Karen Sachs, Omar D. Perez, Garry P. Nolan, David K. Gifford, Tommi S, Douglas A. Lauffenburger
We perform network inference (‘reverse-engineering’) on phospho-specific multi-dimensional flow cytometry measurements of signaling molecules in human T cells using Bayesian networks. Inferred...
Laurie A. Boyer, Tong Ihn Lee, Megan F. Cole, Sarah E. Johnstone, Stuart S. Levine, Jacob P. Zucker, ...
have essential roles in early development and are required for the propagation of undifferentiated embryonic stem (ES) cells in culture. To gain insights into transcriptional regulation of human ES...
Abstract Rover: A Toolkit for Mobile Information Access (2009)
Anthony D. Joseph, Alan F. Delespinasse, Joshua A. Tauber, David K. Gifford, M. Frans Kaashoek
The Rover toolkit combines relocatable dynamic objects and queued remote procedure calls to provide unique services for “roving ” mobile applications. A relocatable dynamic object is an object...
VIEWPOINT Blazing Pathways Through Genetic (2008)
H. Haken, H. C. Wolf, Quantum Physics, A. J. Bhavnagarwala, B. L. Austin, K. A. Bowman, ...
advance from current multibillion transistor chips to the multitrillion transistor range of terascale integration.
Laurie A. Boyer, Tong Ihn Lee, Megan F. Cole, Sarah E. Johnstone, Stuart S. Levine, Jacob P. Zucker, ...
have essential roles in early development and are required for the propagation of undifferentiated embryonic stem (ES) cells in culture. To gain insights into transcriptional regulation of human ES...
Mathur, Divya, Danford, Timothy W., Boyer, Laurie A., Young, Richard A., Gifford, David K., Jaenisch, Rudolf
BACKGROUND: Genome-wide approaches have begun to reveal the transcriptional networks responsible for pluripotency in embryonic stem (ES) cells. Chromatin Immunoprecipitation (ChIP) followed either by...
Mathur, Divya, Danford, Timothy W, Boyer, Laurie A, Young, Richard A, Gifford, David K, Jaenisch, Rudolf
Abstract Background Genome-wide approaches have begun to reveal the transcriptional networks responsible for pluripotency in embryonic stem (ES) cells. Chromatin Immunoprecipitation (ChIP) followed...
Abstract A Caching File System For a Programmer's Workstation (2008)
Michael D. Schroeder, David K. Gifford, Roger M. Needham
This paper describes a file system for a programmer's workstation that has access both to a local disk and to remote file servers. The file system is designed to help programmers manage their...
BIOINFORMATICS ORIGINAL PAPER Sequence analysis (2008)
Kenzie D. Macisaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, ...
A hypothesis-based approach for identifying the binding specificity of regulatory proteins from chromatin immunoprecipitation data Vol. 22 no. 4 2006, pages 423–429 doi:10.1093/bioinformatics/bti815
Ziv Bar-joseph, Therese Biedl, Broňa Brejová, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, ...
Abstract. In this paper, we study how to present gene expression data to display similarities by trying to find a linear ordering of genes such that genes with similar expression profiles will be...
Theory of Computing Systems (2008)
Julia Khodor, David K. Gifford
Abstract. Programmed mutagenesis is a DNA computing system that uses cycles of DNA annealing, ligation, and polymerization to implement programatic rewriting of DNA sequences. We report that...
Networks in Saccharomyces cerevisiae (2008)
S. Nicholson, S. Some, B. Kone, J. Clim, Tong Ihn Lee, Nicola J. Rinaldi, ...
transport (32). The model was also used for tracer forecasts during the MINOS campaign. 40. E. Roeckner et al. “The atmospheric general circulation model ECHAM-4: Model description and simulation...
Abstract Overcast: Reliable Multicasting with an Overlay Network (2008)
John Jannotti, David K. Gifford, Kirk L. Johnson, M. Frans, Kaashoek James, Cisco Systems
Overcast is an application-level multicasting system that can be incrementally deployed using today’s Internet infrastructure. These properties stem from Overcast’s implementation as an overlay...
Algebraic Video for Composition and Content-Based Access (2007)
Ron Weiss, Andrzej Duda, David K. Gifford
We introduce a new data model called algebraic video that provides operations for the composition, search, navigation and playback of digital video presentations. Video presentations are composed...
Richard A. Young, Alexander J. Hartemink, Alexander J. Hartemink, David K. Gifford, David K. Gifford, Tommi S. Jaakkola, ...
