Computational Complexity and Numerical Stability of Linear Problems (2009)
We survey classical and recent developments in numerical linear algebra, focusing on two issues: computational complexity, or arithmetic costs, and numerical stability, or performance under roundoff...
Logistic regression is often used to help make medical decisions with binary outcomes. Here we evaluate the use of several methods for selection of variables in logistic regression. We use a large...
MicroRNA-Biogenesis and Pre-mRNA Splicing Crosstalk (2009)
MicroRNAs (miRNAs) are often hosted in introns of protein-coding genes. Given that the same transcriptional unit can potentially give rise to both miRNA and mRNA transcripts raises the intriguing...
MicroRNA-Biogenesis and Pre-mRNA Splicing Crosstalk (2009)
MicroRNAs (miRNAs) are often hosted in introns of protein-coding genes. Given that the same transcriptional unit can potentially give rise to both miRNA and mRNA transcripts raises the intriguing...
An Evolutionary Perspective of Animal MicroRNAs and Their Targets (2009)
Noam Shomron, David Golan, Eran Hornstein
MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through translational inhibition or mRNA degradation by binding to sequences on the target mRNA. miRNA regulation appears to...
An Evolutionary Perspective of Animal MicroRNAs and Their Targets (2009)
Noam Shomron, David Golan, Eran Hornstein
MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through translational inhibition or mRNA degradation by binding to sequences on the target mRNA. miRNA regulation appears to...
Inference of Splicing Regulatory Activities by Sequence Neighborhood Analysis (2008)
Michael B. Stadler, Noam Shomron, Gene W. Yeo, Aniket Schneider, Xinshu Xiao, Christopher B. Burge
Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with...
Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene (2008)
Amit, Maayan, Sela, Noa, Keren, Hadas, Melamed, Zeev, Muler, Inna, Shomron, Noam, ...
Background: Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization of...
Linear algebra meets Lie algebra: the Kostant-Wallach theory (2008)
Shomron, Noam, Parlett, Beresford N.
In two languages, Linear Algebra and Lie Algebra, we describe the results of Kostant and Wallach on the fibre of matrices with prescribed eigenvalues of all leading principal submatrices. In...
miRNAminer: A tool for homologous microRNA gene search (2008)
Artzi, Shay, Kiezun, Adam, Shomron, Noam
Abstract Background MicroRNAs (miRNAs), present in most metazoans, are small non-coding RNAs that control gene expression by negatively regulating translation through binding to the 3'UTR of mRNA...
Ab initio identification of functionally interacting pairs of cis-regulatory elements (2008)
Friedman, Brad A., Stadler, Michael B., Shomron, Noam, Ding, Ye, Burge, Christopher B.
Cooperatively acting pairs of cis-regulatory elements play important roles in many biological processes. Here, we describe a statistical approach, compositionally orthogonalized co-occurrence...
Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene (2007)
Amit, Maayan, Sela, Noa, Keren, Hadas, Melamed, Ze'ev, Muler, Inna, Shomron, Noam, ...
Abstract Background Gene duplication and exonization of intronic transposed elements are two mechanisms that enhance genomic diversity. We examined whether there is less selection against exonization...
Determinants of targeting by endogenous and exogenous microRNAs and siRNAs (2007)
Nielsen, Cydney B., Shomron, Noam, Sandberg, Rickard, Hornstein, Eran, Kitzman, Jacob, Burge, Christopher B
Vertebrate mRNAs are frequently targeted for post-transcriptional repression by microRNAs (miRNAs) through mechanisms involving pairing of 3′ UTR seed matches to bases at the 5′ end of miRNAs....
Alberstein, Moti, Amit, Maayan, Vaknin, Keren, O'Donnell, Amanda, Farhy, Chen, Lerenthal, Yaniv, ...
Alternative splicing plays a major role in transcriptome diversity and plasticity, but it is largely unknown how tissue-specific and embryogenesis-specific alternative splicing is regulated. The...
Inference of Splicing Regulatory Activities by Sequence Neighborhood Analysis (2006)
Michael B. Stadler, Noam Shomron, Gene W. Yeo, Aniket Schneider, Xinshu Xiao, Christopher B. Burge
Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with...
Inference of Splicing Regulatory Activities by Sequence Neighborhood Analysis (2006)
Michael Stadler, Noam Shomron, Aniket Schneider, Xinshu Xiao, Chris B Burge
Sequence-specific recognition of nucleic acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood-Inference (NI) that predicts sequences with...
Recognition of Unknown Conserved Alternatively Spliced Exons (2005)
Uwe Ohler, Noam Shomron, Christopher B. Burge
The split structure of most mammalian protein-coding genes allows for the potential to produce multiple different mRNA and protein isoforms from a single gene locus through the process of alternative...
Shomron, Noam, Malca, Hadar, Vig, Ida, Ast, Gil
A multicomponent complex of proteins and RNA is assembled on the newly synthesized pre‐mRNA to form the spliceosome. This complex catalyzes a two‐step transesterification reaction required...
Representations of cartan-type lie superalgebras / (2001)
Thesis (Ph. D.)--University of California, Berkeley, 2001.
Blocks of Lie Superalgebras of Type W(n) (2000)
We calculate the blocks of the category of finite-dimensional representations of W(0,n), with n > 2, and show that all are of wild type. As an application, we show that the centre of the universal...
