Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2 (2009)
Kwan, Alan L, Li, Linya, Kulp, David C, Dutcher, Susan K, Stormo, Gary D
Abstract Background The availability of whole-genome sequences allows for the identification of the entire set of protein coding genes as well as their regulatory regions. This can be accomplished...
Predicting Transcription Regulatory Mechanisms by Systematic Promoter Analysis (2008)
Li-wei Chang, Rakesh Nagarajan, Jeffrey A. Magee, Jeffrey Milbr, Gary D. Stormo
An important part of understanding a biological pathway or a cellular function is to delineate the transcriptional regulatory mechanisms of the genes involved. Key participants in these mechanisms...
Noyes, Marcus B., Christensen, Ryan G., Wakabayashi, Atsuya, Stormo, Gary D., Brodsky, Michael H., Wolfe, Scot A.
We describe the comprehensive characterization of homeodomain DNA-binding specificities from a metazoan genome. The analysis of all 84 independent homeodomains from D. melanogaster reveals the...
Yiyong Zhou, Corentin Cras-méneur, Mitsuru Ohsugi, Gary D. Stormo, M. Alan Permutt
A global approach to identify differentially expressed
Structural Alignment, Xing Xu, Yongmei Ji, Gary D. Stormo
Motivation: Non-coding RNA genes and RNA structural regulatory motifs play important roles in gene regulation and other cellular functions. They are often characterized by specific secondary...
Jakob Hull Havgaard, Rune B. Lyngsø, Gary D. Stormo
Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding today as these often are conserved in structure rather than in...
Jan Gorodkin, Rune B. Lyngsø, Gary D. Stormo
When a set of coregulated genes share a common structural RNA motif, e.g. a hairpin, most motif search approaches fail to locate the covarying but structurally conserved motif. There do exist methods...
BIOINFORMATICS ORIGINAL PAPER (2008)
Gene Expression, Ritesh Agrawal, Gary D. Stormo
doi:10.1093/bioinformatics/btl076 Using mRNAs lengths to accurately predict the alternatively spliced gene products in Caenorhabditis elegans
Chang, Li Wei, Payton, Jacqueline E, Yuan, Wenlin, Ley, Timothy J, Nagarajan, Rakesh, Stormo, Gary D
Abstract Background Acute myeloid leukemia (AML) comprises a group of diseases characterized by the abnormal development of malignant myeloid cells. Recent studies have demonstrated an important role...
Zeng, Jue, Yan, Jizhou, Wang, Ting, Mosbrook-Davis, Deborah, Dolan, Kyle T., Christensen, Ryan, ...
Knowledge of all binding sites for transcriptional activators and repressors is essential for computationally aided identification of transcriptional networks. The techniques developed for defining...
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors (2008)
Motivation: Modeling and identifying the DNA-protein recognition code is one of the most challenging problems in computational biology. Several quantitative methods have been developed to model...
The cis-regulatory map of Shewanella genomes (2008)
Liu, Jiajian, Xu, Xing, Stormo, Gary D.
While hundreds of microbial genomes are sequenced, the challenge remains to define their cis-regulatory maps. Here, we present a comparative genomic analysis of the cis-regulatory map of Shewanella...
Debraj Guhathakurta, Gary D. Stormo
Motivation: Transcriptional activation in eukaryotic organisms normally requires combinatorial interactions of multiple transcription factors. Though several methods exist for identification of...
Davies, Sherri R., Chang, Li-Wei, Patra, Debabrata, Xing, Xiaoyun, Posey, Karen, Hecht, Jacqueline, ...
Chondrocyte gene regulation is important for the generation and maintenance of cartilage tissues. Several regulatory factors have been identified that play a role in chondrogenesis, including the...
Zhou, Yiyong, Cras-Méneur, Corentin, Ohsugi, Mitsuru, Stormo, Gary D., Permutt, M. Alan.
Motivation: Currently most of the methods for identifying differentially expressed genes fall into the category of so called single-gene-analysis, performing hypothesis testing on a gene-by-gene...
Xu, Xing, Ji, Yongmei, Stormo, Gary D.
Motivation: Non-coding RNA genes and RNA structural regulatory motifs play important roles in gene regulation and other cellular functions. They are often characterized by specific secondary...
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis (2007)
Chang, Li-Wei, Fontaine, Burr R., Stormo, Gary D., Nagarajan, Rakesh
Given the recent explosion of publications that employ microarray technology to monitor genome-wide expression and that correlate these expression changes to biological processes or to disease...
