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Education and qualifications (2)

Massachusetts Institute of Technology: Cambridge, MA, US

Education
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Massachusetts Institute of Technology

California Institute of Technology: Pasadena, California, US

2010-10 to 2014-06 | B.S. Chemical Engineering
Education
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0000-0002-8271-8723

Funding (1)

Calibration-free quantitation of reaction yields in high-throughput reaction screening through absolute carbon quantification by LC-FID

2024-07-01 to 2025-06-30 | Grant
Research Corporation for Science Advancement (Tucson, AZ, US)
GRANT_NUMBER:

SA-AUT-2024-005b

Part of GRANT_NUMBER:

SA-AUT-2024-005
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Research Corporation for Science Advancement - Symplectic Grant Tracker

Works (50 of 112)

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Page 1 of 3

Empowering natural product science with AI: leveraging multimodal data and knowledge graphs

Natural Product Reports
2025 | Journal article
DOI: 10.1039/D4NP00008K
Contributors: David Meijer; Mehdi A. Beniddir; Connor W. Coley; Yassine M. Mejri; Meltem Öztürk; Justin J. J. van der Hooft; Marnix H. Medema; Adam Skiredj
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Crossref

Rapid prediction of conformationally-dependent DFT-level descriptors using graph neural networks for carboxylic acids and alkyl amines

Digital Discovery
2025 | Journal article
DOI: 10.1039/D4DD00284A
Contributors: Brittany C. Haas; Melissa A. Hardy; Shree Sowndarya S. V.; Keir Adams; Connor W. Coley; Robert S. Paton; Matthew S. Sigman
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Crossref

Schedule optimization for chemical library synthesis

Digital Discovery
2025 | Journal article
DOI: 10.1039/D4DD00327F
Contributors: Qianxiang Ai; Fanwang Meng; Runzhong Wang; J. Cullen Klein; Alexander G. Godfrey; Connor W. Coley
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Crossref

Challenging Reaction Prediction Models to Generalize to Novel Chemistry

ACS Central Science
2025-03-12 | Journal article
DOI: 10.1021/acscentsci.5c00055
Contributors: John Bradshaw; Anji Zhang; Babak Mahjour; David E. Graff; Marwin H. S. Segler; Connor W. Coley
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Crossref

Designing single-polymer-chain nanoparticles to mimic biomolecular hydration frustration

Nature Chemistry
2025-03-12 | Journal article
DOI: 10.1038/s41557-025-01760-9
Contributors: Tianyi Jin; Connor W. Coley; Alfredo Alexander-Katz
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Crossref

Revealing the Relationship between Publication Bias and Chemical Reactivity with Contrastive Learning

Journal of the American Chemical Society
2025-03-12 | Journal article
DOI: 10.1021/jacs.5c01120
Contributors: Wenhao Gao; Priyanka Raghavan; Ron Shprints; Connor W. Coley
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Crossref

Rethinking Evaluation in Compound Potency Prediction

2025-03-07 | Preprint
DOI: 10.21203/rs.3.rs-5899985/v1
Contributors: Brenda Cruz Nogueira; Nuno Moniz; Connor Coley; Nitesh Chawla
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Crossref

A physics-inspired approach to the understanding of molecular representations and models

Molecular Systems Design & Engineering
2024 | Journal article
DOI: 10.1039/D3ME00189J
Contributors: Luke Dicks; David E. Graff; Kirk E. Jordan; Connor W. Coley; Edward O. Pyzer-Knapp
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Crossref

Extracting structured data from organic synthesis procedures using a fine-tuned large language model

Digital Discovery
2024 | Journal article
DOI: 10.1039/D4DD00091A
Contributors: Qianxiang Ai; Fanwang Meng; Jiale Shi; Brenden Pelkie; Connor W. Coley
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Crossref

Pareto optimization to accelerate multi-objective virtual screening

Digital Discovery
2024 | Journal article
DOI: 10.1039/D3DD00227F
Contributors: Jenna C. Fromer; David E. Graff; Connor W. Coley
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Crossref

Comment on “Molecular hypergraph neural networks” [J. Chem. Phys. 160, 144307 (2024)]

The Journal of Chemical Physics
2024-11-28 | Journal article
DOI: 10.1063/5.0239722
Contributors: Nicholas Casetti; Pragnay Nevatia; Junwu Chen; Philippe Schwaller; Connor W. Coley
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Crossref

Reproducing Reaction Mechanisms with Machine‐Learning Models Trained on a Large‐Scale Mechanistic Dataset

