Publications

63 Publications since 2013

  • From the American Chemical Society Journals: Accounts of Chemical Research (2021); ACS Central Science (2018, 2020); Journal of the American Chemical Society [2013, 2015 (×2), 2016, 2019]; ACS Chemical Biology (2016, 2017, 2018, 2020, 2022 (x2); Chemical Reviews (2018); Biochemistry [2013, 2017 (×2)]; Chemical Research in Toxicology (2016, 2022)
  • From the Nature Publishing Group: Nature Chemical Biology (2017, 2018); Nature Protocols [2016, 2023]; Oncogene (2015); Nature Communications (2021); Springer Nature (2022)
  • From the Cell Press: Cell Chemical Biology [2017 (×2), 2018, 2019, 2023]; Trends in Biochemical Sciences [2018 (×2), 2019]; Current Opinion in Chemical Biology [2019 (x2)]; Methods in Enzymology (2019)
  • From the National Academy of Sciences: PNAS (2022)
  • From the eLife Sciences Publications Ltd.: eLife (2022)
  • From the Royal Society of Chemistry Journals: RSC Chemical Biology  (2020, 2022); Chemical Society Reviews (2021); RSC Medicinal Chemistry (2021)
  • From Wiley: ChemBioChem-European Journal of Chemical Biology (2014, 2019, 2021, 2024); Current Protocols in Chemical Biology (2018); BioEssays (2018); Helvetica chimica acta [2020, 2023 (x2)]; ChemMedChem (2021)
  • From the Tetrahedron publications: Biorganic & Medicinal Chemistry Letters (2022)
  • From Frontiers (Switzerland): Frontiers Chemistry (2019); Frontiers Neuroscience (2020)
  • From the Federation of American Societies for Experimental Biology (FASEB): FASEB Journal (2019)
  • From the Swiss Chemical Society: Chimia (2020, 2022)
  • From the Mary Ann Liebert Inc. publishers: Antioxidants & Redox Signaling (2019)

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

    2024In revision (original research)

    Chloe Rogg#, Kuan-Ting Huang#, et al., and Yimon Aye
  • Organ-Specific Responsivity Mapping Unmasks Partitioning between Localized Metabolite Production Governing Global Lipid Storage & Enzyme Inhibition

    2024In revision (original research)

    Jinmin Liu#, et al., and Yimon Aye
  • Climbing into their Skin to Understand Contextual Protein-Protein Associations and Localizations: Functional Investigations in Transgenic Live Model Organisms

    February 2024ChemBioChem (perspective) – invited contribution to EFMC Collections

Marcus J. C. Long# and Yimon Aye


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


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


Chloé Rogg# and Yimon Aye


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

(#first author, *corresponding author)


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*

(#co-first authors, *co-corresponding authors)



 

June 2022 Chimia (invited column)

Yimon Aye*


April 2022 Bioorganic & Medicinal Chemistry Letters (invited perspective)

Marcus J. C. Long and Yimon Aye*


 

April 2022 ACS Chemical Research in Toxicology (invited perspective)

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

(#first authors, *corresponding author)


January 2022PNAS – original research (electrophile signaling program)

Yi Zhao#, Pierre A. Miranda H., Dalu Chang, Romain Hamelin, Marcus J. C. Long*, and Yimon Aye*  (#first author, *co-corresponding authors)


November 2021 Nature Communications – original research (electrophile signaling program)

Jesse R. Poganik#, Kuan-Ting Huang, Saba Parvez, Yi Zhao, Sruthi Raja, Marcus J. C. Long*, and Yimon Aye*(#first author, *co-corresponding authors)


Sept 2021 RSC Medicinal Chemistry – invited review (electrophile signaling program)

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

(#first author, *co-corresponding author)


Aug 2021 RSC Chemical Society Reviews invited review (electrophile signaling program)

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

(#first author, *corresponding author)


April 2021 ChemMedChem

(contribution as part of the 2020 EFMC award)

