| 2011 | BIBE | A Heuristic Algorithm for Detecting Intercellular Interactions. | Fahim Mohammad, Robert M. Flight, Benjamin J. Harrison, Jeffrey C. Petruska, Eric C. Rouchka |
| 2011 | BIBE | Interval Trees for Detection of Overlapping Genetic Entities. | Fahim Mohammad, Robert M. Flight, Benjamin J. Harrison, Jeffrey C. Petruska, Eric C. Rouchka |
| 2010 | ICMLA | A Bayesian Nonparametric Model for Joint Relation Integration and Domain Clustering. | Dazhuo Li, Fahim Mohammad, Eric C. Rouchka |
| 2009 | ICMLA | Feature Selection in Cancer Classification from mRNA Data Based on Localized Dimension Reduction. | Rami N. Mahdi, Eric C. Rouchka |
| 2009 | SNPD | Compute Pairwise Manhattan Distance and Pearson Correlation Coefficient of Data Points with GPU. | Dar-Jen Chang, Ahmed H. Desoky, Ming Ouyang, Eric C. Rouchka |
| 2008 | ICMLA | Model Based Unsupervised Learning Guided by Abundant Background Samples. | Rami N. Mahdi, Eric C. Rouchka |
| 2007 | CIBCB | Biological Sequence Mining Using Plausible Neural Network and its Application to Exon/intron Boundaries Prediction. | Kuo-Chen Li, Dar-Jen Chang, Eric C. Rouchka, Yuan Yan Chen |
| 2000 | ISMB | UTR Reconstruction and Analysis Using Genomically Aligned EST Sequences. | Zhengyan Kan, Warren Gish, Eric C. Rouchka, Jarret Glasscock, David J. States |
| 1999 | ISMB | Identity by Descent Genome Segmentation Based on Single Nucleotide Polymorphism Distributions. | Thomas W. Blackwell, Eric C. Rouchka, David J. States |
| 1998 | ISMB | Sequence Assembly Validation by Multiple Restriction Digest Fragment Coverage Analysis. | Eric C. Rouchka, David J. States |