Cross species analysis of microarray expression data (2009)
Lu, Yong, Huggins, Peter, Bar-Joseph, Ziv
Motivation: Many biological systems operate in a similar manner across a large number of species or conditions. Cross-species analysis of sequence and interaction data is often applied to determine...
The Short Time-series Expression Miner (STEM) (2008)
The Short Time-series Expression Miner (STEM) is a Java application with a graphical user interface (GUI) designed for the analysis of short time-series gene expression microarray data. The software...
A Mixture of Feature Experts Approach for Protein-Protein Interaction Prediction (2008)
Yanjun Qi, Judith Klein-seetharaman, Ziv Bar-joseph
High-throughput methods can directly detect the set of interacting proteins in yeast but the results are often incomplete and exhibit high false positive and false negative rates. A number of...
Yanjun Qi, Judith Klein-seetharaman, Ziv Bar-joseph
mixture of feature experts approach for protein-protein
Yanxin Shi, Michael Klustein, Itamar Simon, Tom Mitchell, Ziv Bar-joseph
Motivation: When analyzing expression experiments, researchers are often interested in identifying the set of biological processes that are up-or down-regulated under the experimental condition...
Peña-Castillo, Lourdes, Tasan, Murat, Myers, Chad L, Lee, Hyunju, Joshi, Trupti, Zhang, Chao, ...
Abstract Background: Several years after sequencing the human genome and the mouse genome, much remains to be discovered about the functions of most human and mouse genes. Computational prediction of...
BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btl676 Systems biology (2008)
Yanxin Shi, Tom Mitchell, Ziv Bar-joseph
Inferring pairwise regulatory relationships from multiple time series datasets
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...
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...
Yong Lu, Roni Rosenfeld, Ziv Bar-joseph
doi:10.1093/bioinformatics/btl229 Identifying cycling genes by combining sequence homology and
Marc Cardle, Stephen Brooks, Ziv Bar-joseph, Peter Robinson
Figure 1 Fully-automated Sound Synthesis: Given a source animation and its associated soundtrack (Left), an unseen target animation of the same nature (Right) is analyzed to automatically synthesize...
Marc Cardle, Stephen Brooks, Ziv Bar-joseph, Peter Robinson
Figure 1 Fully-automated Sound Synthesis: Given a source animation and its associated soundtrack (Left), an unseen target animation of the same nature (Right) is analyzed to automatically synthesize...
Supplementary Methods for: Combining Static and (2008)
Time Series Data, Itamar Simon, Siegfried Zahava, Jason Ernst, Ziv Bar-joseph
problem: max YC P (Y i |Y C ) such that C M i dt = 1 (1) Here we are looking for a curve C with W (C) = M i , such that the observed values for i (Y i ) are a noisy sample of the values used for...
Supplementary Results For: Combining Static and (2008)
Time Series Data, Itamar Simon, Siegfried Zahava, Jason Ernst, Ziv Bar-joseph
this paper, this is not always the case and so we believe that it is better to first use Checksum and only afterwards, when it is determined that the temporal profiles are accurate, to normalize the...
A Patient-Gene Model for Temporal Expression Profiles in Clinical Studies (2008)
Naftali Kaminski, Ziv Bar-joseph
Pharmacogenomics and clinical studies that measure the temporal expression levels of patients can identify important pathways and biomarkers that are activated during disease progression or in...
A probabilistic generative model for GO enrichment analysis (2008)
Lu, Yong, Rosenfeld, Roni, Simon, Itamar, Nau, Gerard J., Bar-Joseph, Ziv
The Gene Ontology (GO) is extensively used to analyze all types of high-throughput experiments. However, researchers still face several challenges when using GO and other functional annotation...
Alignment and classification of time series gene expression in clinical studies (2008)
Lin, Tien-ho, Kaminski, Naftali, Bar-Joseph, Ziv
Motivation: Classification of tissues using static gene-expression data has received considerable attention. Recently, a growing number of expression datasets are measured as a time series. Methods...
Protein complex identification by supervised graph local clustering (2008)
Qi, Yanjun, Balem, Fernanda, Faloutsos, Christos, Klein-Seetharaman, Judith, Bar-Joseph, Ziv
Motivation: Protein complexes integrate multiple gene products to coordinate many biological functions. Given a graph representing pairwise protein interaction data one can search for subgraphs...
