Co-Author
This page shows the publications co-authored by Steven Gygi and Joao Paulo.
Connection Strength
21.394
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Multiplexed proteome profiling of carbon source perturbations in two yeast species with SL-SP3-TMT. J Proteomics. 2020 01 06; 210:103531.
Score: 0.839
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mTMT: An Alternative, Nonisobaric, Tandem Mass Tag Allowing for Precursor-Based Quantification. Anal Chem. 2019 10 01; 91(19):12167-12172.
Score: 0.835
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TKO6: A Peptide Standard To Assess Interference for Unit-Resolved Isobaric Labeling Platforms. J Proteome Res. 2019 01 04; 18(1):565-570.
Score: 0.791
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Isobaric Tag-Based Protein Profiling of a Nicotine-Treated Alpha7 Nicotinic Receptor-Null Human Haploid Cell Line. Proteomics. 2018 06; 18(11):e1700475.
Score: 0.761
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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.
Score: 0.759
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An Internal Standard for Assessing Phosphopeptide Recovery from Metal Ion/Oxide Enrichment Strategies. J Am Soc Mass Spectrom. 2018 07; 29(7):1505-1511.
Score: 0.757
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Proteome-Wide Protein Expression Profiling Across Five Pancreatic Cell Lines. Pancreas. 2017 May/Jun; 46(5):690-698.
Score: 0.708
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Nicotine-induced protein expression profiling reveals mutually altered proteins across four human cell lines. Proteomics. 2017 01; 17(1-2).
Score: 0.691
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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.
Score: 0.670
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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.
Score: 0.670
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Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae. Mol Biol Cell. 2015 Nov 05; 26(22):4063-74.
Score: 0.633
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Global Analysis of Protein Expression and Phosphorylation Levels in Nicotine-Treated Pancreatic Stellate Cells. J Proteome Res. 2015 Oct 02; 14(10):4246-56.
Score: 0.630
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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.
Score: 0.601
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Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10-plex quantitative proteomics and phosphoproteomics. Proteomics. 2015 Jan; 15(2-3):462-73.
Score: 0.594
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Fe3+-NTA magnetic beads as an alternative to spin column-based phosphopeptide enrichment. J Proteomics. 2022 Mar 21; 260:104561.
Score: 0.248
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Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment. J Proteome Res. 2022 02 04; 21(2):494-506.
Score: 0.245
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Assessing interference in isobaric tag-based sample multiplexing using an 18-plex interference standard. Proteomics. 2022 Apr; 22(7):e2100317.
Score: 0.245
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Proteome-wide mapping of short-lived proteins in human cells. Mol Cell. 2021 11 18; 81(22):4722-4735.e5.
Score: 0.241
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A Compendium of Murine (Phospho)Peptides Encompassing Different Isobaric Labeling and Data Acquisition Strategies. J Proteome Res. 2021 07 02; 20(7):3678-3688.
Score: 0.235
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Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell. 2021 05 27; 184(11):3022-3040.e28.
Score: 0.234
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A Semiautomated Paramagnetic Bead-Based Platform for Isobaric Tag Sample Preparation. J Am Soc Mass Spectrom. 2021 Jun 02; 32(6):1519-1529.
Score: 0.234
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TMTpro-18plex: The Expanded and Complete Set of TMTpro Reagents for Sample Multiplexing. J Proteome Res. 2021 05 07; 20(5):2964-2972.
Score: 0.233
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Temporal proteomic changes induced by nicotine in human cells: A quantitative proteomics approach. J Proteomics. 2021 06 15; 241:104244.
Score: 0.233
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Iron Deficiency and Recovery in Yeast: A Quantitative Proteomics Approach. J Proteome Res. 2021 05 07; 20(5):2751-2761.
Score: 0.232
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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.
Score: 0.232
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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.
