Publications

Tools to dissect lipid droplet regulation, players, and mechanisms

2025 – ACS Chemical Biology (invited perspective) - in press

Jinmin Liu# and Yimon Aye

NCBP1 Electrophilic-Stress Signaling in the Nucleus Promotes Alternatively-Spliced S6K1 that Dominantly Inhibits Global Translation

2025 – In revision (original research) 

Dalu Chang#, et al., and Yimon Aye

Metaphiles: A New Concept that Illuminates Structure-Function Basis of Electrophile Sensing & Signaling

2025 – In revision (original research)

Chloe Rogg#, Kuan-Ting Huang#, et al., and Yimon Aye

Atavistic Electrophile Sensing that Confers Animal Fitness Advantage through Selective Amino-Acid Detoxification

2025 – In revision (original research)

Organ-specific electrophile responsivity mapping in live C. elegans

December 2024 – Cell (original research)  -- see highlight 

Jinmin Liu#, Amogh Kulkarni, Yong-Qi Gao, Daniel A. Urul, Romain Hamelin, Marcus J. C. Long, and Yimon Aye

What is Chemical Biology?

September 2024 – Cell Chemical Biology – Invited opinion piece

Contributing authors as arranged by the journal editors

Let’s Get Biophysical – How to Get your Favorite Protein’s Digits

October 2024 – Bioorganic & Medicinal Chemistry – Accepted (perspective) – invited contribution

Marcus J. C. Long and Yimon Aye

Precision Immuno-Chemical Biology: toward Decoding Spatiotemporal Signaling Activities of Reactive Immunometabolites

September 2024 – Communications Chemistry – Perspective – invited contribution

Kuan-Ting Huang# and Yimon Aye

Horner–Wadsworth–Emmons olefination for bioconjugation

June 2024 – Nature Synthesis – News & Views – Invited contribution

Yimon Aye

Formaldehyde Regulates One-Carbon Metabolism and Epigenetics

March 2024 – Trends in Genetics – Spotlight – Invited contribution

Marcus J. C. Long# and Yimon Aye

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

February 2024 – ChemBioChem – Perspective– Invited contribution to EFMC Collections

Tag, you’re it! G-ICAT Identifies p-120 Cysteine Glutathionylation Triggering E-Cadherin Destabilization

December 2023 – Cell Chemical Biology – Preview – Invited contribution

Kevin T. Fridianto# and Yimon Aye

Keap It in the Family: How to Fish out New Paradigms in Keap1-Mediated Cell Signaling

November 2023 – Helvetica (Wiley) – Perspective – Invited contribution to Special Issue in honor of Professor Scott E. Denmark

Marcus J. C. Long#, Kuan-Ting Huang, and Yimon Aye

Z-REX: Shepherding Reactive Electrophiles to Specific Proteins Expressed either Tissue-Specifically or Ubiquitously, and Recording the Resultant Functional Electrophile-Induced Redox Responses in Larval Fish

April 2023 – Nature Protocols – Selected as “This week’s Featured Protocol” by the journal

Kuan-Ting Huang#, Jesse R. Poganik#, Saba Parvez, Sruthi Raja, Brian Miller, Marcus J. C. Long, Joseph R. Fetcho, and Yimon Aye

Monitoring On-Target Signaling Responses in Larval Zebrafish – Z-REX Unmasks Precise Mechanisms of Electrophilic Drugs and Metabolites

March 2023 – JoVE – Invited contribution

Kuan-Ting Huang#, Phillippe Ly#, Jesse R. Poganik, Saba Parvez, Marcus J. C. Long, Yimon Aye

Structural Insights into Electrophiles and Electrophilic Metabolites Sensing and Signaling: The Missing Information

February 2023 – Helvetica (Wiley) – Perspective – Invited contribution for the special issue: Helvetica & Swiss Women in Chemistry

Chloé Rogg# and Yimon Aye

Finding a vocation for validation: Taking proteomics beyond association and location

December 2022 – RSC Chemical Biology – Perspective – Invited contribution: electrophile signaling program

Marcus J. C. Long#, Jinmin Liu, and Yimon Aye

Still no Rest for the Reductases: RNR Structure & Function – an update

November 2022 – Springer Book Series – Subcellular Biochemistry: Macromolecular Protein Complexes IV – Invited contribution

Marcus J. C. Long#, Phillippe Ly, and Yimon Aye

Z-REX uncovers a bifurcation in function of Keap1 paralogs

October 2022 – eLife – Original research

Alexandra Van-Hall Beauvais#, Jesse R. Poganik#, Kuan-Ting Huang#, Saba Parvez, Yi Zhao, Hong-Yu Lin, Xuyu Liu, Marcus J. C. Long*, and Yimon Aye*

