A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs (2009)
Kyoungha Han ¤a, Gene Yeo ¤b, Ping An, Christopher B. Burge, Paula J. Grabowski
Alternative pre-mRNA splicing is widely used to regulate gene expression by tuning the levels of tissue-specific mRNA isoforms. Few regulatory mechanisms are understood at the level of combinatorial...
Most mammalian mRNAs are conserved targets of microRNAs (2009)
Friedman, Robin C., Farh, Kyle Kai-How, Burge, Christopher B., Bartel, David P.
MicroRNAs (miRNAs) are small endogenous RNAs that pair to sites in mRNAs to direct post-transcriptional repression. Many sites that match the miRNA seed (nucleotides 2–7), particularly those in...
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...
1540 BREVIA Vertebrate MicroRNA Genes (2008)
Lee P. Lim, Margaret E. Glasner, Soraya Yekta, Christopher B. Burge, David P. Bartel
MicroRNAs (miRNAs) are an abundant class of �22-nucleotide (nt) noncoding RNAs, some of which are known to control the expression of other genes at the posttranscriptional level (1–4). We...
Stephanie Seneff, Chao Wang, Christopher B. Burge, Stephanie Seneff, Chao Wang, Christopher B. Burge
the only authorised source. All copying of this article including placing on another website requires the written permission of the copyright owner. Seneff, Wang, and Burge, Applied Bioinformatics 2
Splicing regulation: From a parts list of regulatory elements to an integrated splicing code (2008)
Wang, Zefeng, Burge, Christopher B.
Alternative splicing of pre-mRNAs is a major contributor to both proteomic diversity and control of gene expression levels. Splicing is tightly regulated in different tissues and developmental...
Peter F. Arndt, Christopher B. Burge, Terence Hwa
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of models is...
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....
Dynamic regulation of miRNA expression in ordered stages of cellular development (2007)
Neilson, Joel R., Zheng, Grace X.Y., Burge, Christopher B., Sharp, Phillip A.
Short RNA expression in several distinct stages of T-lymphocyte development was comprehensively profiled. The total number of microRNAs (miRNAs) expressed per cell at different stages of development...
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...
The Evolution and Specificity of RNA Splicing (2006)
Brad Aaron Friedman, Christopher B. Burge, Brad Aaron Friedman
Computational Inference of Homologous Gene Structures in the Human Genome (2006)
Human Genome, Ru-fang Yeh, Lee P. Lim, Christopher B. Burge, Email Alerting, Ru-fang Yeh, ...
service
HOLLYWOOD: a comparative relational database of alternative splicing (2006)
Holste, Dirk, Huo, George, Tung, Vivian, Burge, Christopher B.
RNA splicing is an essential step in gene expression, and is often variable, giving rise to multiple alternatively spliced mRNA and protein isoforms from a single gene locus. The design of effective...
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...
A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs (2005)
Kyoungha Han, Gene Yeo, Ping An, Christopher B. Burge, Paula J. Grabowski
Many genes are alternatively spliced, but the signals that regulate the process are unclear. These authors have found a sequence motif that appears to function at many alternatively spliced genes.
A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs (2005)
Kyoungha Han, Gene Yeo, Ping An, Christopher B. Burge, Paula J. Grabowski
Alternative pre-mRNA splicing is widely used to regulate gene expression by tuning the levels of tissue-specific mRNA isoforms. Few regulatory mechanisms are understood at the level of combinatorial...
Patterns of Intron Gain and Loss in Fungi (2004)
Cydney B. Nielsen, Brad Friedman, Bruce Birren, Christopher B. Burge, James E. Galagan
A comparative study of four fungal genomes reveals the patterns of intron gain and loss over several hundred million years of evolution.
Patterns of Intron Gain and Loss in Fungi (2004)
Cydney B. Nielsen, Brad Friedman, Bruce Birren, Christopher B. Burge, James E. Galagan
Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed...
Variation in alternative splicing across human tissues (2004)
Yeo, Gene, Holste, Dirk, Kreiman, Gabriel, Burge, Christopher B
Abstract Background Alternative pre-mRNA splicing (AS) is widely used by higher eukaryotes to generate different protein isoforms in specific cell or tissue types. To compare AS events across human...
Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers (2004)
William G. Fairbrother, Dirk Holste, Christopher B. Burge, Phillip A. Sharp
A computational analysis of single nucleotide polymorphisms showed that one-fifth of mutations that disrupt predicted exonic splicing enhancers have been eliminated by natural selection.
Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers (2004)
William G. Fairbrother, Dirk Holste, Christopher B. Burge, Phillip A. Sharp
Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a...
