Reut Shalgi, Daniel Lieber, Moshe Oren, Yitzhak Pilpel
microRNAs (miRs) are small RNAs that regulate gene expression at the posttranscriptional level. It is anticipated that, in combination with transcription factors (TFs), they span a regulatory network...
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs (2005)
Shalgi, Reut, Lapidot, Michal, Shamir, Ron, Pilpel, Yitzhak
Abstract Background In recent years, intensive computational efforts have been directed towards the discovery of promoter motifs that correlate with mRNA expression profiles. Nevertheless, it is...
Genome-Wide Co-Occurrence of Promoter Elements Reveals a Cis- (2003)
Priya Sudarsanam, Yitzhak Pilpel, George M. Church
Combinatorial regulation is an important feature of eukaryotic transcription. However, only a limited number of studies have characterized this aspect on a whole-genome level. We have conducted a...
Computational Identification of Transcription Factor (2003)
Zhou Zhu, Yitzhak Pilpel, George M. Church
addition, we also made de novo predictions for some unknown TF binding sites. q 2002 Elsevier Science Ltd. All rights reserved Keywords: computational biology; transcription factor; clustering; DNA...
Molecular Biology of the Cell (2002)
Barak A. Cohen, Yitzhak Pilpel, Robi D. Mitra, George M. Church
this report we focus on the response to H 2 O 2, but the full dataset is available at http://arep.med.harvard.edu/ExpressDB
Cohen, Barak A., Pilpel, Yitzhak, Mitra, Robi D., Church, George M.
Ohno [Ohno, S. (1970) in Evolution by Gene Duplication, Springer, New York] proposed that gene duplication with subsequent divergence of paralogs could be a major force in the evolution of new gene...
Lapidot, Michal, Pilpel, Yitzhak
We have generated a WWW interface for automated comprehensive analyses of promoter regulatory motifs and the effect they exert on mRNA expression profiles. The server provides a wide spectrum of...
Sudarsanam, Priya, Pilpel, Yitzhak, Church, George M.
Combinatorial regulation is an important feature of eukaryotic transcription. However, only a limited number of studies have characterized this aspect on a whole-genome level. We have conducted a...
Extraction of transcription regulatory signals from genome-wide DNA–protein interaction data
Garten, Yael, Kaplan, Shai, Pilpel, Yitzhak
Deciphering gene regulatory network architecture amounts to the identification of the regulators, conditions in which they act, genes they regulate, cis-acting motifs they bind, expression profiles...
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs
Shalgi, Reut, Lapidot, Michal, Shamir, Ron, Pilpel, Yitzhak
By analyzing 3' UTR sequences and mRNA decay profiles in yeast, 53 sequence motifs have been identified that may be implicated in stabilization or destabilization of mRNA.
Cohen, Barak A., Pilpel, Yitzhak, Mitra, Robi D., Church, George M.
Ohno [Ohno, S. (1970) in Evolution by Gene Duplication, Springer, New York] proposed that gene duplication with subsequent divergence of paralogs could be a major force in the evolution of new gene...
Lapidot, Michal, Pilpel, Yitzhak
We have generated a WWW interface for automated comprehensive analyses of promoter regulatory motifs and the effect they exert on mRNA expression profiles. The server provides a wide spectrum of...
Sudarsanam, Priya, Pilpel, Yitzhak, Church, George M.
Combinatorial regulation is an important feature of eukaryotic transcription. However, only a limited number of studies have characterized this aspect on a whole-genome level. We have conducted a...
Extraction of transcription regulatory signals from genome-wide DNA–protein interaction data
Garten, Yael, Kaplan, Shai, Pilpel, Yitzhak
Deciphering gene regulatory network architecture amounts to the identification of the regulators, conditions in which they act, genes they regulate, cis-acting motifs they bind, expression profiles...
A catalog of stability-associated sequence elements in 3' UTRs of yeast mRNAs
Shalgi, Reut, Lapidot, Michal, Shamir, Ron, Pilpel, Yitzhak
By analyzing 3' UTR sequences and mRNA decay profiles in yeast, 53 sequence motifs have been identified that may be implicated in stabilization or destabilization of mRNA.
Tabach, Yuval, Milyavsky, Michael, Shats, Igor, Brosh, Ran, Zuk, Or, Yitzhaky, Assif, ...
Deciphering regulatory events that drive malignant transformation represents a major challenge for systems biology. Here, we analyzed genome-wide transcription profiling of an in vitro cancerous...
The regulatory utilization of genetic redundancy through responsive backup circuits
Kafri, Ran, Levy, Melissa, Pilpel, Yitzhak
Functional redundancies, generated by gene duplications, are highly widespread throughout all known genomes. One consequence of these redundancies is a tremendous increase to the robustness of...
Global and Local Architecture of the Mammalian microRNA–Transcription Factor Regulatory Network
Shalgi, Reut, Lieber, Daniel, Oren, Moshe, Pilpel, Yitzhak
microRNAs (miRs) are small RNAs that regulate gene expression at the posttranscriptional level. It is anticipated that, in combination with transcription factors (TFs), they span a regulatory network...
Lapidot, Michal, Pilpel, Yitzhak
Many genomic loci contain transcription units on both strands, therefore two oppositely oriented transcripts can overlap. Often, one strand codes for a protein, whereas the transcript from the other...
Functional Characterization of Variations on Regulatory Motifs
Michal, Lapidot, Mizrahi-Man, Orna, Pilpel, Yitzhak
Transcription factors (TFs) regulate gene expression through specific interactions with short promoter elements. The same regulatory protein may recognize a variety of related sequences. Moreover,...
Kafri, Ran, Dahan, Orna, Levy, Jonathan, Pilpel, Yitzhak
The widely observed dispensability of duplicate genes is typically interpreted to suggest that a proportion of the duplicate pairs are at least partially redundant in their functions, thus allowing...
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...