Score: 0.231
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Categorization of Phosphorylation Site Behavior during the Diauxic Shift in Saccharomyces cerevisiae. J Proteome Res. 2021 05 07; 20(5):2487-2496.
Score: 0.231
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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.
Score: 0.226
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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.
Score: 0.225
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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.
Score: 0.225
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Growth media selection alters the proteome profiles of three model microorganisms. J Proteomics. 2021 01 16; 231:104006.
Score: 0.225
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Selection of Heating Temperatures Improves the Sensitivity of the Proteome Integral Solubility Alteration Assay. J Proteome Res. 2020 05 01; 19(5):2159-2166.
Score: 0.217
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Full-Featured, Real-Time Database Searching Platform Enables Fast and Accurate Multiplexed Quantitative Proteomics. J Proteome Res. 2020 05 01; 19(5):2026-2034.
Score: 0.217
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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.
Score: 0.216
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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.
Score: 0.216
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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.
Score: 0.212
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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.
Score: 0.211
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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.
Score: 0.209
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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.
Score: 0.201
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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.
Score: 0.200
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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.
Score: 0.197
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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.
Score: 0.190
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Proteome-Wide Evaluation of Two Common Protein Quantification Methods. J Proteome Res. 2018 05 04; 17(5):1934-1942.
Score: 0.189
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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.
Score: 0.187
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Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags. J Proteome Res. 2018 01 05; 17(1):590-599.
Score: 0.185
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Improved Method for Determining Absolute Phosphorylation Stoichiometry Using Bayesian Statistics and Isobaric Labeling. J Proteome Res. 2017 11 03; 16(11):4217-4226.
Score: 0.183
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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.
Score: 0.173
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Multiplexed, Proteome-Wide Protein Expression Profiling: Yeast Deubiquitylating Enzyme Knockout Strains. J Proteome Res. 2015 Dec 04; 14(12):5306-17.
Score: 0.160
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The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell. 2015 Jul 16; 162(2):425-440.
Score: 0.156
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Comprehensive Temporal Protein Dynamics during the Diauxic Shift in Saccharomyces cerevisiae. Mol Cell Proteomics. 2015 Sep; 14(9):2454-65.
Score: 0.155
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Rixosomal RNA degradation contributes to silencing of Polycomb target genes. Nature. 2022 Apr; 604(7904):167-174.
Score: 0.062
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NAD+ depletion enhances reovirus-induced oncolysis in multiple myeloma. Mol Ther Oncolytics. 2022 Mar 17; 24:695-706.
Score: 0.062
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Translocation of polyubiquitinated protein substrates by the hexameric Cdc48 ATPase. Mol Cell. 2022 02 03; 82(3):570-584.e8.
Score: 0.061
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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.
Score: 0.061
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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.
Score: 0.060
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Filamin C Cardiomyopathy Variants Cause Protein and Lysosome Accumulation. Circ Res. 2021 09 17; 129(7):751-766.
Score: 0.060
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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.
Score: 0.060
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Mechanism of p38 MAPK-induced EGFR endocytosis and its crosstalk with ligand-induced pathways. J Cell Biol. 2021 07 05; 220(7).
Score: 0.059
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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.
Score: 0.058
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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).
Score: 0.058
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Structures of chaperone-associated assembly intermediates reveal coordinated mechanisms of proteasome biogenesis. Nat Struct Mol Biol. 2021 05; 28(5):418-425.
Score: 0.058
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DPP9 sequesters the C terminus of NLRP1 to repress inflammasome activation. Nature. 2021 04; 592(7856):778-783.
Score: 0.058
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Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. Nat Methods. 2021 03; 18(3):293-302.
Score: 0.058
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Rapid toxin sequestration modifies poison frog physiology. J Exp Biol. 2021 02 09; 224(Pt 3).
Score: 0.057
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Targeting oncoproteins with a positive selection assay for protein degraders. Sci Adv. 2021 Feb; 7(6).
