D. Gifford

Tommi S. Jaakkola, David K. Gifford, Douglas A. Lauffenburger, 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

Genome-wide Map of Nucleosome Acetylation and Methylation in Yeast

Megan F. Cole, N. Hannett, C. T. Harbison, 2005, Cell.

Reasoning about continuations with control effects

Pierre Jouvelot, David K. Gifford, D. Gifford, 1989, PLDI '89.

Tissue-specific transcriptional regulation has diverged significantly between human and mouse

D. Gifford, E. Fraenkel, D. Odom, 2007, Nature Genetics.

Predicting gene expression in massively parallel reporter assays: A comparative study

Michael Wainberg, Manolis Kellis, Anshul Kundaje, 2017, Human mutation.

Polycomb complexes repress developmental regulators in murine embryonic stem cells

J. Zeitlinger, D. Gifford, R. Young, 2006, Nature.

Hierarchical Dirichlet Process-Based Models For Discovery of Cross-species Mammalian Gene Expression

Tommi S. Jaakkola, Robin D. Dowell, David K. Gifford, 2007 .

Control of Pancreas and Liver Gene Expression by HNF Transcription Factors

Nicola J. Rinaldi, T. Volkert, D. Gifford, 2004, Science.

Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells

Megan F. Cole, Richard G. Jenner, Sarah E. Johnstone, 2006, Cell.

Machine learning optimization of peptides for presentation by class II MHCs

D. Gifford, Haoyang Zeng, Siddhartha Jain, 2020, bioRxiv.

Quantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design.

Haoyang Zeng, David K Gifford, D. Gifford, 2019, Cell systems.

Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells

Megan F. Cole, Richard G. Jenner, Sarah E. Johnstone, 2005, Cell.

Modular combinatorial binding among human trans-acting factors reveals direct and indirect factor binding

David K. Gifford, Yuchun Guo, D. Gifford, 2015, bioRxiv.

Reveals Direct and Indirect Factor Binding

D. Gifford, Yuchun Guo, 2015 .

Modular Combinatorial Binding among Human Trans-acting Factors Reveals Direct and Indirect Factor Binding

D. Gifford, Yuchun Guo, 2015, bioRxiv.

Simultaneous computational discovery of dna regulatory motifs and transcription factor binding constraints at high spatial resolution

D. Gifford, Yuchun Guo, 2012 .

A synergistic DNA logic predicts genome-wide chromatin accessibility

Tatsunori B. Hashimoto, Daniel D. Kang, T. Jaakkola, 2016, Genome research.

High-throughput mapping of regulatory DNA

Matthew D. Edwards, D. Gifford, R. Sherwood, 2016, Nature Biotechnology.

Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay

D. Gifford, R. Sherwood, B. Banerjee, 2020, bioRxiv.

Embryonic stem cell-based system for mapping developmental transcriptional programs

Carolyn A. Morrison, D. Gifford, R. Young, 2011 .

Synergistic binding of transcription factors to cell-specific enhancers programs motor neuron identity

Carolyn A. Morrison, D. Gifford, E. Mazzoni, 2013, Nature Neuroscience.

A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction

D. Gifford, Haoyang Zeng, Yuchun Guo, 2017, bioRxiv.

IDR2D identifies reproducible genomic interactions

D. Gifford, Yuchun Guo, Konstantin Krismer, 2019, bioRxiv.

IDR2D identifies reproducible genomic interactions

D. Gifford, Yuchun Guo, Konstantin Krismer, 2020, Nucleic acids research.

Bayesian Network Approach to Cell Signaling Pathway Modeling

T. Jaakkola, K. Sachs, D. Lauffenburger, 2002, Science's STKE.

Coordinated binding of NF-kappaB family members in the response of human cells to lipopolysaccharide.

Richard G. Jenner, D. Gifford, R. Young, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Predicting the impact of non-coding variants on DNA methylation

D. Gifford, Haoyang Zeng, 2016, bioRxiv.

FX-87 Reference Manual. Edition 1.0.

Pierre Jouvelot, Mark A. Sheldon, David K. Gifford, 1987 .

