CoeViz: a web-based tool for coevolution analysis of protein residues. - Frazier N. Baker; Aleksey A. Porollo (BMC Bioinform., 2016)

CoeViz: A Web-Based Integrative Platform for Interactive Visualization of Large Similarity and Distance Matrices. - Frazier N. Baker; Aleksey A. Porollo (Data, 2018)

CoeViz 2: Protein Graphs Derived From Amino Acid Covariance. - Daniel Corcoran; Nicholas Maltbie; Shivchander Sudalairaj; Frazier N. Baker; Joseph Hirschfeld; Aleksey A. Porollo (Frontiers Bioinform., 2021)

RLSynC: Offline-Online Reinforcement Learning for Synthon Completion. - Frazier N. Baker; Ziqi Chen; Xia Ning (CoRR, 2023)

LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset. - Botao Yu; Frazier N. Baker; Ziqi Chen; Xia Ning; Huan Sun 001 (CoRR, 2024)

RLSynC: Offline-Online Reinforcement Learning for Synthon Completion. - Frazier N. Baker; Ziqi Chen; Daniel Adu-Ampratwum; Xia Ning (J. Chem. Inf. Model., 2024)

ScienceAgentBench: Toward Rigorous Assessment of Language Agents for Data-Driven Scientific Discovery. - Ziru Chen; Shijie Chen; Yuting Ning; Qianheng Zhang; Boshi Wang; Botao Yu; Yifei Li 005; Zeyi Liao; Chen Wei; Zitong Lu; Vishal Dey; Mingyi Xue 001; et al. (ICLR, 2025)

Tooling or Not Tooling? The Impact of Tools on Language Agents for Chemistry Problem Solving. - Botao Yu; Frazier N. Baker; Ziru Chen; Garrett Herb; Boyu Gou; Daniel Adu-Ampratwum; Xia Ning; Huan Sun 001 (NAACL (Findings), 2025)

LIDDIA: Language-based Intelligent Drug Discovery Agent. - Reza Averly; Frazier N. Baker; Xia Ning (CoRR, 2025)