Hardware Estimation of Process' Primary Memory Requirements. - David K. Gifford (Commun. ACM, 1977)

Weighted Voting for Replicated Data. - David K. Gifford (SOSP, 1979)

Cryptographic Sealing for Information Secrecy and Authentication (Summary). - David K. Gifford (SOSP, 1981)

Violet, an Experimental Decentralized System. - David K. Gifford (Comput. Networks, 1981)

Cryptographic Sealing for Information Secrecy and Authentication. - David K. Gifford (Commun. ACM, 1982)

Surveyor's Forum: Technical Transactions. - David K. Gifford (ACM Comput. Surv., 1982)

The TWA Reservation System. - David K. Gifford; Alfred Z. Spector (Commun. ACM, 1984)

The Space Shuttle Primary Computer System. - David K. Gifford; Alfred Z. Spector (Commun. ACM, 1984)

Coordinating Independent Atomic Actions. - David K. Gifford; James E. Donahue (COMPCON, 1985)

An Architecture for Large Scale Information Systems. - David K. Gifford; Robert W. Baldwin; Stephen T. Berlin; John M. Lucassen (SOSP, 1985)

A Caching File System For a Programmer's Workstation. - Michael D. Schroeder; David K. Gifford; Roger M. Needham (SOSP, 1985)

The Cirrus Banking Network. - David K. Gifford; Alfred Z. Spector (Commun. ACM, 1985)

The Application of Digital Broadcast Communication to Large Scale Information Systems. - David K. Gifford; John M. Lucassen; Stephen T. Berlin (IEEE J. Sel. Areas Commun., 1985)

Integrating Functional and Imperative Programming. - David K. Gifford; John M. Lucassen (LISP and Functional Programming, 1986)

A Computer Science Perspective of Bridge Design. - Alfred Z. Spector; David K. Gifford (Commun. ACM, 1986)

Case Study: IBM's System/360-370 Architecture. - Alfred Z. Spector; David K. Gifford (Commun. ACM, 1987)

The FX-87 Interpreter. - Pierre Jouvelot; David K. Gifford (ICCL, 1988)

Polymorphic Effect Systems. - John M. Lucassen; David K. Gifford (POPL, 1988)

The Cedar System. - David K. Gifford; Roger M. Needham; Michael D. Schroeder (Commun. ACM, 1988)

Remote Pipes and Procedures for Efficient Distributed Communication. - David K. Gifford; Nathan Glasser (ACM Trans. Comput. Syst., 1988)

Reasoning about Continuations with Control Effects. - Pierre Jouvelot; David K. Gifford (PLDI, 1989)

Type Reconstruction with First-Class Polymorphic Values. - James W. O'Toole Jr.; David K. Gifford (PLDI, 1989)

Static Dependent Types for First Class Modules. - Mark A. Sheldon; David K. Gifford (LISP and Functional Programming, 1990)

Polychannel Systems for Mass Digital Communications. - David K. Gifford (Commun. ACM, 1990)

Remote Evaluation. - James W. Stamos; David K. Gifford (ACM Trans. Program. Lang. Syst., 1990)

Implementing Remote Evaluation. - James W. Stamos; David K. Gifford (IEEE Trans. Software Eng., 1990)

Intelligent File Systems for Object Repositories. - David K. Gifford; James W. O'Toole Jr. (Operating Systems of the 90s and Beyond, 1991)

Algebraic Reconstruction of Types and Effects. - Pierre Jouvelot; David K. Gifford (POPL, 1991)

Semantic File Systems. - David K. Gifford; Pierre Jouvelot; Mark A. Sheldon; James W. O'Toole Jr. (SOSP, 1991)

Names should mean what, not where. - James W. O'Toole Jr.; David K. Gifford (ACM SIGOPS European Workshop, 1992)

Polymorphic Time Systems for Estimating Program Complexity. - Vincent Dornic; Pierre Jouvelot; David K. Gifford (LOPLAS, 1992)

Five Forces Shaping Experimental Computer Science. - David K. Gifford (ACM SIGOPS Oper. Syst. Rev., 1992)

Concurrent Compacting Garbage Collection of a Persistent Heap. - James W. O'Toole Jr.; Scott Nettles; David K. Gifford (SOSP, 1993)

Content Routing for Distributed Information Servers. - Mark A. Sheldon; Andrzej Duda; Ron Weiss; James W. O'Toole Jr.; David K. Gifford (EDBT, 1994)