Blazing Pathways Through Genetic Mountains

D. Gifford, 2001, Science.

Core transcriptional regulatory circuitry in human hepatocytes

Ernest Fraenkel, Robin D Dowell, Richard A Young, 2006, Molecular systems biology.

Genotype to Phenotype: A Complex Problem

Robin D Dowell, Corey Nislow, Charles Boone, 2010, Science.

Global Gene Deletion Analysis Exploring Yeast Filamentous Growth

Anne-Claude Gingras, David K. Gifford, Gerald R. Fink, 2012, Science.

High-resolution computational models of genome binding events

Ernest Fraenkel, Robin D Dowell, Richard A Young, 2006, Nature Biotechnology.

GERV: A Statistical Method for Generative Evaluation of Regulatory Variants for Transcription Factor Binding

Tatsunori B. Hashimoto, Daniel D. Kang, D. Gifford, 2015, bioRxiv.

Saltatory remodeling of Hox chromatin in response to rostro-caudal patterning signals

David K. Gifford, Esteban O. Mazzoni, Hynek Wichterle, 2013, Nature Neuroscience.

Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET

D. Gifford, R. Young, R. Jaenisch, 2008, Genome Biology.

“High resolution discovery of regulatory DNA with synthetic wild-type and ablated genome constructs”

D. Gifford, R. Sherwood, Benjamin Holmes, 2020 .

DNA Based Computers V

Erik Winfree, David K. Gifford, D. Gifford, 2000 .

Wnt Signaling Separates t he Progenitor and Endocrine Compartments during Pancreas Development Graphical

Cole Trapnell, D. Gifford, R. Chawla, 2019 .

A Peninsular Structure Coordinates Asynchronous Differentiation with Morphogenesis to Generate Pancreatic Islets

Cole Trapnell, D. Gifford, R. Chawla, 2019, Cell.

Wnt Signaling Separates the Progenitor and Endocrine Compartments during Pancreas Development.

Cole Trapnell, D. Gifford, R. Chawla, 2019, Cell reports.

Table 2 (Supplemental): Complete data for all 100 expression programs discovered by GeneProgram from the Novartis Gene Atlas v2

Tommi S. Jaakkola, Robin D. Dowell, David K. Gifford, 2007 .

Table 1 (Supplemental): Summary of expression programs discovered by GeneProgram from Novartis Tissue Atlas v2 data

Tommi S. Jaakkola, Robin D. Dowell, David K. Gifford, 2007 .

Bayesian Methods for Elucidating Genetic Regulatory Networks

Tommi S. Jaakkola, Richard A. Young, David K. Gifford, 2002, IEEE Intell. Syst..

A Multiplexed Barcodelet Single-Cell RNA-Seq Approach Elucidates Combinatorial Signaling Pathways that Drive ESC Differentiation.

D. Gifford, R. Sherwood, G. Yeo, 2020, Cell stem cell.

High resolution discovery of chromatin interactions

D. Gifford, H. Wichterle, Michael Closser, 2018, bioRxiv.

Deconvolving cell cycle expression data with complementary information

Ziv Bar-Joseph, Ronald Rosenfeld, David K. Gifford, 2004, ISMB/ECCB.

3. Paper: Semantic File Systems Semantic File Systems

Mark A. Sheldon, D. Gifford, P. Jouvelot, 1997 .

Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay.

D. Gifford, R. Sherwood, B. Banerjee, 2020, Genome research.

seqgra: principled selection of neural network architectures for genomics prediction tasks

D. Gifford, Jennifer Hammelman, Konstantin Krismer, 2022, Bioinformatics.

Discovering DNA motifs and genomic variants associated with DNA methylation

D. Gifford, Haoyang Zeng, 2016 .

A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction

D. Gifford, Haoyang Zeng, Yuchun Guo, 2017, bioRxiv.

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Alexander A. Morgan, Yanay Ofran, Predrag Radivojac, 2017, Human mutation.