Shomron, Noam, Malca, Hadar, Vig, Ida, Ast, Gil
A multicomponent complex of proteins and RNA is assembled on the newly synthesized pre-mRNA to form the spliceosome. This complex catalyzes a two-step transesterification reaction required to remove...
The U1 snRNP Base Pairs with the 5′ Splice Site within a Penta-snRNP Complex
Malca, Hadar, Shomron, Noam, Ast, Gil
Recognition of the 5′ splice site is an important step in mRNA splicing. To examine whether U1 approaches the 5′ splice site as a solitary snRNP or as part of a multi-snRNP complex, we used a...
Shomron, Noam, Reznik, Mika, Ast, Gil
Precursor-mRNA splicing removes the introns and ligates the exons to form a mature mRNA. This process is carried out in a spliceosomal complex containing >150 proteins and five small nuclear...
Recognition of Unknown Conserved Alternatively Spliced Exons
Ohler, Uwe, Shomron, Noam, Burge, Christopher B
The split structure of most mammalian protein-coding genes allows for the potential to produce multiple different mRNA and protein isoforms from a single gene locus through the process of alternative...
Inference of Splicing Regulatory Activities by Sequence Neighborhood Analysis
Stadler, Michael B, Shomron, Noam, Yeo, Gene W, Schneider, Aniket, Xiao, Xinshu, Burge, Christopher B
Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with...
Shomron, Noam, Malca, Hadar, Vig, Ida, Ast, Gil
A multicomponent complex of proteins and RNA is assembled on the newly synthesized pre-mRNA to form the spliceosome. This complex catalyzes a two-step transesterification reaction required to remove...
The U1 snRNP Base Pairs with the 5′ Splice Site within a Penta-snRNP Complex
Malca, Hadar, Shomron, Noam, Ast, Gil
Recognition of the 5′ splice site is an important step in mRNA splicing. To examine whether U1 approaches the 5′ splice site as a solitary snRNP or as part of a multi-snRNP complex, we used a...
Shomron, Noam, Reznik, Mika, Ast, Gil
Precursor-mRNA splicing removes the introns and ligates the exons to form a mature mRNA. This process is carried out in a spliceosomal complex containing >150 proteins and five small nuclear...
Recognition of Unknown Conserved Alternatively Spliced Exons
Ohler, Uwe, Shomron, Noam, Burge, Christopher B
The split structure of most mammalian protein-coding genes allows for the potential to produce multiple different mRNA and protein isoforms from a single gene locus through the process of alternative...
Inference of Splicing Regulatory Activities by Sequence Neighborhood Analysis
Stadler, Michael B, Shomron, Noam, Yeo, Gene W, Schneider, Aniket, Xiao, Xinshu, Burge, Christopher B
Sequence-specific recognition of nucleic-acid motifs is critical to many cellular processes. We have developed a new and general method called Neighborhood Inference (NI) that predicts sequences with...
Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene
Amit, Maayan, Sela, Noa, Keren, Hadas, Melamed, Ze'ev, Muler, Inna, Shomron, Noam, ...
Determinants of targeting by endogenous and exogenous microRNAs and siRNAs
Nielsen, Cydney B., Shomron, Noam, Sandberg, Rickard, Hornstein, Eran, Kitzman, Jacob, Burge, Christopher B
Vertebrate mRNAs are frequently targeted for post-transcriptional repression by microRNAs (miRNAs) through mechanisms involving pairing of 3′ UTR seed matches to bases at the 5′ end of miRNAs....
Alberstein, Moti, Amit, Maayan, Vaknin, Keren, O'Donnell, Amanda, Farhy, Chen, Lerenthal, Yaniv, ...
Alternative splicing plays a major role in transcriptome diversity and plasticity, but it is largely unknown how tissue-specific and embryogenesis-specific alternative splicing is regulated. The...
Kiezun, Adam, Lee, I-Ting Angelina, Shomron, Noam
Logistic regression is often used to help make medical decisions with binary outcomes. Here we evaluate the use of several methods for selection of variables in logistic regression. We use a large...
Ab initio identification of functionally interacting pairs of cis-regulatory elements
Friedman, Brad A., Stadler, Michael B., Shomron, Noam, Ding, Ye, Burge, Christopher B.
Cooperatively acting pairs of cis-regulatory elements play important roles in many biological processes. Here, we describe a statistical approach, compositionally orthogonalized co-occurrence...
MicroRNA-Biogenesis and Pre-mRNA Splicing Crosstalk
MicroRNAs (miRNAs) are often hosted in introns of protein-coding genes. Given that the same transcriptional unit can potentially give rise to both miRNA and mRNA transcripts raises the intriguing...
An Evolutionary Perspective of Animal MicroRNAs and Their Targets
Shomron, Noam, Golan, David, Hornstein, Eran
MicroRNAs (miRNAs) are short noncoding RNAs that regulate gene expression through translational inhibition or mRNA degradation by binding to sequences on the target mRNA. miRNA regulation appears to...
MicroRNAs are essential for development and function of inner ear hair cells in vertebrates
Friedman, Lilach M., Dror, Amiel A., Mor, Eyal, Tenne, Tamar, Toren, Ginat, Satoh, Takunori, ...
MicroRNAs (miRNAs) inhibit the translation of target mRNAs and affect, directly or indirectly, the expression of a large portion of the protein-coding genes. This study focuses on miRNAs that are...