Content-Based Access to Algebraic Video. - Ron Weiss; Andrzej Duda; David K. Gifford (ICMCS, 1994)

Static Dependent Costs for Estimating Execution Time. - Brian Reistad; David K. Gifford (LISP and Functional Programming, 1994)

Payment for Open Networks. - David K. Gifford; Lawrence C. Stewart; Andrew C. Payne; G. Winfield Treese (COMPCON, 1995)

Rover: A Toolkit for Mobile Information Access. - Anthony D. Joseph; Alan F. deLespinasse; Joshua A. Tauber; David K. Gifford; M. Frans Kaashoek (SOSP, 1995)

Payment Switches for Open Networks. - David K. Gifford; Lawrence C. Stewart; Andrew C. Payne; G. Winfield Treese (USENIX Workshop on Electronic Commerce, 1995)

Discover: A Resource Discovery System Based on Content Routing. - Mark A. Sheldon; Andrzej Duda; David K. Gifford (Comput. Networks ISDN Syst., 1995)

Composition and Search with a Video Algebra. - Ron Weiss; Andrzej Duda; David K. Gifford (IEEE Multim., 1995)

HyPursuit: A Hierarchical Network Search Engine that Exploits Content-Link Hypertext Clustering. - Ron Weiss; Bienvenido Vélez; Mark A. Sheldon; Chanathip Namprempre; Péter Szilágyi; Andrzej Duda; David K. Gifford (Hypertext, 1996)

Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation. - Alexander J. Hartemink; David K. Gifford (DNA Based Computers, 1997)

The efficiency of sequence-specific separation of DNA mixtures for biological computing. - Julia Khodor; David K. Gifford (DNA Based Computers, 1997)

Fast and Effective Query Refinement. - Bienvenido Vélez; Ron Weiss; Mark A. Sheldon; David K. Gifford (SIGIR, 1997)

Simulating biological reactions: A modular approach. - Alexander J. Hartemink; Tarjei S. Mikkelsen; David K. Gifford (DNA Based Computers, 1999)

Overcast: Reliable Multicasting with an Overlay Network. - John Jannotti; David K. Gifford; Kirk L. Johnson; M. Frans Kaashoek; James W. O'Toole Jr. (OSDI, 2000)

Programmed Mutagenesis Is a Universal Model of Computation. - Julia Khodor; David K. Gifford (DNA, 2001)

Fast optimal leaf ordering for hierarchical clustering. - Ziv Bar-Joseph; David K. Gifford; Tommi S. Jaakkola (ISMB (Supplement of Bioinformatics), 2001)

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 (Pacific Symposium on Biocomputing, 2001)

Mesh Based Content Routing using XML. - Alex C. Snoeren; Kenneth Conley; David K. Gifford (SOSP, 2001)

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 (Pacific Symposium on Biocomputing, 2002)

A new approach to analyzing gene expression time series data. - Ziv Bar-Joseph; Georg K. Gerber; David K. Gifford; Tommi S. Jaakkola; Itamar Simon (RECOMB, 2002)

Bayesian Methods for Elucidating Genetic Regulatory Networks. - Alexander J. Hartemink; David K. Gifford; Tommi S. Jaakkola; Richard A. Young (IEEE Intell. Syst., 2002)

Programmed Mutagenesis Is Universal. - Julia Khodor; David K. Gifford (Theory Comput. Syst., 2002)

Experimental Efficiency of Programmed Mutagenesis. - Julia Khodor; David K. Gifford (New Gener. Comput., 2002)

K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. - Ziv Bar-Joseph; Erik D. Demaine; David K. Gifford; Nathan Srebro; Angèle M. Hamel; Tommi S. Jaakkola (Bioinform., 2003)

Continuous Representations of Time-Series Gene Expression Data. - Ziv Bar-Joseph; Georg K. Gerber; David K. Gifford; Tommi S. Jaakkola; Itamar Simon (J. Comput. Biol., 2003)

Analysis of Signaling Pathways in Human T-Cells Using Bayesian Network Modeling of Single Cell Data. - Karen Sachs; Omar D. Perez; Dana Pe'er; Garry P. Nolan; David K. Gifford; Tommi S. Jaakkola; Douglas A. Lauffenburger (CSB, 2004)

