My Bibliography

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Rogers J, Cardani L, Shah N, AlQuraishi M. Quantitative machine learning of protein interactions reveals the multiscale organization and molecular syntax of signaling networks. [Preprint]. 2026 September. doi: 10.64898/2026.09.25.754499.

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Lee M, Johns AC, Wang Z, Semoy DA, Shah NH. Substrate-Derived Peptides for Selective Covalent Inhibition of Protein Tyrosine Kinases. ACS Chem Biol. 2026 Aug 24;. doi: 10.1021/acschembio.6c00468. [Epub ahead of print] PubMed PMID: 42669292; PubMed Central PMCID: PMC13590119.

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Johns AC, Goonatilleke YS, Cabanero DC, Ma Y, Lee M, van Vlimmeren AE, Jovanovic M, Shah NH. In situ identification of substrates of the protein tyrosine phosphatase PTP1B using site-specific photo-crosslinking. bioRxiv [Preprint]. Version v1. 2026 July. Available from: https://doi.org/10.64898/2026.07.06.736850.

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Johns A, Goonatilleke Y, Cabanero D, Ma Y, Lee M, van Vlimmeren A, Jovanovic M, Shah N. Identification of substrates of the protein tyrosine phosphatase PTP1B using <i>in situ</i> site-specific photo-crosslinking. [Preprint]. 2026 July. doi: 10.64898/2026.07.06.736850.

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van Vlimmeren AE, Giglio RM, Jiang Z, Lee M, McFaline-Figueroa JL, Shah NH. Multiplexed single-cell transcriptomics reveals diverse phenotypic outcomes for pathogenic SHP2 variants. Sci Adv. 2026 May 22;12(21):eaea9389. doi: 10.1126/sciadv.aea9389. Epub 2026 May 22. PubMed PMID: 42172315; PubMed Central PMCID: PMC13196782.

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Lee M, Wang Z, Johns AC, Shah NH. Substrate-derived peptides for selective covalent inhibition of protein tyrosine kinases. bioRxiv. 2026 May 14;. doi: 10.64898/2026.05.11.724146. PubMed PMID: 42182222; PubMed Central PMCID: PMC13192911.

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Semoy DA, Shah NH. A bis-phosphorylated peptide wrangles the SHP2 tandem SH2 domains into shape. Structure. 2026 Mar 5;34(3):388-390. doi: 10.1016/j.str.2026.02.003. PubMed PMID: 41795456.

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Karaj E, Venkatarangan V, Sindi SH, Siriwongsup S, Lee C, Pergu R, Sreekanth V, Kailass K, Tran K, Singh P, Singh S, Kawai J, Fung JE, Tefera M, Dhaliwal R, Chaudhary SK, Keyes A, Sadagopan A, Boatner L, Shah NH, Fehl C, Backus KM, Choudhary A. A Scalable Design for Proximity-Inducing Molecules. bioRxiv. 2026 Feb 21;. doi: 10.64898/2026.02.20.706349. PubMed PMID: 41756985; PubMed Central PMCID: PMC12934950.

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Shah NH. Pervanadate: So much more than a protein tyrosine phosphatase inhibitor. Sci Signal. 2026 Jan 20;19(921):eaed6832. doi: 10.1126/scisignal.aed6832. Epub 2026 Jan 20. PubMed PMID: 41557760.

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Lee M, Shah NH. Profiling tyrosine kinase substrate recognition using bacterial peptide display and deep sequencing. bioRxiv. 2025 Dec 30;. doi: 10.64898/2025.12.28.696772. PubMed PMID: 41509325; PubMed Central PMCID: PMC12776416.

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van Vlimmeren AE, Tang LC, Jiang Z, Iyer A, Voleti R, Krismer K, Gaublomme JT, Jovanovic M, Shah NH. Proximity-labeling proteomics reveals remodeled interactomes and altered localization of pathogenic SHP2 variants. EMBO Rep. 2026 Feb;27(3):793-826. doi: 10.1038/s44319-025-00674-4. Epub 2025 Dec 22. PubMed PMID: 41429940; PubMed Central PMCID: PMC12894930.

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van Vlimmeren AE, Jiang Z, Karandur D, Applebaum Licht AT, Shah NH. The pathogenic E139D mutation stabilizes a non-canonical active state of the multi-domain phosphatase SHP2. Protein Sci. 2025 Dec;34(12):e70373. doi: 10.1002/pro.70373. PubMed PMID: 41225768; PubMed Central PMCID: PMC12611872.