Untangling influences of hydrophobicity on protein sequences and structures (2004)
Yahyanejad, Mehdi, Burge, Christopher B., Kardar, Mehran
We fit the Fourier transforms of solvent accessibility and hydrophobicity profiles of a representative set of proteins to a joint multi-variable Gaussian. This allows us to separate the intrinsic...
William G. Fairbrother, Gene W. Yeo, Rufang Yeh, Paul Goldstein, Matthew Mawson, Phillip A. Sharp, ...
identifies candidate exonic splicing
Gene Yeo, Dirk Holste, Gabriel Kreiman, Christopher B Burge
The electronic version of this article is the complete one and can be
Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals (2004)
Gene Yeo, Christopher B. Burge
We propose a framework for modeling sequence motifs based on the Maximum Entropy principle (MEP). We recommend approximating short sequence motif distributions with the Maximum Entropy Distribution...
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons (2004)
Fairbrother, William G., Yeo, Gene W., Yeh, Rufang, Goldstein, Paul, Mawson, Matthew, Sharp, Phillip A., ...
A typical gene contains two levels of information: a sequence that encodes a particular protein and a host of other signals that are necessary for the correct expression of the transcript. While much...
OHLER, UWE, YEKTA, SORAYA, LIM, LEE P., BARTEL, DAVID P., BURGE, CHRISTOPHER B.
MicroRNAs are ~22-nucleotide (nt) RNAs processed from foldback segments of endogenous transcripts. Some are known to play important gene regulatory roles during animal and plant development by...
DNA sequence evolution with neighbor-dependent mutation (2003)
Arndt,Peter F., Burge,Christopher B., Hwa,Terence
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of models is...
DNA sequence evolution with neighbor-dependent mutation (2003)
Arndt, Peter F., Burge, Christopher B., Hwa, Terence
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of models is...
The microRNAs of Caenorhabditis elegans (2003)
Lee P. Lim, Nelson C. Lau, Earl G. Weinstein, Aliaa Abdelhakim, Soraya Yekta, Matthew W. Rhoades, ...
MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals. In the present study, we describe a computational procedure to...
Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes (2003)
Katz, Luba, Burge, Christopher B.
Redundancy of the genetic code dictates that a given protein can be encoded by a large collection of distinct mRNA species, potentially allowing mRNAs to simultaneously optimize desirable RNA...
The microRNAs of Caenorhabditis elegans (2003)
Lim, Lee P., Lau, Nelson C., Weinstein, Earl G., Abdelhakim, Aliaa, Yekta, Soraya, Rhoades, Matthew W., ...
A uniform system for microRNA annotation (2003)
AMBROS, VICTOR, BARTEL, BONNIE, BARTEL, DAVID P., BURGE, CHRISTOPHER B., CARRINGTON, JAMES C., CHEN, XUEMEI, ...
MicroRNAs (miRNAs) are small noncoding RNA gene products about 22 nt long that are processed by Dicer from precursors with a characteristic hairpin secondary structure. Guidelines are presented for...
The microRNAs of Caenorhabditis elegans (2003)
Lim, Lee P., Lau, Nelson C., Weinstein, Earl G., Abdelhakim, Aliaa, Yekta, Soraya, Rhoades, Matthew W., ...
DNA sequence evolution with neighbor-dependent mutation (2002)
Peter F. Arndt, Christopher B. Burge, Terence Hwa
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of models is...
DNA Sequence Evolution with Neighbor-Dependent Mutation (2001)
Arndt, Peter F., Burge, Christopher B., Hwa, Terence
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of...
Zefeng Wang, Michael E. Rolish, Gene Yeo, Vivian Tung, Matthew Mawson, Christopher B. Burge
Exonic splicing silencers (ESSs) are cis-regulatory elements that inhibit the use of adjacent splice sites, often contributing to alternative splicing (AS). To sys-tematically identify ESSs, an in...
A computational analysis of sequence features involved in recognition of short introns
Lim, Lee P., Burge, Christopher B.
Splicing of short introns by the nuclear pre-mRNA splicing machinery is thought to proceed via an “intron definition” mechanism, in which the 5′ and 3′ splice sites (5′ss, 3′ss,...
The microRNAs of Caenorhabditis elegans
Lim, Lee P., Lau, Nelson C., Weinstein, Earl G., Abdelhakim, Aliaa, Yekta, Soraya, Rhoades, Matthew W., ...
MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals. In the present study, we describe a computational procedure to...
Computational Inference of Homologous Gene Structures in the Human Genome
Yeh, Ru-Fang, Lim, Lee P., Burge, Christopher B.
With the human genome sequence approaching completion, a major challenge is to identify the locations and encoded protein sequences of all human genes. To address this problem we have developed a new...
Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes
Katz, Luba, Burge, Christopher B.
Redundancy of the genetic code dictates that a given protein can be encoded by a large collection of distinct mRNA species, potentially allowing mRNAs to simultaneously optimize desirable RNA...