Identification of muscle-specific regulatory modules in Caenorhabditis elegans (2007)
Zhao, Guoyan, Schriefer, Lawrence A., Stormo, Gary D.
Transcriptional regulation is the major regulatory mechanism that controls the spatial and temporal expression of genes during development. This is carried out by transcription factors (TFs), which...
An improved map of conserved regulatory sites for Saccharomyces cerevisiae (2006)
MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest
Abstract Background The regulatory map of a genome consists of the binding sites for proteins that determine the transcription of nearby genes. An initial regulatory map for S. cerevisiae was...
Chang, Li-Wei, Nagarajan, Rakesh, Magee, Jeffrey A., Milbrandt, Jeffrey, Stormo, Gary D.
An important aspect of understanding a biological pathway is to delineate the transcriptional regulatory mechanisms of the genes involved. Two important tasks are often encountered when studying...
Agrawal, Ritesh, Stormo, Gary D.
Motivation: Computational gene prediction methods are an important component of whole genome analyses. While ab initio gene finders have demonstrated major improvements in accuracy, the most reliable...
Chang, Li-Wei, Nagarajan, Rakesh, Magee, Jeffrey A., Milbrandt, Jeffrey, Stormo, Gary D.
An important aspect of understanding a biological pathway is to delineate the transcriptional regulatory mechanisms of the genes involved. Two important tasks are often encountered when studying...
Abstract Background Recognition codes for protein-DNA interactions typically assume that the interacting positions contribute additively to the binding energy. While this is known to not be precisely...
Kai Tan, Lee Ann Mccue, Gary D. Stormo, Email Alerting, Kai Tan, Lee Ann Mccue, ...
Making connections between novel transcription factors and their DNA motifs
enoLOGOS: a versatile web tool for energy normalized sequence logos (2005)
Workman, Christopher T., Yin, Yutong, Corcoran, David L., Ideker, Trey, Stormo, Gary D., Benos, Panayiotis V.
enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a...
Editing efficiency of a Drosophila gene correlates with a distant splice site selection (2005)
AGRAWAL, RITESH, STORMO, GARY D.
RNA editing and alternative splicing are two processes that increase protein diversity. The relationship between the two processes is not well understood. There are a few examples of correlations...
Gershenzon, Naum I., Stormo, Gary D., Ioshikhes, Ilya P.
Position-weight matrices (PWMs) are broadly used to locate transcription factor binding sites in DNA sequences. The majority of existing PWMs provide a low level of both sensitivity and specificity....
Making connections between novel transcription factors and their DNA motifs (2005)
Tan, Kai, McCue, Lee Ann, Stormo, Gary D.
The key components of a transcriptional regulatory network are the connections between trans-acting transcription factors and cis-acting DNA-binding sites. In spite of several decades of intense...
Making connections between novel transcription factors and their DNA motifs (2005)
Tan, Kai, McCue, Lee Ann, Stormo, Gary D.
The key components of a transcriptional regulatory network are the connections between trans-acting transcription factors and cis-acting DNA-binding sites. In spite of several decades of intense...
Models for the specificity of DNA-binding transcription factors are often based on small amounts of qualitative data and therefore have limited accuracy. In this study we demonstrate a simple and...
Procom: a web-based tool to compare multiple eukaryotic proteomes (2005)
Li, Jin Billy, Zhang, Miao, Dutcher, Susan K., Stormo, Gary D.
Summary: Each organism has traits that are shared with some, but not all, organisms. Identification of genes needed for a particular trait can be accomplished by a comparative genomics approach using...
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40% (2005)
Havgaard, Jakob Hull, Lyngsø, Rune B., Stormo, Gary D., Gorodkin, Jan
Motivation: Searching for non-coding RNA (ncRNA) genes and structural RNA elements (eleRNA) are major challenges in gene finding today as these often are conserved in structure rather than in...
ILM: a web server for predicting RNA secondary structures with pseudoknots (2004)
Jianhua Ruan, Gary D. Stormo, Weixiong Zhang
The ILM web server provides a web interface to two algorithms, iterated loop matching and maximum weighted matching, for efficiently predicting RNA secondary structures with pseudoknots. The...
Jianhua Ruan, Gary D. Stormo, Weixiong Zhang
In this paper we present a heuristic algorithm, iterative loop matching, for predicting RNA pseudoknots. The method can utilize either thermodynamic or comparative information or both, thus is able...