Go to the Board: A Journey through the Life of Professor David A. Evans

July 2022 – ACS Chemical Biology – A tribute to Professor Dave Evans

Yimon Aye, Kevin R. Campos, and David W. C. MacMillan

Hiding in Plain Sight: The Issue of Hidden Variables

June 2022 – ACS Chemical Biology – Perspective

Marcus J. C. Long#, Mahdi Assari, and Yimon Aye

Bringing Functional Context to Emerging Proximity-mapping Proteomics Tools

June 2022 – Chimia – Invited column

Yimon Aye

Keap 1: The new Janus word on the block

April 2022 – Bioorganic & Medicinal Chemistry Letters – Perspective – Invited contribution

Marcus J. C. Long and Yimon Aye

Hitting the Bullseye: Endogenous Electrophiles Show Remarkable Nuance in Signaling Regulation

April 2022 – ACS Chemical Research in Toxicology –  Perspective – Invited contribution

Marcus J. C. Long#, Pierre A. Miranda H.#, and Yimon Aye

Function-guided proximity mapping unveils electrophilic-metabolite sensing by proteins not present in their canonical locale

January 2022 – PNAS – Original research

Wdr1 and cofilin are necessary mediators of immune-cell-specific apoptosis triggered by Tecfidera

November 2021 – Nature Communications – Original research

Jesse R. Poganik#, Kuan-Ting Huang, Saba Parvez, Yi Zhao, Sruthi Raja, Marcus J. C. Long*, and Yimon Aye*

A primer on harnessing non-enzymatic post-translational modifications for drug design

September 2021 – RSC Medicinal Chemistry – Review – Invited contribution

Marcus J. C. Long#, Phillippe Ly, and Yimon Aye*

The not-so-identical twins: (Dis)similarities between reactive electrophile and oxidant sensing & signaling

August 2021 – RSC Chemical Society Reviews – Review – Invited contribution

Marcus J. C. Long#, Kuan-Ting (Tim) Huang, and Yimon Aye*

Science’s response to CoVID-19

April 2021 – ChemMedChem – Review – Invited contribution as part of the 2020 EFMC award

Marcus J. C. Long#, Amogh Kulkarni and Yimon Aye*

Can Precision Electrophile Signaling Make a Meaningful and Lasting Impression in Drug Design?

April 2021 – ChemBioChem – Viewpoint – Invited contribution

Dalu Chang#, et al., and Yimon Aye

Precision Immuno-Chemical Biology: toward Decoding Spatiotemporal Signaling Activities of Reactive Immunometabolites

September 2024 – Communications Chemistry – Original research

Kuan-Ting Huang# and Yimon Aye

Horner–Wadsworth–Emmons olefination for bioconjugation

June 2024 – Nature Synthesis – News & Views – Invited contribution

Yimon Aye

Formaldehyde Regulates One-Carbon Metabolism and Epigenetics

March 2024 – Trends in Genetics – Spotlight – Invited contribution

Marcus J. C. Long# and Yimon Aye

Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

February 2024 – ChemBioChem – Perspective– Invited contribution to EFMC Collections

An oculus to profile and probe target engagement in vivo: How T-REX was born and its evolution into G-REX

Nov 2020 – Accounts of Chemical Research – Accounts – Invited contribution – Selected for Cover Art of Feb 2021 issue

Marcus J. C. Long#, Chloe Rogg, and Yimon Aye*

Where Electrophile Signaling and Covalent Ligand-Target Mining Converge

September 2020 – Chimia – News – Contribution to Voices of Chemical Biology

Yimon Aye

Voices of Chemical Biology

May 2020 – Nature Chemical Biology – Feature – Invited partial contribution

Yimon Aye

Precision targeting of pten-null triple-negative breast tumors guided by electrophilic metabolite sensing

May 2020 – ACS Central Science – Original research

Xuyu Liu#, Marcus J. C. Long, Benjamin Hopkins, Chaosheng Luo, Lingxi Wang, and Yimon Aye*

Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities

May 2020 – RSC Chemical Biology – Perspective

Marcus J. C. Long#, Yi Zhao, and Yimon Aye*

Empowering global chemical biology at the dawn of the new decade

April 2020 – ACS Chemical Biology – Perspective – Contribution to NCCR Chemical Biology (UNIGE/EPFL)

Sascha Hoogendoorn* and Yimon Aye*

The mRNA-binding protein HuR is a kinetically-privileged electrophile sensor

April 2020 – Helvetica Chimica Acta – Orginial research – Invited contribution to special issue dedicated to Professor Michael Graetzel

