Harvard Catalyst Profiles

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Joao A Paulo, Ph.D.

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Research
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. K01DK098285 (PAULO, JOAO A) Sep 16, 2013 - Aug 31, 2018
    NIH/NIDDK
    Resolving the role of nicotine-mediated phosphorylation on pancreatic fibrosis
    Role: Principal Investigator
  2. F32DK085835 (PAULO, JOAO A) May 1, 2010 - Apr 30, 2013
    NIH/NIDDK
    Proteomics of Pancreatic Fluid and Urine in Chronic Pancreatitis
    Role: Principal Investigator

Bibliographic
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. 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 Feb 04. PMID: 30658528.
    Citations:    Fields:    
  2. Schweppe DK, Prasad S, Belford MW, Navarrete-Perea J, Bailey D, 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 Jan 23. PMID: 30672687.
    Citations:    Fields:    
  3. 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. PMID: 30530686.
    Citations:    Fields:    
  4. 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. 2018 Nov 27. PMID: 30481031.
    Citations:    Fields:    
  5. 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 Feb 01; 18(2):687-693. PMID: 30451507.
    Citations:    Fields:    
  6. Heo JM, Ordureau A, Swarup S, Paulo JA, Shen K, Sabatini DM, Harper JW. RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway. Sci Adv. 2018 Nov; 4(11):eaav0443. PMID: 30627666.
    Citations:    Fields:    
  7. 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. PMID: 30473739.
    Citations:    
  8. 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 Oct 24; 140(42):13542-13545. PMID: 30285435.
    Citations:    Fields:    
  9. Mulcahy MJ, Paulo JA, Hawrot E. Proteomic Investigation of Murine Neuronal a7-Nicotinic Acetylcholine Receptor Interacting Proteins. J Proteome Res. 2018 Nov 02; 17(11):3959-3975. PMID: 30285449.
    Citations:    Fields:    
  10. 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 Nov 29; 132(22):2375-2388. PMID: 30181176.
    Citations:    Fields:    
  11. 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 Aug 28; 24(9):2381-2391.e5. PMID: 30157431.
    Citations:    Fields:    
  12. 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. PMID: 30051891.
    Citations:    Fields:    
  13. 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 Jun 01; 17(6):2226-2236. PMID: 29734811.
    Citations:    Fields:    
  14. Paulo JA, Gygi SP. Isobaric Tag-Based Protein Profiling of a Nicotine-Treated Alpha7 Nicotinic Receptor-Null Human Haploid Cell Line. Proteomics. 2018 Jun; 18(11):e1700475. PMID: 29663646.
    Citations:    Fields:    
  15. 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 May; 18(10):e1700326. PMID: 29660237.
    Citations:    Fields:    
  16. O'Connell JD, Paulo JA, O'Brien JJ, Gygi SP. Proteome-Wide Evaluation of Two Common Protein Quantification Methods. J Proteome Res. 2018 May 04; 17(5):1934-1942. PMID: 29635916.
    Citations: 1     Fields:    
  17. 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 Jul; 29(7):1505-1511. PMID: 29671274.
    Citations:    Fields:    
  18. 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. PMID: 29656925.
    Citations:    Fields:    
  19. Berberich MJ, Paulo JA, Everley RA. MS3-IDQ: Utilizing MS3 Spectra beyond Quantification Yields Increased Coverage of the Phosphoproteome in Isobaric Tag Experiments. J Proteome Res. 2018 Apr 06; 17(4):1741-1747. PMID: 29461835.
    Citations:    Fields:    
  20. 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. PMID: 29402085.
    Citations: 1     Fields:    Translation:HumansCells
  21. 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. PMID: 29273634.
    Citations:    Fields:    Translation:HumansAnimalsCells
  22. 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. PMID: 29195270.
    Citations: 2     Fields:    
  23. 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. PMID: 28985074.
    Citations:    Fields:    Translation:HumansCells
  24. Pontano Vaites L, Paulo JA, Huttlin EL, Harper JW. Systematic analysis of human cells lacking ATG8 proteins uncovers roles for GABARAPs and the CCZ1/MON1 regulator C18orf8/RMC1 in macro and selective autophagic flux. Mol Cell Biol. 2017 Oct 16. PMID: 29038162.
    Citations: 4     Fields:    
  25. 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. PMID: 28945737.
