Wang, Haidong, Segal, Eran, Ben-Hur, Asa, Li, Qian-Ru, Vidal, Marc, Koller, Daphne
Abstract We propose InSite, a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs. We compared our...
A Transcriptional Program Mediating Entry into Cellular Quiescence (2007)
Helen Liu, Adam S. Adler, Eran Segal, Howard Y. Chang
The balance of quiescence and cell division is critical for tissue homeostasis and organismal health. Serum stimulation of fibroblasts is well studied as a classic model of entry into the cell...
A Transcriptional Profile of Aging in the Human Kidney (2004)
Rebecca Sonu, Jacob M. Zahn, James Lund, Julie Wilhelmy, Lingli Wang, ...
A study of human aging in the kidney reveals similar changes in the transcriptional profile in cortex and medulla, suggesting that a common underlying aging process is taking place.
A Transcriptional Profile of Aging in the Human Kidney (2004)
Rebecca Sonu, Jacob M. Zahn, James Lund, Julie Wilhelmy, Lingli Wang, ...
In this study, we found 985 genes that change expression in the cortex and the medulla of the kidney with age. Some of the genes whose transcripts increase in abundance with age are known to be...
Rich probabilistic models for genomic data / (2004)
Segal, Eran., Koller, Daphne Advisor
Submitted to the Department of Computer Science.
Learning Module Networks (2003)
Eran Segal, Bauer Ctr, Daphne Koller, Nir Friedman
Methods for learning Bayesian networks can discover dependency structure between observed variables. Although these methods are useful in many applications, they run into computational and...
Learning Module Networks (2003)
Eran Segal, Bauer Ctr, Daphne Koller, Nir Friedman
Methods for learning Bayesian networks can discover dependency structure between observed variables. Although these methods are useful in many applications, they run into computational and...
Module Networks: Discovering Regulatory (2003)
Eran Segal, David Botstein, Daphne Koller, Nir Friedman
Introduction The complex functions of a living cell are carried out through the concerted activity of many genes and gene products. This activity is often coordinated by the organization of Computer...
The modular era of functional genomics (2003)
A report on the Keystone Symposium 'Functional Genomics: Global Analysis of Complex Biological Systems', Santa Fe, USA, 20-24 February 2003.
Boosting Density Estimation (2002)
Several authors have suggested viewing boosting as a gradient descent search for a good fit in function space. We apply gradient-based boosting methodology to the unsupervised learning problem of...
From Promoter Sequence to Expression: A Probabilistic Framework (2002)
Eran Segal, Yoseph Barash, Itamar Simon, Nir Friedman, Daphne Keller
We present a probabilistic framework that models the process by which transcriptional binding explains the mRNA expression of different genes. Our joint probabilistic model unifies the two key...
Probabilistic Abstraction Hierarchies (2002)
Eran Segal, Daphne Koller, Dirk Ormoneit
Many domains are naturally organized in an abstraction hierarchy or taxonomy, where the instances in "nearby" classes in the taxonomy are similar. In this paper, we provide a general probabilistic...
From Promoter Sequence to Expression: A Probabilistic Framework (2002)
Eran Segal, Yoseph Barash, Itamar Simon, Nir Friedman, Daphne Koller
We present a probabilistic framework that models the process by which transcriptional binding explains the mRNA expression of different genes. Our joint probabilistic model unifies the two key...
Probabilistic Hierarchical Clustering for Biological Data (2002)
Biological data, such as gene expression profiles or protein sequences, is often organized in a hierarchy of classes, where the instances assigned to "nearby" classes in the tree are similar. Most...
From Promoter Sequence to Expression: (2002)
Eran Segal, Yoseph Barash, Itamar Simon, Nir Friedman, Daphne Koller
We present a probabilistic framework that models the process by which transcriptional binding explains the mRNA expression of different genes. Our joint probabilistic model unifies the two key...