Angewandte Chemie
2024-10-21 | Journal article
DOI: 10.1002/ange.202411296
Contributors: Joonyoung F. Joung; Mun Hong Fong; Jihye Roh; Zhengkai Tu; John Bradshaw; Connor W. Coley
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Crossref

Reproducing Reaction Mechanisms with Machine‐Learning Models Trained on a Large‐Scale Mechanistic Dataset

Angewandte Chemie International Edition
2024-09-02 | Journal article
DOI: 10.1002/anie.202411296
Contributors: Joonyoung F. Joung; Mun Hong Fong; Jihye Roh; Zhengkai Tu; John Bradshaw; Connor W. Coley
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Crossref

OpenChemIE: An Information Extraction Toolkit for Chemistry Literature

Journal of Chemical Information and Modeling
2024-07-22 | Journal article
DOI: 10.1021/acs.jcim.4c00572
Contributors: Vincent Fan; Yujie Qian; Alex Wang; Amber Wang; Connor W. Coley; Regina Barzilay
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Crossref

Decoding protein language models: insights from embedding space analysis

2024-06-27 | Preprint
DOI: 10.1101/2024.06.21.600139
Contributors: Pia Francesca Rissom; Paulo Yanez Sarmiento; Jordan Safer; Connor W. Coley; Bernhard Y. Renard; Henrike O. Heyne; Sumaiya Iqbal
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Crossref

An algorithmic framework for synthetic cost-aware decision making in molecular design

Nature Computational Science
2024-06-17 | Journal article
DOI: 10.1038/s43588-024-00639-y
Contributors: Jenna C. Fromer; Connor W. Coley
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Crossref

Data-Efficient, Chemistry-Aware Machine Learning Predictions of Diels–Alder Reaction Outcomes

Journal of the American Chemical Society
2024-06-12 | Journal article
DOI: 10.1021/jacs.4c03131
Contributors: Angus Keto; Taicheng Guo; Morgan Underdue; Thijs Stuyver; Connor W. Coley; Xiangliang Zhang; Elizabeth H. Krenske; Olaf Wiest
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Crossref

Incorporating Synthetic Accessibility in Drug Design: Predicting Reaction Yields of Suzuki Cross-Couplings by Leveraging AbbVie’s 15-Year Parallel Library Data Set

Journal of the American Chemical Society
2024-06-05 | Journal article
DOI: 10.1021/jacs.4c00098
Contributors: Priyanka Raghavan; Alexander J. Rago; Pritha Verma; Majdi M. Hassan; Gashaw M. Goshu; Amanda W. Dombrowski; Abhishek Pandey; Connor W. Coley; Ying Wang
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Crossref

RDCanon: A Python Package for Canonicalizing the Order of Tokens in SMARTS Queries

Journal of Chemical Information and Modeling
2024-04-22 | Journal article
DOI: 10.1021/acs.jcim.4c00138
Contributors: Babak A. Mahjour; Connor W. Coley
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Crossref

Automation of air-free synthesis

Nature Reviews Chemistry
2024-04-11 | Journal article
DOI: 10.1038/s41570-024-00599-x
Contributors: Babak A. Mahjour; Connor W. Coley
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Crossref

MIST-CF: Chemical Formula Inference from Tandem Mass Spectra

Journal of Chemical Information and Modeling
2024-04-08 | Journal article
DOI: 10.1021/acs.jcim.3c01082
Contributors: Samuel Goldman; Jiayi Xin; Joules Provenzano; Connor W. Coley
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Crossref

DNA-encoded library-enabled discovery of proximity-inducing small molecules

Nature Chemical Biology
2024-02 | Journal article
DOI: 10.1038/s41589-023-01458-4
Contributors: Jeremy W. Mason; Yuen Ting Chow; Liam Hudson; Antonin Tutter; Gregory Michaud; Matthias V. Westphal; Wei Shu; Xiaolei Ma; Zher Yin Tan; Connor W. Coley et al.
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Crossref

Generating Molecular Fragmentation Graphs with Autoregressive Neural Networks

Analytical Chemistry
2024-02-27 | Journal article
DOI: 10.1021/acs.analchem.3c04654
Contributors: Samuel Goldman; Janet Li; Connor W. Coley
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Crossref

Evaluating the roughness of structure–property relationships using pretrained molecular representations

Digital Discovery
2023 | Journal article
DOI: 10.1039/D3DD00088E
Contributors: David E. Graff; Edward O. Pyzer-Knapp; Kirk E. Jordan; Eugene I. Shakhnovich; Connor W. Coley
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Crossref

Predictive chemistry: machine learning for reaction deployment, reaction development, and reaction discovery

