| 2023 | AIED | Implementing and Evaluating ASSISTments Online Math Homework Support At large Scale over Two Years: Findings and Lessons Learned. | Mingyu Feng, Neil T. Heffernan, Kelly Collins, Cristina Heffernan, Robert F. Murphy |
| 2018 | WACV | Learning Generative Models of Tissue Organization with Supervised GANs. | Ligong Han, Robert F. Murphy, Deva Ramanan |
| 2015 | RECOMB | Deciding When to Stop: Efficient Experimentation to Learn to Predict Drug-Target Interactions (Extended Abstract). | Maja Temerinac-Ott, Armaghan W. Naik, Robert F. Murphy |
| 2014 | ITS | Implementation of an Intelligent Tutoring System for Online Homework Support in an Efficacy Trial. | Mingyu Feng, Jeremy Roschelle, Neil T. Heffernan, Janet Fairman, Robert F. Murphy |
| 2011 | RECOMB | Learning Cellular Sorting Pathways Using Protein Interactions and Sequence Motifs. | Tien-ho Lin, Ziv Bar-Joseph, Robert F. Murphy |
| 2009 | ICML | Workshop summary: Automated interpretation and modelling of cell images. | Robert F. Murphy, Chun-Nan Hsu, Loris Nanni |
| 2009 | KDD | Structured correspondence topic models for mining captioned figures in biological literature. | Amr Ahmed, Eric P. Xing, William W. Cohen, Robert F. Murphy |
| 2008 | ISMB | Structured Literature Image Finder: Extracting Information from Text and Images in Biomedical Literature. | Lus Pedro Coelho, Amr Ahmed, Andrew Arnold, Joshua D. Kangas, Abdul-Saboor Sheikh, Eric P. Xing, William W. Cohen, Robert F. Murphy |
| 2008 | ISMB | Principles of Bioimage Informatics: Focus on Machine Learning of Cell Patterns. | Lus Pedro Coelho, Estelle Glory-Afshar, Joshua D. Kangas, Shannon Quinn, Aabid Shariff, Robert F. Murphy |
| 2007 | ICIP | Efficient Acquisition and Learning of Fluorescence Microscope Data Models. | Charles Jackson, Robert F. Murphy, Jelena Kovacevic |
| 2007 | ISMB | Automated image analysis of protein localization in budding yeast. | Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, Robert F. Murphy |
| 2007 | PSB | A Stacked Graphical Model for Associating Sub-Images with Sub-Captions. | Zhenzhen Kou, William W. Cohen, Robert F. Murphy |
| 2006 | CIBCB | A Novel Graphical Model Approach to Segmenting Cell Images. | Shann-Ching Chen, Ting Zhao, Geoffrey J. Gordon, Robert F. Murphy |
| 2005 | ICASSP | Adaptive Multirate Data Acquisition of 3D Cell Images. | Thomas E. Merryman, Jelena Kovacevic, Elvira Garcia Osuna, Robert F. Murphy |
| 2005 | ISMB | High-recall protein entity recognition using a dictionary. | Zhenzhen Kou, William W. Cohen, Robert F. Murphy |
| 2005 | SIGMOD | Research issues in protein location image databases. | Robert F. Murphy, Christos Faloutsos |
| 2003 | KDD | Understanding captions in biomedical publications. | William W. Cohen, Richard C. Wang, Robert F. Murphy |
| 2003 | KDD | Extracting information from text and images for location proteomics. | Zhenzhen Kou, William W. Cohen, Robert F. Murphy |
| 2001 | BIBE | Searching Online Journals for Fluorescence Microscope Images Depicting Protein Subcellular Location Patterns. | Robert F. Murphy, Meel Velliste, Jie Yao, Gregory Porreca |
| 2000 | ISMB | Towards a Systematics for Protein Subcellular Location: Quantitative Description of Protein Localization Patterns and Automated Analysis of Fluorescence Microscope Images. | Robert F. Murphy, Michael V. Boland, Meel Velliste |