibrahim JG, Gygi SP, Qaqish BF. The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments. Ann Appl Stat. 2018 Dec; 12(4):2075-2095.
    View in: PubMed
    Score: 0.055
  61. Martin SES, Tan ZW, Itkonen HM, Duveau DY, Paulo JA, Janetzko J, Boutz PL, Törk L, Moss FA, Thomas CJ, Gygi SP, Lazarus MB, Walker S. Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors. J Am Chem Soc. 2018 10 24; 140(42):13542-13545.
    View in: PubMed
    Score: 0.054
  62. Bretones G, Álvarez MG, Arango JR, Rodríguez D, Nadeu F, Prado MA, Valdés-Mas R, Puente DA, Paulo JA, Delgado J, Villamor N, López-Guillermo A, Finley DJ, Gygi SP, Campo E, Quesada V, López-Otín C. Altered patterns of global protein synthesis and translational fidelity in RPS15-mutated chronic lymphocytic leukemia. Blood. 2018 11 29; 132(22):2375-2388.
    View in: PubMed
    Score: 0.054
  63. Murphy JP, Giacomantonio MA, Paulo JA, Everley RA, Kennedy BE, Pathak GP, Clements DR, Kim Y, Dai C, Sharif T, Gygi SP, Gujar S. The NAD+ Salvage Pathway Supports PHGDH-Driven Serine Biosynthesis. Cell Rep. 2018 08 28; 24(9):2381-2391.e5.
    View in: PubMed
    Score: 0.054
  64. Iglesias N, Currie MA, Jih G, Paulo JA, Siuti N, Kalocsay M, Gygi SP, Moazed D. Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability. Nature. 2018 08; 560(7719):504-508.
    View in: PubMed
    Score: 0.054
  65. Ordureau A, Paulo JA, Zhang W, Ahfeldt T, Zhang J, Cohn EF, Hou Z, Heo JM, Rubin LL, Sidhu SS, Gygi SP, Harper JW. Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Mol Cell. 2018 04 19; 70(2):211-227.e8.
    View in: PubMed
    Score: 0.052
  66. Fraile JM, Campos-Iglesias D, Rodríguez F, Astudillo A, Vilarrasa-Blasi R, Verdaguer-Dot N, Prado MA, Paulo JA, Gygi SP, Martín-Subero JI, Freije JMP, López-Otín C. Loss of the deubiquitinase USP36 destabilizes the RNA helicase DHX33 and causes preimplantation lethality in mice. J Biol Chem. 2018 02 09; 293(6):2183-2194.
    View in: PubMed
    Score: 0.051
  67. Navarrete-Perea J, Isasa M, Paulo JA, Corral-Corral R, Flores-Bautista J, Hernández-Téllez B, Bobes RJ, Fragoso G, Sciutto E, Soberón X, Gygi SP, Laclette JP. Quantitative multiplexed proteomics of Taenia solium cysts obtained from the skeletal muscle and central nervous system of pigs. PLoS Negl Trop Dis. 2017 Sep; 11(9):e0005962.
    View in: PubMed
    Score: 0.051
  68. Whiteley AM, Prado MA, Peng I, Abbas AR, Haley B, Paulo JA, Reichelt M, Katakam A, Sagolla M, Modrusan Z, Lee DY, Roose-Girma M, Kirkpatrick DS, McKenzie BS, Gygi SP, Finley D, Brown EJ. Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins. Elife. 2017 09 21; 6.
    View in: PubMed
    Score: 0.050
  69. Clements DR, Murphy JP, Sterea A, Kennedy BE, Kim Y, Helson E, Almasi S, Holay N, Konda P, Paulo JA, Sharif T, Lee PW, Weekes MP, Gygi SP, Gujar S. Quantitative Temporal in Vivo Proteomics Deciphers the Transition of Virus-Driven Myeloid Cells into M2 Macrophages. J Proteome Res. 2017 09 01; 16(9):3391-3406.
    View in: PubMed
    Score: 0.050
  70. Nguyen AT, Prado MA, Schmidt PJ, Sendamarai AK, Wilson-Grady JT, Min M, Campagna DR, Tian G, Shi Y, Dederer V, Kawan M, Kuehnle N, Paulo JA, Yao Y, Weiss MJ, Justice MJ, Gygi SP, Fleming MD, Finley D. UBE2O remodels the proteome during terminal erythroid differentiation. Science. 2017 08 04; 357(6350).
