| 2023 | AAAI | Constrained Submodular Optimization for Vaccine Design. | Zheng Dai, David K. Gifford |
| 2022 | ICLR | Maximum n-times Coverage for Vaccine Design. | Ge Liu, Alexander Dimitrakakis, Brandon Carter, David K. Gifford |
| 2022 | RECOMB | Ultra High Diversity Factorizable Libraries for Efficient Therapeutic Discovery. | Zheng Dai, Sachit D. Saksena, Geraldine Horny, Christine Banholzer, Stefan Ewert, David K. Gifford |
| 2019 | AISTATS | What made you do this? Understanding black-box decisions with sufficient input subsets. | Brandon Carter, Jonas Mueller, Siddhartha Jain, David K. Gifford |
| 2017 | ICML | Sequence to Better Sequence: Continuous Revision of Combinatorial Structures. | Jonas Mueller, David K. Gifford, Tommi S. Jaakkola |
| 2017 | RECOMB | K-mer Set Memory (KSM) Motif Representation Enables Accurate Prediction of the Impact of Regulatory Variants. | Yuchun Guo, Kevin Tian, Haoyang Zeng, David K. Gifford |
| 2016 | ICML | Learning Population-Level Diffusions with Generative RNNs. | Tatsunori B. Hashimoto, David K. Gifford, Tommi S. Jaakkola |
| 2014 | RECOMB | An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding. | Shaun Mahony, Matthew D. Edwards, Esteban O. Mazzoni, Richard Sherwood, Akshay Kakumanu, Carolyn A. Morrison, Hynek Wichterle, David K. Gifford |
| 2010 | RECOMB | Discovering Regulatory Overlapping RNA Transcripts. | Timothy Danford, Robin D. Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David K. Gifford |
| 2008 | PSB | GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data. | Timothy Danford, P. Alexander Rolfe, David K. Gifford |
| 2006 | ISMB | Semi-supervised analysis of gene expression profiles for lineage-specific development in the | Yuan (Alan) Qi, Patrycja E. Missiuro, Ashish Kapoor, Craig P. Hunter, Tommi S. Jaakkola, David K. Gifford, Hui Ge |
| 2005 | ICML | Active learning for sampling in time-series experiments with application to gene expression analysis. | Rohit Singh, Nathan P. Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph |
| 2004 | ISMB | Deconvolving cell cycle expression data with complementary information. | Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, Roni Rosenfeld |
| 2004 | PSB | Negative Information for Motif Discovery. | Ken T. Takusagawa, David K. Gifford |
| 2002 | PSB | Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models. | Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young |
| 2002 | RECOMB | A new approach to analyzing gene expression time series data. | Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon |
| 2002 | WABI | K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. | Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angle M. Hamel, Tommi S. Jaakkola, Nathan Srebro |
| 2001 | DNA | Programmed Mutagenesis Is a Universal Model of Computation. | Julia Khodor, David K. Gifford |
| 2001 | ISMB | Fast optimal leaf ordering for hierarchical clustering. | Ziv Bar-Joseph, David K. Gifford, Tommi S. Jaakkola |
| 2001 | PSB | Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks. | Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young |
| 2001 | SOSP | Mesh Based Content Routing using XML. | Alex C. Snoeren, Kenneth Conley, David K. Gifford |
| 2000 | OSDI | Overcast: Reliable Multicasting with an Overlay Network. | John Jannotti, David K. Gifford, Kirk L. Johnson, M. Frans Kaashoek, James W. O'Toole Jr. |
| 1997 | SIGIR | Fast and Effective Query Refinement. | Bienvenido Vlez, Ron Weiss, Mark A. Sheldon, David K. Gifford |
| 1995 | SOSP | Rover: A Toolkit for Mobile Information Access. | Anthony D. Joseph, Alan F. deLespinasse, Joshua A. Tauber, David K. Gifford, M. Frans Kaashoek |
| 1994 | EDBT | Content Routing for Distributed Information Servers. | Mark A. Sheldon, Andrzej Duda, Ron Weiss, James W. O'Toole Jr., David K. Gifford |
| 1993 | SOSP | Concurrent Compacting Garbage Collection of a Persistent Heap. | James W. O'Toole Jr., Scott Nettles, David K. Gifford |
| 1991 | POPL | Algebraic Reconstruction of Types and Effects. | Pierre Jouvelot, David K. Gifford |
| 1991 | SAS | Polymorphic Time Systems for Estimating Program Complexity. | Vincent Dornic, Pierre Jouvelot, David K. Gifford |
| 1991 | SOSP | Semantic File Systems. | David K. Gifford, Pierre Jouvelot, Mark A. Sheldon, James W. O'Toole Jr. |
| 1989 | PLDI | Reasoning about Continuations with Control Effects. | Pierre Jouvelot, David K. Gifford |
| 1989 | PLDI | Type Reconstruction with First-Class Polymorphic Values. | James W. O'Toole Jr., David K. Gifford |
| 1988 | POPL | Polymorphic Effect Systems. | John M. Lucassen, David K. Gifford |
| 1985 | SOSP | An Architecture for Large Scale Information Systems. | David K. Gifford, Robert W. Baldwin, Stephen T. Berlin, John M. Lucassen |
| 1985 | SOSP | A Caching File System For a Programmer's Workstation. | Michael D. Schroeder, David K. Gifford, Roger M. Needham |
| 1981 | SOSP | Cryptographic Sealing for Information Secrecy and Authentication (Summary). | David K. Gifford |
| 1979 | SOSP | Weighted Voting for Replicated Data. | David K. Gifford |