    Citations:    Fields:    Translation:Animals
  26. 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. PMID: 28933694.
    Citations:    Fields:    Translation:HumansAnimalsCells
  27. 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. PMID: 28768414.
    Citations: 1     Fields:    Translation:AnimalsCells
  28. 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). PMID: 28774900.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  29. 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. PMID: 29031721.
    Citations:    
  30. 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. PMID: 28684784.
    Citations: 3     Fields:    
  31. 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. PMID: 28671190.
    Citations: 8     Fields:    Translation:HumansAnimalsCells
  32. 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. PMID: 28682306.
    Citations: 2     Fields:    Translation:AnimalsCells
  33. Scott DC, Hammill JT, Min J, Rhee DY, Connelly M, Sviderskiy VO, Bhasin D, Chen Y, Ong SS, Chai SC, Goktug AN, Huang G, Monda JK, Low J, Kim HS, Paulo JA, Cannon JR, Shelat AA, Chen T, Kelsall IR, Alpi AF, Pagala V, Wang X, Peng J, Singh B, Harper JW, Schulman BA, Guy RK. Blocking an N-terminal acetylation-dependent protein interaction inhibits an E3 ligase. Nat Chem Biol. 2017 Aug; 13(8):850-857. PMID: 28581483.
    Citations: 6     Fields:    Translation:HumansCells
  34. 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. PMID: 28539327.
    Citations: 2     Fields:    Translation:HumansCells
  35. 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. PMID: 28514442.
    Citations: 42     Fields:    Translation:HumansCells
  36. 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. PMID: 28514666.
    Citations: 7     Fields:    Translation:HumansCells
  37. Paulo JA, Mancias JD, Gygi SP. Proteome-Wide Protein Expression Profiling Across Five Pancreatic Cell Lines. Pancreas. 2017 May/Jun; 46(5):690-698. PMID: 28375945.
    Citations: 1     Fields:    Translation:HumansCells
  38. 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. PMID: 28388415.
    Citations: 4     Fields:    Translation:HumansCells
  39. 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 03 06; 2:17038. PMID: 28263306.
    Citations:    Fields:    
  40. 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. PMID: 28171727.
    Citations: 1     Fields:    Translation:HumansCells
  41. 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. PMID: 28211852.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  42. 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. PMID: 28186488.
    Citations: 6     Fields:    Translation:HumansCells
  43. Anikster Y, Haack TB, Vilboux T, Pode-Shakked B, Thöny B, Shen N, Guarani V, Meissner T, Mayatepek E, Trefz FK, Marek-Yagel D, Martinez A, Huttlin EL, Paulo JA, Berutti R, Benoist JF, Imbard A, Dorboz I, Heimer G, Landau Y, Ziv-Strasser L, Malicdan MCV, Gemperle-Britschgi C, Cremer K, Engels H, Meili D, Keller I, Bruggmann R, Strom TM, Meitinger T, Mullikin JC, Schwartz G, Ben-Zeev B, Gahl WA, Harper JW, Blau N, Hoffmann GF, Prokisch H, Opladen T, Schiff M. Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability. Am J Hum Genet. 2017 02 02; 100(2):257-266. PMID: 28132689.
    Citations: 3     Fields:    Translation:HumansCells
  44. 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. PMID: 28065596.
    Citations: 6     Fields:    Translation:HumansCells
  45. Paulo JA, Gygi SP. Nicotine-induced protein expression profiling reveals mutually altered proteins across four human cell lines. Proteomics. 2017 01; 17(1-2). PMID: 27862958.
    Citations: 3     Fields:    Translation:HumansCells
  46. 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. PMID: 27984722.
    Citations: 27     Fields:    Translation:HumansAnimalsCells
  47. 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. PMID: 27489273.
    Citations: 4     Fields:    Translation:HumansAnimalsCells
  48. 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. PMID: 27666594.
    Citations: 3     Fields:    Translation:HumansCells
  49. Guarani V, Jardel C, Chrétien D, Lombès A, Bénit P, Labasse C, Lacène E, Bourillon A, Imbard A, Benoist JF, Dorboz I, Gilleron M, Goetzman ES, Gaignard P, Slama A, Elmaleh-Bergès M, Romero NB, Rustin P, Ogier de Baulny H, Paulo JA, Harper JW, Schiff M. QIL1 mutation causes MICOS disassembly and early onset fatal mitochondrial encephalopathy with liver disease. Elife. 2016 09 13; 5. PMID: 27623147.