A mixture of feature experts approach for protein-protein interaction prediction (2007)
Qi, Yanjun, Klein-Seetharaman, Judith, Bar-Joseph, Ziv
Abstract Background High-throughput methods can directly detect the set of interacting proteins in model species but the results are often incomplete and exhibit high false positive and false...
A Fault-Tolerant Dynamic Atomic Broadcast Algorithm with QoS Guarantees (2007)
Ziv Bar-joseph, Idit Keidar, Nancy Lynch
We present a fault-tolerant algorithm for an atomic broadcast service with a dynamic set of participants; that is, reliable totally ordered multicast for dynamic groups. The algorithm preserves QoS...
(Guest Editors) Abstract Hierarchical Context-based Pixel Ordering (2007)
Eurographics P. Brunet, D. Fellner, Ziv Bar-joseph, Daniel Cohen-or
We present a context-based scanning algorithm which reorders the input image using a hierarchical representation of the image. Our algorithm optimally orders (permutes) the leaves corresponding to...
Ziv Bar-joseph, Tal Anker, Idit Keidar, Nancy Lynch
This paper studies the Quality of Service (QoS) guarantees of totally ordered multicast algorithms. The paper shows that totally ordered multicast can coexist with guaranteed predictable delays in...
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...
(Guest Editors) Abstract Hierarchical Context-based Pixel Ordering (2007)
Eurographics P. Brunet, D. Fellner, Ziv Bar-joseph, Daniel Cohen-or
We present a context-based scanning algorithm which reorders the input image using a hierarchical representation of the image. Our algorithm optimally orders (permutes) the leaves corresponding to...
Synthesis of Sound Textures by Learning and Resampling of Wavelet Trees (2007)
Shlomo Dubnov, Ziv Bar-joseph, Ran El-Yaniv, Dani Lischinski, Michael Werman
In this paper we present a statistical learning algorithm for synthesizing new random instances of a sound texture given an example of such a texture as input. A large class of natural and artificial...
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...
Combined analysis reveals a core set of cycling genes (2007)
Lu, Yong, Mahony, Shaun, Benos, Panayiotis V, Rosenfeld, Roni, Simon, Itamar, Breeden, Linda L, ...
Abstract Background Global transcript levels throughout the cell cycle have been characterized using microarrays in several species. Early analysis of these experiments focused on individual species....
Continuous hidden process model for time series expression experiments (2007)
Shi, Yanxin, Klustein, Michael, Simon, Itamar, Mitchell, Tom, Bar-Joseph, Ziv
Motivation: When analyzing expression experiments, researchers are often interested in identifying the set of biological processes that are up-or down-regulated under the experimental condition...
Inferring pairwise regulatory relationships from multiple time series datasets (2007)
Shi, Yanxin, Mitchell, Tom, Bar-Joseph, Ziv
Motivation: Time series expression experiments have emerged as a popular method for studying a wide range of biological systems under a variety of conditions. One advantage of such data is the...
STEM: a tool for the analysis of short time series gene expression data (2006)
Abstract Background Time series microarray experiments are widely used to study dynamical biological processes. Due to the cost of microarray experiments, and also in some cases the limited...
Yanjun Qi, Ziv Bar-joseph, Judith Klein-seetharaman
ABSTRACT Protein–protein interactions play a key role in many biological systems. High-throughput methods can directly detect the set of interacting proteins in yeast, but the results are often...
Identifying cycling genes by combining sequence homology and expression data (2006)
Lu, Yong, Rosenfeld, Roni, Bar-Joseph, Ziv
Motivation: The expression of genes during the cell division process has now been studied in many different species. An important goal of these studies is to identify the set of cycling genes. To...
Jason Ernst, Gerard J. Nau, Ziv Bar-joseph
Vol. 21 Suppl. 1 2005, pages i159–i168 doi:10.1093/bioinformatics/bti1022
A Mixture of Experts Approach for Protein-Protein Interaction (2005)
Prediction Yanjun Qi, Yanjun Qi, Judith Klein-seetharaman, Ziv Bar-joseph
High-throughput methods can directly detect the set of interacting proteins in yeast but the results are often incomplete and exhibit high false positive and false negative rates. A number of...
Clustering Short Time Series Gene Expression Data (2005)
Jason Ernst, Gerard J. Nau, Ziv Bar-Joseph
Motivation: Time series expression experiments are used to study a wide range of biological systems. More than 80% of all time series expression datasets are short (8 time points or fewer). These...
