Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. - Edward Y. Chen; Christopher M. Tan; Yan Kou; Qiaonan Duan; Zichen Wang 002; Gabriela Vaz Meirelles; Neil R. Clark; Avi Ma'ayan (BMC Bioinform., 2013)

Drug/Cell-line Browser: interactive canvas visualization of cancer drug/cell-line viability assay datasets. - Qiaonan Duan; Zichen Wang 002; Nicolas F. Fernandez; Andrew D. Rouillard; Christopher M. Tan; Cyril H. Benes; Avi Ma'ayan (Bioinform., 2014)

Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool. - Neil R. Clark; Maciej Szymkiewicz; Zichen Wang 002; Caroline D. Monteiro; Matthew R. Jones; Avi Ma'ayan (BIBM, 2015)

Dynamics of the discovery process of protein-protein interactions from low content studies. - Zichen Wang 002; Neil R. Clark; Avi Ma'ayan (BMC Syst. Biol., 2015)

Reprint of "Abstraction for data integration: Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction". - Andrew D. Rouillard; Zichen Wang 002; Avi Ma'ayan (Comput. Biol. Chem., 2015)

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. - Andrew D. Rouillard; Gregory W. Gundersen; Nicolas F. Fernandez; Zichen Wang 002; Caroline D. Monteiro; Michael G. McDermott; Avi Ma'ayan (Database J. Biol. Databases Curation, 2016)

Drug-induced adverse events prediction with the LINCS L1000 data. - Zichen Wang 002; Neil R. Clark; Avi Ma'ayan (Bioinform., 2016)

An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study. - Zichen Wang 002; Avi Ma'ayan (F1000Research, 2016)

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. - Maxim V. Kuleshov; Matthew R. Jones; Andrew D. Rouillard; Nicolas F. Fernandez; Qiaonan Duan; Zichen Wang 002; Simon Koplev; Sherry L. Jenkins; Kathleen M. Jagodnik; Alexander Lachmann; Michael G. McDermott; Caroline D. Monteiro; et al. (Nucleic Acids Res., 2016)

Predicting age by mining electronic medical records with deep learning characterizes differences between chronological and physiological age. - Zichen Wang 002; Li Li 062; Benjamin S. Glicksberg; Ariel Israel; Joel T. Dudley; Avi Ma'ayan (J. Biomed. Informatics, 2017)

Cell-specific prediction and application of drug-induced gene expression . - Rachel Hodos; Ping Zhang 016; Hao-Chih Lee; Qiaonan Duan; Zichen Wang 002; Neil R. Clark; Avi Ma'ayan; Fei Wang 001; Brian A. Kidd; Jianying Hu; David A. Sontag; Joel Dudley (PSB, 2018)

L1000FWD: fireworks visualization of drug-induced transcriptomic signatures. - Zichen Wang 002; Alexander Lachmann; Alexandra B. Keenan; Avi Ma'ayan (Bioinform., 2018)

eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. - Daniel J. B. Clarke; Maxim V. Kuleshov; Brian M. Schilder; Denis Torre; Mary E. Duffy; Alexandra B. Keenan; Alexander Lachmann; Axel S. Feldmann; Gregory W. Gundersen; Moshe C. Silverstein; Zichen Wang 002; Avi Ma'ayan (Nucleic Acids Res., 2018)

Predicting opioid dependence from electronic health records with machine learning. - Randall J. Ellis; Zichen Wang 002; Nicholas Genes; Avi Ma'ayan (BioData Min., 2019)

Drug Gene Budger (DGB): an application for ranking drugs to modulate a specific gene based on transcriptomic signatures. - Zichen Wang 002; Edward He 002; Kevin Sani; Kathleen M. Jagodnik; Moshe C. Silverstein; Avi Ma'ayan (Bioinform., 2019)

ChEA3: transcription factor enrichment analysis by orthogonal omics integration. - Alexandra B. Keenan; Denis Torre; Alexander Lachmann; Ariel K. Leong; Megan L. Wojciechowicz; Vivian Utti; Kathleen M. Jagodnik; Eryk Kropiwnicki; Zichen Wang 002; Avi Ma'ayan (Nucleic Acids Res., 2019)

Graph Neural Networks in Life Sciences: Opportunities and Solutions. - Zichen Wang 002; Vassilis N. Ioannidis; Huzefa Rangwala; Tatsuya Arai; Ryan Brand; Mufei Li; Yohei Nakayama (KDD, 2022)

