| 2014 | AMIA | Application of Bayesian Logistic Regression to Mining Biomedical Data. | Viji R. Avali, Gregory F. Cooper, Vanathi Gopalakrishnan |
| 2009 | AMIA | Measuring Stability of Feature Selection in Biomedical Datasets. | Jonathan L. Lustgarten, Vanathi Gopalakrishnan, Shyam Visweswaran |
| 2008 | AMIA | Improving Classification Performance with Discretization on Biomedical Datasets. | Jonathan L. Lustgarten, Vanathi Gopalakrishnan, Himanshu Grover, Shyam Visweswaran |
| 2007 | IJCAI | Protein Quaternary Fold Recognition Using Conditional Graphical Models. | Yan Liu, Jaime G. Carbonell, Vanathi Gopalakrishnan, Peter Weigele |
| 2006 | CVPR | Segmentation of fMRI Data by Maximization of Region Contrast. | Pinaki S. Mitra, Vanathi Gopalakrishnan, Rebecca L. McNamee |
| 2006 | PAKDD | Rule Learning for Disease-Specific Biomarker Discovery from Clinical Proteomic Mass Spectra. | Vanathi Gopalakrishnan, Philip Ganchev, Srikanth Ranganathan, Robert P. Bowser |
| 2005 | RECOMB | Segmentation Conditional Random Fields (SCRFs): A New Approach for Protein Fold Recognition. | Yan Liu, Jaime G. Carbonell, Peter Weigele, Vanathi Gopalakrishnan |
| 2004 | SIGIR | Context sensitive vocabulary and its application in protein secondary structure prediction. | Yan Liu, Jaime G. Carbonell, Judith Klein-Seetharaman, Vanathi Gopalakrishnan |
| 2000 | ISMB | Intelligent Aids for Parallel Experiment Planning and Macromolecular Crystallization. | Vanathi Gopalakrishnan, Bruce G. Buchanan, John M. Rosenberg |
| 1998 | TIME | Representing and Learning Temporal Relationships among Experimental Variables. | Vanathi Gopalakrishnan, Bruce G. Buchanan |
| 1996 | AAAI | Inducing Design Biases that Characterize Successful Experimentation in Weak-Theory Domains: TIPS. | Vanathi Gopalakrishnan |
| 1994 | AAAI | The Crystallographer's Assistant. | Vanathi Gopalakrishnan, Daniel N. Hennessy, Bruce G. Buchanan, Devika Subramanian |
| 1994 | ISMB | Induction of Rules for Biological Macromolecular Crystallization. | Daniel N. Hennessy, Vanathi Gopalakrishnan, Bruce G. Buchanan, John M. Rosenberg, Devika Subramanian |