Random Forest Similarity for Protein-Protein Interaction Prediction (2005)
Y. Qi, J. Klein-seetharaman, Z. Bar-joseph, Yanjun Qi, Ziv Bar-joseph
One of the most important, but often ignored, parts of any clustering and classification algorithm is the computation of the similarity matrix. This is especially important when integrating high...
Clustering short time series gene expression data (2005)
Ernst, Jason, Nau, Gerard J., Bar-Joseph, Ziv
Motivation: Time series expression experiments are used to study a wide range of biological systems. More than 80% of all time series expression datasets are short (8 time points or fewer). These...
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
Analyzing time series gene expression data (2004)
Motivation: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. However, when analyzing these experiments researchers face many new...
Analyzing time series gene expression data (2004)
Motivation: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. However, when analyzing these experiments researchers face many new...
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...
Analyzing time series gene expression data (2004)
Motivation: Time series expression experiments are an increasingly popular method for studying a wide range of biological systems. However, when analyzing these experiments researchers face many new...
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...
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...
Early-delivery dynamic atomic broadcast (2002)
Ziv Bar-joseph, Idit Keidar, Nancy Lynch
Abstract. We consider a problem of atomic broadcast in a dynamic setting where processes may join, leave voluntarily, or fail (by stopping) during the course of computation. We provide a formal...
Early-delivery dynamic atomic broadcast (2002)
Ziv Bar-joseph, Idit Keidar, Nancy Lynch
We consider a problem of atomic broadcast in a dynamic setting where processes may join, leave voluntarily, or fail (by stopping) during the course of computation. We provide a formal definition of...
Early-delivery dynamic atomic broadcast (2002)
Ziv Bar-joseph, Idit Keidar, Nancy Lynch
We consider a problem of atomic broadcast in a dynamic setting where processes may join, leave voluntarily, or fail (by stopping) during the course of computation. We provide a formal de nition of...
Early-delivery dynamic atomic broadcast (2002)
Ziv Bar-joseph, Idit Keidar, Nancy Lynch
We consider a problem of atomic broadcast in a dynamic setting where processes may join, leave voluntarily, or fail (by stopping) during the course of computation. We provide a formal definition of...
Early-delivery dynamic atomic broadcast (2002)
Ziv Bar-joseph, Idit Keidar, Nancy Lynch
Abstract. We consider a problem of atomic broadcast in a dynamic setting where processes may join, leave voluntarily, or fail (by stopping) during the course of computation. We provide a formal...
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....
Early-delivery dynamic atomic broadcast (2002)
Abstract We consider a problem of atomic broadcast in a dynamic setting where processes may join, leave voluntarily, or fail (by stopping) during the course of computation. We provide a formal...
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...
Texture Mixing and Texture Movie Synthesis using Statistical Learning (2001)
Ziv Bar-joseph, Ran El-Yaniv, Dani Lischinski, Michael Werman
We present an algorithm based on statistical learning for synthesizing static and time-varying textures matching the appearance of an input texture. Our algorithm is general and automatic, and it...
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...
QoS preserving totally ordered multicast (2000)
Ziv Bar-joseph, Idit Keidar, Tal Anker, Nancy Lynch
Abstract. This paper presents an algorithm for totally ordered multicast which preserves Quality of Service (QoS) guarantees. The paper assumes a QoS reservation model in which the network allows for...
QoS Preserving Totally Ordered Multicast (2000)
Ziv Bar-joseph, Idit Keidar, Tal Anker, Nancy Lynch
This paper studies the Quality of Service (QoS) guarantees of totally ordered multicast algorithms. The paper shows that totally ordered multicast can coexist with guaranteed predictable delays in...
Granular Synthesis of Sound Textures using Statistical Learning (1999)
Ziv Bar-Joseph (Institute Of Computer Science, The Hebrew University Of Jerusalem, Israel), Dani Lischinski (Institute Of Computer Science, The Hebrew University Of Jerusalem, Israel), Michael Werman (Institute Of Computer Science, The Hebrew University Of Jerusalem, Israel), Shlomo Dubnov (Communication Systems Engineering, Ben-Gurion University, Beer-Sheva, Israel), Ran El-Yaniv (Department Of Computer Science, Technion - Israel Institute Of Technology)
Statistical Learning of Multi-Dimensional Textures (1999)
1 1 Introduction 2 1.1 OverviewofApproach ............................ 3 1.2 Thesis Outline . . . .............................. 4 2 Definitions 5 2.1 Textures.................................... 5...