Marcus J. C. Long# and Yimon Aye*

(#first author, *corresponding author)


April 2021 ChemBioChem

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


 
Selected for Cover Art of Feb 2021 issue:

Nov 2020 Accounts of Chemical Research

(electrophile signaling program: invited accounts)

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

(#first author, *corresponding author)


Sep 2020 – Chimia

Author: Yimon Aye


May 2020 – Nature Chemical Biology

Author: Yimon Aye


May 2020 ACS Central Science

(electrophile signaling program: original research)

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

(#first author, *corresponding author)


May 2020 RSC Chemical Biology

(electrophile signaling program: perspective)

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

(#first author, *corresponding author)


April 2020 – contribution to NCCR Chemical Biology (UNIGE/EPFL)

ACS Chemical Biology (symposium report)

Sascha Hoogendoorn* and Yimon Aye*

(*co-corresponding authors)


April 2020 – invited contribution to special issue dedicated to Professor Michael Graetzel

Helvetica Chimica Acta (Wiley)

(electrophile signaling program: original research)

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

(#co-first authors, *corresponding author)


February 2020– invited contribution to special issue:

‘Molecular mechanisms of thiol-based redox homeostasis and signaling in the brain’

Frontiers Neuroscience

(electrophile signaling program: review article)

Jesse R. Poganik#,, and Yimon Aye*

(#first author, *corresponding author)


January 2020– Cell Chemical Biology

(nucleotide signaling program: original research)

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

(#co-first authors, *corresponding author)


September 2019– FASEB Journal

(electrophile signaling program: original research)

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

(#first author, *corresponding author)


September 2019 – Current Opinion in Chemical Biology

(nucleotide signaling program: invited review)

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

(#first author, *corresponding author)


September 2019– Antioxidants & Redox Signaling

(electrophile signaling program: invited review)

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

(#first author, *corresponding author)


February 2019Trends in Biochemical Sciences (technology of the month)

(electrophile signaling program)

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

(#first author, *corresponding author)


February 2019 – Current Opinion in Chemical Biology (Chemical Genetics opinion piece)

(electrophile signaling program)

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

(#co-first authors, *corresponding author)


February 2019 – Methods in Enzymology (Techniques review for Synthetic Biology special issue)

(electrophile signaling program)

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

(#first author, *corresponding author)


February 2019 – Journal of the American Chemical Society (Collaboration with the Nargony Lab)

Just accepted


February 2019ChemBioChem (invited contribution to ChemBioTalents special issue)

(Review integrating both electrophile and nucleotide signaling programs)

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

(#first author, §joint second-author, *corresponding author)


February 2019nominated contribution to the Rising Stars in Chemistry Frontiers Special Issue (Perspective)

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

(#, co-first authors. *, corresponding author)


October 2018Cell Chemical Biology (Preview)

Jesse R. Poganik#, and Yimon Aye*

(#, first author *, corresponding author)


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

(#, co-first authors. *, corresponding author)

September 2018 – Trends in Biochemical Sciences (Review) (electrophile signaling program)


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*

(#, co-first authors. *, corresponding author)

August 2018 – Nature Chemical Biology (Original Research) (nucleotide signaling program)


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

(#, co-first authors. *, corresponding author)

August 2018 – Chemical Reviews (Review Article) (electrophile signaling program)


Sanjna L. Surya#, Marcus J. C. Long#, Daniel A. Urul, Yi Zhao, Emily J. Mercer, Islam M. Elsaid, Todd Evans, and Yimon Aye*  (#, co-first authors. *, corresponding author)

February 2018 – ACS Chemical Biology (Original Research) (electrophile signaling program) Invited contribution to the 2018 “Biosensors” Special Issue of ACS Chemical Biology


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

(#, first author. *, corresponding author)

DOI: 10.1002/cpch.43

February 2018 – Current Protocols in Chemical Biology (Wiley) (Protocols) (electrophile signaling program in cultured cells and C. elegans)


