The Shuken LabHKUST

Publications

Papers

Synced from PubMed and ORCID using Shuken SR[Author] and 0000-0002-2782-2165.

2026

Multi-omic characterization of axolotl perilymph-cerebrospinal fluid reveals shifts in composition during limb regeneration

Noah Lopez, Bingsen Zhang, Steven R. Shuken, Yudong Zhou, Duygu Payzin-Dogru, Julia C. Paoli, Anthony E. Striker, S. Y. Celeste Wu, Tia S. Patel, Karly Chan, Sebastian Böhm, Hani D. Singer, Ashley R. Juarez, Ryan T. Kim, Laurel Shugart, Edward T Chouchani, Jessica L. Whited

Preprint, 2026 Aug 28

Next-generation multiplexed targeted proteomics quantifies post-translational modifications in disease and compound-protein interactions with high throughput

Shuken SR, Frere GA, Beard CR, McGann CD, Canterbury JD, Zuniga NR, Gassaway BM, Dawson SL, Ooi KH, Paulo JA, McNerney MW, Gygi SP, Yu Q

Nature communications. 2026; 17(1)

Altered Molecular Regulation of TUG Is a Central Feature of Insulin-Resistant Human Adipose Tissue

Strober JW, Ter Horst KW, Sung D, Jongejan A, Slusher AL, Gassaway BM, Tarabra E, Paulo JA, Shuken SR, Gygi SP, Santoro N, Caprio S, Serlie MJ, Bogan JS, Vatner DF

Diabetes. 2026; 75(2): 341-350

2025

Library-Free Multiplexed Targeted Proteomics Enables Quantitative Protein-Level Genotyping

Shuken SR, Gygi SP

bioRxiv : the preprint server for biology, 2025 Sep 16

Cell-surface proteomic profiling identifies CD72 as a regulator of microglial tiling

Chan TC, Rastogi M, Williams MX, Zhang S, Shi SM, Shuken SR, Bartling T, Wild K, Atkins M, Hahn O, Paulo JA, Jereb S, Shuster SA, Yoo Y, Napole A, Hernandez VG, Luo L, Buckwalter MS, Stevens B, Deverman BE, Kronenberg-Versteeg D, Gygi SP, Wyss-Coray T, Wernig M

bioRxiv : the preprint server for biology, 2025 Jun 5

2024

Disagreement on foundational principles of biological aging

Gladyshev VN, Anderson B, Barlit H, Barré B, Beck S, Behrouz B, Belsky DW, Chaix A, Chamoli M, Chen BH, Cheng K, Chuprin J, Churchill GA, Cipriano A, Colville A, Deelen J, Deigin Y, Edmonds KK, English BW, Fang R, Florea M, Gershteyn IM, Gill D, Goetz LH, Gorbunova V, Griffin PT, Horvath S, Borch Jensen M, Jin X, Jovanovska S, Kajderowicz KM, Kasahara T, Kerepesi C, Kulkarni S, Labunskyy VM, Levine ME, Libert S, Lu JY, Lu YR, Marioni RE, McCoy BM, Mitchell W, Moqri M, Nasirian F, Niimi P, Oh HS, Okundaye B, Parkhitko AA, Peshkin L, Petljak M, Poganik JR, Pridham G, Promislow DEL, Prusisz W, Quiniou M, Raj K, Richard D, Ricon JL, Rutledge J, Scheibye-Knudsen M, Schork NJ, Seluanov A, Shadpour M, Shindyapina AV, Shuken SR, Sivakumar S, Stoeger T, Sugiura A, Sutton NR, Suvorov A, Tarkhov AE, Teeling EC, Trapp A, Tyshkovskiy A, Unfried M, Ward-Caviness CK, Yim SH, Ying K, Yunes J, Zhang B, Zhavoronkov A

PNAS nexus. 2024; 3(12): pgae499

Inserting Pre-analytical Chromatographic Priming Runs Significantly Improves Targeted Pathway Proteomics with Sample Multiplexing

Shuken SR, Yu Q, Gygi SP

Journal of proteome research. 2024; 23(5): 1834-1843

2023

Deep Proteomic Compound Profiling with the Orbitrap Ascend Tribrid Mass Spectrometer Using Tandem Mass Tags and Real-Time Search

Shuken SR, McAlister GC, Barshop WD, Canterbury JD, Bergen D, Huang J, Huguet R, Paulo JA, Zabrouskov V, Gygi SP, Yu Q

Analytical chemistry. 2023; 95(41): 15180-15188

An Introduction to Mass Spectrometry-Based Proteomics

Shuken SR

Journal of proteome research. 2023; 22(7): 2151-2171

Costs and Benefits of Popular P-Value Correction Methods in Three Models of Quantitative Omic Experiments

Shuken SR, McNerney MW

Analytical chemistry. 2023; 95(5): 2732-2740

Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression

Yu Q, Liu X, Keller MP, Navarrete-Perea J, Zhang T, Fu S, Vaites LP, Shuken SR, Schmid E, Keele GR, Li J, Huttlin EL, Rashan EH, Simcox J, Churchill GA, Schweppe DK, Attie AD, Paulo JA, Gygi SP

Nature communications. 2023; 14(1): 555

2022

Limited Proteolysis-Mass Spectrometry Reveals Aging-Associated Changes in Cerebrospinal Fluid Protein Abundances and Structures

Shuken SR, Rutledge J, Iram T, Losada PM, Wilson EN, Andreasson KI, Leib RD, Wyss-Coray T

Nature aging. 2022; 2(5): 379-388

Young CSF restores oligodendrogenesis and memory in aged mice via Fgf17

Iram T, Kern F, Kaur A, Myneni S, Morningstar AR, Shin H, Garcia MA, Yerra L, Palovics R, Yang AC, Hahn O, Lu N, Shuken SR, Haney MS, Lehallier B, Iyer M, Luo J, Zetterberg H, Keller A, Zuchero JB, Wyss-Coray T

Nature. 2022; 605(7910): 509-515

2020

Halogenation-Dependent Effects of the Chlorosulfolipids of Ochromonas danica on Lipid Bilayers

Moss Iii FR, Cabrera GE, McKenna GM, Salerno GJ, Shuken SR, Landry ML, Weiss TM, Burns NZ, Boxer SG

ACS chemical biology. 2020; 15(11): 2986-2995

2019

CD22 blockade restores homeostatic microglial phagocytosis in ageing brains

Pluvinage JV, Haney MS, Smith BAH, Sun J, Iram T, Bonanno L, Li L, Lee DP, Morgens DW, Yang AC, Shuken SR, Gate D, Scott M, Khatri P, Luo J, Bertozzi CR, Bassik MC, Wyss-Coray T

Nature. 2019; 568(7751): 187-192

2018

Ladderane phospholipids form a densely packed membrane with normal hydrazine and anomalously low proton/hydroxide permeability

Moss FR 3rd, Shuken SR, Mercer JAM, Cohen CM, Weiss TM, Boxer SG, Burns NZ

Proceedings of the National Academy of Sciences of the United States of America. 2018; 115(37): 9098-9103

2016

Chemical Synthesis and Self-Assembly of a Ladderane Phospholipid

Mercer JA, Cohen CM, Shuken SR, Wagner AM, Smith MW, Moss FR 3rd, Smith MD, Vahala R, Gonzalez-Martinez A, Boxer SG, Burns NZ

Journal of the American Chemical Society. 2016; 138(49): 15845-15848