Jesse R. Poganik#, Alexandra K. Van Hall-Beauvais#, Marcus J. C. Long, Michael T. Disare, Yi Zhao, and Yimon Aye*

Electrophile signaling and emerging immuno- and neuro-modulatory electrophilic pharmaceuticals

February 2020 – Frontiers Neuroscience – Review – Invited contribution to special issue: ‘Molecular mechanisms of thiol-based redox homeostasis and signaling in the brain’

Marcus J. C. Long# and Yimon Aye

Clofarabine commandeers the RNR-α-ZRANB3 nuclear signaling axis

January 2020 – Cell Chemical Biology – Original research

Post-transcriptional regulation of Nrf2-mRNA by the mRNA-binding proteins HuR and AUF1

September 2019 – FASEB Journal – Original research

Jesse R. Poganik#, Marcus J. C. Long, Michael T. Disare, Xuyu Liu, Sung-Hee Chang, Timothy Hla, and Yimon Aye*

The more the merrier: How homo-oligomerization alters the interactome and function of ribonucleotide reductase

September 2019 – Current Opinion in Chemical Biology – Review – Invited contribution

Marcus J. C. Long#, Alexandra Van Hall-Beauvais, and Yimon Aye*

Getting the right grip? How understanding electrophile selectivity profiles could illuminate our understanding of redox signaling

September 2019 – Antioxidants & Redox Signaling – Review – Invited contribution

Marcus J. C. Long#, Lingxi Wang, and Yimon Aye*

Interrogating precision electrophile signaling

February 2019 – Trends in Biochemical Sciences – Technology of the month

Jesse R. Poganik#, Marcus J. C. Long, and Yimon Aye*

Genie in a bottle: Controlled release help tame natural polypharmacology

February 2019 – Current Opinion in Chemical Biology – Review – Chemical Genetics opinion piece

Xuyu Liu#, Marcus J. C. Long#, and Yimon Aye*

REX technologies for profiling and decoding the electrophile signaling axes mediated by Rosetta Stone proteins

February 2019 – Methods in Enzymology – Review – Synthetic Biology special issue

Marcus J. C. Long#, Daniel A. Urul, and Yimon Aye*

Modular total synthesis and cell-based anticancer activity evaluation of ouabagenin and other cardiotonic steroids with varying degrees of oxygenation

February 2019 – Journal of the American Chemical Society – Original research

Hem Raj Khatri#, Bijay Bhattarai, Will Kaplan, Zhongzheng Li, Marcus John Curtis Long*, Yimon Aye*, and Pavel Nagorny*

Breaking the fourth wall: Modulating quaternary associations for protein regulation and drug discovery

February 2019 – ChemBioChem – Review – Invited contribution to ChemBioTalents special issue

Marcus J. C. Long#, Dziyana Hnedzko§, Bo Kyoung Kim§, and Yimon Aye*

Chemical biology gateways to mapping location, association, and pathway responsivity

February 2019 – Frontiers in Chemistry – Review – Nominated contribution to the Rising Stars in Chemistry Frontiers Special Issue

Weighing up the selenocysteome uncovers new sec-rets

October 2018 – Cell Chemical Biology – Preview

Jesse R. Poganik#, and Yimon Aye*

Proteomics and Beyond: Cell decision making shaped by reactive electrophiles

September 2018 – Trends in Biochemical Sciences – Review

Xuyu Liu#, Marcus J. C. Long#, and Yimon Aye*

Nuclear RNR-α Antagonizes Cell Proliferation by Directly Inhibiting ZRANB3

August 2018 – Nature Chemical Biology – Original research

Yuan Fu#, Marcus J. C. Long#, Somsinee Wisitpitthaya, Huma Inayat, Timothy M. Pierpont, Islam M. Elsaid, Jordana C. Bloom, Joaquin Ortega, Robert S. Weiss, and Yimon Aye*

Redox Signaling by Reactive Electrophiles and Oxidants

August 2018 – Chemical Reviews – Review

Saba Parvez#, Marcus J. C. Long#, Jesse R. Poganik, and Yimon Aye*

Cardiovascular small heat shock protein HSPB7 is a kinetically-privileged reactive electrophilic species (RES) sensor

February 2018 – ACS Chemical Biology – Original Research – Invited contribution to the 2018 “Biosensors” Special Issue of ACS Chemical Biology

Sanjna L. Surya#, Marcus J. C. Long#, Daniel A. Urul, Yi Zhao, Emily J. Mercer, Islam M. Elsaid, Todd Evans, and Yimon Aye*