    Citations: 2     Fields:    Translation:Humans
  50. Scott DC, Rhee DY, Duda DM, Kelsall IR, Olszewski JL, Paulo JA, de Jong A, Ovaa H, Alpi AF, Harper JW, Schulman BA. Two Distinct Types of E3 Ligases Work in Unison to Regulate Substrate Ubiquitylation. Cell. 2016 Aug 25; 166(5):1198-1214.e24. PMID: 27565346.
    Citations: 15     Fields:    Translation:HumansCells
  51. 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. PMID: 27432472; PMCID: PMC5035620.
    Citations: 14     Fields:    Translation:Animals
  52. Paulo JA. Sample preparation for proteomic analysis using a GeLC-MS/MS strategy. J Biol Methods. 2016; 3(3). PMID: 27482532.
    Citations: 2     
  53. 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. PMID: 27400695.
    Citations: 12     Fields:    Translation:Animals
  54. 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. PMID: 27374330; PMCID: PMC4947008.
    Citations: 16     Fields:    Translation:AnimalsCells
  55. 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. PMID: 26503604; PMCID: PMC4802358.
    Citations: 9     Fields:    Translation:AnimalsCells
  56. 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. PMID: 26399295; PMCID: PMC4710237.
    Citations: 5     Fields:    Translation:AnimalsCells
  57. Heo JM, Ordureau A, Paulo JA, Rinehart J, Harper JW. The PINK1-PARKIN Mitochondrial Ubiquitylation Pathway Drives a Program of OPTN/NDP52 Recruitment and TBK1 Activation to Promote Mitophagy. Mol Cell. 2015 Oct 01; 60(1):7-20. PMID: 26365381; PMCID: PMC4592482.
    Citations: 98     Fields:    Translation:HumansCells
  58. 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. PMID: 26265067; PMCID: PMC4868188.
    Citations: 11     Fields:    Translation:HumansCells
  59. 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. PMID: 26278051; PMCID: PMC4802359.
    Citations: 69     Fields:    Translation:HumansCells
  60. 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. PMID: 26186194; PMCID: PMC4617211.
    Citations: 216     Fields:    Translation:Humans
  61. 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. PMID: 26077900; PMCID: PMC4563728.
    Citations: 16     Fields:    Translation:Animals
  62. 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. PMID: 25997101; PMCID: PMC4439739.
    Citations: 21     Fields:    Translation:HumansAnimalsCells
  63. Ordureau A, Heo JM, Duda DM, Paulo JA, Olszewski JL, Yanishevski D, Rinehart J, Schulman BA, Harper JW. Defining roles of PARKIN and ubiquitin phosphorylation by PINK1 in mitochondrial quality control using a ubiquitin replacement strategy. Proc Natl Acad Sci U S A. 2015 May 26; 112(21):6637-42. PMID: 25969509; PMCID: PMC4450373.
    Citations: 51     Fields:    Translation:HumansCells
  64. 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. PMID: 25954012.
    Citations: 24     Fields:    Translation:HumansAnimalsCells
  65. Marchegiani G, Paulo JA, Sahora K, Fernández-Del Castillo C. The proteome of postsurgical pancreatic juice. Pancreas. 2015 May; 44(4):574-82. PMID: 25875796; PMCID: PMC4506756.
    Citations: 2     Fields:    Translation:HumansCTClinical Trials
  66. 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. PMID: 25315811; PMCID: PMC4511088.
    Citations: 14     Fields:    Translation:AnimalsCells
  67. 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. PMID: 25195567; PMCID: PMC4515953.
    Citations: 21     Fields:    Translation:HumansAnimalsCells
  68. Paulo JA. Nicotine alters the proteome of two human pancreatic duct cell lines. JOP. 2014 Sep 28; 15(5):465-74. PMID: 25262714; PMCID: PMC4500938.
    Citations: 4     Fields:    
  69. 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. PMID: 24344204; PMCID: PMC4023825.