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Gagoski D, Rube HT, Rastogi C, Melo LAN, Li X, Voleti R, Shah NH, Bussemaker HJ. Accurate affinity models for SH2 domains from peptide binding assays and free-energy regression. Protein Sci. 2025 Nov;34(11):e70317. doi: 10.1002/pro.70317. PubMed PMID: 41088778; PubMed Central PMCID: PMC12521615.

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van Vlimmeren AE, Jiang Z, Karandur D, Licht ATA, Shah NH. The pathogenic E139D mutation stabilizes a non-canonical active state of the multi-domain phosphatase SHP2. bioRxiv. 2025 Oct 1;. doi: 10.1101/2025.07.02.662799. PubMed PMID: 40631229; PubMed Central PMCID: PMC12236607.

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van Vlimmeren AE, Tang LC, Jiang Z, Iyer A, Voleti R, Krismer K, Gaublomme JT, Jovanovic M, Shah NH. Proximity-labeling proteomics reveals remodeled interactomes and altered localization of pathogenic SHP2 variants. bioRxiv. 2025 Sep 8;. doi: 10.1101/2025.02.26.640373. PubMed PMID: 40661614; PubMed Central PMCID: PMC12258515.

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van Vlimmeren AE, Giglio RM, Jiang Z, Lee M, McFaline-Figueroa JL, Shah NH. Multiplexed single-cell transcriptomics reveals diverse phenotypic outcomes for pathogenic SHP2 variants. bioRxiv. 2025 Jul 2;. doi: 10.1101/2025.06.30.662374. PubMed PMID: 40631144; PubMed Central PMCID: PMC12236728.

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Jiang Z, van Vlimmeren AE, Karandur D, Semmelman A, Shah NH. Deep mutational scanning of the multi-domain phosphatase SHP2 reveals mechanisms of regulation and pathogenicity. Nat Commun. 2025 Jul 1;16(1):5464. doi: 10.1038/s41467-025-60641-4. PubMed PMID: 40595497; PubMed Central PMCID: PMC12216643.

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Makrides N, Sun E, Mir H, Jiang Z, Wu Y, Serra C, Cardoso WV, Shah NH, Zhang X. Allosteric inhibition rescues hydrocephalus caused by catalytically inactive Shp2. bioRxiv. 2025 Feb 1;. doi: 10.1101/2025.01.28.635289. PubMed PMID: 39974929; PubMed Central PMCID: PMC11838390.

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Doron-Mandel E, Bokor BJ, Ma Y, Street LA, Tang LC, Abdou AA, Shah NH, Rosenberger G, Jovanovic M. SEC-MX: an approach to systematically study the interplay between protein assembly states and phosphorylation. Nat Commun. 2025 Jan 30;16(1):1176. doi: 10.1038/s41467-025-56303-0. PubMed PMID: 39885126; PubMed Central PMCID: PMC11782603.

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Gagoski D, Rube HT, Rastogi C, Melo LAN, Li X, Voleti R, Shah NH, Bussemaker HJ. Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression. bioRxiv. 2025 Jan 5;. doi: 10.1101/2024.12.23.630085. PubMed PMID: 39764007; PubMed Central PMCID: PMC11703206.

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Chartier CA, Woods VA, Xu Y, van Vlimmeren AE, Johns AC, Jovanovic M, McDermott AE, Keedy DA, Shah NH. Allosteric regulation of the tyrosine phosphatase PTP1B by a protein-protein interaction. Protein Sci. 2025 Jan;34(1):e70016. doi: 10.1002/pro.70016. PubMed PMID: 39723820; PubMed Central PMCID: PMC11670308.

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Doron-Mandel E, Bokor BJ, Ma Y, Street LA, Tang LC, Abdou AA, Shah NH, Rosenberger G, Jovanovic M. A Multiplexed SEC-MS Approach to Systematically Study the Interplay Between Protein Assembly-States and Phosphorylation Events. bioRxiv. 2024 Aug 1;. doi: 10.1101/2023.01.12.523793. PubMed PMID: 36711903; PubMed Central PMCID: PMC9882152.

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Lamartina C, Chartier C, Hirano J, Shah N, Rovis T. Crafting Unnatural Peptide Macrocycles via Rh(III)-Catalyzed Carboamidation. Journal of the American Chemical Society. 2024 July; 146(30):20868-20877. doi: 10.1021/jacs.4c05248.

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van Vlimmeren AE, Voleti R, Chartier CA, Jiang Z, Karandur D, Humphries PA, Lo WL, Shah NH. The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain. Proc Natl Acad Sci U S A. 2024 Jul 23;121(30):e2407159121. doi: 10.1073/pnas.2407159121. Epub 2024 Jul 16. PubMed PMID: 39012820; PubMed Central PMCID: PMC11287265.

