David K. Gifford

Tatsunori Hashimoto, Tommi Jaakkola, Richard Sherwood, Esteban O. Mazzoni, Hynek Wichterle, David K. Gifford: Lineage-based identification of cellular states and expression programs. Bioinformatics 28(12): 250-257 (2012)

Matthew D. Edwards, David K. Gifford: High-resolution genetic mapping with pooled sequencing. BMC Bioinformatics 13(S-6): S8 (2012)

Yuchun Guo, Shaun Mahony, David K. Gifford: High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints. PLoS Computational Biology 8(8) (2012)

P. Alexander Rolfe, David K. Gifford: ReadDB Provides Efficient Storage for Mapped Short Reads. BMC Bioinformatics 12: 278 (2011)

Timothy Danford, Robin D. Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David K. Gifford: Discovering Regulatory Overlapping RNA Transcripts. Journal of Computational Biology 18(3): 295-303 (2011)

Yuchun Guo, Georgios Papachristoudis, Robert C. Altshuler, Georg K. Gerber, Tommi Jaakkola, David K. Gifford, Shaun Mahony: Discovering homotypic binding events at high spatial resolution. Bioinformatics 26(24): 3028-3034 (2010)

Timothy Danford, Robin D. Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David K. Gifford: Discovering Regulatory Overlapping RNA Transcripts. RECOMB 2010: 110-122

Timothy Danford, P. Alexander Rolfe, David K. Gifford: GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data. Pacific Symposium on Biocomputing 2008: 539-550

Georg K. Gerber, Robin D. Dowell, Tommi Jaakkola, David K. Gifford: Automated Discovery of Functional Generality of Human Gene Expression Programs. PLoS Computational Biology 3(8) (2007)

Kenzie D. MacIsaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, Richard A. Young, Ernest Fraenkel: A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data. Bioinformatics 22(4): 423-429 (2006)

Kenzie D. MacIsaac, Ting Wang, D. Benjamin Gordon, David K. Gifford, Gary D. Stormo, Ernest Fraenkel: An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7: 113 (2006)

Yuan (Alan) Qi, Patrycja E. Missiuro, Ashish Kapoor, Craig P. Hunter, Tommi Jaakkola, David K. Gifford, Hui Ge: Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo. ISMB (Supplement of Bioinformatics) 2006: 417-423

Rohit Singh, Nathan Palmer, David K. Gifford, Bonnie Berger, Ziv Bar-Joseph: Active learning for sampling in time-series experiments with application to gene expression analysis. ICML 2005: 832-839

Karen Sachs, Omar D. Perez, Dana Pe'er, Garry P. Nolan, David K. Gifford, Tommi Jaakkola, Douglas A. Lauffenburger: Analysis of Signaling Pathways in Human T-Cells Using Bayesian Network Modeling of Single Cell Data. CSB 2004: 644

Ziv Bar-Joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, Roni Rosenfeld: Deconvolving cell cycle expression data with complementary information. ISMB/ECCB (Supplement of Bioinformatics) 2004: 23-30

Ken T. Takusagawa, David K. Gifford: Negative Information for Motif Discovery. Pacific Symposium on Biocomputing 2004: 360-371

Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Nathan Srebro, Angèle M. Hamel, Tommi Jaakkola: K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. Bioinformatics 19(9): 1070-1078 (2003)

Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi Jaakkola, Itamar Simon: Continuous Representations of Time-Series Gene Expression Data. Journal of Computational Biology 10(3/4): 341-356 (2003)

Alexander J. Hartemink, David K. Gifford, Tommi Jaakkola, Richard A. Young: Bayesian Methods for Elucidating Genetic Regulatory Networks. IEEE Intelligent Systems 17(2): 37-43 (2002)

Julia Khodor, David K. Gifford: Programmed Mutagenesis Is Universal. Theory Comput. Syst. 35(5): 483-500 (2002)