  • Yi Zhao#, Marcus J. C. Long, Yiran Wang, Sheng Zhang, and Yimon Aye* (#, first author. *, corresponding author)

Highlight in Cornell Chronicle

February 2018 – ACS Central Science (Original Research) (electrophile signaling program in cultured cells and in zebrafish)


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

(#, co-first authors. *, corresponding author)

February 2018 – BioEssays (Wiley) (Problems & Paradigms) (electrophile signaling program)


Selected as an “ACS Editors’ Choice” communication!
Click Here For LiveSlides Of The Paper

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

(#, co-first authors. +, co-second authors. *, corresponding author)

Invited contribution to “Future of Biochemistry” Special Issue of ACS Biochemistry (scheduled for January 2018)

September 2017 – Original Research Communication


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

(#, co-first authors. *, corresponding author)

 Highlighted in Cornell Chronicle: Group discovers avenue for precision cancer treatment

July 22 2017 – Cell Chemical Biology (Original research) (electrophile signaling program)


Jeremy M. Baskin*, and Yimon Aye*

(*, co-corresponding authors)

May 24 2017   Symposium report contribution


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

(#, first author. *, corresponding author)

May 24 2017 Cell Chemical Biology (Perspective) (electrophile signaling program in cells and fish)


2017 13(3):333-338

Marcus J. C. Long#, Saba Parvez#, Yi Zhao, Sanjna L. Surya, Yiran Wang, Sheng Zhang, and Yimon Aye*

(#, co-first authors. *, corresponding author)

Highlighted in Nature Chemical Biology “News & Views”    2017 13(3):244-245

Highlighted in Cornell Chronicle: Group uses its own ‘toolset’ to probe chemical responses

March 2017 – Nature Chemical Biology (Original Research) (electrophile signaling program in cultured cells and in zebrafish)


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

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

(#, first author. §, shared second-author. *, corresponding author)

January 2017 – ACS Chemical Biology (Review Article) DOI: 10.1021/acschembio.6b01148


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

(#, co-first authors. †, co-second authors. *, corresponding author)

Nature Protocols 201611 2328-2356

December 2016Nature Protocols (electrophile signaling program)


Selected as an “ACS Editors’ Choice” communication!

– peer-reviewed article contributed as part of 2016 ACS CRT young investigator award to Aye Lab

Marcus J. C. Long#, and Yimon Aye*   (#, first author. *, corresponding author)

September 2016 – ACS Chem Res Toxicol (Perspective)- (electrophile signaling program)

AlsoSelected for the Journal Cover Art !


ACS Chemical Biology (research article) 2016 11 2021-2032

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

(#, first author.*, corresponding author)

May 2016ACS Chem Bio (Original Research) (nucleotide signaling program)


Click Here For ACS LiveSlides on the journal website


“Chemical Biology On Demand and In High-Definition”

Journal of the American Chemical Society (Spotlights) 2016 138 4269-4269

Journal of the American Chemical Society (Perspective) 2016 138 3610-22

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

(#, first author. *, corresponding author)

Feb 2016 – J Am Chem Soc (Perspective) ACS OPEN ACCESS ARTICLE (electrophile signaling program)


Journal of the American Chemical Society (research article) 2015 137 6232-44

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

(#, first author. *, corresponding author)

Apr 2015J Am Chem Soc (Original Research) (electrophile signaling program)


Journal of the American Chemical Society (research communication) 2015 137 10-3

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

(#, co-first authors. *, corresponding author)

Jan 2015 – J Am Chem Soc (Original Research) (electrophile signaling program)


Oncogene(mini review2015  34 2011–2021 Yimon Aye*, Minxing Li#, Marcus J. C. Long and Robert S. Weiss* (#, first author. *, co-corresponding authors)

Apr 2015 – Oncogene Mini Review (nucleotide signaling program)


ChemBioChem (research article) 2014 15  2598-604

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

(#, co-2nd authors. *, corresponding author)

Aug 2014 – ChemBioChem (Original Research) (nucleotide signaling program)