Score: 0.057
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Membrane skeleton modulates erythroid proteome remodeling and organelle clearance. Blood. 2021 01 21; 137(3):398-409.
Score: 0.057
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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.
Score: 0.057
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Global proteomics of Ubqln2-based murine models of ALS. J Biol Chem. 2021 Jan-Jun; 296:100153.
Score: 0.057
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ADAM17 cytoplasmic domain modulates Thioredoxin-1 conformation and activity. Redox Biol. 2020 10; 37:101735.
Score: 0.056
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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.
Score: 0.056
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pH-Gated Succinate Secretion Regulates Muscle Remodeling in Response to Exercise. Cell. 2020 10 01; 183(1):62-75.e17.
Score: 0.056
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Mitochondrial fatty acid synthesis coordinates oxidative metabolism in mammalian mitochondria. Elife. 2020 08 17; 9.
Score: 0.056
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Co-option of Plasmodium falciparum PP1 for egress from host erythrocytes. Nat Commun. 2020 07 15; 11(1):3532.
Score: 0.055
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PHD3 Loss Promotes Exercise Capacity and Fat Oxidation in Skeletal Muscle. Cell Metab. 2020 08 04; 32(2):215-228.e7.
Score: 0.055
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O-GlcNAc regulates gene expression by controlling detained intron splicing. Nucleic Acids Res. 2020 06 04; 48(10):5656-5669.
Score: 0.055
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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.
Score: 0.054
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Selective Alanine Transporter Utilization Creates a Targetable Metabolic Niche in Pancreatic Cancer. Cancer Discov. 2020 07; 10(7):1018-1037.
Score: 0.054
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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.
Score: 0.054
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Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics. Anal Chem. 2020 05 05; 92(9):6478-6485.
Score: 0.054
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Targeting the cyclin-dependent kinase 5 in metastatic melanoma. Proc Natl Acad Sci U S A. 2020 04 07; 117(14):8001-8012.
Score: 0.054
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Chromatin accessibility promotes hematopoietic and leukemia stem cell activity. Nat Commun. 2020 03 16; 11(1):1406.
Score: 0.054
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Paradoxical mitotic exit induced by a small molecule inhibitor of APC/CCdc20. Nat Chem Biol. 2020 05; 16(5):546-555.
Score: 0.054
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A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging. Cell. 2020 03 05; 180(5):968-983.e24.
Score: 0.054
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Dynamic proteome profiling of human pluripotent stem cell-derived pancreatic progenitors. Stem Cells. 2020 04; 38(4):542-555.
Score: 0.053
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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.
Score: 0.053
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Thiol-based direct threat sensing by the stress-activated protein kinase Hog1. Sci Signal. 2019 11 26; 12(609).
Score: 0.053
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Native Chromatin Proteomics Reveals a Role for Specific Nucleoporins in Heterochromatin Organization and Maintenance. Mol Cell. 2020 01 02; 77(1):51-66.e8.
Score: 0.053
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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.
Score: 0.052
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Epstein-Barr-Virus-Induced One-Carbon Metabolism Drives B Cell Transformation. Cell Metab. 2019 09 03; 30(3):539-555.e11.
Score: 0.051
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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.
Score: 0.051
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Tissue-Specific Oncogenic Activity of KRASA146T. Cancer Discov. 2019 06; 9(6):738-755.
Score: 0.051
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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.
Score: 0.050
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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.
Score: 0.049
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The effects of nonignorable missing data on label-free mass spectrometry proteomics experiments. Ann Appl Stat. 2018 Dec; 12(4):2075-2095.
Score: 0.049
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Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors. J Am Chem Soc. 2018 10 24; 140(42):13542-13545.
Score: 0.049
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Altered patterns of global protein synthesis and translational fidelity in RPS15-mutated chronic lymphocytic leukemia. Blood. 2018 11 29; 132(22):2375-2388.