Man, Tsz-Kwong, Yang, Joshua SungWoo, Stormo, Gary D.
Understanding DNA–protein recognition quantitatively is essential to developing computational algorithms for accurate transcriptional binding site prediction. Using a quantitative, multiple...
Ji, Yongmei, Xu, Xing, Stormo, Gary D.
Motivation: RNA structure motifs contained in mRNAs have been found to play important roles in regulating gene expression. However, identification of novel RNA regulatory motifs using computational...
Ruan, Jianhua, Stormo, Gary D., Zhang, Weixiong
Motivation: Pseudoknots have generally been excluded from the prediction of RNA secondary structures due to its difficulty in modeling. Although, several dynamic programming algorithms exist for the...
Ji, Yongmei, Xu, Xing, Stormo, Gary D.
Motivation: RNA structure motifs contained in mRNAs have been discovered to play important roles in regulating gene expression. However, identification of novel RNA regulatory motifs using...
Procom: a web-based tool to compare multiple eukaryotic proteomes (2004)
Li, Jin Billy, Zhang, Miao, Dutcher, Susan K., Stormo, Gary D.
Summary: Each organism has traits that are shared with some, but not all organisms. Identification of genes needed for a particular trait can be accomplished by a comparative genomics approach using...
Procom: a web-based tool to compare multiple eukaryotic proteomes (2004)
Li, Jin Billy, Zhang, Miao, Dutcher, Susan K., Stormo, Gary D.
Summary: Each organism has traits that are shared with some, but not all organisms. Identification of genes needed for a particular trait can be accomplished by a comparative genomics approach using...
ILM: a web server for predicting RNA secondary structures with pseudoknots (2004)
Ruan, Jianhua, Stormo, Gary D., Zhang, Weixiong
The ILM web server provides a web interface to two algorithms, iterated loop matching and maximum weighted matching, for efficiently predicting RNA secondary structures with pseudoknots. The...
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes (2004)
GuhaThakurta, Debraj, Schriefer, Lawrence A., Waterston, Robert H., Stormo, Gary D.
We report the identification of three new transcription regulatory elements that are associated with muscle gene expression in the nematode Caenorhabditis elegans. Starting from a subset of...
Ji, Yongmei, Xu, Xing, Stormo, Gary D.
Motivation: RNA structure motifs contained in mRNAs have been discovered to play important roles in regulating gene expression. However, identification of novel RNA regulatory motifs using...
Procom: a web-based tool to compare multiple eukaryotic proteomes (2004)
Li, Jin Billy, Zhang, Miao, Dutcher, Susan K., Stormo, Gary D.
Summary: Each organism has traits that are shared with some, but not all organisms. Identification of genes needed for a particular trait can be accomplished by a comparative genomics approach using...
Procom: a web-based tool to compare multiple eukaryotic proteomes (2004)
Li, Jin Billy, Zhang, Miao, Dutcher, Susan K., Stormo, Gary D.
Summary: Each organism has traits that are shared with some, but not all organisms. Identification of genes needed for a particular trait can be accomplished by a comparative genomics approach using...
JIN BILLY LI, SHAOPING LIN, HONGGUI JIA, HONGMIN WU, BRUCE A. ROE, DAVID KULP, ...
Chlamydomonas reinhardtii is a unicellular green alga that has been used as a model organism for the study of flagella and basal bodies as well as photosynthesis. This report analyzes finished...
Combining phylogenetic data with co-regulated genes to identify regulatory motifs (2003)
Motivation: Discovery of regulatory motifs in unaligned DNA sequences remains a fundamental problem in computational biology. Two categories of algorithms have been developed to identify common...
Liu, Jiajian, Tan, Kai, Stormo, Gary D.
Spo0A‐phosphate is essential for the initiation of cellular differentiation and developmental processes in Gram‐positive spore‐forming bacteria. Here we combined comparative genomics...
Probabilistic code for DNA recognition by proteins of the EGR family (2002)
Panayiotis V. Benos, Alan S. Lapedes, Gary D. Stormo
Unravelling the rules that govern the recognition of the target DNA sequences by transcription factors is one of the great challenges in computational biology today. The regulation of the
Debraj Guhathakurta, Lisanne Palomar, Gary D. Stormo, Pat Tedesco, Christopher D. Link
this article were defrayed in part by payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 USC section 1734 solely to indicate this...
Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections (2002)
Silbaq, Fauzi S., Ruttenberg, Steven E., Stormo, Gary D.
Mnt is a repressor from phage P22 that belongs to the ribbon–helix–helix family of DNA binding factors. Four amino acids from the N‐terminus of the protein, Arg2, His6, Asn8 and Arg10,...
Identifying target sites for cooperatively binding factors (2001)
GuhaThakurta, Debraj, Stormo, Gary D.
Motivation: Transcriptional activation in eukaryotic organisms normally requires combinatorial interactions of multiple transcription factors. Though several methods exist for identification of...
Man, Tsz-Kwong, Stormo, Gary D.
Salmonella bacteriophage repressor Mnt belongs to the ribbon–helix–helix class of transcription factors. Previous SELEX results suggested that interactions of Mnt with positions 16 and 17 of the...
Selection of optimal DNA oligos for gene expression arrays (2001)
Motivation: High density DNA oligo microarrays are widely used in biomedical research. Selection of optimal DNA oligos that are deposited on the microarrays is critical. Based on sequence information...
A Comparative Genomics Approach to Prediction of New Members of Regulons (2001)
Tan, Kai, Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio, Stormo, Gary D.
Selecting optimum DNA oligos for microarrays (2000)
High-density DNA oligo microarrays are widely used in biomedical research. In this paper we describe algorithms to optimize the selection of specific probes for each gene in an entire genome. Having...
Improved statistical methods reveal direct interactions between 16S and 23S rRNA (2000)
Kelley, Scott T., Akmaev, Viatcheslav R., Stormo, Gary D.
Recent biochemical studies have indicated a number of regions in both the 16S and 23S rRNA that are exposed on the ribosomal subunit surface. In order to predict potential interactions between these...
Phylogenetically enhanced statistical tools for RNA structure prediction (2000)
Akmaev, Viatcheslav R., Kelley, Scott T., Stormo, Gary D.
Motivation: Methods that predict the structure of molecules by looking for statistical correlation have been quite effective. Unfortunately, these methods often disregard phylogenetic information in...
DNA binding sites: representation and discovery (2000)
The purpose of this article is to provide a brief history of the development and application of computer algorithms for the analysis and prediction of DNA binding sites. This problem can be...
Yuhai Cui, Qing Wang, Gary D. Stormo, Joseph M. Calvo
Lrp (leucine-responsive regulatory protein) is a major regulatory protein involved in the expression of numerous operons in Escherichia coli. For ilvIH, one of the operons positively regulated by...
Chen, Qing K., Hertz, Gerald Z., Stormo, Gary D.
The information matrix database (IMD), a database of weight matrices of transcription factor binding sites, is developed. MATRIX SEARCH, a program which can find potential transcription factor...
Optimally Parsing a Sequence into Different Classes Based on Multiple Types of Evidence (1994)
Gary D. Stormo, David Haussler
We consider the problem of parsing a sequence into different classes of subsequences. Two common examples are finding the exons and introns in genomic sequences and identifying the secondary...
Quantitative analysis of ribosome binding sites in E.coli (1994)
Barrick, Doug, Villanueba, Keith, Childs, John, Kalil, Rhonda, Schneider, Thomas D., Lawrence, Charles E., ...
185 clones with randomized ribosome binding sites, from position −11 to 0 preceding the coding region of β-galactosidase, were selected and sequenced. The translatlonal yield of each clone was...
Detection of deletions in the mitochondrial genome of Caenorhabditis elegans (1994)
Melov, Simon, Hertz, Gerald Z., Stormo, Gary D., Johnson, Thomas E.
We have examined an aging population of Caenorhabditis elegans via a PCR assay to determine if deletions in the mitochondrial genome occur in the nematode. We detected eight such deletions,...
Snyder, Eric E., Stormo, Gary D.
Dynamic programming (DP) is applied to the problem of precisely identifying internal exons and introns in genomic DNA sequences. The program GeneParser first scores the sequence of interest for...
Splicing signals in Drosophila: intron size, information content, and consensus sequences (1992)
Mount, Stephen M., Burks, Christian, Herts, Gerald, Stormo, Gary D., White, Owen, Fields, Chris
A database of 209 Drosophila Introns was extracted from Genbank (release number 64.0) and examined by a number of methods in order to characterize features that might serve as signals for messenger...
Hertz, Gerald Z., Hartzell, George W., Stormo, Gary D.
We have developed a method for identifying consensus patterns in a set of unaligned DNA sequences known to bind a common protein or to have some other common biochemical function. The method is based...