    Citations: 20     Fields:    Translation:HumansCells
  70. Low HP, Tiwari A, Janjanam J, Qiu L, Chang CI, Strohsnitter WC, Norwitz ER, Tam SW, Evans JE, Green KM, Paulo JA, Lambe M, Hsieh CC. Screening preeclamptic cord plasma for proteins associated with decreased breast cancer susceptibility. Genomics Proteomics Bioinformatics. 2013 Dec; 11(6):335-44. PMID: 24296084; PMCID: PMC4357835.
    Citations: 2     Fields:    Translation:Humans
  71. Paulo JA. Practical and Efficient Searching in Proteomics: A Cross Engine Comparison. Webmedcentral. 2013 Oct 01; 4(10). PMID: 25346847.
    Citations: 4     
  72. Paulo JA, Kadiyala V, Brizard S, Banks PA, Steen H, Conwell DL. A proteomic comparison of formalin-fixed paraffin-embedded pancreatic tissue from autoimmune pancreatitis, chronic pancreatitis, and pancreatic cancer. JOP. 2013 Jul 10; 14(4):405-14. PMID: 23846938; PMCID: PMC4506757.
    Citations: 4     Fields:    Translation:Humans
  73. Paulo JA, Urrutia R, Kadiyala V, Banks P, Conwell DL, Steen H. Cross-species analysis of nicotine-induced proteomic alterations in pancreatic cells. Proteomics. 2013 May; 13(9):1499-1512. PMID: 23456891; PMCID: PMC4036444.
    Citations: 5     Fields:    Translation:HumansAnimalsCells
  74. 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. PMID: 23565203; PMCID: PMC3615023.
    Citations: 6     Fields:    Translation:Animals
  75. Paulo JA, Kadiyala V, Banks PA, Conwell DL, Steen H. Mass spectrometry-based quantitative proteomic profiling of human pancreatic and hepatic stellate cell lines. Genomics Proteomics Bioinformatics. 2013 Apr; 11(2):105-13. PMID: 23528454; PMCID: PMC4123426.
    Citations: 4     Fields:    Translation:HumansCells
  76. Paulo JA, Kadiyala V, Brizard S, Banks PA, Steen H, Conwell DL. Post-translational modifications of pancreatic fluid proteins collected via the endoscopic pancreatic function test (ePFT). J Proteomics. 2013 Oct 30; 92:216-27. PMID: 23500127; PMCID: PMC3731404.
    Citations: 3     Fields:    Translation:HumansCellsCTClinical Trials
  77. Paulo JA, Kadiyala V, Gaun A, Sauld JF, Ghoulidi A, Banks PA, Steen H, Conwell DL. Analysis of endoscopic pancreatic function test (ePFT)-collected pancreatic fluid proteins precipitated via ultracentrifugation. JOP. 2013 Mar 10; 14(2):176-86. PMID: 23474565; PMCID: PMC4506755.
    Citations:    Fields:    Translation:HumansCells
  78. Lusczek ER, Paulo JA, Saltzman JR, Kadiyala V, Banks PA, Beilman G, Conwell DL. Urinary 1H-NMR metabolomics can distinguish pancreatitis patients from healthy controls. JOP. 2013 Mar 10; 14(2):161-70. PMID: 23474563; PMCID: PMC4500934.
    Citations: 5     Fields:    Translation:Humans
  79. Paulo JA, Gaun A, Kadiyala V, Ghoulidi A, Banks PA, Conwell DL, Steen H. Subcellular fractionation enhances proteome coverage of pancreatic duct cells. Biochim Biophys Acta. 2013 Apr; 1834(4):791-7. PMID: 23352835; PMCID: PMC3618666.
    Citations: 3     Fields:    Translation:Cells
  80. Kadiyala V, Lee LS, Banks PA, Suleiman S, Paulo JA, Wang W, Rosenblum J, Sainani NI, Mortele K, Conwell DL. Cigarette smoking impairs pancreatic duct cell bicarbonate secretion. JOP. 2013 Jan 10; 14(1):31-8. PMID: 23306332; PMCID: PMC4498578.
    Citations: 7     Fields:    Translation:Humans
  81. Serang O, Paulo J, Steen H, Steen JA. A non-parametric cutout index for robust evaluation of identified proteins. Mol Cell Proteomics. 2013 Mar; 12(3):807-12. PMID: 23292186; PMCID: PMC3591671.