Single-protein-specific redox targeting in live mammalian cells and C. elegans

February 2018 – Current Protocols in Chemical Biology – Protocol

Alexandra Van Hall-Beauvais#, Yi Zhao, Daniel A. Urul, Marcus J. C. Long, and Yimon Aye*

Ube2V2 is a Rosetta Stone bridging redox and ubiquitin codes, coordinating DNA damage responses

February 2018 – ACS Central Science – Original Research – Highlighted in Cornell Chronicle

Yi Zhao#, Marcus J. C. Long, Yiran Wang, Sheng Zhang, and Yimon Aye*

Getting the message? Native reactive electrophiles pass two out of three thresholds to be bona fide signaling mediators

February 2018 – BioEssays  – Problems & Paradigms

Jesse R. Poganik#, Marcus J. C. Long#, and Yimon Aye*

Precision electrophile tagging in C. elegans

September 2017 – Biochemistry – Original research – Invited contribution to “Future of Biochemistry” special issue of ACS Biochemistry – Selected as an “ACS Editors’ Choice” communication

Marcus J. C. Long#, Daniel A. Urul#, Shivansh Chawla#, Hong-Yu Lin+, Yi Zhao+, Joseph A. Haegele, Yiran Wang, and Yimon Aye*

β-TrCP1 is a vacillatory regulator of Wnt signaling

July 2017 – Cell Chemical Biology – Original research – Highlighted in Cornell Chronicle: Group discovers avenue for precision cancer treatment

Marcus J. C. Long#, Hong-Yu Lin#, Saba Parvez, Yi Zhao, Jesse R. Poganik, Paul Huang, and Yimon Aye*

Quo vadis: The boundless trajectories of chemical biology

May 2017 – Biochemistry – Correspondence – Symposium report contribution

Jeremy M. Baskin*, and Yimon Aye*

Privileged electrophile sensors: a resource for covalent drug development

May 2017 – Cell Chemical Biology – Perspective

Marcus J. C. Long#, and Yimon Aye*

Akt3 is a privileged first responder in isozyme-specific electrophile response

March 2017 – Nature Chemical Biology – Original research – Highlighted in Nature Chemical Biology “News & Views”, Highlighted in Cornell Chronicle: Group uses its own ‘toolset’ to probe chemical responses

Dalu Chang#, et al., and Yimon Aye

Subcellular Redox Targeting: Bridging In Vitro and In Vivo Chemical Biology

January 2017 – ACS Chemical Biology – Review

Marcus J. C. Long#, Jesse R. Poganik§, Souradyuti Ghosh§, and Yimon Aye*

T-REX on-demand redox targeting in live cells

December 2016 – Nature Protocols – Protocol

Saba Parvez#, Marcus J. C. Long#,  Hong-Yu Lin†, Yi Zhao†, Joseph A. Haegele, Vanha N. Pham, Dustin K. Lee, and Yimon Aye*

The Die is Cast: Precision electrophilic modifications contribute to cellular decision making

September 2016 – ACS Chem Res Toxicol – Perspective – Contributed as part of 2016 ACS CRT young investigator award to Aye Lab, selected as an “ACS Editors’ Choice” & Journal Cover Art

Marcus J. C. Long#, and Yimon Aye*

Cladribine and fludarabine nucleotides induce distinct hexamers defining a common mode of reversible RNR inhibition

May 2016 – ACS Chemical Biology – Original research

Somsinee Wisitpitthaya#, Yi Zhao, Marcus J. C. Long, Minxing Li, Elaine A. Fletcher, William A. Blessing, Robert S. Weiss, and Yimon Aye*

On-demand targeting: Investigating biology with proximity-directed chemistry

February 2016 – Journal of the American Chemical Society – Perspective – Selected as a Spotlights article on recent JACS publications

Marcus J. C. Long#,  Jesse R. Poganik, and Yimon Aye*

A generalizable platform for interrogating target- and signal-specific consequences of electrophilic modifications in redox-dependent cell signaling

April 2015 – Journal of the American Chemical Society – Original research

Hong-Yu Lin#, Joseph A. Haegele, Michael T. Disare, Qishan Lin, and Yimon Aye*

Ribonucleotide reductase and cancer: biological mechanisms and targeted therapies

April 2015 – Oncogene – Review

Yimon Aye*, Minxing Li#, Marcus J. C. Long and Robert S. Weiss*

Substoichiometric hydroxynonenylation of a single protein recapitulates whole-cell-stimulated antioxidant response

December 2014 – Journal of the American Chemical Society – Original research

Saba Parvez#, Yuan Fu#, Jiayang Li, Marcus J. C. Long, Hong-Yu Lin, Dustin K. Lee, Gene S. Hu, and Yimon Aye*

