Evolutionary conservation of domain-domain interactions (2006)
Itzhaki, Zohar, Akiva, Eyal, Altuvia, Yael, Margalit, Hanah
Abstract Background Recently, there has been much interest in relating domain-domain interactions (DDIs) to protein-protein interactions (PPIs) and vice versa , in an attempt to understand the...
Co-evolution of transcription factors and their targets depends on mode of regulation (2006)
Hershberg, Ruth, Margalit, Hanah
Abstract Background Differences in the transcription regulation network are at the root of much of the phenotypic variation observed among organisms. These differences may be achieved either by...
Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge (2005)
Tommy Kaplan, Nir Friedman, Hanah Margalit
Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structure-based approach applicable...
IntAct: an open source molecular interaction database (2004)
Hermjakob,Henning, Montecchi-Palazzi,Luisa, Lewington,Chris, Mudali,Sugath, Kerrien,Samuel, Orchard,Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
IntAct: an open source molecular interaction database (2004)
Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
Markovian Domain Fingerprinting: Statistical Segmentation of Protein Sequences (2001)
Gill Bejerano, Yevgeny Seldin, Hanah Margalit, Naftali Tishby
Motivation: Characterization of a protein family by its distinct sequence domains is crucial for functional annotation and correct classification of newly discovered proteins. Conventional Multiple...
Novel small RNA-encoding genes in the intergenic regions of Escherichia Coli (2001)
Liron Argaman, Ruth Hershberg, Gill Bejerano, E. Gerhart, H. Wagner, Hanah Margalit, ...
tributed equally to this work. to the prediction of 24 putative sRNA-encoding genes, of which 23 were Received: 2 May 2001 tested experimentally. Here we report on the discovery of 14 genes Revised:...
Gill Bejerano, Yevgeny Seldin, Hanah Margalit, Naftali Tishby
We present a novel information theoretic method for protein domain and statistical signature extraction. We apply a new algorithm [20] for unsupervised segmentation of sequences into alternating...
Mishmar, Dan, Rahat, Ayelet, Scherer, Stephen W., Nyakatura, Gerald, Hinzmann, Bernd, Kohwi, Yoshinori, ...
Common fragile sites are chromosomal loci prone to breakage and rearrangement, hypothesized to provide targets for foreign DNA integration. We cloned a simian virus 40 integration site and showed by...
Hershberg, Ruti, Bejerano, Gill, Santos-Zavaleta, Alberto, Margalit, Hanah
PromEC is an updated compilation of Escherichia coli mRNA promoter sequences. It includes documentation on the location of experimentally identified mRNA transcriptional start sites on the E.coli...
Conserved sequence elements associated with exon skipping
Miriami, Elana, Margalit, Hanah, Sperling, Ruth
One of the major forms of alternative splicing, which generates multiple mRNA isoforms differing in the precise combinations of their exon sequences, is exon skipping. While in constitutive splicing...
SURVEY AND SUMMARY: A survey of small RNA-encoding genes in Escherichia coli
Hershberg, Ruth, Altuvia, Shoshy, Margalit, Hanah
Small RNA (sRNA) molecules have gained much interest lately, as recent genome-wide studies have shown that they are widespread in a variety of organisms. The relatively small family of 10 known...
Yeger-Lotem, Esti, Margalit, Hanah
The post-genomic era is marked by huge amounts of data generated by large-scale functional genomic and proteomic experiments. A major challenge is to integrate the various types of genome-scale...
Molecular Basis for Expression of Common and Rare Fragile Sites
Zlotorynski, Eitan, Rahat, Ayelet, Skaug, Jennifer, Ben-Porat, Neta, Ozeri, Efrat, Hershberg, Ruth, ...
Fragile sites are specific loci that form gaps, constrictions, and breaks on chromosomes exposed to partial replication stress and are rearranged in tumors. Fragile sites are classified as rare or...
IntAct: an open source molecular interaction database
Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
Yeger-Lotem, Esti, Sattath, Shmuel, Kashtan, Nadav, Itzkovitz, Shalev, Milo, Ron, Pinter, Ron Y., ...
Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of...
Hierarchy of Sequence-Dependent Features Associated With Prokaryotic Translation
Lithwick, Gila, Margalit, Hanah
Protein expression in the cell is affected by various sequence-dependent features. Several such sequence-dependent features have been individually studied,yet they have not been compared...
Relative predicted protein levels of functionally associated proteins are conserved across organisms
Lithwick, Gila, Margalit, Hanah
We show that the predicted protein levels of functionally related proteins change in a coordinated fashion over many unicellular organisms. For each protein, we created a profile containing a protein...
Clustering and conservation patterns of human microRNAs
Altuvia, Yael, Landgraf, Pablo, Lithwick, Gila, Elefant, Naama, Pfeffer, Sébastien, Aravin, Alexei, ...
MicroRNAs (miRNAs) are ∼22 nt-long non-coding RNA molecules, believed to play important roles in gene regulation. We present a comprehensive analysis of the conservation and clustering patterns of...
Zick, Aviad, Onn, Itay, Bezalel, Rachel, Margalit, Hanah, Shlomai, Joseph
Assigning functions to genes is one of the major challenges of the post-genomic era. Usually, functions are assigned based on similarity of the coding sequences to sequences of known genes, or by...
Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
Kaplan, Tommy, Friedman, Nir, Margalit, Hanah
Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structure-based approach applicable...
Mishmar, Dan, Rahat, Ayelet, Scherer, Stephen W., Nyakatura, Gerald, Hinzmann, Bernd, Kohwi, Yoshinori, ...