    Citations: 6     Fields:    Translation:HumansCells
  82. Paulo JA, Kadiyala V, Brizard S, Banks PA, Conwell DL, Steen H. Short Gel, Long Gradient Liquid Chromatography Tandem Mass Spectrometry to Discover Urinary Biomarkers of Chronic Pancreatitis. Open Proteomics J. 2013; 6:1-13. PMID: 25346780.
    Citations: 3     
  83. Lee LS, Bellizzi AM, Banks PA, Sainani NI, Kadiyala V, Suleiman S, Conwell DL, Paulo JA. Differentiating Branch Duct and Mixed IPMN in Endoscopically Collected Pancreatic Cyst Fluid via Cytokine Analysis. Gastroenterol Res Pract. 2012; 2012:247309. PMID: 23326260; PMCID: PMC3543798.
    Citations: 2     
  84. Kentsis A, Shulman A, Ahmed S, Brennan E, Monuteaux MC, Lee YH, Lipsett S, Paulo JA, Dedeoglu F, Fuhlbrigge R, Bachur R, Bradwin G, Arditi M, Sundel RP, Newburger JW, Steen H, Kim S. Urine proteomics for discovery of improved diagnostic markers of Kawasaki disease. EMBO Mol Med. 2013 Feb; 5(2):210-20. PMID: 23281308; PMCID: PMC3569638.
    Citations: 17     Fields:    Translation:HumansAnimalsCells
  85. Lee LS, Banks PA, Bellizzi AM, Sainani NI, Kadiyala V, Suleiman S, Conwell DL, Paulo JA. Inflammatory protein profiling of pancreatic cyst fluid using EUS-FNA in tandem with cytokine microarray differentiates between branch duct IPMN and inflammatory cysts. J Immunol Methods. 2012 Aug 31; 382(1-2):142-149. PMID: 22683544.
    Citations: 10     Fields:    Translation:Humans
  86. Paulo JA, Kadiyala V, Banks PA, Steen H, Conwell DL. Mass Spectrometry-Based (GeLC-MS/MS) Comparative Proteomic Analysis of Endoscopically (ePFT) Collected Pancreatic and Gastroduodenal Fluids. Clin Transl Gastroenterol. 2012 May 03; 3:e14. PMID: 23238231; PMCID: PMC3367612.
    Citations: 4     
  87. Paulo JA, Kadiyala V, Banks PA, Steen H, Conwell DL. Mass spectrometry-based proteomics for translational research: a technical overview. Yale J Biol Med. 2012 Mar; 85(1):59-73. PMID: 22461744; PMCID: PMC3313540.
    Citations: 6     Fields:    Translation:HumansAnimals
  88. Paulo JA, Lee LS, Banks PA, Steen H, Conwell DL. Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry. Pancreas. 2012 Mar; 41(2):175-85. PMID: 22015969; PMCID: PMC3368275.
    Citations: 11     Fields:    Translation:Humans
  89. Paulo JA, Kadiyala V, Lee LS, Banks PA, Conwell DL, Steen H. Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitis. J Proteome Res. 2012 Mar 02; 11(3):1897-912. PMID: 22243521; PMCID: PMC3294251.
    Citations: 14     Fields:    Translation:Humans
  90. Broadbelt KG, Rivera KD, Paterson DS, Duncan JR, Trachtenberg FL, Paulo JA, Stapels MD, Borenstein NS, Belliveau RA, Haas EA, Stanley C, Krous HF, Steen H, Kinney HC. Brainstem deficiency of the 14-3-3 regulator of serotonin synthesis: a proteomics analysis in the sudden infant death syndrome. Mol Cell Proteomics. 2012 Jan; 11(1):M111.009530. PMID: 21976671; PMCID: PMC3270099.
    Citations: 14     Fields:    Translation:Humans
  91. Paulo JA, Urrutia R, Banks PA, Conwell DL, Steen H. Proteomic analysis of a rat pancreatic stellate cell line using liquid chromatography tandem mass spectrometry (LC-MS/MS). J Proteomics. 2011 Dec 21; 75(2):708-17. PMID: 21968429; PMCID: PMC3238025.
    Citations: 16     Fields:    Translation:AnimalsCells
  92. Paulo JA, Urrutia R, Banks PA, Conwell DL, Steen H. Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs nonproliferating cell states. J Proteome Res. 2011 Oct 07; 10(10):4835-44. PMID: 21838295; PMCID: PMC3189387.
