| 2008 | CBMS | Generating GO Slim Using Relational Database Management Systems to Support Proteomics Analysis. | Getiria Onsongo, Hongwei Xie, Timothy J. Griffin, John V. Carlis |
| 2005 | SAC | A complex biological database querying method. | Jake Yue Chen, John V. Carlis, Ning Gao |
| 2003 | SAC | Similar_Join: Extending DBMS with a Bio-specific Operator. | Jake Yue Chen, John V. Carlis |
| 2003 | SIGCSE | Using scientific data to teach a database systems course. | Paul J. Wagner, Elizabeth Shoop, John V. Carlis |
| 2001 | Interact | The Effects of Interruptions on Task Performance, Annoyance, and Anxiety in the User Interface. | Brian P. Bailey, Joseph A. Konstan, John V. Carlis |
| 2001 | WWW | WebMacros - a Proxy-based System for Recording and Replaying User Interactions with the Web. | Alex Safonov, Joseph A. Konstan, John V. Carlis |
| 2000 | SMC | Measuring the effects of interruptions on task performance in the user interface. | Brian P. Bailey, Joseph A. Konstan, John V. Carlis |
| 1998 | KDD | Blurring the Distinction between Command and Data in Scientific KDD. | John V. Carlis, Elizabeth Shoop, Scott Krieger |
| 1998 | UIST | Interactive Visualization of Serial Periodic Data. | John V. Carlis, Joseph A. Konstan |
| 1997 | CHI | The Neighborhood Viewer: A Paradigm for Exploring Image Databases. | John V. Carlis, Alex Safonov, Douglas P. Perrin, Joseph A. Konstan |
| 1990 | ICDE | A Shared Conceptual Schema for Four Medical Expert Systems. | James P. Held, John V. Carlis |
| 1986 | ICDE | HAS, a Relational Algebra Operator or Divide is not Enough to Conquer. | John V. Carlis |
| 1985 | ER | Conceptual Data Modelling of an Expert System. | James P. Held, John V. Carlis |
| 1984 | ICDE | A Descriptive Model of Physical Database Design Problems and Solutions. | John V. Carlis, Salvatore T. March |
| 1981 | ICIS | Physical Database Design: A DSS Approach. | John V. Carlis, Salvatore T. March, Gary W. Dickson |