A multi-parametric flow cytometric assay to analyze DNA–protein interactions

D. Gifford, S. Gygi, R. Sherwood, 2012, Nucleic acids research.

Accurate eQTL prioritization with an ensemble‐based framework

Matthew D. Edwards, D. Gifford, Haoyang Zeng, 2017, Human mutation.

Methods for Identifying Regulatory Grammars by Tahin Fahmid

D. Gifford, Tahin Syed, 2013 .

Robust computational design and evaluation of peptide vaccines for cellular immunity with application to SARS-CoV-2

D. Gifford, M. Carrington, Siddhartha Jain, 2020, bioRxiv.

Computational counterselection identifies nonspecific therapeutic biologic candidates

Sachit D. Saksena, D. Gifford, Geraldine Horny, 2022, Cell Reports Methods.

Extracting and Interpreting the Effects of Higher Order Sequence Features on Peptide MHC Binding

D. Gifford, M. Birnbaum, Zheng Dai, 2020, bioRxiv.

Gene co-regulation by Fezf2 selects neurotransmitter identity and connectivity of corticospinal neurons

J. Rinn, D. Gifford, S. Lodato, 2014, Nature Neuroscience.

Publishing RPC Services

D. Gifford, 2009 .

Transcriptional dynamics of murine motor neuron maturation in vivo and in vitro

D. Gifford, H. Wichterle, Michael Closser, 2022, Nature Communications.

A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding

D. Gifford, M. Birnbaum, Zheng Dai, 2022, bioRxiv.

A Cdx4-Sall4 Regulatory Module Controls the Transition from Mesoderm Formation to Embryonic Hematopoiesis

D. Gifford, L. Zon, R. White, 2013, Stem cell reports.

A pan-variant mRNA-LNP T cell vaccine protects HLA transgenic mice from mortality after infection with SARS-CoV-2 Beta

D. Gifford, Qiaobing Xu, Ying K. Tam, 2022, bioRxiv.

A Cdx 4-Sall 4 Regulatory Module Controls the Transition from Mesoderm Formation to Embryonic Hematopoiesis Citation

D. Gifford, L. Zon, R. White, 2013 .

Image classifiers can not be made robust to small perturbations

D. Gifford, Zheng Dai, 2021, ArXiv.

Information storage in a decentralized computer system

David Kenneth Gifford, D. Gifford, 1981 .

Small molecule inhibition of ATM kinase increases CRISPR-Cas9 1-bp insertion frequency

Sannie J. Culbertson, Max W. Shen, D. Gifford, 2021, Nature Communications.

Author Correction: Predictable and precise template-free CRISPR editing of pathogenic variants

David K. Gifford, Christopher A. Cassa, David R. Liu, 2019, Nature.

Predictable and precise template-free CRISPR editing of pathogenic variants

David K. Gifford, Christopher A. Cassa, David R. Liu, 2018, Nature.

Machine learning based CRISPR gRNA design for therapeutic exon skipping

Max W. Shen, D. Gifford, R. Sherwood, 2021, PLoS Comput. Biol..

An improved map of conserved regulatory sites for Saccharomyces cerevisiae

Ting Wang, Gary D. Stormo, Ernest Fraenkel, 2006, BMC Bioinformatics.

Convolutional neural network architectures for predicting DNA–protein binding

David K. Gifford, Matthew D. Edwards, Ge Liu, 2016, Bioinform..

GERV: A Statistical Method for Generative Evaluation of Regulatory Variants for Transcription Factor Binding

David K. Gifford, Tatsunori B. Hashimoto, Haoyang Zeng, 2015, bioRxiv.

Disentangled Representations of Cellular Identity

Ziheng Wang, Richard Sherwood, David Gifford, 2019, RECOMB.

Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

Robin D. Dowell, David K. Gifford, Gerald R. Fink, 2009, Proceedings of the National Academy of Sciences.

Sequence analysis A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data

Ernest Fraenkel, Richard A. Young, David K. Gifford, 2006 .

seqgra: principled selection of neural network architectures for genomics prediction tasks

D. Gifford, Jennifer Hammelman, Konstantin Krismer, 2021, bioRxiv.

Accurate eQTL prioritization with an ensemble-based framework

Matthew D. Edwards, D. Gifford, Haoyang Zeng, 2016, bioRxiv.