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
Fairbrother, William G., Yeo, Gene W., Yeh, Rufang, Goldstein, Paul, Mawson, Matthew, Sharp, Phillip A., ...
A typical gene contains two levels of information: a sequence that encodes a particular protein and a host of other signals that are necessary for the correct expression of the transcript. While much...
Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers
Fairbrother, William G, Holste, Dirk, Burge, Christopher B, Sharp, Phillip A
Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a...
Variation in sequence and organization of splicing regulatory elements in vertebrate genes
Yeo, Gene, Hoon, Shawn, Venkatesh, Byrappa, Burge, Christopher B.
Although core mechanisms and machinery of premRNA splicing are conserved from yeast to human, the details of intron recognition often differ, even between closely related organisms. For example,...
Patterns of Intron Gain and Loss in Fungi
Nielsen, Cydney B, Friedman, Brad, Birren, Bruce, Burge, Christopher B, Galagan, James E
Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed...
Variation in alternative splicing across human tissues
Yeo, Gene, Holste, Dirk, Kreiman, Gabriel, Burge, Christopher B
Analysis of the alternative splicing patterns of genomically aligned ESTs revealed that human brain, testis and liver have unusually high levels of alternative splicing and identified candidate...
A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs
Han, Kyoungha, Yeo, Gene, An, Ping, Burge, Christopher B, Grabowski, Paula J
Alternative pre-mRNA splicing is widely used to regulate gene expression by tuning the levels of tissue-specific mRNA isoforms. Few regulatory mechanisms are understood at the level of combinatorial...
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...
Goranov, Alexi I., Katz, Luba, Breier, Adam M., Burge, Christopher B., Grossman, Alan D.
Organisms respond to perturbations in DNA replication. We characterized the global transcriptional response to inhibition of DNA replication in Bacillus subtilis. We focused on changes that were...
Hollywood: a comparative relational database of alternative splicing
Holste, Dirk, Huo, George, Tung, Vivian, Burge, Christopher B.
RNA splicing is an essential step in gene expression, and is often variable, giving rise to multiple alternatively spliced mRNA and protein isoforms from a single gene locus. The design of effective...
A uniform system for microRNA annotation
AMBROS, VICTOR, BARTEL, BONNIE, BARTEL, DAVID P., BURGE, CHRISTOPHER B., CARRINGTON, JAMES C., CHEN, XUEMEI, ...
MicroRNAs (miRNAs) are small noncoding RNA gene products about 22 nt long that are processed by Dicer from precursors with a characteristic hairpin secondary structure. Guidelines are presented for...
OHLER, UWE, YEKTA, SORAYA, LIM, LEE P., BARTEL, DAVID P., BURGE, CHRISTOPHER B.
MicroRNAs are ~22-nucleotide (nt) RNAs processed from foldback segments of endogenous transcripts. Some are known to play important gene regulatory roles during animal and plant development by...
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...
A computational analysis of sequence features involved in recognition of short introns
Lim, Lee P., Burge, Christopher B.
Splicing of short introns by the nuclear pre-mRNA splicing machinery is thought to proceed via an “intron definition” mechanism, in which the 5′ and 3′ splice sites (5′ss, 3′ss,...
The microRNAs of Caenorhabditis elegans
Lim, Lee P., Lau, Nelson C., Weinstein, Earl G., Abdelhakim, Aliaa, Yekta, Soraya, Rhoades, Matthew W., ...
MicroRNAs (miRNAs) are an abundant class of tiny RNAs thought to regulate the expression of protein-coding genes in plants and animals. In the present study, we describe a computational procedure to...
Computational Inference of Homologous Gene Structures in the Human Genome
Yeh, Ru-Fang, Lim, Lee P., Burge, Christopher B.
With the human genome sequence approaching completion, a major challenge is to identify the locations and encoded protein sequences of all human genes. To address this problem we have developed a new...
Widespread Selection for Local RNA Secondary Structure in Coding Regions of Bacterial Genes
Katz, Luba, Burge, Christopher B.
Redundancy of the genetic code dictates that a given protein can be encoded by a large collection of distinct mRNA species, potentially allowing mRNAs to simultaneously optimize desirable RNA...
RESCUE-ESE identifies candidate exonic splicing enhancers in vertebrate exons
Fairbrother, William G., Yeo, Gene W., Yeh, Rufang, Goldstein, Paul, Mawson, Matthew, Sharp, Phillip A., ...
A typical gene contains two levels of information: a sequence that encodes a particular protein and a host of other signals that are necessary for the correct expression of the transcript. While much...