We demonstrate how graphical models, and Bayesian networks in particular, can be used to model genetic regulatory networks. These models can be scored in a principled manner in the presence of...
Deoxyoligonucleotide Hybridization, Er J. Hartemink, David K. Gifford
for DNA Computation
Abstract Rover: A Toolkit for Mobile Information Access (2007)
Anthony D. Joseph, Alan F. Delespinasse, Joshua A. Tauber, David K. Gifford, M. Frans Kaashoek
The Rover toolkit combines relocatable dynamic objects and queued remote procedure calls to provide unique services for “roving ” mobile applications. A relocatable dynamic object is an object...
Alex C. Snoeren, Kenneth Conley, David K. Gifford
We have developed a new approach for reliably multicasting timecritical data to heterogeneous clients over mesh-based overlay networks. To facilitate intelligent content pruning, data streams are...
Mark A. Sheldon, Andrzej Duda, Ron Weiss, James W. O'toole, David K. Gifford
(DARPA) under contract DABT63-92-C-0012. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either...
Abstract Mesh-Based Content Routing using XML (2007)
Alex C. Snoeren, Kenneth Conley, David K. Gifford
We have developed a new approach for reliably multicasting timecritical data to heterogeneous clients over mesh-based overlay networks. To facilitate intelligent content pruning, data streams are...
Ecole des Mines de Paris (2007)
Pierre Jouvelot, David K. Gifford
We present the first algorithm for reconstructing the types and effects of expressions in the presence of first class procedures in a polymorphic typed language. Effects are static descriptions of...
ary Clustering with Optimal Leaf Ordering (2007)
For Gene Expression, Ziv Bar-joseph, Erik D. Demaine, David K. Gifford, Nathan Srebro, Angèle M. Hamel, ...
Motivation: A major challenge in gene expression analysis is effective data organization and visualization. One of the most popular tools for this task is hierarchical clustering. Hierarchical...
Alex C. Snoeren, Kenneth Conley, David K. Gifford
We have developed a new approach for reliably multicasting timecritical data to heterogeneous clients over mesh-based overlay networks. To facilitate intelligent content pruning, data streams are...
Continuous Representations of Time Series Gene Expression Data (2007)
Ziv Bar-joseph, Georg Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon
We present algorithms for time-series gene expression analysis that permit the principled estimation of unobserved time-points, clustering, and dataset alignment. Each expression profile is modeled...
Automated Discovery of Functional Generality of Human Gene Expression Programs (2007)
Georg K. Gerber, Robin D. Dowell, Tommi S. Jaakkola, David K. Gifford
An important research problem in computational biology is the identification of expression programs, sets of co-expressed genes orchestrating normal or pathological processes, and the...
Gerber, Georg K., Dowell, Robin D., Jaakkola, Tommi S., Gifford, David K.
An important research problem in computational biology is theidentification of expression programs, sets of co-activatedgenes orchestrating physiological processes, and thecharacterization of the...
Gerber, Georg K., Dowell, Robin D., Jaakkola, Tommi S., Gifford, David K.
An important research problem in computational biology is theidentification of expression programs, sets of co-activatedgenes orchestrating physiological processes, and thecharacterization of the...
Gerber, Georg K., Dowell, Robin D., Jaakkola, Tommi S., Gifford, David K.
Table 1 (Supplemental): Summary of recurrent expression programs (EPs) discovered by GeneProgram. The columns are: (1) the EP identifier (an arbitrarily assigned number), (2) the number of genes in...
Gerber, Georg K., Dowell, Robin D., Jaakkola, Tommi S., Gifford, David K.
Table 2 (Supplemental): Complete data for all 100 recurrent expression programs (EPs) discovered by GeneProgram. Each EP has two identifying rows, a list of meta-genes, and a list of significantly...
Gerber, Georg K., Dowell, Robin D., Jaakkola, Tommi S., Gifford, David K.
Table 2 (Supplemental): Complete data for all 100 recurrent expression programs (EPs) discovered by GeneProgram. Each EP has two identifying rows, a list of meta-genes, and a list of significantly...
Gerber, Georg K., Dowell, Robin D., Jaakkola, Tommi S., Gifford, David K.
Table 1 (Supplemental): Summary of recurrent expression programs (EPs) discovered by GeneProgram. The columns are: (1) the EP identifier (an arbitrarily assigned number), (2) the number of genes in...
Georg K. Gerber, Robin D. Dowell, Tommi S. Jaakkola, David K. Gifford
An important research problem in computational biology is the identification of expression programs, sets of coexpressed genes orchestrating normal or pathological processes, and the characterization...