Schneider, Thomas D., Stormo, Gary D.
In our previous analysis of the information at binding sites on nucleic acids, we found that most of the sites examined contain the amount of information expected from their frequency in the genome....
Quantitative analysis of the relationship between nucleotide sequence and functional activity (1986)
Stormo, Gary D., Schneider, Thomas D., Gold, Larry
Matrices can be used to evaluate sequences for functional activity. Multiple regression can solve for the matrix that gives the best fit between sequence evaluations and quantitative activities. This...
Characterization of translational initiation sites in E. coli (1982)
Stormo, Gary D., Schneider, Thomas D., Gold, Larry M.
We characterize the Shine and Dalgarno sequence of 124 known gene beginnings This information is used to make “rules” which help distinguish gene beginning from other sites in a library of over...
Use of the 'Perceptron' algorithm to distinguish translational initiation sites in E. coli (1982)
Stormo, Gary D., Schneider, Thomas D., Gold, Larry, Ehrenfeucht, Andrzej
We have used a “Perceptron” algorithm to find a weighting function which distinguishes E. coli translational initiation sites from all other sites in a library of over 78,000 nucleotides of mRNA...
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation (1982)
Schneider, Thomas D., Stormo, Gary D., Haemer, Jeffrey S., Gold, Larry
He have designed and built a data-base system for the storage of nucleic-acid sequences. The system consists of a data base (“the library”) and software that manages and provides access to that...
Discovering common stem–loop motifs in unaligned RNA sequences
Gorodkin, Jan, Stricklin, Shawn L., Stormo, Gary D.
Post-transcriptional regulation of gene expression is often accomplished by proteins binding to specific sequence motifs in mRNA molecules, to affect their translation or stability. The motifs are...
Man, Tsz-Kwong, Stormo, Gary D.
Salmonella bacteriophage repressor Mnt belongs to the ribbon–helix–helix class of transcription factors. Previous SELEX results suggested that interactions of Mnt with positions 16 and 17 of the...
Improved statistical methods reveal direct interactions between 16S and 23S rRNA
Kelley, Scott T., Akmaev, Viatcheslav R., Stormo, Gary D.
Recent biochemical studies have indicated a number of regions in both the 16S and 23S rRNA that are exposed on the ribosomal subunit surface. In order to predict potential interactions between these...
Lin, Yiing, Han, Mei, Shimada, Brian, Wang, Lin, Gibler, Therese M., Amarakone, Aloka, ...
We measured daily gene expression in heads of control and period mutant Drosophila by using oligonucleotide microarrays. In control flies, 72 genes showed diurnal rhythms in light-dark cycles; 22 of...
Additivity in protein–DNA interactions: how good an approximation is it?
Benos, Panayiotis V., Bulyk, Martha L., Stormo, Gary D.
Man and Stormo and Bulyk et al. recently presented their results on the study of the DNA binding affinity of proteins. In both of these studies the main conclusion is that the additivity assumption,...
Specificity of Mnt ‘master residue’ obtained from in vivo and in vitro selections
Silbaq, Fauzi S., Ruttenberg, Steven E., Stormo, Gary D.
Mnt is a repressor from phage P22 that belongs to the ribbon–helix–helix family of DNA binding factors. Four amino acids from the N-terminus of the protein, Arg2, His6, Asn8 and Arg10, interact...
GuhaThakurta, Debraj, Palomar, Lisanne, Stormo, Gary D., Tedesco, Pat, Johnson, Thomas E., Walker, David W., ...
We report here the identification of a previously unknown transcription regulatory element for heat shock (HS) genes in Caenorhabditis elegans. We monitored the expression pattern of 11,917 genes...
Liu, Jiajian, Tan, Kai, Stormo, Gary D.
Spo0A-phosphate is essential for the initiation of cellular differentiation and developmental processes in Gram-positive spore-forming bacteria. Here we combined comparative genomics with analyses of...
A Comparative Genomics Approach to Prediction of New Members of Regulons
Tan, Kai, Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio, Stormo, Gary D.
Identifying the complete transcriptional regulatory network for an organism is a major challenge. For each regulatory protein, we want to know all the genes it regulates, that is, its regulon....
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation
Schneider, Thomas D., Stormo, Gary D., Haemer, Jeffrey S., Gold, Larry
We have designed and built a data-base system for the storage of nucleic-acid sequences. The system consists of a data base (“the library”) and software that manages and provides access to that...