Score: 0.049
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The NAD+ Salvage Pathway Supports PHGDH-Driven Serine Biosynthesis. Cell Rep. 2018 08 28; 24(9):2381-2391.e5.
Score: 0.049
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Automethylation-induced conformational switch in Clr4 (Suv39h) maintains epigenetic stability. Nature. 2018 08; 560(7719):504-508.
Score: 0.048
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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.
Score: 0.047
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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.
Score: 0.046
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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.
Score: 0.045
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Ubiquilin1 promotes antigen-receptor mediated proliferation by eliminating mislocalized mitochondrial proteins. Elife. 2017 09 21; 6.
Score: 0.045
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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.
Score: 0.045
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UBE2O remodels the proteome during terminal erythroid differentiation. Science. 2017 08 04; 357(6350).
Score: 0.045
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Cdkal1, a type 2 diabetes susceptibility gene, regulates mitochondrial function in adipose tissue. Mol Metab. 2017 10; 6(10):1212-1225.
Score: 0.045
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Probing the missing mature ß-cell proteomic landscape in differentiating patient iPSC-derived cells. Sci Rep. 2017 07 06; 7(1):4780.
Score: 0.045
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Compensatory metabolic networks in pancreatic cancers upon perturbation of glutamine metabolism. Nat Commun. 2017 07 03; 8:15965.
Score: 0.045
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Unique roles for histone H3K9me states in RNAi and heritable silencing of transcription. Nature. 2017 07 27; 547(7664):463-467.
Score: 0.045
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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.
Score: 0.044
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Architecture of the human interactome defines protein communities and disease networks. Nature. 2017 05 25; 545(7655):505-509.
Score: 0.044
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A Temporal Proteomic Map of Epstein-Barr Virus Lytic Replication in B Cells. Cell Rep. 2017 05 16; 19(7):1479-1493.
Score: 0.044
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Multidimensional Tracking of GPCR Signaling via Peroxidase-Catalyzed Proximity Labeling. Cell. 2017 04 06; 169(2):338-349.e11.
Score: 0.044
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Erratum: Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. Nat Microbiol. 2017 Mar 06; 2:17038.
Score: 0.044
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Multiplexed Phosphoproteomic Profiling Using Titanium Dioxide and Immunoaffinity Enrichments Reveals Complementary Phosphorylation Events. J Proteome Res. 2017 04 07; 16(4):1506-1514.
Score: 0.044
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Plasmodium falciparum CRK4 directs continuous rounds of DNA replication during schizogony. Nat Microbiol. 2017 Feb 17; 2:17017.
Score: 0.044
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Control of immune ligands by members of a cytomegalovirus gene expansion suppresses natural killer cell activation. Elife. 2017 02 10; 6.
Score: 0.044
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An Ancient, Unified Mechanism for Metformin Growth Inhibition in C. elegans and Cancer. Cell. 2016 Dec 15; 167(7):1705-1718.e13.
Score: 0.043
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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.
Score: 0.042
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Bromodomain Inhibitors Correct Bioenergetic Deficiency Caused by Mitochondrial Disease Complex I Mutations. Mol Cell. 2016 10 06; 64(1):163-175.
Score: 0.042
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The Secreted Enzyme PM20D1 Regulates Lipidated Amino Acid Uncouplers of Mitochondria. Cell. 2016 Jul 14; 166(2):424-435.
Score: 0.042
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Detection and Quantitation of Circulating Human Irisin by Tandem Mass Spectrometry. Cell Metab. 2015 Oct 06; 22(4):734-740.
Score: 0.039
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QIL1 is a novel mitochondrial protein required for MICOS complex stability and cristae morphology. Elife. 2015 May 21; 4.
Score: 0.039
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Malaria. A forward genetic screen identifies erythrocyte CD55 as essential for Plasmodium falciparum invasion. Science. 2015 May 08; 348(6235):711-4.
Score: 0.039
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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.
Score: 0.035
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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.
Score: 0.033
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.