CV

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Experience

Senior Staff Engineer, Head of ML Engineering, Drug Discovery — SandboxAQ (2024–Present)

• Key contributor on 10+ small molecule and antibody programs with academic, biotech, and pharmaceutical collaborators.
• Designed, built, and maintained cloud-native cheminformatics, ML, antibody design, and workflow optimization platforms.
• Managed a team of 3 engineers and led cross-functional scientific teams of up to 10.

Principal Scientist, CADD — Bristol Myers Squibb (2021–2024)

• Contributed to small molecule and targeted protein degradation drug discovery projects. Drove hit ID with high hit rates (up to 30% in prospective virtual screens) and advanced a lead optimization project to IND-enabling study readiness.
• Led development of ML and cheminformatics infrastructure for activity prediction, ADMET modeling, Bayesian optimization, virtual screening, generative design, and more.
• Recognized with BMS “Leadership Award in Synthetic and Medicinal Chemistry” (2023).

Postdoctoral Researcher — Adams & Doyle Labs, Princeton University (2019–2021)

• Led development of Bayesian optimization and ML frameworks for chemical reaction optimization and modeling of reaction outcomes, resulting in 2 publications in Nature.

Education

• Ph.D. in Chemistry, Princeton University (2016–2019)
• M.A. in Chemistry, with distinction, Princeton University (2014–2016)
• B.S. in Chemistry, with highest honors, University of North Carolina Asheville (2010–2014)
• B.A. in Applied Mathematics, with highest honors, University of North Carolina Asheville (2010–2014)

Publications

Direct C(sp³)–H Cross Coupling Enabled by Catalytic Generation of Chlorine Radicals

Shields, Benjamin J.; Doyle, Abigail G. “Direct C(sp3)–H Cross Coupling Enabled by Catalytic Generation of Chlorine Radicals” J. Am. Chem. Soc., 2016, 138, 12719–12722.

Mild Redox-Neutral Formylation of Aryl Chlorides through the Photocatalytic Generation of Chlorine Radicals

Nielsen, Matthew K.^; Shields, Benjamin J.^; Liu, Junyi; Williams, M. J.; Zacuto, M. J.; Doyle, Abigail G. “Mild Redox-Neutral Formylation of Aryl Chlorides through the Photocatalytic Generation of Chlorine Radicals” Angew. Chem. Int. Ed. 2017, 56 7191–7194. ^Equal contributions.

Long-Lived Charge Transfer States of Nickel(II) Aryl Halide Complexes Facilitate Bimolecular Photoinduced Electron Transfer

Shields, Benjamin J.; Kudisch, Bryan; Scholes, Gregory, D.; Doyle, Abigail G. “Long-Lived Charge Transfer States of Nickel(II) Aryl Halide Complexes Facilitate Bimolecular Photoinduced Electron Transfer” J. Am. Chem. Soc., 2018, 140, 3035–3039.

³d-d Excited States of Ni(II) Complexes Relevant to Photoredox Catalysis, Spectroscopic Identification and Mechanistic Implications

Ting, Stephen I.; Garakyaraghi, Sofia; Taliaferro, Chelsea M.; Shields, Benjamin J.; Scholes, Gregory D.; Castellano, Felix N.; and Doyle, Abigail G. “3d-d Excited States of Ni(II) Complexes Relevant to Photoredox Catalysis, Spectroscopic Identification and Mechanistic Implications” J. Am. Chem. Soc., 2020, 142, 1859–1869.

Nickel/Photoredox-Catalyzed Methylation of (Hetero)aryl Chlorides Using Trimethyl Orthoformate as a Methyl Radical Source

Kariofillis, Stavros K.; Shields, Benjamin J.; Tekle-Smith, Makeda; Zacuto, Michael. J.; Doyle, Abigail G. “Nickel/Photoredox-Catalyzed Methylation of (Hetero)aryl Chlorides Using Trimethyl Orthoformate as a Methyl Radical Source” J. Am. Chem. Soc., 2020, 142, 7683–7689.