    Citations: 21     Fields:    Translation:AnimalsCells
  93. Lysaght AC, Kao SY, Paulo JA, Merchant SN, Steen H, Stankovic KM. Proteome of human perilymph. J Proteome Res. 2011 Sep 02; 10(9):3845-51. PMID: 21740021; PMCID: PMC3179892.
    Citations: 11     Fields:    Translation:Humans
  94. Paulo JA, Lee LS, Banks PA, Steen H, Conwell DL. Difference gel electrophoresis identifies differentially expressed proteins in endoscopically collected pancreatic fluid. Electrophoresis. 2011 Aug; 32(15):1939-51. PMID: 21792986; PMCID: PMC3374332.
    Citations: 5     Fields:    Translation:Humans
  95. Paulo JA, Lee LS, Wu B, Banks PA, Steen H, Conwell DL. Cytokine profiling of pancreatic fluid using the ePFT collection method in tandem with a multiplexed microarray assay. J Immunol Methods. 2011 Jun 30; 369(1-2):98-107. PMID: 21569776; PMCID: PMC3116066.
    Citations: 8     Fields:    Translation:Humans
  96. Paulo JA, Lee LS, Wu B, Banks PA, Steen H, Conwell DL. Mass spectrometry-based proteomics of endoscopically collected pancreatic fluid in chronic pancreatitis research. Proteomics Clin Appl. 2011 Apr; 5(3-4):109-20. PMID: 21360826; PMCID: PMC3085141.
    Citations: 11     Fields:    Translation:Humans
  97. Paulo JA, Lee LS, Wu B, Repas K, Banks PA, Conwell DL, Steen H. Proteomic analysis of endoscopically (endoscopic pancreatic function test) collected gastroduodenal fluid using in-gel tryptic digestion followed by LC-MS/MS. Proteomics Clin Appl. 2010 Sep; 4(8-9):715-25. PMID: 21137089; PMCID: PMC3210639.
    Citations: 14     Fields:    Translation:Humans
  98. Paulo JA, Lee LS, Wu B, Repas K, Mortele KJ, Banks PA, Steen H, Conwell DL. Identification of pancreas-specific proteins in endoscopically (endoscopic pancreatic function test) collected pancreatic fluid with liquid chromatography--tandem mass spectrometry. Pancreas. 2010 Aug; 39(6):889-96. PMID: 20182389; PMCID: PMC2891328.
    Citations: 17     Fields:    Translation:Humans
  99. Paulo JA, Lee LS, Wu B, Repas K, Banks PA, Conwell DL, Steen H. Optimized sample preparation of endoscopic collected pancreatic fluid for SDS-PAGE analysis. Electrophoresis. 2010 Jul; 31(14):2377-87. PMID: 20589857; PMCID: PMC3019099.
    Citations: 13     Fields:    Translation:HumansCells
  100. Paulo JA, Hawrot E. Effect of homologous serotonin receptor loop substitutions on the heterologous expression in Pichia of a chimeric acetylcholine-binding protein with alpha-bungarotoxin-binding activity. Protein Expr Purif. 2009 Oct; 67(2):76-81. PMID: 19427904; PMCID: PMC2713376.
    Citations: 2     Fields:    Translation:AnimalsCells
  101. Paulo JA, Brucker WJ, Hawrot E. Proteomic analysis of an alpha7 nicotinic acetylcholine receptor interactome. J Proteome Res. 2009 Apr; 8(4):1849-58. PMID: 19714875; PMCID: PMC2891571.
    Citations: 30     Fields:    Translation:AnimalsCells
  102. Paulo JA, Hawrot E. A radioisotope label-free alpha-bungarotoxin-binding assay using BIAcore sensor chip technology for real-time analysis. Anal Biochem. 2009 Jun 01; 389(1):86-8. PMID: 19289092; PMCID: PMC2684811.
    Citations:    Fields:    
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Funded by the NIH/NCATS Clinical and Translational Science Award (CTSA) program, grant number UL1TR001102, and through institutional support from Harvard University, Harvard Medical School, Harvard T.H. Chan School of Public Health, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Brigham and Women's Hospital, Massachusetts General Hospital and the Dana Farber Cancer Institute.