Probabilistic Models of Text and Link Structure for Hypertext Classification (2001)
Lise Getoor, Eran Segal, Ben Taskar, Daphne Koller
Most text classification methods treat each document as an independent instance. However, in many text domains, documents are linked and the topics of linked documents are correlated.
Probabilistic Abstraction Hierarchies (2001)
Eran Segal, Daphne Koller, Dirk Ormoneit
Many domains are naturally organized in an abstraction hierarchy or taxonomy, where the instances in "nearby" classes in the taxonomy are similar. In this paper, we provide a general probabilistic...
Exact Inference in Networks with Discrete Children of Continuous Parents (2001)
Uri Lerner, Eran Segal, Daphne Koller
Many real life domains contain a mixture of discrete
Efficient Bundle Sorting (2001)
Yossi Matias, Eran Segal, Jerey Scott Vitter
Many data sets to be sorted consist of a limited number of distinct keys. Sorting such data sets can be thought of as bundling together identical keys and having the bundles placed in order; we...
Probabilistic Models of Text and Link Structure for Hypertext Classification (2001)
Lise Getoor, Eran Segal, Ben Taskar, Daphne Koller
Most text classification methods treat each document as an independent instance. However, in many text domains, documents are linked and the topics of linked documents are correlated. For example,...
Probabilistic Classification and Clustering in Relational Data (2001)
Ben Taskar, Eran Segal, Daphne Koller
Supervised and unsupervised learning methods have traditionally focused on data consisting of independent instances of a single type. However, many real-world domains are best described by relational...
Rich Probabilistic Models for Gene Expression (2001)
Eran Segal, Ben Taskar, Audrey Gasch, Nir Friedman, Daphne Koller
Clustering is commonly used for analyzing gene expression data. Despite their successes, clustering methods suffer from a number of limitations. First, these methods reveal similarities that exist...
The modular era of functional genomics
A report on the Keystone Symposium 'Functional Genomics: Global Analysis of Complex Biological Systems', Santa Fe, USA, 20-24 February 2003.
Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression
Marion, Rosa M., Regev, Aviv, Segal, Eran, Barash, Yoseph, Koller, Daphne, Friedman, Nir, ...
Yeast cells modulate their protein synthesis capacity in response to physiological needs through the transcriptional control of ribosomal protein (RP) genes. Here we demonstrate that the...
Disruption of Yeast Forkhead-associated Cell Cycle Transcription by Oxidative StressD⃞
Shapira, Michael, Segal, Eran, Botstein, David
The effects of oxidative stress on yeast cell cycle depend on the stress-exerting agent. We studied the effects of two oxidative stress agents, hydrogen peroxide (HP) and the superoxide-generating...
A Transcriptional Profile of Aging in the Human Kidney
Rodwell, Graham E. J, Sonu, Rebecca, Zahn, Jacob M, Lund, James, Wilhelmy, Julie, Wang, Lingli, ...
In this study, we found 985 genes that change expression in the cortex and the medulla of the kidney with age. Some of the genes whose transcripts increase in abundance with age are known to be...
The modular era of functional genomics
A report on the Keystone Symposium 'Functional Genomics: Global Analysis of Complex Biological Systems', Santa Fe, USA, 20-24 February 2003.
Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression
Marion, Rosa M., Regev, Aviv, Segal, Eran, Barash, Yoseph, Koller, Daphne, Friedman, Nir, ...
Yeast cells modulate their protein synthesis capacity in response to physiological needs through the transcriptional control of ribosomal protein (RP) genes. Here we demonstrate that the...
Disruption of Yeast Forkhead-associated Cell Cycle Transcription by Oxidative StressD⃞
Shapira, Michael, Segal, Eran, Botstein, David
The effects of oxidative stress on yeast cell cycle depend on the stress-exerting agent. We studied the effects of two oxidative stress agents, hydrogen peroxide (HP) and the superoxide-generating...