Chemical Science
2023 | Journal article
DOI: 10.1039/D2SC05089G
Contributors: Zhengkai Tu; Thijs Stuyver; Connor W. Coley
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Crossref

Computer‐aided evaluation and exploration of chemical spaces constrained by reaction pathways

AIChE Journal
2023-12 | Journal article
DOI: 10.1002/aic.18234
Contributors: Itai Levin; Michael E. Fortunato; Kian L. Tan; Connor W. Coley
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Crossref

Dataset Design for Building Models of Chemical Reactivity

ACS Central Science
2023-12-27 | Journal article
DOI: 10.1021/acscentsci.3c01163
Contributors: Priyanka Raghavan; Brittany C. Haas; Madeline E. Ruos; Jules Schleinitz; Abigail G. Doyle; Sarah E. Reisman; Matthew S. Sigman; Connor W. Coley
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Crossref

A Computationally Informed Unified View on the Effect of Polarity and Sterics on the Glass Transition in Vinyl-based Polymer Melts

ACS Macro Letters
2023-11-21 | Journal article
DOI: 10.1021/acsmacrolett.3c00553
Contributors: Tianyi Jin; Connor W. Coley; Alfredo Alexander-Katz
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Crossref

Opportunities for Machine Learning and Artificial Intelligence to Advance Synthetic Drug Substance Process Development

Organic Process Research & Development
2023-11-17 | Journal article
DOI: 10.1021/acs.oprd.3c00229
Contributors: Daniel J. Griffin; Connor W. Coley; Scott A. Frank; Joel M. Hawkins; Klavs F. Jensen
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Crossref

Combining Molecular Quantum Mechanical Modeling and Machine Learning for Accelerated Reaction Screening and Discovery

Chemistry – A European Journal
2023-10-26 | Journal article
DOI: 10.1002/chem.202301957
Contributors: Nicholas Casetti; Javier E. Alfonso‐Ramos; Connor W. Coley; Thijs Stuyver
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Crossref

Neural scaling of deep chemical models

Nature Machine Intelligence
2023-10-23 | Journal article
DOI: 10.1038/s42256-023-00740-3
Contributors: Nathan C. Frey; Ryan Soklaski; Simon Axelrod; Siddharth Samsi; Rafael Gómez-Bombarelli; Connor W. Coley; Vijay Gadepally
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Crossref

Annotating metabolite mass spectra with domain-inspired chemical formula transformers

Nature Machine Intelligence
2023-08-17 | Journal article
DOI: 10.1038/s42256-023-00708-3
Contributors: Samuel Goldman; Jeremy Wohlwend; Martin Stražar; Guy Haroush; Ramnik J. Xavier; Connor W. Coley
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Crossref

Data Sharing in Chemistry: Lessons Learned and a Case for Mandating Structured Reaction Data

Journal of Chemical Information and Modeling
2023-07-24 | Journal article
DOI: 10.1021/acs.jcim.3c00607
Contributors: Rocío Mercado; Steven M. Kearnes; Connor W. Coley
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Crossref

RxnScribe: A Sequence Generation Model for Reaction Diagram Parsing

Journal of Chemical Information and Modeling
2023-07-10 | Journal article
DOI: 10.1021/acs.jcim.3c00439
Contributors: Yujie Qian; Jiang Guo; Zhengkai Tu; Connor W. Coley; Regina Barzilay
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Crossref

The promise and pitfalls of AI for molecular and materials synthesis

Nature Computational Science
2023-05-18 | Journal article
DOI: 10.1038/s43588-023-00446-x
Contributors: Nicholas David; Wenhao Sun; Connor W. Coley
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Crossref

Machine Learning‐Guided Computational Screening of New Candidate Reactions with High Bioorthogonal Click Potential

Chemistry – A European Journal
2023-05-16 | Journal article
DOI: 10.1002/chem.202300387
Contributors: Thijs Stuyver; Connor W. Coley
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Crossref

Negative Data in Data Sets for Machine Learning Training

Organic Letters
2023-05-05 | Journal article
DOI: 10.1021/acs.orglett.3c01282
Contributors: Michael P. Maloney; Connor W. Coley; Samuel Genheden; Nessa Carson; Paul Helquist; Per-Ola Norrby; Olaf Wiest
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Crossref

Negative Data in Data Sets for Machine Learning Training

The Journal of Organic Chemistry
2023-05-05 | Journal article
DOI: 10.1021/acs.joc.3c00844
Contributors: Michael P. Maloney; Connor W. Coley; Samuel Genheden; Nessa Carson; Paul Helquist; Per-Ola Norrby; Olaf Wiest
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Crossref