Global position and recruitment of HATs and HDACs in the yeast genome.

Nicola J. Rinaldi, Richard A Young, David K Gifford, 2004, Molecular cell.

Control of Transcription by Cell Size

D. Gifford, G. Fink, P. A. Rolfe, 2010, PLoS biology.

Feed-Forward Regulation of a Cell Fate Determinant by an RNA-Binding Protein Generates Asymmetry in Yeast

D. Gifford, G. Fink, Shaun Mahony, 2010, Genetics.

Control of Transcription by Cell Size Citation

D. Gifford, G. Fink, P. A. Rolfe, 2010 .

Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo

Yuan Qi, Ashish Kapoor, Tommi S. Jaakkola, 2006, ISMB.

Generative modeling of single-cell population time series for inferring cell differentiation landscapes

David K. Gifford, Grace H.T. Yeo, Sachit D. Saksena, 2020, bioRxiv.

DeepLigand: accurate prediction of MHC class I ligands using peptide embedding

Haoyang Zeng, David K Gifford, D. Gifford, 2019, Bioinform..

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

Yuchun Guo, David K. Gifford, Shaun Mahony, 2012, PLoS Comput. Biol..

Generative modeling of single-cell time series with PRESCIENT enables prediction of cell trajectories with interventions

Sachit D. Saksena, D. Gifford, G. Yeo, 2021, Nature Communications.

GSE: A Comprehensive Database System for the Representation, Retrieval, and Analysis of Microarray Data

David K. Gifford, Timothy Danford, P. Alexander Rolfe, 2007, Pacific Symposium on Biocomputing.

Computational discovery of gene modules, regulatory networks and expression programs

David K. Gifford, Georg K. Gerber, D. Gifford, 2007 .

Differentiated human stem cells resemble fetal, not adult, β cells

D. Gifford, Sinisa Hrvatin, D. Melton, 2014, Proceedings of the National Academy of Sciences.

A new approach to analyzing gene expression time series data

Tommi S. Jaakkola, Ziv Bar-Joseph, David K. Gifford, 2002, RECOMB '02.

Predictable and precise template-free CRISPR editing of pathogenic variants

David R. Liu, Jonathan Y. Hsu, Sannie J. Culbertson, 2018, Nature.

Expression of Terminal Effector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers

D. Gifford, H. Wichterle, Michael Closser, 2016, Neuron.

Expression of Terminal Ef fector Genes in Mammalian Neurons Is Maintained by a Dynamic Relay of Transient Enhancers Highlights

D. Gifford, H. Wichterle, Michael Closser, 2016 .

An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity

D. Gifford, E. Mazzoni, H. Wichterle, 2021, Neuron.

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal–fetal interface

Chad A. Cowan, T. Mikkelsen, J. Rinn, 2016, Proceedings of the National Academy of Sciences.

An Integrated Model of Multiple-Condition ChIP-Seq Data Reveals Predeterminants of Cdx2 Binding

David K. Gifford, Matthew D. Edwards, Richard Sherwood, 2014, RECOMB.

Global Control of Motor Neuron Topography Mediated by the Repressive Actions of a Single Hox Gene

Jonathan D. Grinstein, D. Gifford, R. Young, 2010, Neuron.

Discovering differential genome sequence activity with interpretable and efficient deep learning

D. Gifford, Jennifer Hammelman, 2021, bioRxiv.

Perspectives on ENCODE

Xintao Wei, Christopher B. Burge, Jason Liu, 2020, Nature.

MARIS: Method for Analyzing RNA following Intracellular Sorting

D. Gifford, Sinisa Hrvatin, D. Melton, 2014, PloS one.

Systematic elucidation of genetic mechanisms underlying cholesterol uptake

D. Gifford, R. Sherwood, G. Lettre, 2023, bioRxiv.

Identification of new branch points and unconventional introns in Saccharomyces cerevisiae

Eric T. Wang, Joseph M. Paggi, D. Gifford, 2016, RNA.