Georg K. Gerber, Robin D. Dowell, Tommi S, David K. Gifford, Georg K. Gerber, Robin D. Dowell, ...
An important research problem in computational biology is the identification of expression programs, sets of co-activated genes orchestrating physiological processes, and the characterization of the...
An improved map of conserved regulatory sites for Saccharomyces cerevisiae (2006)
MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest
Abstract Background The regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was...
Kenzie D. Macisaac, D. Benjamin Gordon, Lena Nekludova, Duncan T. Odom, Joerg Schreiber, David K. Gifford, ...
Motivation: Genome-wide chromatin-immunoprecipitation (ChIPchip) detects binding of transcriptional regulators to DNA in vivo at low resolution. Motif discovery algorithms can be used to discover...
Qi, Yuan, Missiuro, Patrycja E., Kapoor, Ashish, Hunter, Craig P., Jaakkola, Tommi S., Gifford, David K., ...
Motivation: Gene expression profiling is a powerful approach to identify genes that may be involved in a specific biological process on a global scale. For example, gene expression profiling of...
Polychannel Systems for Mass Digital Communication. (2005)
We describe a new type of distributed computer system that looks beyond workstation and local area network assumptions towards the time when computers will be used by everyone at both home and the...
MacIsaac, Kenzie D., Gordon, D. Benjamin, Nekludova, Lena, Odom, Duncan T., Schreiber, Joerg, Gifford, David K., ...
Motivation: Genome-wide chromatin-immunoprecipitation (ChIP-chip) detects binding of transcriptional regulators to DNA in vivo at low resolution. Motif discovery algorithms can be used to discover...
DOI: 10.1093/bioinformatics/bth915 (2004)
Ziv Bar-joseph, Shlomit Farkash, David K. Gifford, Itamar Simon, Roni Rosenfeld
Vol. 20 Suppl. 1 2004, pages i23–i30
Deconvolving cell cycle expression data with complementary information (2004)
Bar-Joseph, Ziv, Farkash, Shlomit, Gifford, David K., Simon, Itamar, Rosenfeld, Roni
Motivation: In the study of many systems, cells are first synchronized so that a large population of cells exhibit similar behavior. While synchronization can usually be achieved for a short...
K-ary clustering with optimal leaf ordering for gene expression data (2003)
Ziv Bar-joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi S. Jaakkola, Nathan Srebro
Abstract. A major challenge in gene expression analysis is effective data organization and visualization. One of the most popular tools for this task is hierarchical clustering. Hierarchical...
K-ary clustering with optimal leaf ordering for gene expression data (2003)
Ziv Bar-joseph, Erik D. Demaine, David K. Gifford, Ang`ele M. Hamel, Tommi S. Jaakkola, Nathan Srebro
K-ary clustering with optimal leaf ordering for gene expression data (2003)
Ziv Bar-joseph, Erik D. Demaine, David K. Gifford, Angèle M. Hamel, Tommi S. Jaakkola, Nathan Srebro
Abstract. A major challenge in gene expression analysis is effective data organization and visualization. One of the most popular tools for this task is hierarchical clustering. Hierarchical...
Continuous Representations of Time-Series Gene Expression Data (2003)
Ziv Bar-joseph, Georg K. Gerber, David K. Gifford, Tommi S. Jaakkola, Itamar Simon
We present algorithms for time-series gene expression analysis that permit the principled estimation of unobserved time points, clustering, and dataset alignment. Each expression pro# le is modeled...
Do the Time-Warp: Continuous Alignment of Gene Expression Time-Series Data (2003)
David K. Gifford, Georg Kurt Gerber, Georg Kurt Gerber
expression levels of thousands of genes simultaneously, with time-series data o#ering particularly rich opportunities for understanding dynamic biological processes. Unfortunately, DNA microarray...
K-ary clustering with optimal leaf ordering for gene expression data (2003)
Ziv Bar-joseph, Erik D. Demaine, David K. Gifford, Ang`ele M. Hamel, Tommi S. Jaakkola, Nathan Srebro
K-ary clustering with optimal leaf ordering for gene expression data (2003)
Bar-Joseph, Ziv, Demaine, Erik D., Gifford, David K., Srebro, Nathan, Hamel, Angèle M., Jaakkola, Tommi S.
Motivation: A major challenge in gene expression analysis is effective data organization and visualization. One of the most popular tools for this task is hierarchical clustering. Hierarchical...