Hu, Yan, Wang, Ting, Stormo, Gary D., Gordon, Jeffrey I.
We have previously characterized a transgenic mouse model (CR2-TAg) of metastatic prostate cancer arising in the neuroendocrine (NE) cell lineage. Biomarkers of NE differentiation in this model are...
Friedman, Charles P., Altman, Russ B., Kohane, Isaac S., McCormick, Kathleen A., Miller, Perry L., Ozbolt, Judy G., ...
In 2002–2003, the American College of Medical Informatics (ACMI) undertook a study of the future of informatics training. This project capitalized on the rapidly expanding interest in the role of...
ILM: a web server for predicting RNA secondary structures with pseudoknots
Ruan, Jianhua, Stormo, Gary D., Zhang, Weixiong
The ILM web server provides a web interface to two algorithms, iterated loop matching and maximum weighted matching, for efficiently predicting RNA secondary structures with pseudoknots. The...
Man, Tsz-Kwong, Yang, Joshua SungWoo, Stormo, Gary D.
Understanding DNA–protein recognition quantitatively is essential to developing computational algorithms for accurate transcriptional binding site prediction. Using a quantitative, multiple...
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes
GuhaThakurta, Debraj, Schriefer, Lawrence A., Waterston, Robert H., Stormo, Gary D.
We report the identification of three new transcription regulatory elements that are associated with muscle gene expression in the nematode Caenorhabditis elegans. Starting from a subset of...
Making connections between novel transcription factors and their DNA motifs
Tan, Kai, McCue, Lee Ann, Stormo, Gary D.
The key components of a transcriptional regulatory network are the connections between trans-acting transcription factors and cis-acting DNA-binding sites. In spite of several decades of intense...
Gershenzon, Naum I., Stormo, Gary D., Ioshikhes, Ilya P.
Position-weight matrices (PWMs) are broadly used to locate transcription factor binding sites in DNA sequences. The majority of existing PWMs provide a low level of both sensitivity and specificity....
enoLOGOS: a versatile web tool for energy normalized sequence logos
Workman, Christopher T., Yin, Yutong, Corcoran, David L., Ideker, Trey, Stormo, Gary D., Benos, Panayiotis V.
enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a...
Models for the specificity of DNA-binding transcription factors are often based on small amounts of qualitative data and therefore have limited accuracy. In this study we demonstrate a simple and...
Editing efficiency of a Drosophila gene correlates with a distant splice site selection
AGRAWAL, RITESH, STORMO, GARY D.
RNA editing and alternative splicing are two processes that increase protein diversity. The relationship between the two processes is not well understood. There are a few examples of correlations...
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
A major focus of genome research has been to decipher the cis-regulatory code that governs complex transcriptional regulation. We report a computational approach for identifying conserved regulatory...
Chang, Li-Wei, Nagarajan, Rakesh, Magee, Jeffrey A., Milbrandt, Jeffrey, Stormo, Gary D.
An important aspect of understanding a biological pathway is to delineate the transcriptional regulatory mechanisms of the genes involved. Two important tasks are often encountered when studying...
Discovering common stem–loop motifs in unaligned RNA sequences
Gorodkin, Jan, Stricklin, Shawn L., Stormo, Gary D.
Post-transcriptional regulation of gene expression is often accomplished by proteins binding to specific sequence motifs in mRNA molecules, to affect their translation or stability. The motifs are...
Man, Tsz-Kwong, Stormo, Gary D.
Salmonella bacteriophage repressor Mnt belongs to the ribbon–helix–helix class of transcription factors. Previous SELEX results suggested that interactions of Mnt with positions 16 and 17 of the...
Improved statistical methods reveal direct interactions between 16S and 23S rRNA
Kelley, Scott T., Akmaev, Viatcheslav R., Stormo, Gary D.
Recent biochemical studies have indicated a number of regions in both the 16S and 23S rRNA that are exposed on the ribosomal subunit surface. In order to predict potential interactions between these...
Lin, Yiing, Han, Mei, Shimada, Brian, Wang, Lin, Gibler, Therese M., Amarakone, Aloka, ...
We measured daily gene expression in heads of control and period mutant Drosophila by using oligonucleotide microarrays. In control flies, 72 genes showed diurnal rhythms in light-dark cycles; 22 of...
Additivity in protein–DNA interactions: how good an approximation is it?
Benos, Panayiotis V., Bulyk, Martha L., Stormo, Gary D.