Julia Khodor, David K. Gifford: Experimental Efficiency of Programmed Mutagenesis. New Generation Comput. 20(3): 307-315 (2002)

Alexander J. Hartemink, David K. Gifford, Tommi Jaakkola, Richard A. Young: Combining Location and Expression Data for Principled Discovery of Genetic Regulatory Network Models. Pacific Symposium on Biocomputing 2002: 437-449

Ziv Bar-Joseph, Georg K. Gerber, David K. Gifford, Tommi Jaakkola, Itamar Simon: A new approach to analyzing gene expression time series data. RECOMB 2002: 39-48

Ziv Bar-Joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi Jaakkola, Nathan Srebro: K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data. WABI 2002: 506-520

Julia Khodor, David K. Gifford: Programmed Mutagenesis Is a Universal Model of Computation. DNA 2001: 300-307

Ziv Bar-Joseph, David K. Gifford, Tommi Jaakkola: Fast optimal leaf ordering for hierarchical clustering. ISMB (Supplement of Bioinformatics) 2001: 22-29

Alexander J. Hartemink, David K. Gifford, Tommi Jaakkola, Richard A. Young: Using Graphical Models and Genomic Expression Data to Statistically Validate Models of Genetic Regulatory Networks. Pacific Symposium on Biocomputing 2001: 422-433

Alex C. Snoeren, Kenneth Conley, David K. Gifford: Mesh Based Content Routing using XML. SOSP 2001: 160-173

John Jannotti, David K. Gifford, Kirk L. Johnson, M. Frans Kaashoek, James O'Toole Jr.: Overcast: Reliable Multicasting with an Overlay Network. OSDI 2000: 197-212

Bienvenido Vélez, Ron Weiss, Mark A. Sheldon, David K. Gifford: Fast and Effective Query Refinement. SIGIR 1997: 6-15

Ron Weiss, Bienvenido Vélez, Mark A. Sheldon, Chanathip Namprempre, Péter Szilágyi, Andrzej Duda, David K. Gifford: HyPursuit: A Hierarchical Network Search Engine that Exploits Content-Link Hypertext Clustering. Hypertext 1996: 180-193

Mark A. Sheldon, Andrzej Duda, David K. Gifford: Discover: A Resource Discovery System Based on Content Routing. Computer Networks and ISDN Systems 27(6): 953-972 (1995)

Ron Weiss, Andrzej Duda, David K. Gifford: Composition and Search with a Video Algebra. IEEE MultiMedia 2(1): 12-25 (1995)

David K. Gifford, Lawrence C. Stewart, Andrew C. Payne, G. Winfield Treese: Payment for Open Networks. COMPCON 1995: 26-31

Anthony D. Joseph, Alan F. deLespinasse, Joshua A. Tauber, David K. Gifford, M. Frans Kaashoek: Rover: A Toolkit for Mobile Information Access. SOSP 1995: 156-171

Mark A. Sheldon, Andrzej Duda, Ron Weiss, James O'Toole, David K. Gifford: Content Routing for Distributed Information Servers. EDBT 1994: 109-122

Ron Weiss, Andrzej Duda, David K. Gifford: Content-Based Access to Algebraic Video. ICMCS 1994: 140-151

Brian Reistad, David K. Gifford: Static Dependent Costs for Estimating Execution Time. LISP and Functional Programming 1994: 65-78

James O'Toole, Scott Nettles, David K. Gifford: Concurrent Compacting Garbage Collection of a Persistent Heap. SOSP 1993: 161-174

Vincent Dornic, Pierre Jouvelot, David K. Gifford: Polymorphic Time Systems for Estimating Program Complexity. LOPLAS 1(1): 33-45 (1992)

David K. Gifford: Five Forces Shaping Experimental Computer Science. Operating Systems Review 26(1): 6 (1992)

James O'Toole, David K. Gifford: Names should mean what, not where. ACM SIGOPS European Workshop 1992