Ranking Reprogramming Factors for Directed Differentiation

D. Gifford, H. Wichterle, Michael Closser, 2021, bioRxiv.

Ruler Arrays Reveal Haploid Genomic Structural Variation

D. Gifford, G. Fink, P. A. Rolfe, 2012, PloS one.

Ruler Arrays Reveal Haploid Genomic Structural Variation Citation

D. Gifford, G. Fink, P. A. Rolfe, 2012 .

Supplemental Data Core Transcriptional Regulatory Circuitry in Human Embryonic Stem Cells

Richard G. Jenner, D. Gifford, R. Young, 2005 .

Rapid haplotype inference for nuclear families

David K Gifford, Amy L Williams, D. Gifford, 2010, Genome Biology.

Differential chromatin profiles partially determine transcription factor binding

David K. Gifford, D. Gifford, Rujian Chen, 2017, PloS one.

Ligand-dependent dynamics of retinoic acid receptor binding during early neurogenesis

Hynek Wichterle, Shaun Mahony, Richard A Young, 2011, Genome Biology.

Discovering Regulatory Overlapping RNA Transcripts

Robin D. Dowell, David K. Gifford, Timothy Danford, 2010, RECOMB.

Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets

D. Gifford, Brandon Carter, Ge Liu, 2020, bioRxiv.

High Resolution Modeling of Chromatin Interactions

David Gifford, Christopher Reeder, D. Gifford, 2013, RECOMB.

High-resolution genetic mapping with pooled sequencing

David K. Gifford, Matthew D. Edwards, D. Gifford, 2012, BMC Bioinformatics.

Antibody complementarity determining region design using high-capacity machine learning

Ziheng Wang, Jonas Mueller, Brandon Carter, 2019, bioRxiv.

Static dependent costs for estimating execution time

David K. Gifford, Brian Reistad, D. Gifford, 1994, LFP '94.

Transfer of cell type information across single-cell datasets using adversarial neural networks

David K. Gifford, Hui Ting Grace Yeo, D. Gifford, 2018, Annual International Conference on Research in Computational Molecular Biology.

Coordinating Independent Atomic Actions

David K. Gifford, James E. Donahue, D. Gifford, 1985, COMPCON.

Cryptographic Sealing for Information Secrecy and Authentication (Summary).

David K. Gifford, D. Gifford, 1981, Symposium on Operating Systems Principles.

Polychannel systems for mass digital communication

David K. Gifford, D. Gifford, 1988 .

Visualizing complex feature interactions and feature sharing in genomic deep neural networks

David K. Gifford, Ge Liu, Haoyang Zeng, 2019, BMC Bioinformatics.

An architecture for large scale information systems

David K. Gifford, Robert W. Baldwin, John M. Lucassen, 1985, Symposium on Operating Systems Principles.

Fast and effective query refinement

Ron Weiss, Mark A. Sheldon, David K. Gifford, 1997, SIGIR '97.

Content Routing for Distributed Information Servers

Mark A. Sheldon, David K. Gifford, James O'Toole, 1994, EDBT.

Polychannel systems for mass digital communications

David K. Gifford, D. Gifford, 1990, Commun. ACM.

Remote pipes and procedures for efficient distributed communication

David K. Gifford, Nathan Glasser, D. Gifford, 1988, TOCS.

Communication Models for Distributed Computation

David K. Gifford, D. Gifford, 1987 .

The Application of Digital Broadcast Communication to Large Scale Information Systems

D. Gifford, J. Lucassen, S. Berlin, 1985, IEEE J. Sel. Areas Commun..

High Resolution Mapping of Enhancer-Promoter Interactions

Hynek Wichterle, Christopher Reeder, David Gifford, 2015, PloS one.

Deconvolving cell cycle expression data with complementary information

I. Simon, D. Gifford, Z. Bar-Joseph, 2004, ISMB/ECCB.

Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions

Brandon Carter, Siddhartha Jain, David K. Gifford, 2020, Cell Systems.