    View in: PubMed
    Score: 0.050
  71. Palmer CJ, Bruckner RJ, Paulo JA, Kazak L, Long JZ, Mina AI, Deng Z, LeClair KB, Hall JA, Hong S, Zushin PH, Smith KL, Gygi SP, Hagen S, Cohen DE, Banks AS. Cdkal1, a type 2 diabetes susceptibility gene, regulates mitochondrial function in adipose tissue. Mol Metab. 2017 10; 6(10):1212-1225.
    View in: PubMed
    Score: 0.050
  72. Vethe H, Bjørlykke Y, Ghila LM, Paulo JA, Scholz H, Gygi SP, Chera S, Ræder H. Probing the missing mature ß-cell proteomic landscape in differentiating patient iPSC-derived cells. Sci Rep. 2017 07 06; 7(1):4780.
    View in: PubMed
    Score: 0.050
  73. Biancur DE, Paulo JA, Malachowska B, Quiles Del Rey M, Sousa CM, Wang X, Sohn ASW, Chu GC, Gygi SP, Harper JW, Fendler W, Mancias JD, Kimmelman AC. Compensatory metabolic networks in pancreatic cancers upon perturbation of glutamine metabolism. Nat Commun. 2017 07 03; 8:15965.
    View in: PubMed
    Score: 0.050
  74. Jih G, Iglesias N, Currie MA, Bhanu NV, Paulo JA, Gygi SP, Garcia BA, Moazed D. Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription. Nature. 2017 07 27; 547(7664):463-467.
    View in: PubMed
    Score: 0.050
  75. Mohideen F, Paulo JA, Ordureau A, Gygi SP, Harper JW. Quantitative Phospho-proteomic Analysis of TNFa/NF?B Signaling Reveals a Role for RIPK1 Phosphorylation in Suppressing Necrotic Cell Death. Mol Cell Proteomics. 2017 07; 16(7):1200-1216.
    View in: PubMed
    Score: 0.049
  76. Huttlin EL, Bruckner RJ, Paulo JA, Cannon JR, Ting L, Baltier K, Colby G, Gebreab F, Gygi MP, Parzen H, Szpyt J, Tam S, Zarraga G, Pontano-Vaites L, Swarup S, White AE, Schweppe DK, Rad R, Erickson BK, Obar RA, Guruharsha KG, Li K, Artavanis-Tsakonas S, Gygi SP, Harper JW. Architecture of the human interactome defines protein communities and disease networks. Nature. 2017 05 25; 545(7655):505-509.
    View in: PubMed
    Score: 0.049
  77. Ersing I, Nobre L, Wang LW, Soday L, Ma Y, Paulo JA, Narita Y, Ashbaugh CW, Jiang C, Grayson NE, Kieff E, Gygi SP, Weekes MP, Gewurz BE. A Temporal Proteomic Map of Epstein-Barr Virus Lytic Replication in B Cells. Cell Rep. 2017 05 16; 19(7):1479-1493.
    View in: PubMed
    Score: 0.049
  78. Paek J, Kalocsay M, Staus DP, Wingler L, Pascolutti R, Paulo JA, Gygi SP, Kruse AC. Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling. Cell. 2017 04 06; 169(2):338-349.e11.
    View in: PubMed
    Score: 0.049
  79. Ganter M, Goldberg JM, Dvorin JD, Paulo JA, King JG, Tripathi AK, Paul AS, Yang J, Coppens I, Jiang RH, Elsworth B, Baker DA, Dinglasan RR, Gygi SP, Duraisingh MT. Erratum: Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. Nat Microbiol. 2017 Mar 06; 2:17038.
    View in: PubMed
    Score: 0.049
  80. Possemato AP, Paulo JA, Mulhern D, Guo A, Gygi SP, Beausoleil SA. Multiplexed Phosphoproteomic Profiling Using Titanium Dioxide and Immunoaffinity Enrichments Reveals Complementary Phosphorylation Events. J Proteome Res. 2017 04 07; 16(4):1506-1514.
    View in: PubMed
    Score: 0.049
  81. Ganter M, Goldberg JM, Dvorin JD, Paulo JA, King JG, Tripathi AK, Paul AS, Yang J, Coppens I, Jiang RH, Elsworth B, Baker DA, Dinglasan RR, Gygi SP, Duraisingh MT. Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. Nat Microbiol. 2017 Feb 17; 2:17017.
    View in: PubMed
    Score: 0.048
  82. Fielding CA, Weekes MP, Nobre LV, Ruckova E, Wilkie GS, Paulo JA, Chang C, Suárez NM, Davies JA, Antrobus R, Stanton RJ, Aicheler RJ, Nichols H, Vojtesek B, Trowsdale J, Davison AJ, Gygi SP, Tomasec P, Lehner PJ, Wilkinson GW. Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation. Elife. 2017 02 10; 6.