Boston Community Information System User Manual, (2002)
Lucassen,John M., Gifford,David K., Berlin,Steven T., Burmaster,David E.
The Boston Community Information System turns your computer into a personal information assistant that monitors the news as it happens. This experiment, CommInS, tests a new way of distributing world...
Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young
We develop principled methods for the automatic induction (discovery) of genetic regulatory network models from multiple data sources and data modalities. Models of regulatory networks are...
Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young
We develop principled methods for the automatic induction (discovery) of genetic regulatory network models from multiple data sources and data modalities. Models of regulatory networks are...
A new approach to analyzing gene expression time series data (2002)
Ziv Bar-joseph, Georg Gerber, David K. Gifford, Tommi S. Jaakkola
1 Introduction Principled methods for estimating unobserved time-points,clustering, and aligning microarray gene expression timeseries are needed to make such data useful for detailed anal-ysis....
David K. Gifford, Tommi S. Jaakkola
We develop principled methods for the automatic induction (discovery) of genetic regulatory network models from multiple data sources and data modalities. Models of regulatory networks are...
A New Approach to Analyzing Gene Expression Time Series Data (2002)
Ziv Bar-joseph, Georg Gerber, David K. Gifford, Tommi S. Jaakkola
We present algorithms for time-series gene expression analysis that permit the principled estimation of unobserved timepoints, clustering, and dataset alignment. Each expression profile is modeled as...
David K. Gifford, Tommi S. Jaakkola
We propose a model-driven approach for analyzing genomic expression data that permits genetic regulatory networks to be represented in a biologically interpretable computational form. Our models...
Alexander J. Hartemink, David K. Gifford, Tommi S. Jaakkola, Richard A. Young
this paper, we present a principled method for using genomic expression data to elucidate these genetic regulatory networks
Fast Optimal Leaf Ordering For Hierarchical Clustering (2001)
Ziv Bar-joseph, David K. Gifford, Tommi S. Jaakkola
We present the first practical algorithm for the optimal linear leaf ordering of trees that are generated by hierarchical clustering. Hierarchical clustering has been extensively used to analyze gene...
Fast optimal leaf ordering for hierarchical clustering (2001)
Bar-Joseph, Ziv, Gifford, David K., Jaakkola, Tommi S.
We present the first practical algorithm for the optimal linear leaf ordering of trees that are generated by hierarchical clustering. Hierarchical clustering has been extensively used to analyze gene...
Overcast: Reliable multicasting with an overlay network (2000)
John Jannotti, David K. Gifford, Kirk L. Johnson, M. Frans, Kaashoek James
Overcast is an application-level multicasting system that can be incrementally deployed using today's Internet infrastructure. These properties stem from Overcast's implementation as an...
Simulating Biological Reactions: A Modular Approach (1999)
Er J. Hartemink, Tarjei S. Mikkelsen, David K. Gifford
Abstract. We develop a general framework for simulating a sequence of biological reactions using small simulation modules. We demonstrate the usefulness of such a framework by implementing a...
Boston Community Information System 1986 Experimental Test Results. (1998)
Gifford, David K., Heitmann, Dawn, Segal, David A., Cote, Robert G., Tanacea, Kendra
This report describes the first year of an experimental test of the Boston Community Information System (Boston COMMINS). The experiment implements new ideas of data communication and database design...
FX-87 Reference Manual. Edition 1.0. (1998)
Gifford, David K., Jouvelot, Pierre, Lucassen, John M., Sheldon, Mark A.
The FX programming language is designed to support the parallel implementation of applications that perform both symbolic and scientific computations. Unlike previous languages, FX uses an effect...
Boston Community Information System User's Manual (Version 8.17). (1998)
Segal, David A., Gifford, David K., Lucassen, John M., Henderson, James B., Berlin, Stephen T.
The Boston Community Information System turns your computer into a personal information assistant that monitors the news as it happens. This experiment, CommInS, tests a new way of distributing world...
Walter User's Manual (Version 1.0). (1998)
Gifford, David K., Cote, Robert G., Segal, David A.
Walter is one of the experimental computer systems that is part of the Boston Community Information System Project. Walter allows you to use a UNIX system (including DEC Vaxes, IBM RTs, and Sun...
Clipping Service User's Manual (Version 1.2). (1998)
Gifford, David K., Cote, Robert G., Segal, David A.
The Clipping Service is a program that will send selected stories from the New York Times and other information sources to you via electronic mail. In order to use the Clipping Service, you first...