Preliminary Immunogenicity of a Pan-COVID-19 T Cell Vaccine in HLA-A*02:01 Mice

D. Gifford, Qiaobing Xu, G. Gaiha, 2021, bioRxiv.

Chemogenetic System Demonstrates That Cas9 Longevity Impacts Genome Editing Outcomes

D. Gifford, R. Sherwood, Vedagopuram Sreekanth, 2020, ACS central science.

Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells

D. Gifford, A. Meissner, G. Weir, 2014, Nature Biotechnology.

Detection of gene cis-regulatory element perturbations in single-cell transcriptomes

Max W. Shen, D. Gifford, R. Sherwood, 2021, PLoS Comput. Biol..

K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data

Erik D. Demaine, Tommi S. Jaakkola, Ziv Bar-Joseph, 2002, WABI.

Fast optimal leaf ordering for hierarchical clustering

T. Jaakkola, D. Gifford, Z. Bar-Joseph, 2001, ISMB.

- ary Clustering with Optimal Leaf Ordering for Gene Expression Data

Erik D. Demaine, Nathan Srebro, David K. Gifford, 2022 .

Elucidating Genetic Regulatory Networks Using Graphical Models and Genomic Expression Data Authors:

D. Gifford, 2022 .

Interactions between chromosomal and nonchromosomal elements reveal missing heritability

Matthew D. Edwards, D. Gifford, G. Fink, 2014, Proceedings of the National Academy of Sciences.

Automated Discovery of Functional Generality of Human Gene Expression Programs

Tommi S. Jaakkola, Robin D. Dowell, David K. Gifford, 2007, PLoS Comput. Biol..

General and cell-type-specific aspects of the motor neuron maturation transcriptional program

D. Gifford, H. Wichterle, Michael Closser, 2021, bioRxiv.

Sequence to Better Sequence: Continuous Revision of Combinatorial Structures

Tommi S. Jaakkola, Jonas Mueller, David K. Gifford, 2017, ICML.

Design Concepts in Programming Languages

David K. Gifford, Franklyn Turbak, D. Gifford, 2008 .

Payment switches for open networks

Andrew C. Payne, Lawrence C. Stewart, G. Winfield Treese, 1995, Digest of Papers. COMPCON'95. Technologies for the Information Superhighway.

Ultra-high-diversity factorizable libraries for efficient therapeutic discovery

Sachit D. Saksena, D. Gifford, Zheng Dai, 2022, bioRxiv.

Comprehensive Mapping of Key Regulatory Networks that Drive Oncogene Expression

Max W. Shen, D. Gifford, R. Sherwood, 2020, Cell reports.

Active learning for sampling in time-series experiments with application to gene expression analysis

Ziv Bar-Joseph, David K. Gifford, Nathan P. Palmer, 2005, ICML.

Algebraic reconstruction of types and effects

Pierre Jouvelot, David K. Gifford, D. Gifford, 1991, POPL '91.

Names should mean what, not where

David K. Gifford, James O'Toole, D. Gifford, 1992, EW 5.

Polymorphic effect systems

David K. Gifford, John M. Lucassen, D. Gifford, 1988, POPL '88.

What made you do this? Understanding black-box decisions with sufficient input subsets

Jonas Mueller, Brandon Carter, Siddhartha Jain, 2018, AISTATS.

Systematic elucidation of genetic mechanisms underlying cholesterol uptake

D. Gifford, R. Sherwood, G. Lettre, 2023, Cell genomics.

The space shuttle primary computer system

David K. Gifford, Alfred Z. Spector, D. Gifford, 1984, CACM.

The TWA reservation system

David K. Gifford, Alfred Z. Spector, D. Gifford, 1984, CACM.

Static dependent types for first class modules

Mark A. Sheldon, David K. Gifford, D. Gifford, 1990, LISP and Functional Programming.

spatzie: an R package for identifying significant transcription factor motif co-enrichment from enhancer–promoter interactions

D. Gifford, Jennifer Hammelman, K. Krismer, 2021, bioRxiv.

Modeling Persistent Trends in Distributions

Tommi S. Jaakkola, David K. Gifford, Jonas Mueller, 2015, Journal of the American Statistical Association.