Variational Causal Inference. - Yulun Wu; Layne C. Price; Zichen Wang 002; Vassilis N. Ioannidis; George Karypis (CoRR, 2022)

Training self-supervised peptide sequence models on artificially chopped proteins. - Gil Sadeh; Zichen Wang 002; Jasleen Grewal; Huzefa Rangwala; Layne Price (CoRR, 2022)

Improving postpartum hemorrhage risk prediction using longitudinal electronic medical records. - Amanda B. Zheutlin; Luciana Vieira; Ryan A. Shewcraft; Shilong Li; Zichen Wang 002; Emilio Schadt; Susan Gross; Siobhan M. Dolan; Joanne Stone; Eric E. Schadt; Li Li 062 (J. Am. Medical Informatics Assoc., 2022)

A comprehensive digital phenotype for postpartum hemorrhage. - Amanda B. Zheutlin; Luciana Vieira; Ryan A. Shewcraft; Shilong Li; Zichen Wang 002; Emilio Schadt; Yu-Han Kao; Susan Gross; Siobhan M. Dolan; Joanne Stone; Eric E. Schadt; Li Li 062 (J. Am. Medical Informatics Assoc., 2022)

Improving preeclampsia risk prediction by modeling pregnancy trajectories from routinely collected electronic medical record data. - Shilong Li; Zichen Wang 002; Luciana Vieira; Amanda B. Zheutlin; Boshu Ru; Emilio Schadt; Pei Wang 014; Alan B. Copperman; Joanne Stone; Susan Gross; Yu-Han Kao; Yan Kwan Lau; et al. (npj Digit. Medicine, 2022)

Predicting Cellular Responses with Variational Causal Inference and Refined Relational Information. - Yulun Wu; Robert A. Barton; Zichen Wang 002; Vassilis N. Ioannidis; Carlo De Donno; Layne C. Price; Luis F. Voloch; George Karypis (ICLR, 2023)

DATALORE: Can a Large Language Model Find All Lost Scrolls in a Data Repository? - Yuze Lou; Chuan Lei; Xiao Qin 003; Zichen Wang 002; Christos Faloutsos; Rishita Anubhai; Huzefa Rangwala (ICDE, 2024)

BioBridge: Bridging Biomedical Foundation Models via Knowledge Graphs. - Zifeng Wang 008; Zichen Wang 002; Balasubramaniam Srinivasan; Vassilis N. Ioannidis; Huzefa Rangwala; Rishita Anubhai (ICLR, 2024)

GraphStorm: All-in-one Graph Machine Learning Framework for Industry Applications. - Da Zheng; Xiang Song 003; Qi Zhu 008; Jian Zhang; Theodore Vasiloudis; Runjie Ma; Houyu Zhang; Zichen Wang 002; Soji Adeshina; Israt Nisa; Alejandro Mottini; Qingjun Cui; et al. (KDD, 2024)

GraphStorm: all-in-one graph machine learning framework for industry applications. - Da Zheng; Xiang Song 003; Qi Zhu 008; Jiani Zhang 003; Theodore Vasiloudis; Runjie Ma; Houyu Zhang; Zichen Wang 002; Soji Adeshina; Israt Nisa; Alejandro Mottini; Qingjun Cui; et al. (CoRR, 2024)

Long-context Protein Language Model. - Yingheng Wang; Zichen Wang 002; Gil Sadeh; Luca Zancato; Alessandro Achille; George Karypis; Huzefa Rangwala (CoRR, 2024)

Pushing the Limits of All-Atom Geometric Graph Neural Networks: Pre-Training, Scaling, and Zero-Shot Transfer. - Zihan Pengmei; Zhengyuan Shen; Zichen Wang 002; Marcus D. Collins; Huzefa Rangwala (ICLR, 2025)

LC-PLM: Long-context Protein Language Modeling Using Bidirectional Mamba with Shared Projection Layers. - Yingheng Wang; Zichen Wang 002; Gil Sadeh; Luca Zancato; Alessandro Achille; George Karypis; Huzefa Rangwala (Trans. Mach. Learn. Res., 2025)

Protein Structure Tokenization: Benchmarking and New Recipe. - Xinyu Yuan; Zichen Wang 002; Marcus D. Collins; Huzefa Rangwala (CoRR, 2025)