A fluorimetric readout reporting the kinetics of nucleotide-induced human ribonucleotide reductase oligomerization

August 2014 – ChemBioChem – Original research

Yuan Fu, Hong-Yu Lin#, Somsinee (Sine) Wisitpitthaya#, William A. Blessing, and Yimon Aye*

Uncoupling of allosteric and oligomeric regulation in a functional hybrid enzyme constructed from Escherichia coli and human ribonucleotide reductase

September 2013 – Biochemistry – Original research

Yuan Fu#, Marcus J. C. Long, Mike Rigney, Saba Parvez, William A. Blessing, and Yimon Aye*

Temporally controlled targeting of 4-hydroxynonenal to specific proteins in living cells

September 2013 – Journal of the American Chemical Society – Original research

Xinqiang Fang#, Yuan Fu#, Marcus J. C. Long, Joseph A. Haegele, Eva J. Ge, Saba Parvez, and Yimon Aye*

From postdoctoral research (MIT, USA): 08/2009 – 06/2012

3.3-Å resolution cryo-EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound

Feb 2018 – eLife – Original research

Edward J. Brignole#, Kuang-Lei Tsai, Johnathan Chittuluru, Haoran Li, Yimon Aye, Pawel A Penczek, JoAnne Stubbe*, Catherine L. Drennan*, Francisco Asturias*

Mechanistic Studies of Semicarbazone Triapine Targeting Ribonucleotide Reductase in Vitro and in Mammalian Cells: Tyrosyl Radical Quenching Not Involving Reactive Oxygen Species

August 2012 – Journal of Biological Chemistry – Original research

Yimon Aye#, Marcus J. C. Long and JoAnne Stubbe*

Clofarabine Targets the Large Subunit (α) of Human Ribonucleotide Reductase in Live Cells by Assembly into Persistent Hexamers

July 2012 – Chemistry and Biology – Original research

Yimon Aye#, Edward J. Brignole, Marcus J. C. Long, Johnathan Chitturulu, Catherine L. Drennan, Francisco J. Asturias, and JoAnne Stubbe*

Clofarabine 5´-Di and –Triphosphates Inhibit Human Ribonucleotide Reductase by Altering the Quaternary Structure of its Large Subunit

May 2011 – PNAS – Original research

Yimon Aye# and JoAnne Stubbe*

From PhD thesis research (Harvard University, USA): 07/2004 – 05/2009

Vinyl-, Propargyl- and Allenylsilicon Reagents in Asymmetric Synthesis: Relatively Untapped Resource of Environmentally-Benign Reagents

May 2009 – Chemistry (wiley) – Review

Marcus J. Curtis Long# and Yimon Aye*

Structural Report for Sc[(R,R)-norephedrine-pybox](OTf)3 Dimeric Complex

November 2007 – Journal of Chemical Crystallography – Original research

Richard J. Staples* and Yimon Aye

Aluminum-catalyzed Enantio- and Diastereoselective Carbonyl Addition of Propargylsilanes. A New Approach to Enantioenriched Vinyl Epoxides

July 2007 – Journal of the American Chemical Society – Original research

David A. Evans* and Yimon Aye

Enantioselective Scandium-catalyzed Vinylsilane Additions: A New Approach to the Synthesis of β,γ-Unsaturated α-Amino Acid Derivatives

August 2006 – Journal of the American Chemical Society – Original research

David A. Evans* and Yimon Aye

Asymmetric, Anti–selective Scandium-catalyzed Sakurai Additions to Glyoxamide. Applications to the Syntheses of N-Boc- D-Alloisoleucine and D-Isoleucine

May 2006 – Organic Letters – Original research

David A. Evans*, Yimon Aye and Jimmy Wu

From undergraduate master’s thesis research (Oxford University, UK): 10/2003 – 05/2004

Parallel kinetic resolution of tert-butyl (RS)-3-oxy-substituted cyclopent-1-ene-carboxylates for the asymmetric synthesis of 3-oxy-substituted cispentacin and transpentacin derivatives

April 2008 – Organic and Biomolecular Chemistry – Original research

Yimon Aye#, Stephen G. Davies,* A. Christopher Garner, Paul M. Roberts, Andrew D. Smith and James E. Thomson

From undergraduate summer research (MIT, USA):

Copper-catalyzed Asymmetric Conjugate Reduction as a Route to Novel β-Azaheterocyclic Acid Derivatives

April 2004 – PNAS – Original research

Matthew P. Rainka#, Yimon Aye and Stephen L. Buchwald*