ReadDB Provides Efficient Storage for Mapped Short Reads

David K. Gifford, P. Alexander Rolfe, D. Gifford, 2011, BMC Bioinformatics.

Integrating functional and imperative programming

David K. Gifford, John M. Lucassen, D. Gifford, 1986, LFP '86.

Supporting online material for : Transcriptional Regulatory Networks in Saccharomyces cerevisiae

Nicola J. Rinaldi, John J. Wyrick, I. Simon, 2002 .

Training Data Attribution for Diffusion Models

D. Gifford, Zheng Dai, 2023, ArXiv.

Sequence analysis A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data

D. Gifford, R. Young, E. Fraenkel, 2006 .

Implementing Remote Evaluation

David K. Gifford, James W. Stamos, D. Gifford, 1990, IEEE Trans. Software Eng..

Mesh-based content routing using XML

Alex C. Snoeren, David K. Gifford, Kenneth Conley, 2001, SOSP.

Remote evaluation

David K. Gifford, James W. Stamos, D. Gifford, 1990, TOPL.

Surveyor's Forum: Technical Transactions

David K. Gifford, D. Gifford, 1982, CSUR.

Embryonic stem cell-based system for mapping developmental transcriptional programs

Carolyn A. Morrison, D. Gifford, R. Young, 2011, Nature Methods.

MIT Open Access Articles Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

D. Gifford, R. Young, S. Mccuine, 2022 .

Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation

David K. Gifford, Alexander J. Hartemink, D. Gifford, 1997, DNA Based Computers.

On the path to computation with DNA.

D K Gifford, D. Gifford, 1994, Science.

Cas9 Functionally Opens Chromatin

Tatsunori B. Hashimoto, D. Gifford, R. Sherwood, 2016, PloS one.

Universal Count Correction for High-Throughput Sequencing

David K. Gifford, Matthew D. Edwards, Tatsunori B. Hashimoto, 2014, PLoS Comput. Biol..

Local and global model interpretability via backward selection and clustering

Jonas Mueller, Brandon Carter, Siddhartha Jain, 2018 .

High-throughput mapping of regulatory DNA

Matthew D. Edwards, D. Gifford, R. Sherwood, 2016, Nature Biotechnology.

Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells

D. Gifford, A. Meissner, G. Weir, 2014, Nature Biotechnology.

Differentiated human stem cells resemble fetal, not adult, β cells

D. Gifford, D. Melton, P. Diiorio, 2014, Proceedings of the National Academy of Sciences.

Genotype to Phenotype: A Complex Problem

D. Gifford, G. Fink, G. Giaever, 2010, Science.

Polycomb complexes repress developmental regulators in murine embryonic stem cells

J. Zeitlinger, D. Gifford, R. Jaenisch, 2006, Nature.

Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

D. Gifford, G. Fink, R. Dowell, 2009, Proceedings of the National Academy of Sciences.

Bioinformatics Original Paper a Hypothesis-based Approach for Identifying the Binding Specificity of Regulatory Proteins from Chromatin Immunoprecipitation Data

D. Gifford, D. B. Gordon, E. Fraenkel, 2022 .

Global Control of Motor Neuron Topography Mediated by the Repressive Actions of a Single Hox Gene

D. Gifford, K. Anderson, E. Mazzoni, 2010, Neuron.

A distant trophoblast-specific enhancer controls HLA-G expression at the maternal–fetal interface

Chad A. Cowan, T. Mikkelsen, J. Rinn, 2016, Proceedings of the National Academy of Sciences.

Mapping Neuronal Diversity One Cell at a Time

D. Gifford, E. Mazzoni, H. Wichterle, 2013, Science.

A caching file system for a programmer's workstation

David K. Gifford, Roger M. Needham, Michael D. Schroeder, 1985, SOSP '85.

Comparing the continuous representation of time-series expression profiles to identify differentially expressed genes

T. Jaakkola, I. Simon, D. Gifford, 2003, Proceedings of the National Academy of Sciences of the United States of America.