Single Nucleotide Polymorphism–Based Validation of Exonic Splicing Enhancers
Fairbrother, William G, Holste, Dirk, Burge, Christopher B, Sharp, Phillip A
Because deleterious alleles arising from mutation are filtered by natural selection, mutations that create such alleles will be underrepresented in the set of common genetic variation existing in a...
Variation in sequence and organization of splicing regulatory elements in vertebrate genes
Yeo, Gene, Hoon, Shawn, Venkatesh, Byrappa, Burge, Christopher B.
Although core mechanisms and machinery of premRNA splicing are conserved from yeast to human, the details of intron recognition often differ, even between closely related organisms. For example,...
Patterns of Intron Gain and Loss in Fungi
Nielsen, Cydney B, Friedman, Brad, Birren, Bruce, Burge, Christopher B, Galagan, James E
Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed...
Variation in alternative splicing across human tissues
Yeo, Gene, Holste, Dirk, Kreiman, Gabriel, Burge, Christopher B
Analysis of the alternative splicing patterns of genomically aligned ESTs revealed that human brain, testis and liver have unusually high levels of alternative splicing and identified candidate...
Identification and analysis of alternative splicing events conserved in human and mouse
Yeo, Gene W., Van Nostrand, Eric, Holste, Dirk, Poggio, Tomaso, Burge, Christopher B.
Alternative pre-mRNA splicing affects a majority of human genes and plays important roles in development and disease. Alternative splicing (AS) events conserved since the divergence of human and...
A Combinatorial Code for Splicing Silencing: UAGG and GGGG Motifs
Han, Kyoungha, Yeo, Gene, An, Ping, Burge, Christopher B, Grabowski, Paula J
Alternative pre-mRNA splicing is widely used to regulate gene expression by tuning the levels of tissue-specific mRNA isoforms. Few regulatory mechanisms are understood at the level of combinatorial...
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...
Goranov, Alexi I., Katz, Luba, Breier, Adam M., Burge, Christopher B., Grossman, Alan D.
Organisms respond to perturbations in DNA replication. We characterized the global transcriptional response to inhibition of DNA replication in Bacillus subtilis. We focused on changes that were...
Hollywood: a comparative relational database of alternative splicing
Holste, Dirk, Huo, George, Tung, Vivian, Burge, Christopher B.
RNA splicing is an essential step in gene expression, and is often variable, giving rise to multiple alternatively spliced mRNA and protein isoforms from a single gene locus. The design of effective...
A uniform system for microRNA annotation
AMBROS, VICTOR, BARTEL, BONNIE, BARTEL, DAVID P., BURGE, CHRISTOPHER B., CARRINGTON, JAMES C., CHEN, XUEMEI, ...
MicroRNAs (miRNAs) are small noncoding RNA gene products about 22 nt long that are processed by Dicer from precursors with a characteristic hairpin secondary structure. Guidelines are presented for...
OHLER, UWE, YEKTA, SORAYA, LIM, LEE P., BARTEL, DAVID P., BURGE, CHRISTOPHER B.
MicroRNAs are ~22-nucleotide (nt) RNAs processed from foldback segments of endogenous transcripts. Some are known to play important gene regulatory roles during animal and plant development by...
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...
Dynamic regulation of miRNA expression in ordered stages of cellular development
Neilson, Joel R., Zheng, Grace X.Y., Burge, Christopher B., Sharp, Phillip A.
Short RNA expression in several distinct stages of T-lymphocyte development was comprehensively profiled. The total number of microRNAs (miRNAs) expressed per cell at different stages of development...
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....
Coevolutionary networks of splicing cis-regulatory elements
Xiao, Xinshu, Wang, Zefeng, Jang, Minyoung, Burge, Christopher B.
Accurate and efficient splicing of eukaryotic pre-mRNAs requires recognition by trans-acting factors of a complex array of cis-acting RNA elements. Here, we developed a generalized Bayesian network...
Splicing regulation: From a parts list of regulatory elements to an integrated splicing code
Wang, Zefeng, Burge, Christopher B.
Alternative splicing of pre-mRNAs is a major contributor to both proteomic diversity and control of gene expression levels. Splicing is tightly regulated in different tissues and developmental...
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...
Most mammalian mRNAs are conserved targets of microRNAs
Friedman, Robin C., Farh, Kyle Kai-How, Burge, Christopher B., Bartel, David P.
MicroRNAs (miRNAs) are small endogenous RNAs that pair to sites in mRNAs to direct post-transcriptional repression. Many sites that match the miRNA seed (nucleotides 2–7), particularly those in...
A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart
Kalsotra, Auinash, Xiao, Xinshu, Ward, Amanda J., Castle, John C., Johnson, Jason M., Burge, Christopher B., ...
From a large-scale screen using splicing microarrays and RT-PCR, we identified 63 alternative splicing (AS) events that are coordinated in 3 distinct temporal patterns during mouse heart development....