| 2018 | CIKM | Extracting Figures and Captions from Scientific Publications. | Pengyuan Li, Xiangying Jiang, Hagit Shatkay |
| 2016 | ECAI | Improved Multi-Label Classification Using Inter-Dependence Structure via a Generative Mixture Model. | Ramanuja Simha, Hagit Shatkay |
| 2016 | MICCAI | Prostate Cancer: Improved Tissue Characterization by Temporal Modeling of Radio-Frequency Ultrasound Echo Data. | Layan Nahlawi, Farhad Imani, Mena Gaed, Jose A. Gomez, Madeleine Moussa, Eli Gibson, Aaron Fenster, Aaron D. Ward, Purang Abolmaesumi, Hagit Shatkay, Parvin Mousavi |
| 2015 | ICIP | Utilizing image-based features in biomedical document classification. | Kaidi Ma, Hogyeong Jeong, M. V. Rohith, Gowri Somanath, Ryan Tarpine, Kyle Schutter, Dorothea Blostein, Sorin Istrail, Chandra Kambhamettu, Hagit Shatkay |
| 2013 | WABI | Protein (Multi-)Location Prediction: Using Location Inter-dependencies in a Probabilistic Framework. | Ramanuja Simha, Hagit Shatkay |
| 2010 | CIKM | DTMBIO workshop summary. | Hagit Shatkay, Doheon Lee, Min Song, Shamkant B. Navathe |
| 2008 | AMIA | Ranking single nucleotide polymorphisms by potential deleterious effects. | Phil Hyoun Lee, Hagit Shatkay |
| 2008 | ISMB | Overview of the Ninth Annual Meeting of the BioLINK SIG at ISMB: Linking Literature, Information and Knowledge for Biology. | Christian Blaschke, Lynette Hirschman, Hagit Shatkay, Alfonso Valencia |
| 2008 | ISMB | Toward Computer-Assisted Text Curation: Classification Is Easy (Choosing Training Data Can Be Hard...). | Robert Denroche, Ramana Madupu, Shibu Yooseph, Granger G. Sutton, Hagit Shatkay |
| 2008 | PSB | EpiLoc: A (Working) Text-Based System for Predicting Protein Subcellular Location. | Scott Brady, Hagit Shatkay |
| 2007 | AMIA | Using Cluster Ensemble and Validation to Identify Subtypes of Pervasive Developmental Disorders. | Jess J. Shen, Phil Hyoun Lee, Jeanette J. A. Holden, Hagit Shatkay |
| 2007 | WABI | Two Birds, One Stone: Selecting Functionally Informative Tag SNPs for Disease Association Studies. | Phil Hyoun Lee, Hagit Shatkay |
| 2006 | ISMB | BNTagger: improved tagging SNP selection using Bayesian networks. | Phil Hyoun Lee, Hagit Shatkay |
| 2006 | ISMB | Integrating image data into biomedical text categorization. | Hagit Shatkay, Nawei Chen, Dorothea Blostein |
| 2006 | PSB | Significantly Improved Prediction of Subcellular Localization by Integrating Text and Protein Sequence Data . | Annette Hglund, Torsten Blum, Scott Brady, Pierre Dnnes, John San Miguel, Matthew Rocheford, Oliver Kohlbacher, Hagit Shatkay |
| 2000 | ISMB | Genes, Themes, and Microarrays: Using Information Retrieval for Large-Scale Gene Analysis. | Hagit Shatkay, Stephen Edwards, W. John Wilbur, Mark Boguski |
| 1999 | UAI | Learning Hidden Markov Models with Geometrical Constraints. | Hagit Shatkay |
| 1998 | ICML | Heading in the Right Direction. | Hagit Shatkay, Leslie Pack Kaelbling |
| 1997 | IJCAI | Learning Topological Maps with Weak Local Odometric Information. | Hagit Shatkay, Leslie Pack Kaelbling |
| 1996 | ICDE | Approximate Queries and Representations for Large Data Sequences. | Hagit Shatkay, Stanley B. Zdonik |