Deconvolving cell cycle expression data with complementary information. - Ziv Bar-Joseph; Shlomit Farkash; David K. Gifford; Itamar Simon; Roni Rosenfeld (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Negative Information for Motif Discovery. - Ken T. Takusagawa; David K. Gifford (Pacific Symposium on Biocomputing, 2004)

Active learning for sampling in time-series experiments with application to gene expression analysis. - Rohit Singh 001; Nathan P. Palmer; David K. Gifford; Bonnie Berger; Ziv Bar-Joseph (ICML, 2005)

Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo. - Yuan (Alan) Qi; Patrycja E. Missiuro; Ashish Kapoor; Craig P. Hunter; Tommi S. Jaakkola; David K. Gifford; Hui Ge (ISMB (Supplement of Bioinformatics), 2006)

A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. - Kenzie D. MacIsaac; D. Benjamin Gordon; Lena Nekludova; Duncan T. Odom; Joerg Schreiber; David K. Gifford; Richard A. Young; Ernest Fraenkel (Bioinform., 2006)

An improved map of conserved regulatory sites for Saccharomyces cerevisiae. - Kenzie D. MacIsaac; Ting Wang; D. Benjamin Gordon; David K. Gifford; Gary D. Stormo; Ernest Fraenkel (BMC Bioinform., 2006)

Automated Discovery of Functional Generality of Human Gene Expression Programs. - Georg K. Gerber; Robin D. Dowell; Tommi S. Jaakkola; David K. Gifford (PLoS Comput. Biol., 2007)

GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data. - Timothy Danford; P. Alexander Rolfe; David K. Gifford (Pacific Symposium on Biocomputing, 2008)

Discovering homotypic binding events at high spatial resolution. - Yuchun Guo; Georgios Papachristoudis; Robert C. Altshuler; Georg K. Gerber; Tommi S. Jaakkola; David K. Gifford; Shaun Mahony (Bioinform., 2010)

ReadDB Provides Efficient Storage for Mapped Short Reads. - P. Alexander Rolfe; David K. Gifford (BMC Bioinform., 2011)

Stochastic motion planning and applications to traffic. - Sejoon Lim; Hari Balakrishnan; David Gifford 001; Samuel Madden 001; Daniela Rus (Int. J. Robotics Res., 2011)

Discovering Regulatory Overlapping RNA Transcripts. - Timothy Danford; Robin D. Dowell; Sudeep Agarwala; Paula Grisafi; Gerald Fink; David K. Gifford (J. Comput. Biol., 2011)

Lineage-based identification of cellular states and expression programs. - Tatsunori B. Hashimoto; Tommi S. Jaakkola; Richard Sherwood; Esteban O. Mazzoni; Hynek Wichterle; David K. Gifford (Bioinform., 2012)

High-resolution genetic mapping with pooled sequencing. - Matthew D. Edwards; David K. Gifford (BMC Bioinform., 2012)

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints. - Yuchun Guo; Shaun Mahony; David K. Gifford (PLoS Comput. Biol., 2012)

High Resolution Modeling of Chromatin Interactions. - Christopher Reeder; David Gifford 001 (RECOMB, 2013)

Universal Count Correction for High-Throughput Sequencing. - Tatsunori B. Hashimoto; Matthew D. Edwards; David K. Gifford (PLoS Comput. Biol., 2014)

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding. - Shaun Mahony; Matthew D. Edwards; Esteban O. Mazzoni; Richard I. Sherwood; Akshay Kakumanu; Carolyn A. Morrison; Hynek Wichterle; David K. Gifford (PLoS Comput. Biol., 2014)

Learning Population-Level Diffusions with Generative RNNs. - Tatsunori B. Hashimoto; David K. Gifford; Tommi S. Jaakkola (ICML, 2016)

Convolutional neural network architectures for predicting DNA-protein binding. - Haoyang Zeng; Matthew D. Edwards; Ge Liu; David K. Gifford (Bioinform., 2016)

GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding. - Haoyang Zeng; Tatsunori B. Hashimoto; Daniel D. Kang; David K. Gifford (Bioinform., 2016)

Sequence to Better Sequence: Continuous Revision of Combinatorial Structures. - Jonas Mueller 001; David K. Gifford; Tommi S. Jaakkola (ICML, 2017)

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 (RECOMB, 2017)