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Jiang Z, van Vlimmeren A, Karandur D, Semmelman A, Shah N. Deep mutational scanning of a multi-domain signaling protein reveals mechanisms of regulation and pathogenicity. [Preprint]. 2024 May. doi: 10.1101/2024.05.13.593907.

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van Vlimmeren AE, Voleti R, Chartier CA, Jiang Z, Karandur D, Humphries PA, Lo WL, Shah NH. The pathogenic T42A mutation in SHP2 rewires the interaction specificity of its N-terminal regulatory domain. bioRxiv. 2024 Apr 9;. doi: 10.1101/2023.07.10.548257. PubMed PMID: 37502916; PubMed Central PMCID: PMC10369915.

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Cabanero DC, Kariofillis SK, Johns AC, Kim J, Ni J, Park S, Parker DL Jr, Ramil CP, Roy X, Shah NH, Rovis T. Photocatalytic Activation of Aryl(trifluoromethyl) Diazos to Carbenes for High-Resolution Protein Labeling with Red Light. J Am Chem Soc. 2024 Jan 17;146(2):1337-1345. doi: 10.1021/jacs.3c09545. Epub 2024 Jan 2. PubMed PMID: 38165744; NIHMSID:NIHMS1971853.

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Tsai YL, Arias-Badia M, Kadlecek TA, Lwin YM, Srinath A, Shah NH, Wang ZE, Barber D, Kuriyan J, Fong L, Weiss A. TCR signaling promotes formation of an STS1-Cbl-b complex with pH-sensitive phosphatase activity that suppresses T cell function in acidic environments. Immunity. 2023 Dec 12;56(12):2682-2698.e9. doi: 10.1016/j.immuni.2023.11.010. PubMed PMID: 38091950; PubMed Central PMCID: PMC10785950.

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Hong SH, Xi SY, Johns AC, Tang LC, Li A, Hum MN, Chartier CA, Jovanovic M, Shah NH. Mapping the Chemical Space of Active-Site Targeted Covalent Ligands for Protein Tyrosine Phosphatases. Chembiochem. 2023 May 16;24(10):e202200706. doi: 10.1002/cbic.202200706. Epub 2023 Apr 26. PubMed PMID: 36893077; PubMed Central PMCID: PMC10192133.

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Li A, Voleti R, Lee M, Gagoski D, Shah NH. High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display. Elife. 2023 Mar 16;12. doi: 10.7554/eLife.82345. PubMed PMID: 36927728; PubMed Central PMCID: PMC10065799.

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Li A, Voleti R, Lee M, Gagoski D, Shah N. High-throughput profiling of sequence recognition by tyrosine kinases and SH2 domains using bacterial peptide display. eLife. 2023 March; 12:-. doi: 10.7554/eLife.82345.

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Lamartina C, Chartier C, Lee S, Shah N, Rovis T. Modular Synthesis of Unnatural Peptides via Rh(III)-Catalyzed Diastereoselective Three-Component Carboamidation Reaction. Journal of the American Chemical Society. 2022 December; 145(2):1129-1135. doi: 10.1021/jacs.2c10793.

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Hobbs HT, Shah NH, Shoemaker SR, Amacher JF, Marqusee S, Kuriyan J. Saturation mutagenesis of a predicted ancestral Syk-family kinase. Protein Sci. 2022 Oct;31(10):e4411. doi: 10.1002/pro.4411. PubMed PMID: 36173161; PubMed Central PMCID: PMC9601881.

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Rube HT, Rastogi C, Feng S, Kribelbauer JF, Li A, Becerra B, Melo LAN, Do BV, Li X, Adam HH, Shah NH, Mann RS, Bussemaker HJ. Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning. Nat Biotechnol. 2022 Oct;40(10):1520-1527. doi: 10.1038/s41587-022-01307-0. Epub 2022 May 23. PubMed PMID: 35606422; PubMed Central PMCID: PMC9546773.

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Hidalgo F, Nocka L, Shah N, Gorday K, Latorraca N, Bandaru P, Templeton S, Lee D, Karandur D, Pelton J, Marqusee S, Wemmer D, Kuriyan J. A saturation-mutagenesis analysis of the interplay between stability and activation in Ras. eLife. 2022 March; 11:-. doi: 10.7554/eLife.76595.

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Hidalgo F, Nocka L, Shah N, Gorday K, Latorraca N, Bandaru P, Templeton S, Lee D, Karandur D, Pelton J, Marqusee S, Wemmer D, Kuriyan J. A Saturation-Mutagenesis Analysis of the Interplay Between Stability and Activation in Ras. [Preprint]. 2022 January. doi: 10.1101/2022.01.06.475190.