A Transcriptional Profile of Aging in the Human Kidney
Rodwell, Graham E. J, Sonu, Rebecca, Zahn, Jacob M, Lund, James, Wilhelmy, Julie, Wang, Lingli, ...
In this study, we found 985 genes that change expression in the cortex and the medulla of the kidney with age. Some of the genes whose transcripts increase in abundance with age are known to be...
A Transcriptional Program Mediating Entry into Cellular Quiescence
Liu, Helen, Adler, Adam S, Segal, Eran, Chang, Howard Y
The balance of quiescence and cell division is critical for tissue homeostasis and organismal health. Serum stimulation of fibroblasts is well studied as a classic model of entry into the cell...
Reconstruction of Cell Lineage Trees in Mice
Wasserstrom, Adam, Adar, Rivka, Shefer, Gabi, Frumkin, Dan, Itzkovitz, Shalev, Stern, Tomer, ...
The cell lineage tree of a multicellular organism represents its history of cell divisions from the very first cell, the zygote. A new method for high-resolution reconstruction of parts of such cell...
Estimating Cell Depth from Somatic Mutations
Wasserstrom, Adam, Frumkin, Dan, Adar, Rivka, Itzkovitz, Shalev, Stern, Tomer, Kaplan, Shai, ...
The depth of a cell of a multicellular organism is the number of cell divisions it underwent since the zygote, and knowing this basic cell property would help address fundamental problems in several...
Wang, Haidong, Segal, Eran, Ben-Hur, Asa, Li, Qian-Ru, Vidal, Marc, Koller, Daphne
InSite is a computational method that integrates high-throughput protein and sequence data to infer the specific binding regions of interacting protein pairs.
Motif module map reveals enforcement of aging by continual NF-κB activity
Adler, Adam S., Sinha, Saurabh, Kawahara, Tiara L.A., Zhang, Jennifer Y., Segal, Eran, Chang, Howard Y.
Aging is characterized by specific alterations in gene expression, but their underlying mechanisms and functional consequences are not well understood. Here we develop a systematic approach to...
Baruch, Leehod, Itzkovitz, Shalev, Golan-Mashiach, Michal, Shapiro, Ehud, Segal, Eran
Synaptic wiring of neurons in Caenorhabditis elegans is largely invariable between animals. It has been suggested that this feature stems from genetically encoded molecular markers that guide the...
A Feature-Based Approach to Modeling Protein–DNA Interactions
Sharon, Eilon, Lubliner, Shai, Segal, Eran
Transcription factor (TF) binding to its DNA target site is a fundamental regulatory interaction. The most common model used to represent TF binding specificities is a position specific scoring...
Preferentially Quantized Linker DNA Lengths in Saccharomyces cerevisiae
Wang, Ji-Ping, Fondufe-Mittendorf, Yvonne, Xi, Liqun, Tsai, Guei-Feng, Segal, Eran, Widom, Jonathan
The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths...
Systematic functional characterization of cis-regulatory motifs in human core promoters
Sinha, Saurabh, Adler, Adam S., Field, Yair, Chang, Howard Y., Segal, Eran
A large number of cis-regulatory motifs involved in transcriptional control have been identified, but the regulatory context and biological processes in which many of them function are unknown. Here,...
Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals
Field, Yair, Kaplan, Noam, Fondufe-Mittendorf, Yvonne, Moore, Irene K., Sharon, Eilon, Lubling, Yaniv, ...
The detailed positions of nucleosomes profoundly impact gene regulation and are partly encoded by the genomic DNA sequence. However, less is known about the functional consequences of this encoding....
Shalem, Ophir, Dahan, Orna, Levo, Michal, Martinez, Maria Rodriguez, Furman, Itay, Segal, Eran, ...
The state of the transcriptome reflects a balance between mRNA production and degradation. Yet how these two regulatory arms interact in shaping the kinetics of the transcriptome in response to...