Biochemistry (research article) 2013 52 7050-9

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

(#, first author. *, corresponding author)

Sept 2013 – Biochemistry (Original Research)(nucleotide signaling program)


Journal of the American Chemical Society (research communication) 2013 135 14496-9

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

(#, co-first authors. *, corresponding author)

Sept 2013 – J Am Chem Soc (Original Research) (electrophile signaling program)


PUBLICATIONS DURING TRAINING From postdoctoral research (MIT, USA): 08/2009 — 06/2012

Original research:

Clofarabine 5´-Di and –Triphosphates Inhibit Human Ribonucleotide Reductase by Altering the Quaternary Structure of its Large Subunit” Yimon Aye and JoAnne Stubbe*; Proceedings to the National Academy of Sciences USA (Direct Submission) 2011, 108, 9815.

Clofarabine Targets the Large Subunit (α) of Human Ribonucleotide Reductase in Live Cells by Assembly into Persistent Hexamers” Yimon Aye, Edward J. Brignole, Marcus J. C. Long, Johnathan Chitturulu, Catherine L. Drennan, Francisco J. Asturias, and JoAnne Stubbe*; Chemistry and Biology 2012, 19, 799.

Mechanistic Studies of Semicarbazone Triapine Targeting Ribonucleotide Reductase in Vitro and in Mammalian Cells: Tyrosyl Radical Quenching Not Involving Reactive Oxygen Species” Yimon Aye, Marcus J. C. Long and JoAnne Stubbe*; Journal of Biological Chemistry 2012, 287, 35768.

“3.3-Å resolution cryo-EM structure of human ribonucleotide reductase with substrate and allosteric regulators bound” Edward J. Brignole, Kuang-Lei Tsai, Johnathan Chittuluru, Haoran Li, Yimon Aye, Pawel A Penczek, JoAnne Stubbe*, Catherine L. Drennan*, Francisco Asturias*; eLife 2018;7:e31502 doi: 10.7554/eLife.31502

From PhD thesis research (Harvard University, USA):

07/2004 — 05/2009

Independent review article:

“Vinyl-, Propargyl- and Allenylsilicon Reagents in Asymmetric Synthesis: Relatively Untapped Resource of Environmentally-Benign Reagents” Marcus J. Curtis-¬Long and Yimon Aye*; Chemistry, A European Journal 2009, 15, 5402.

Original research:

“Structural Report for Sc[(R,R)-norephedrine-pybox](OTf)3 Dimeric Complex” Richard J. Staples* and Yimon Aye; Journal of Chemical Crystallography 2008, 38, 49.

“Aluminum-catalyzed Enantio- and Diastereoselective Carbonyl Addition of Propargylsilanes. A New Approach to Enantioenriched Vinyl Epoxides” David A. Evans* and Yimon Aye; Journal of the American Chemical Society 2007, 129, 9606.

“Enantioselective Scandium-catalyzed Vinylsilane Additions: A New Approach to the Synthesis of β,γ-Unsaturated α-Amino Acid Derivatives” David A. Evans* and Yimon Aye; Journal of the American Chemical Society 2006, 128, 11034.

“Asymmetric, Anti–selective Scandium-catalyzed Sakurai Additions to Glyoxamide. Applications to the Syntheses of N-Boc- D-Alloisoleucine and D-Isoleucine” David A. Evans*, Yimon Aye and Jimmy Wu; Organic Letters 2006, 8, 2071.

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” Yimon Aye, Stephen G. Davies,* A. Christopher Garner, Paul M. Roberts, Andrew D. Smith and James E. Thomson; Organic and Biomolecular Chemistry, 2018, 6, 2195.

From undergraduate summer research (MIT, USA):

Summer 2003

“Copper-catalyzed Asymmetric Conjugate Reduction as a Route to Novel β-Azaheterocyclic Acid Derivatives” Matthew P. Rainka, Yimon Aye and Stephen L. Buchwald*; Proceedings to the National Academy of Sciences USA, 2004, 101, 5821.