A Tight Lower Bound for Randomized Synchronous Consensus (1999)
Ziv Bar-joseph, Michael Ben-or
We prove tight upper and lower bounds of \Theta(t= n) on the expected number of rounds needed for randomized synchronous consensus protocols for a fail-stop, full information, adaptive adversary. In...
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...
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...
Reconstructing dynamic regulatory maps
Ernst, Jason, Vainas, Oded, Harbison, Christopher T, Simon, Itamar, Bar-Joseph, Ziv
Even simple organisms have the ability to respond to internal and external stimuli. This response is carried out by a dynamic network of protein–DNA interactions that allows the specific regulation...
A Semi-Supervised Method for Predicting Transcription Factor–Gene Interactions in Escherichia coli
Ernst, Jason, Beg, Qasim K., Kay, Krin A., Balázsi, Gábor, Oltvai, Zoltán N., Bar-Joseph, Ziv
While Escherichia coli has one of the most comprehensive datasets of experimentally verified transcriptional regulatory interactions of any organism, it is still far from complete. This presents a...
Impact of the solvent capacity constraint on E. coli metabolism
Vazquez, Alexei, Beg, Qasim K, DeMenezes, Marcio A, Ernst, Jason, Bar-Joseph, Ziv, Barabási, Albert-László, ...
Combined analysis reveals a core set of cycling genes
Lu, Yong, Mahony, Shaun, Benos, Panayiotis V, Rosenfeld, Roni, Simon, Itamar, Breeden, Linda L, ...
The simultaneous analysis of expression data from multiple species reveals a core set of conserved cycling genes that is much larger than previously thought.
Bar-Joseph, Ziv, Siegfried, Zahava, Brandeis, Michael, Brors, Benedikt, Lu, Yong, Eils, Roland, ...
Characterization of the transcriptional regulatory network of the normal cell cycle is essential for understanding the perturbations that lead to cancer. However, the complete set of cycling genes in...
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence
Peña-Castillo, Lourdes, Tasan, Murat, Myers, Chad L, Lee, Hyunju, Joshi, Trupti, Zhang, Chao, ...
A probabilistic generative model for GO enrichment analysis
Lu, Yong, Rosenfeld, Roni, Simon, Itamar, Nau, Gerard J., Bar-Joseph, Ziv
The Gene Ontology (GO) is extensively used to analyze all types of high-throughput experiments. However, researchers still face several challenges when using GO and other functional annotation...
Backup in gene regulatory networks explains differences between binding and knockout results
Gitter, Anthony, Siegfried, Zehava, Klutstein, Michael, Fornes, Oriol, Oliva, Baldo, Simon, Itamar, ...
The complementarity of gene expression and protein–DNA interaction data led to several successful models of biological systems. However, recent studies in multiple species raise doubts about the...
Alignment and classification of time series gene expression in clinical studies
Lin, Tien-ho, Kaminski, Naftali, Bar-Joseph, Ziv
Motivation: Classification of tissues using static gene-expression data has received considerable attention. Recently, a growing number of expression datasets are measured as a time series. Methods...
Protein complex identification by supervised graph local clustering
Qi, Yanjun, Balem, Fernanda, Faloutsos, Christos, Klein-Seetharaman, Judith, Bar-Joseph, Ziv
Motivation: Protein complexes integrate multiple gene products to coordinate many biological functions. Given a graph representing pairwise protein interaction data one can search for subgraphs...
IL-3 and Oncogenic Abl Regulate the Myeloblast Transcriptome by Altering mRNA Stability
Ernst, Jason, Ghanem, Louis, Bar-Joseph, Ziv, McNamara, Michael, Brown, Jason, Steinman, Richard A.
The growth factor interleukin-3 (IL-3) promotes the survival and growth of multipotent hematopoietic progenitors and stimulates myelopoiesis. It has also been reported to oppose terminal...
Li, Lihong, Lu, Yong, Qin, Li-Xuan, Bar-Joseph, Ziv, Werner-Washburne, Margaret, Breeden, Linda L.
Ssd1 is an RNA-binding protein that affects literally hundreds of different processes and is polymorphic in both wild and lab yeast strains. We have used transcript microarrays to compare mRNA levels...