FX-87 Performance Measurements: Dataflow Implementation. (1998)
Hammel, R. T., Gifford, David K.
This report documents a series of experiments performed to explore the thesis that the FX-87 effect system permits a compiler to schedule imperative programs (i.e., programs that may contain...
Type Reconstruction with First-Class Polymorphic Values. (1998)
O'Toole, James W., Gifford, David K.
We present the first type reconstruction system which combines the implicit typing of ML with the full power of the explicity typed second-order polymorphic lambda calculus. The system will accept...
Boston Community Information System 1987-1988 Experimental Test Results. (1998)
Gifford, David K., Segal, David A.
The goal of Boston Community Information System Project is to explore new information system technologies that can provide sophisticated new services to entire metropolitan areas at moderate cost....
Report on the FX-91 Programming Language. (1998)
Gifford, David K., Jouvelot, Pierre, Sheldon, Mark A., O'Toole, James W.
This report gives a defining description of the programming language FX-91. The FX (short for FX-91) programming language is designed to support the parallel implementation of applications that...
Automated constraint-based nucleotide sequence selection for DNA computation (1998)
Er J. Hartemink, David K. Gifford, Julia Khodor
Computation
Ron Weiss, Peter Szilagyi, Andrzej Duda, David K. Gifford
ABSTRACT HyPursuit is a new hierarchical network search engine that clusters hypertext documents to structure a given information space for browsing and search activities. Our content-link clustering...
Payment Switches for Open Networks (1995)
David Gifford, David K. Gifford, Lawrence Stewart, Lawrence C. Stewart, Andrew C. Payne, Andrew C. Payne, ...
We describe the first operational Internet payment switch that provides real-time authorization suitable for direct use by merchant servers. A payment switch is a server that creates digital...
Rover: A Toolkit for Mobile Information Access (1995)
Anthony Joseph, Alan F. Delespinasse, Joshua A. Tauber, David K. Gifford, M. Frans Kaashoek
The Rover toolkit combines relocatable dynamic objects andqueued remote procedure calls to provide unique services for "roving" mobile applications. A relocatable dynamic object is an...
Discover: A Resource Discovery System based on Content Routing (1995)
Mark Sheldon, Andrzej Duda, Ron Weiss, David K. Gifford
. We have built an HTTP based resource discovery system called Discover that provides a single point of access to over 500 WAIS servers. Discover provides two key services: query refinement and query...
Discover: A Resource Discovery System based on Content Routing (1995)
Mark A. Sheldon, Andrzej Duda, Ron Weiss, David K. Gifford
. We have built an HTTP based resource discovery system called Discover that provides a single point of access to over 500 WAIS servers. Discover provides two key services: query refinement and query...
Content-based access to algebraic video (1994)
Andrzej Duda, Ron Weiss, David K. Gifford
Algebraic video uses a set of basic operations on video segments to create a desired video stream. The video algebra consists of operations for combining video segments, temporally organizing video...
Content Routing for Distributed Information Servers (1994)
Mark A. Sheldon, Andrzej Duda, Ron Weiss, James W. O'Toole, David K. Gifford
. We describe a system that provides query based associative access to the contents of distributed information servers. In typical distributed information systems there are so many objects that...
Static dependent costs for estimating execution time (1994)
Brian Reistad, David K. Gifford
We present the first system for estimating and using datadependent expression execution times in a language with first-class procedures and imperative constructs. Thepresence of first-class...
Names should mean what, not where (1992)
James W. O'toole, David K. Gifford
Naming is a fundamental issue in distributed systems that is growing in importance as the number of directly accessible systems and resources grows to the point that it is difficult to discover the...
Report on the fx programming language (1992)
David K. Gifford, Pierre Jouvelot, Mark A. Sheldon, James W. O'toole
This report gives a de ning description of the programming language FX. The FX programming language is designed to support the parallel implementation of applications that perform both symbolic and...
Names should mean what, not where (1992)
James W. O'toole, David K. Gifford
Naming is a fundamental issue in distributed systems that is growing in importance as the number of directly accessible systems and resources grows to the point that it is difficult to discover the...
David K. Gifford, Pierre Jouvelot, Mark A. Sheldon, James W. O'toole
A semantic file system is an information storage system that provides flexible associative access to the system's contents by automatically extracting attributes from files with file type...
Type Reconstruction with First-Class Polymorphic Values (1989)
James William OToole, David K. Gifford
We present the first type reconstruction system which combines the implicit typing of ML with the full power of the explicitly typed second-order polymorphic lambda calculus. The system will accept...