Man and Stormo and Bulyk et al. recently presented their results on the study of the DNA binding affinity of proteins. In both of these studies the main conclusion is that the additivity assumption,...
Specificity of Mnt ‘master residue’ obtained from in vivo and in vitro selections
Silbaq, Fauzi S., Ruttenberg, Steven E., Stormo, Gary D.
Mnt is a repressor from phage P22 that belongs to the ribbon–helix–helix family of DNA binding factors. Four amino acids from the N-terminus of the protein, Arg2, His6, Asn8 and Arg10, interact...
GuhaThakurta, Debraj, Palomar, Lisanne, Stormo, Gary D., Tedesco, Pat, Johnson, Thomas E., Walker, David W., ...
We report here the identification of a previously unknown transcription regulatory element for heat shock (HS) genes in Caenorhabditis elegans. We monitored the expression pattern of 11,917 genes...
Liu, Jiajian, Tan, Kai, Stormo, Gary D.
Spo0A-phosphate is essential for the initiation of cellular differentiation and developmental processes in Gram-positive spore-forming bacteria. Here we combined comparative genomics with analyses of...
A Comparative Genomics Approach to Prediction of New Members of Regulons
Tan, Kai, Moreno-Hagelsieb, Gabriel, Collado-Vides, Julio, Stormo, Gary D.
Identifying the complete transcriptional regulatory network for an organism is a major challenge. For each regulatory protein, we want to know all the genes it regulates, that is, its regulon....
A design for computer nucleic-acid-sequence storage, retrieval, and manipulation
Schneider, Thomas D., Stormo, Gary D., Haemer, Jeffrey S., Gold, Larry
We have designed and built a data-base system for the storage of nucleic-acid sequences. The system consists of a data base (“the library”) and software that manages and provides access to that...
Hu, Yan, Wang, Ting, Stormo, Gary D., Gordon, Jeffrey I.
We have previously characterized a transgenic mouse model (CR2-TAg) of metastatic prostate cancer arising in the neuroendocrine (NE) cell lineage. Biomarkers of NE differentiation in this model are...
Friedman, Charles P., Altman, Russ B., Kohane, Isaac S., McCormick, Kathleen A., Miller, Perry L., Ozbolt, Judy G., ...
In 2002–2003, the American College of Medical Informatics (ACMI) undertook a study of the future of informatics training. This project capitalized on the rapidly expanding interest in the role of...
ILM: a web server for predicting RNA secondary structures with pseudoknots
Ruan, Jianhua, Stormo, Gary D., Zhang, Weixiong
The ILM web server provides a web interface to two algorithms, iterated loop matching and maximum weighted matching, for efficiently predicting RNA secondary structures with pseudoknots. The...
Man, Tsz-Kwong, Yang, Joshua SungWoo, Stormo, Gary D.
Understanding DNA–protein recognition quantitatively is essential to developing computational algorithms for accurate transcriptional binding site prediction. Using a quantitative, multiple...
Novel transcription regulatory elements in Caenorhabditis elegans muscle genes
GuhaThakurta, Debraj, Schriefer, Lawrence A., Waterston, Robert H., Stormo, Gary D.
We report the identification of three new transcription regulatory elements that are associated with muscle gene expression in the nematode Caenorhabditis elegans. Starting from a subset of...
Making connections between novel transcription factors and their DNA motifs
Tan, Kai, McCue, Lee Ann, Stormo, Gary D.
The key components of a transcriptional regulatory network are the connections between trans-acting transcription factors and cis-acting DNA-binding sites. In spite of several decades of intense...
Gershenzon, Naum I., Stormo, Gary D., Ioshikhes, Ilya P.
Position-weight matrices (PWMs) are broadly used to locate transcription factor binding sites in DNA sequences. The majority of existing PWMs provide a low level of both sensitivity and specificity....
enoLOGOS: a versatile web tool for energy normalized sequence logos
Workman, Christopher T., Yin, Yutong, Corcoran, David L., Ideker, Trey, Stormo, Gary D., Benos, Panayiotis V.
enoLOGOS is a web-based tool that generates sequence logos from various input sources. Sequence logos have become a popular way to graphically represent DNA and amino acid sequence patterns from a...
Models for the specificity of DNA-binding transcription factors are often based on small amounts of qualitative data and therefore have limited accuracy. In this study we demonstrate a simple and...
