| 2022 | RECOMB | Transcription Factor-Centric Approach to Identify Non-recurring Putative Regulatory Drivers in Cancer. | Jingkang Zhao, Vincentius Martin, Raluca Gordn |
| 2017 | RECOMB | Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. | Jingkang Zhao, Dongshunyi Li, Jungkyun Seo, Andrew S. Allen, Raluca Gordn |
| 2013 | RECOMB | Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors. | Alina Munteanu, Raluca Gordn |
| 2012 | PSB | Identification of Cell Cycle-Regulated, Putative Hyphal Genes in Candida Albicans. | Raluca Gordn, Saumyadipta Pyne, Martha L. Bulyk |
| 2010 | RECOMB | Distinguishing Direct versus Indirect Transcription Factor-DNA Interactions. | Raluca Gordn, Alexander J. Hartemink, Martha L. Bulyk |
| 2008 | PSB | Using DNA Duplex Stability Information for Transcription Factor Binding Site Discovery. | Raluca Gordn, Alexander J. Hartemink |
| 2008 | RECOMB | A Fast, Alignment-Free, Conservation-Based Method for Transcription Factor Binding Site Discovery. | Raluca Gordn, Leelavati Narlikar, Alexander J. Hartemink |
| 2007 | RECOMB | Nucleosome Occupancy Information Improves | Leelavati Narlikar, Raluca Gordn, Alexander J. Hartemink |
| 2006 | ISMB | Informative priors based on transcription factor structural class improve | Leelavati Narlikar, Raluca Gordn, Uwe Ohler, Alexander J. Hartemink |