Regioselective Cross-Electrophile Coupling of Epoxides and (Hetero)aryl Iodides via Ni/Ti/Photoredox Catalysis

Parasram, Marvin; Shields, Benjamin J.; Ahmad, Omar; Knauber, Thomas; Doyle, Abigail G. “Regioselective Cross-Electrophile Coupling of Epoxides and (Hetero)aryl Iodides via Ni/Ti/Photoredox Catalysis” ACS Catalysis, 2020, 10, 5821–5827.

Bayesian reaction optimization as a tool for chemical synthesis

Shields, Benjamin J.; Stevens, Jason; Li, Jun; Parasram, Marvin; Damani, Farhan; Martinez Alvarado, Jesus; Janey, Jacob; Adams, Ryan; Doyle, Abigail G. "Bayesian Reaction Optimization as A Tool for Chemical Synthesis", Nature, 2021, 590, 89–96.

Predicting Reaction Yields via Supervised Learning

Zuranski, Andrzej M.; Martinez Alvarado, Jesus; Shields, Benjamin J.; Doyle, Abigail G. "Predicting Reaction Yields via Supervised Learning", Acc. Chem. Res., 2021, 54, 1856–1865.

Auto-QChem an automated workflow for the generation and storage of DFT calculations for organic molecules

Zuranski, Andrzej M.; Wang, J. Y.; Shields, Benjamin J.; Doyle, Abigail G. "Auto-QChem an automated workflow for the generation and storage of DFT calculations for organic molecules", React. Chem. Eng., 2022, 7, 1276.

Scoring Methods in Lead Optimization of Molecular Glues

Jia, Lei; Weiss, Dahlia; Shields, Benjamin J.; Claus, Brian; Shanmugasundaram, Veerabahu; Johnson, Stephen; Riggs, Jennifer; Zapf, Christoph "Scoring Methods in Lead Optimization of Molecular Glues", ChemRxiv, 2023.

Identifying general reaction conditions by bandit optimization

Wang, Jason Y.; Stevens, Jason M.; Kariofillis, Stavros K.; Tom Mai-Jan; Li, Jun; Tabora, Jose E.; Parasram, Marvin; Shields, Benjamin J.; Primer, David; Hao, Bo; Valle, David D.; DiSomma, Stacey; Furman, Ariel; Zipp, Greg G.; Melnikov, Sergey; Paulson, James; Doyle, Abigail G. "Identifying general reaction conditions by bandit optimization", Nature, 2024.

MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics

Bruechner, Alexander; Shields, Benjamin J.; Kirubakaran, Palani; Suponya, Alexander; Panda, Manoranjan; Posy, Shana; Johnson, Stephen; Lakkaraju, Sirish K. "MDFit, Automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics", Journal of Computer-Aided Molecular Design, 2024.

SAIR: Enabling Deep Learning for Protein-Ligand Interactions with a Synthetic Structural Dataset

Lemos, Pablo; Beckwith, Zane; Bandi, Sasaank; van Damme, Maarten; Crivelli-Decker, Jordan; Shields, Benjamin J.; Merth, Thomas; Jha, Punit K.; De Mitri, Nicola; Callahan, Tiffany J.; Nish AJ; Abruzzo, Paul; Salomon-Ferrer, Romelia; Ganahl, Martin. "SAIR, Enabling Deep Learning for Protein-Ligand Interactions with a Synthetic Structural Dataset", BioRxiv, 2025.

On improving experimental binding affinity predictions with synthetic data

Ryczko, Kevin; Zin, Phyo Phyo; Crivelli-Decker, Jordan; Le, Ly; Jha, Punit K.; Shields, Benjamin J.; Lemos, Pablo; Bandi, Sasaank; van Damme, Maarten; Sood, Amogh; Huntington, Lee; Pitman, Mary; Ganahl, Martin; Bortolato, Andrea. "On improving experimental binding affinity predictions with synthetic data", BioRxiv, 2026.

Teaching

Princeton University

• Chemistry 304: Organic Chemistry (2016)
• Chemistry 201: General Chemistry (2015)

University of North Carolina Asheville

• Chemistry department tutor: general, organic, inorganic, physical (2012-2014)
• Chemistry 222: Organic Chemistry Laboratory TA (2012-2013)
• Chemistry 111: General Chemistry Laboratory TA (2012)