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Hobbs H, Shah N, Badroos J, Gee C, Marqusee S, Kuriyan J. Differences in the dynamics of the <scp>tandem‐SH2</scp> modules of the Syk and <scp>ZAP</scp> ‐70 tyrosine kinases. Protein Science. 2021 October; 30(12):2373-2384. doi: 10.1002/pro.4199.

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Hobbs H, Shah N, Badroos J, Gee C, Marqusee S, Kuriyan J. Differences in the dynamics of the tandem-SH2 modules of the Syk and ZAP-70 tyrosine kinases. [Preprint]. 2021 July. doi: 10.1101/2021.07.20.453126.

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Tomas Rube H, Rastogi C, Feng S, Kribelbauer J, Li A, Becerra B, Melo L, Do B, Li X, Adam H, Shah N, Mann R, Bussemaker H. Probing molecular specificity with deep sequencing and biophysically interpretable machine learning. [Preprint]. 2021 July. doi: 10.1101/2021.06.30.450414.

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Shah NH, Stevens AJ. Identification, Characterization, and Optimization of Split Inteins. Methods Mol Biol. 2020;2133:31-54. doi: 10.1007/978-1-0716-0434-2_3. PubMed PMID: 32144662.

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Shah N, Stevens A. Identification, Characterization, and Optimization of Split Inteins. In: Methods in Molecular Biology [Internet] New York, NY: Springer US; 2020. Chapter Chapter 3; 31-54p. Available from: http://link.springer.com/10.1007/978-1-0716-0434-2_3.

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Lo WL, Shah NH, Rubin SA, Zhang W, Horkova V, Fallahee IR, Stepanek O, Zon LI, Kuriyan J, Weiss A. Slow phosphorylation of a tyrosine residue in LAT optimizes T cell ligand discrimination. Nat Immunol. 2019 Nov;20(11):1481-1493. doi: 10.1038/s41590-019-0502-2. Epub 2019 Oct 14. PubMed PMID: 31611699; PubMed Central PMCID: PMC6858552.

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Hong SH, Shah NH. Learning from ancestors. Elife. 2019 Aug 13;8. doi: 10.7554/eLife.49976. PubMed PMID: 31407665; PubMed Central PMCID: PMC6692129.

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McSpadden E, Xia Z, Chi C, Susa A, Shah N, Gee C, Williams E, Kuriyan J. Variation in assembly stoichiometry in non‐metazoan homologs of the hub domain of Ca <sup>2+</sup> /calmodulin‐dependent protein kinase II. Protein Science. 2019 April; 28(6):1071-1082. doi: 10.1002/pro.3614.

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McSpadden E, Xia Z, Chi C, Susa A, Shah N, Gee C, Williams E, Kuriyan J. Variation in assembly stoichiometry in non-metazoan homologs of the hub domain of Ca2+/Calmodulin-dependent protein kinase II. [Preprint]. 2019 January. doi: 10.1101/536094.

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Shah NH, Kuriyan J. Understanding molecular mechanisms in cell signaling through natural and artificial sequence variation. Nat Struct Mol Biol. 2019 Jan;26(1):25-34. doi: 10.1038/s41594-018-0175-9. Epub 2018 Dec 31. Review. PubMed PMID: 30598552; PubMed Central PMCID: PMC6463301.

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Shah NH, Amacher JF, Nocka LM, Kuriyan J. The Src module: an ancient scaffold in the evolution of cytoplasmic tyrosine kinases. Crit Rev Biochem Mol Biol. 2018 Oct;53(5):535-563. doi: 10.1080/10409238.2018.1495173. Epub 2018 Sep 5. Review. PubMed PMID: 30183386; PubMed Central PMCID: PMC6328253.

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Cantor AJ, Shah NH, Kuriyan J. Deep mutational analysis reveals functional trade-offs in the sequences of EGFR autophosphorylation sites. Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):E7303-E7312. doi: 10.1073/pnas.1803598115. Epub 2018 Jul 16. PubMed PMID: 30012625; PubMed Central PMCID: PMC6077704.

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Lo WL, Shah NH, Ahsan N, Horkova V, Stepanek O, Salomon AR, Kuriyan J, Weiss A. Lck promotes Zap70-dependent LAT phosphorylation by bridging Zap70 to LAT. Nat Immunol. 2018 Jul;19(7):733-741. doi: 10.1038/s41590-018-0131-1. Epub 2018 Jun 18. PubMed PMID: 29915297; PubMed Central PMCID: PMC6202249.

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Au-Yeung B, Shah N, Shen L, Weiss A. ZAP-70 in Signaling, Biology, and Disease. Annual Review of Immunology. 2018 April; 36(1):127-156. doi: 10.1146/annurev-immunol-042617-053335.