David K. Gifford, James O'Toole: Intelligent File Systems for Object Repositories. Operating Systems of the 90s and Beyond 1991: 20-24

Pierre Jouvelot, David K. Gifford: Algebraic Reconstruction of Types and Effects. POPL 1991: 303-310

Vincent Dornic, Pierre Jouvelot, David K. Gifford: Polymorphic Time Systems for Estimating Program Complexity. JTASPEFT/WSA 1991: 9-17

David K. Gifford, Pierre Jouvelot, Mark A. Sheldon, James O'Toole: Semantic File Systems. SOSP 1991: 16-25

David K. Gifford: Polychannel Systems for Mass Digital Communications. Commun. ACM 33(2): 141-151 (1990)

James W. Stamos, David K. Gifford: Remote Evaluation. ACM Trans. Program. Lang. Syst. 12(4): 537-565 (1990)

James W. Stamos, David K. Gifford: Implementing Remote Evaluation. IEEE Trans. Software Eng. 16(7): 710-722 (1990)

Mark A. Sheldon, David K. Gifford: Static Dependent Types for First Class Modules. LISP and Functional Programming 1990: 20-29

James O'Toole, David K. Gifford: Type Reconstruction with First-Class Polymorphic Values. PLDI 1989: 207-217

Pierre Jouvelot, David K. Gifford: Reasoning about Continuations with Control Effects. PLDI 1989: 218-226

David K. Gifford, Roger M. Needham, Michael D. Schroeder: The Cedar System. Commun. ACM 31(3): 288-298 (1988)

David K. Gifford, Nathan Glasser: Remote Pipes and Procedures for Efficient Distributed Communication. ACM Trans. Comput. Syst. 6(3): 258-283 (1988)

Pierre Jouvelot, David K. Gifford: The FX-87 Interpreter. ICCL 1988: 65-72

John M. Lucassen, David K. Gifford: Polymorphic Effect Systems. POPL 1988: 47-57

Alfred Z. Spector, David K. Gifford: A Computer Science Perspective of Bridge Design. Commun. ACM 29(4): 267-283 (1986)

David K. Gifford, John M. Lucassen: Integrating Functional and Imperative Programming. LISP and Functional Programming 1986: 28-38

David K. Gifford, Alfred Z. Spector: The Cirrus Banking Network. Commun. ACM 28(8): 797-807 (1985)

David K. Gifford, James E. Donahue: Coordinating Independent Atomic Actions. COMPCON 1985: 92-95

Michael D. Schroeder, David K. Gifford, Roger M. Needham: A Caching File System For a Programmer's Workstation. SOSP 1985: 25-34

David K. Gifford, Robert W. Baldwin, Stephen T. Berlin, John M. Lucassen: An Architecture for Large Scale Information Systems. SOSP 1985: 161-170

David K. Gifford, Alfred Z. Spector: The TWA Reservation System. Commun. ACM 27(7): 649-665 (1984)

David K. Gifford, Alfred Z. Spector: The Space Shuttle Primary Computer System. Commun. ACM 27(9): 872-900 (1984)

Alfred Z. Spector, David K. Gifford: Case Study: IBM's System/360-370 Architecture. Commun. ACM 30(4): 291-307 (1984)

David K. Gifford: Cryptographic Sealing for Information Secrecy and Authentication. Commun. ACM 25(4): 274-286 (1982)

David K. Gifford: Surveyor's Forum: Technical Transactions. ACM Comput. Surv. 14(2): 316 (1982)

David K. Gifford: Violet, an Experimental Decentralized System. Computer Networks 5: 423-433 (1981)

David K. Gifford: Cryptographic Sealing for Information Secrecy and Authentication (Summary). SOSP 1981: 123-124

David K. Gifford: Weighted Voting for Replicated Data. SOSP 1979: 150-162

David K. Gifford: Hardware Estimation of Process' Primary Memory Requirements. Commun. ACM 20(9): 655-663 (1977)