A high-throughput platform for efficient exploration of functional polypeptide chemical space

Nature Synthesis
2023-05-01 | Journal article
DOI: 10.1038/s44160-023-00294-7
Contributors: Guangqi Wu; Haisen Zhou; Jun Zhang; Zi-You Tian; Xingyi Liu; Shuo Wang; Connor W. Coley; Hua Lu
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Crossref

MolScribe: Robust Molecular Structure Recognition with Image-to-Graph Generation

Journal of Chemical Information and Modeling
2023-04-10 | Journal article
DOI: 10.1021/acs.jcim.2c01480
Contributors: Yujie Qian; Jiang Guo; Zhengkai Tu; Zhening Li; Connor W. Coley; Regina Barzilay
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Crossref

Adsorption of Biomimetic Amphiphilic Heteropolymers onto Graphene and Its Derivatives

Macromolecules
2023-03-14 | Journal article
DOI: 10.1021/acs.macromol.2c02413
Contributors: Tianyi Jin; Connor W. Coley; Alfredo Alexander-Katz
Source: check_circle
Crossref

Computer-aided multi-objective optimization in small molecule discovery

Patterns
2023-02 | Journal article
DOI: 10.1016/j.patter.2023.100678
Contributors: Jenna C. Fromer; Connor W. Coley
Source: check_circle
Crossref

A graph representation of molecular ensembles for polymer property prediction

Chemical Science
2022 | Journal article
DOI: 10.1039/D2SC02839E
Contributors: Matteo Aldeghi; Connor W. Coley
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Crossref

Equivariant Shape-Conditioned Generation of 3D Molecules for Ligand-Based Drug Design

2022 | Journal article
DOI: 10.48550/ARXIV.2210.04893
Contributors: Keir Adams; Connor W. Coley
Source: Self-asserted source
0000-0002-8271-8723

Sample Efficiency Matters: A Benchmark for Practical Molecular Optimization

2022 | Conference paper
DOI: 10.48550/ARXIV.2206.12411
Contributors: Wenhao Gao; Tianfan Fu; Jimeng Sun; Connor W. Coley
Source: Self-asserted source
0000-0002-8271-8723

Similarity based enzymatic retrosynthesis

Chemical Science
2022 | Journal article
DOI: 10.1039/D2SC01588A
Contributors: Karthik Sankaranarayanan; Esther Heid; Connor W. Coley; Deeptak Verma; William H. Green; Klavs F. Jensen
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Crossref

Improving the performance of models for one-step retrosynthesis through re-ranking

Journal of Cheminformatics
2022-12 | Journal article
DOI: 10.1186/s13321-022-00594-8
Contributors: Min Htoo Lin; Zhengkai Tu; Connor W. Coley
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Crossref

Merging enzymatic and synthetic chemistry with computational synthesis planning

Nature Communications
2022-12-14 | Journal article
DOI: 10.1038/s41467-022-35422-y
Contributors: Itai Levin; Mengjie Liu; Christopher A. Voigt; Connor W. Coley
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Crossref

Roughness of Molecular Property Landscapes and Its Impact on Modellability

Journal of Chemical Information and Modeling
2022-10-10 | Journal article
DOI: 10.1021/acs.jcim.2c00903
Contributors: Matteo Aldeghi; David E. Graff; Nathan Frey; Joseph A. Morrone; Edward O. Pyzer-Knapp; Kirk E. Jordan; Connor W. Coley
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Crossref

Self-Focusing Virtual Screening with Active Design Space Pruning

Journal of Chemical Information and Modeling
2022-08-22 | Journal article
DOI: 10.1021/acs.jcim.2c00554
Contributors: David E. Graff; Matteo Aldeghi; Joseph A. Morrone; Kirk E. Jordan; Edward O. Pyzer-Knapp; Connor W. Coley
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Crossref
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Peer review (54 reviews for 15 publications/grants)

Review activity for Accounts of chemical research. (3)
Review activity for ACS catalysis. (1)
Review activity for ACS central science. (5)
Review activity for ACS chemical biology. (3)
Review activity for ACS omega. (1)
Review activity for ACS synthetic biology. (1)
Review activity for Analytical chemistry. (2)
Review activity for Chemical reviews. (2)
Review activity for Chemistry methods. (1)
Review activity for Energy & fuels. (1)
Review activity for Journal of chemical information and modeling. (12)
Review activity for Journal of medicinal chemistry. (4)
Review activity for Journal of the American Chemical Society. (16)
Review activity for Nature (1)
Review activity for Nature chemistry. (1)
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