    View in: PubMed
    Score: 0.048
  83. Wu L, Zhou B, Oshiro-Rapley N, Li M, Paulo JA, Webster CM, Mou F, Kacergis MC, Talkowski ME, Carr CE, Gygi SP, Zheng B, Soukas AA. An Ancient, Unified Mechanism for Metformin Growth Inhibition in C. elegans and Cancer. Cell. 2016 Dec 15; 167(7):1705-1718.e13.
    View in: PubMed
    Score: 0.048
  84. Turnbull ML, Wise HM, Nicol MQ, Smith N, Dunfee RL, Beard PM, Jagger BW, Ligertwood Y, Hardisty GR, Xiao H, Benton DJ, Coburn AM, Paulo JA, Gygi SP, McCauley JW, Taubenberger JK, Lycett SJ, Weekes MP, Dutia BM, Digard P. Role of the B Allele of Influenza A Virus Segment 8 in Setting Mammalian Host Range and Pathogenicity. J Virol. 2016 10 15; 90(20):9263-84.
    View in: PubMed
    Score: 0.047
  85. Barrow JJ, Balsa E, Verdeguer F, Tavares CD, Soustek MS, Hollingsworth LR, Jedrychowski M, Vogel R, Paulo JA, Smeitink J, Gygi SP, Doench J, Root DE, Puigserver P. Bromodomain Inhibitors Correct Bioenergetic Deficiency Caused by Mitochondrial Disease Complex I Mutations. Mol Cell. 2016 10 06; 64(1):163-175.
    View in: PubMed
    Score: 0.047
  86. Long JZ, Svensson KJ, Bateman LA, Lin H, Kamenecka T, Lokurkar IA, Lou J, Rao RR, Chang MR, Jedrychowski MP, Paulo JA, Gygi SP, Griffin PR, Nomura DK, Spiegelman BM. The Secreted Enzyme PM20D1 Regulates Lipidated Amino Acid Uncouplers of Mitochondria. Cell. 2016 Jul 14; 166(2):424-435.
    View in: PubMed
    Score: 0.046
  87. Jedrychowski MP, Wrann CD, Paulo JA, Gerber KK, Szpyt J, Robinson MM, Nair KS, Gygi SP, Spiegelman BM. Detection and Quantitation of Circulating Human Irisin by Tandem Mass Spectrometry. Cell Metab. 2015 Oct 06; 22(4):734-740.
    View in: PubMed
    Score: 0.044
  88. Guarani V, McNeill EM, Paulo JA, Huttlin EL, Fröhlich F, Gygi SP, Van Vactor D, Harper JW. QIL1 is a novel mitochondrial protein required for MICOS complex stability and cristae morphology. Elife. 2015 May 21; 4.
    View in: PubMed
    Score: 0.043
  89. Egan ES, Jiang RH, Moechtar MA, Barteneva NS, Weekes MP, Nobre LV, Gygi SP, Paulo JA, Frantzreb C, Tani Y, Takahashi J, Watanabe S, Goldberg J, Paul AS, Brugnara C, Root DE, Wiegand RC, Doench JG, Duraisingh MT. Malaria. A forward genetic screen identifies erythrocyte CD55 as essential for Plasmodium falciparum invasion. Science. 2015 May 08; 348(6235):711-4.
    View in: PubMed
    Score: 0.043
  90. Guarani V, Paulo J, Zhai B, Huttlin EL, Gygi SP, Harper JW. TIMMDC1/C3orf1 functions as a membrane-embedded mitochondrial complex I assembly factor through association with the MCIA complex. Mol Cell Biol. 2014 Mar; 34(5):847-61.
    View in: PubMed
    Score: 0.039
  91. Ræder H, Vesterhus M, El Ouaamari A, Paulo JA, McAllister FE, Liew CW, Hu J, Kawamori D, Molven A, Gygi SP, Njølstad PR, Kahn CR, Kulkarni RN. Absence of diabetes and pancreatic exocrine dysfunction in a transgenic model of carboxyl-ester lipase-MODY (maturity-onset diabetes of the young). PLoS One. 2013; 8(4):e60229.
    View in: PubMed
    Score: 0.037
Connection Strength
The connection strength for co-authors is the sum of the scores for each of their shared publications.

Publication scores are based on many factors, including how long ago they were written and whether the person is a first or senior author.
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Funded by the NIH National Center for Advancing Translational Sciences through its Clinical and Translational Science Awards Program, grant number UL1TR002541.