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
A major focus of genome research has been to decipher the cis-regulatory code that governs complex transcriptional regulation. We report a computational approach for identifying conserved regulatory...
Editing efficiency of a Drosophila gene correlates with a distant splice site selection
AGRAWAL, RITESH, STORMO, GARY D.
RNA editing and alternative splicing are two processes that increase protein diversity. The relationship between the two processes is not well understood. There are a few examples of correlations...
Chang, Li-Wei, Nagarajan, Rakesh, Magee, Jeffrey A., Milbrandt, Jeffrey, Stormo, Gary D.
An important aspect of understanding a biological pathway is to delineate the transcriptional regulatory mechanisms of the genes involved. Two important tasks are often encountered when studying...
An improved map of conserved regulatory sites for Saccharomyces cerevisiae
MacIsaac, Kenzie D, Wang, Ting, Gordon, D Benjamin, Gifford, David K, Stormo, Gary D, Fraenkel, Ernest
Zhao, Guoyan, Chang, Kuan Y., Varley, Katherine, Stormo, Gary D.
Inverted repeats have been found to occur in both prokaryotic and eukaryotic genomes. Usually they are short and some have important functions in various biological processes. However, long inverted...
Beverley, Stephen M, Akopyants, Natalia S, Goyard, Sophie, Matlib, Robin S, Gordon, Jennifer L, Brownstein, Bernard H, ...
Leishmania are important protozoan pathogens of humans in temperate and tropical regions. The study of gene expression during the infectious cycle, in mutants or after environmental or chemical...
PAP: a comprehensive workbench for mammalian transcriptional regulatory sequence analysis
Chang, Li-Wei, Fontaine, Burr R., Stormo, Gary D., Nagarajan, Rakesh
Given the recent explosion of publications that employ microarray technology to monitor genome-wide expression and that correlate these expression changes to biological processes or to disease...
Identification of muscle-specific regulatory modules in Caenorhabditis elegans
Zhao, Guoyan, Schriefer, Lawrence A., Stormo, Gary D.
Transcriptional regulation is the major regulatory mechanism that controls the spatial and temporal expression of genes during development. This is carried out by transcription factors (TFs), which...
Zeng, Jue, Yan, Jizhou, Wang, Ting, Mosbrook-Davis, Deborah, Dolan, Kyle T., Christensen, Ryan, ...
Knowledge of all binding sites for transcriptional activators and repressors is essential for computationally aided identification of transcriptional networks. The techniques developed for defining...
Davies, Sherri R., Chang, Li-Wei, Patra, Debabrata, Xing, Xiaoyun, Posey, Karen, Hecht, Jacqueline, ...
Chondrocyte gene regulation is important for the generation and maintenance of cartilage tissues. Several regulatory factors have been identified that play a role in chondrogenesis, including the...
Chang, Li Wei, Payton, Jacqueline E, Yuan, Wenlin, Ley, Timothy J, Nagarajan, Rakesh, Stormo, Gary D
A dissection of the genetic networks and circuitries is described for two form of leukaemia. Integrating transcription factor binding and gene expression profiling, networks are revealed that underly...
The cis-regulatory map of Shewanella genomes
Liu, Jiajian, Xu, Xing, Stormo, Gary D.
While hundreds of microbial genomes are sequenced, the challenge remains to define their cis-regulatory maps. Here, we present a comparative genomic analysis of the cis-regulatory map of Shewanella...
Neural Networks for Determining Protein Specificity and Multiple Alignment of Binding Sites
John M. Heumann, Alan S. Lapedes, Gary D. Stormo
We use a quantitative definition of specificity to develop a neural network for the identification of common protein binding sites in a collection of unaligned DNA fragments. We demonstrate the...
Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines
Xu, Xing, Ji, Yongmei, Stormo, Gary D.
An increasing number of cis-regulatory RNA elements have been found to regulate gene expression post-transcriptionally in various biological processes in bacterial systems. Effective computational...
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs
Foat, Barrett C, Stormo, Gary D
Gene expression is regulated at each step from chromatin remodeling through translation and degradation. Several known RNA-binding regulatory proteins interact with specific RNA secondary structures...
Improving Gene-finding in Chlamydomonas reinhardtii:GreenGenie2
Kwan, Alan L, Li, Linya, Kulp, David C, Dutcher, Susan K, Stormo, Gary D
Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors
Motivation: Modeling and identifying the DNA-protein recognition code is one of the most challenging problems in computational biology. Several quantitative methods have been developed to model...