FX-87 Performance Measurements: Dataflow Implementation (1988)
R. Todd Hammel, R. Todd Hammel, R. Todd Hammel, David K. Gifford, David K. Gifford, David K. Gifford
We analyze how much the FX-87 static effect system can improve the execution times of five benchmark programs on a parallel graph interpreter. Three of our benchmark programs do not use side-effects...
FX-87 Performance Measurements: Dataflow Implementation (1988)
R. Todd Hammel, R. Todd Hammel, R. Todd Hammel, David K. Gifford, David K. Gifford, David K. Gifford
We analyze how much the FX-87 static effect system can improve the execution times of five benchmark programs on a parallel graph interpreter. Three of our benchmark programs do not use side-effects...
Polymorphic effect systems (1988)
John M. Lucassen, David K. Gifford
We present a new approach to programming lan-guages for parallel computers that uses an effect sys-tem to discover expression scheduling constraints. This effect system is part of a ‘kinded ’...
David K. Gifford, Pierre Jouvelotl, Mark A. Sheldon, James W. O’toole
A semantic jile s~stem is an information storage system that provides flexible associative access to the system’s contents by automatically extracting attributes from files with file type specific...
A Caching File System for a Programmer's Workstation (1985)
Michael D. Schroeder, David K. Gifford, Roger M. Needham
This paper describes a workstation file system that supports a group of cooperating programmers by allowing them both to manage local naming environments and to share consistent versions of...
Information storage in a decentralized computer system /--by David K. Gifford. (1981)
Thesis (Ph. D.)--Stanford University, 1981.
Information storage in a decentralized computer system / (1981)
Gifford, David K. (David Kenneth)
Typescript (photocopy).
Weighted voting for replicated data (1979)
In a new aliorithm for maintainhi replicated data, every. copy of a replicated file is ssiined some number of votes. Every. transaction collects a read quorum of votes to read a file, and a write...
Weighted voting for replicated data (1979)
In a new algorithm for maintaining replicated data, every copy of a replicated file is assigned some number of votes. Every transaction collects a read quorum of r votes to read a file, and a write...
Bar-Joseph, Ziv, Gerber, Georg, Simon, Itamar, Gifford, David K., Jaakkola, Tommi S.
We present a general algorithm to detect genes differentially expressed between two nonhomogeneous time-series data sets. As increasing amounts of high-throughput biological data become available, a...
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest
Coordinated binding of NF-κB family members in the response of human cells to lipopolysaccharide
Schreiber, Joerg, Jenner, Richard G., Murray, Heather L., Gerber, Georg K., Gifford, David K., Young, Richard A.
The NF-κB family of transcription factors plays a critical role in numerous cellular processes, particularly the immune response. Our understanding of how the different NF-κB subunits act...
Bar-Joseph, Ziv, Gerber, Georg, Simon, Itamar, Gifford, David K., Jaakkola, Tommi S.
We present a general algorithm to detect genes differentially expressed between two nonhomogeneous time-series data sets. As increasing amounts of high-throughput biological data become available, a...
Coordinated binding of NF-κB family members in the response of human cells to lipopolysaccharide
Schreiber, Joerg, Jenner, Richard G., Murray, Heather L., Gerber, Georg K., Gifford, David K., Young, Richard A.
The NF-κB family of transcription factors plays a critical role in numerous cellular processes, particularly the immune response. Our understanding of how the different NF-κB subunits act...
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest
Core transcriptional regulatory circuitry in human hepatocytes
Odom, Duncan T, Dowell, Robin D, Jacobsen, Elizabeth S, Nekludova, Lena, Rolfe, P Alexander, Danford, Timothy W, ...
We mapped the transcriptional regulatory circuitry for six master regulators in human hepatocytes using chromatin immunoprecipitation and high-resolution promoter microarrays. The results show that...
Automated Discovery of Functional Generality of Human Gene Expression Programs
Gerber, Georg K, Dowell, Robin D, Jaakkola, Tommi S, Gifford, David K
An important research problem in computational biology is the identification of expression programs, sets of co-expressed genes orchestrating normal or pathological processes, and the...
Analysis of the mouse embryonic stem cell regulatory networks obtained by ChIP-chip and ChIP-PET
Mathur, Divya, Danford, Timothy W, Boyer, Laurie A, Young, Richard A, Gifford, David K, Jaenisch, Rudolf
OCT4 and NANOG genomic targets were identified in mouse embryonic stem cells by ChIP-chip and were compared with previously reported ChIP-PET results.