Common fragile sites are chromosomal loci prone to breakage and rearrangement, hypothesized to provide targets for foreign DNA integration. We cloned a simian virus 40 integration site and showed by...
Hershberg, Ruti, Bejerano, Gill, Santos-Zavaleta, Alberto, Margalit, Hanah
PromEC is an updated compilation of Escherichia coli mRNA promoter sequences. It includes documentation on the location of experimentally identified mRNA transcriptional start sites on the E.coli...
Conserved sequence elements associated with exon skipping
Miriami, Elana, Margalit, Hanah, Sperling, Ruth
One of the major forms of alternative splicing, which generates multiple mRNA isoforms differing in the precise combinations of their exon sequences, is exon skipping. While in constitutive splicing...
SURVEY AND SUMMARY: A survey of small RNA-encoding genes in Escherichia coli
Hershberg, Ruth, Altuvia, Shoshy, Margalit, Hanah
Small RNA (sRNA) molecules have gained much interest lately, as recent genome-wide studies have shown that they are widespread in a variety of organisms. The relatively small family of 10 known...
Yeger-Lotem, Esti, Margalit, Hanah
The post-genomic era is marked by huge amounts of data generated by large-scale functional genomic and proteomic experiments. A major challenge is to integrate the various types of genome-scale...
Molecular Basis for Expression of Common and Rare Fragile Sites
Zlotorynski, Eitan, Rahat, Ayelet, Skaug, Jennifer, Ben-Porat, Neta, Ozeri, Efrat, Hershberg, Ruth, ...
Fragile sites are specific loci that form gaps, constrictions, and breaks on chromosomes exposed to partial replication stress and are rearranged in tumors. Fragile sites are classified as rare or...
IntAct: an open source molecular interaction database
Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...
Yeger-Lotem, Esti, Sattath, Shmuel, Kashtan, Nadav, Itzkovitz, Shalev, Milo, Ron, Pinter, Ron Y., ...
Genes and proteins generate molecular circuitry that enables the cell to process information and respond to stimuli. A major challenge is to identify characteristic patterns in this network of...
Hierarchy of Sequence-Dependent Features Associated With Prokaryotic Translation
Lithwick, Gila, Margalit, Hanah
Protein expression in the cell is affected by various sequence-dependent features. Several such sequence-dependent features have been individually studied,yet they have not been compared...
Relative predicted protein levels of functionally associated proteins are conserved across organisms
Lithwick, Gila, Margalit, Hanah
We show that the predicted protein levels of functionally related proteins change in a coordinated fashion over many unicellular organisms. For each protein, we created a profile containing a protein...
Clustering and conservation patterns of human microRNAs
Altuvia, Yael, Landgraf, Pablo, Lithwick, Gila, Elefant, Naama, Pfeffer, Sébastien, Aravin, Alexei, ...
MicroRNAs (miRNAs) are ∼22 nt-long non-coding RNA molecules, believed to play important roles in gene regulation. We present a comprehensive analysis of the conservation and clustering patterns of...
Zick, Aviad, Onn, Itay, Bezalel, Rachel, Margalit, Hanah, Shlomai, Joseph
Assigning functions to genes is one of the major challenges of the post-genomic era. Usually, functions are assigned based on similarity of the coding sequences to sequences of known genes, or by...
Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
Kaplan, Tommy, Friedman, Nir, Margalit, Hanah
Current approaches for identification and detection of transcription factor binding sites rely on an extensive set of known target genes. Here we describe a novel structure-based approach applicable...
Co-evolution of transcription factors and their targets depends on mode of regulation
Hershberg, Ruth, Margalit, Hanah
Analysis of transcription regulatory networks in γ-proteobacteria reveals that repressors co-evolve tightly with their target genes, whereas activators can be lost independently of their targets.
Evolutionary conservation of domain-domain interactions
Itzhaki, Zohar, Akiva, Eyal, Altuvia, Yael, Margalit, Hanah
Mapping of domain-domain interactions onto the cellular protein-protein interaction networks of different organisms demonstrates that there is a catalogue of domain pairs that is used for mediating...
Characterization and prediction of protein–protein interactions within and between complexes
Sprinzak, Einat, Altuvia, Yael, Margalit, Hanah
Databases of experimentally determined protein interactions provide information on binary interactions and on involvement in multiprotein complexes. These data are valuable for understanding the...
Regulation of gene expression by small non-coding RNAs: a quantitative view
Shimoni, Yishai, Friedlander, Gilgi, Hetzroni, Guy, Niv, Gali, Altuvia, Shoshy, Biham, Ofer, ...
The importance of post-transcriptional regulation by small non-coding RNAs has recently been recognized in both pro- and eukaryotes. Small RNAs (sRNAs) regulate gene expression post-transcriptionally...
A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval
Habib, Naomi, Kaplan, Tommy, Margalit, Hanah, Friedman, Nir
Characterizing the DNA-binding specificities of transcription factors is a key problem in computational biology that has been addressed by multiple algorithms. These usually take as input sequences...
Padalon-Brauch, Gilly, Hershberg, Ruth, Elgrably-Weiss, Maya, Baruch, Kobi, Rosenshine, Ilan, Margalit, Hanah, ...
The emergence of pathogenic strains of enteric bacteria and their adaptation to unique niches are associated with the acquisition of foreign DNA segments termed ‘genetic islands’. We explored...
Friedberg, Iddo, Margalit, Hanah
Many protein pairs that share the same fold do not have any detectable sequence similarity, providing a valuable source of information for studying sequence-structure relationship. In this study, we...