Predictable and precise template-free CRISPR editing of pathogenic variants. - Max W. Shen; Mandana Arbab; Jonathan Y. Hsu; Daniel Worstell; Sannie J. Culbertson; Olga Krabbe; Christopher A. Cassa; David R. Liu; David K. Gifford; Richard I. Sherwood (Nat., 2018)

What made you do this? Understanding black-box decisions with sufficient input subsets. - Brandon Carter 001; Jonas Mueller 001; Siddhartha Jain 001; David K. Gifford (AISTATS, 2019)

Disentangled Representations of Cellular Identity. - Ziheng Wang; Grace H. T. Yeo; Richard Sherwood; David Gifford 001 (RECOMB, 2019)

DeepLigand: accurate prediction of MHC class I ligands using peptide embedding. - Haoyang Zeng; David K. Gifford (Bioinform., 2019)

Visualizing complex feature interactions and feature sharing in genomic deep neural networks. - Ge Liu; Haoyang Zeng; David K. Gifford (BMC Bioinform., 2019)

Maximizing Overall Diversity for Improved Uncertainty Estimates in Deep Ensembles. - Siddhartha Jain 001; Ge Liu; Jonas Mueller 001; David Gifford 001 (AAAI, 2020)

Antibody complementarity determining region design using high-capacity machine learning. - Ge Liu; Haoyang Zeng; Jonas Mueller 001; Brandon Carter 001; Ziheng Wang; Jonas Schilz; Geraldine Horny; Michael E. Birnbaum; Stefan Ewert; David K. Gifford (Bioinform., 2020)

Information Condensing Active Learning. - Siddhartha Jain 001; Ge Liu; David K. Gifford (CoRR, 2020)

Lost in Pruning: The Effects of Pruning Neural Networks beyond Test Accuracy. - Lucas Liebenwein; Cenk Baykal; Brandon Carter 001; David Gifford 001; Daniela Rus (MLSys, 2021)

Overinterpretation reveals image classification model pathologies. - Brandon Carter 001; Siddhartha Jain 001; Jonas Mueller 001; David Gifford 001 (NeurIPS, 2021)

Machine learning optimization of peptides for presentation by class II MHCs. - Zheng Dai; Brooke D. Huisman; Haoyang Zeng; Brandon Carter 001; Siddhartha Jain 001; Michael E. Birnbaum; David K. Gifford (Bioinform., 2021)

Maximum n-times Coverage for COVID-19 Vaccine Design. - Ge Liu; Brandon Carter 001; David K. Gifford (CoRR, 2021)

Image classifiers can not be made robust to small perturbations. - Zheng Dai; David K. Gifford (CoRR, 2021)

Discovering differential genome sequence activity with interpretable and efficient deep learning. - Jennifer Hammelman; David K. Gifford (PLoS Comput. Biol., 2021)

Machine learning based CRISPR gRNA design for therapeutic exon skipping. - Wilson Louie; Max W. Shen; Zakir Tahiry; Sophia Zhang; Daniel Worstell; Christopher A. Cassa; Richard I. Sherwood; David K. Gifford (PLoS Comput. Biol., 2021)

Detection of gene cis-regulatory element perturbations in single-cell transcriptomes. - Grace Hui Ting Yeo; Oscar Juez; Qing Chen; Budhaditya Banerjee; Lendy Chu; Max W. Shen; May Sabry; Ive Logister; Richard I. Sherwood; David K. Gifford (PLoS Comput. Biol., 2021)

Maximum n-times Coverage for Vaccine Design. - Ge Liu; Alexander Dimitrakakis; Brandon Carter 001; David K. Gifford (ICLR, 2022)

Ultra High Diversity Factorizable Libraries for Efficient Therapeutic Discovery. - Zheng Dai; Sachit D. Saksena; Geraldine Horny; Christine Banholzer; Stefan Ewert; David K. Gifford (RECOMB, 2022)

seqgra: principled selection of neural network architectures for genomics prediction tasks. - Konstantin Krismer; Jennifer Hammelman; David K. Gifford (Bioinform., 2022)

Constrained Submodular Optimization for Vaccine Design. - Zheng Dai; David K. Gifford (AAAI, 2023)

Fundamental limits on the robustness of image classifiers. - Zheng Dai; David Gifford 001 (ICLR, 2023)

Training Data Attribution for Diffusion Models. - Zheng Dai; David K. Gifford (CoRR, 2023)

Ablation Based Counterfactuals. - Zheng Dai; David K. Gifford (CoRR, 2024)