Centroid estimation in discrete high-dimensional spaces with applications (2008)
Luis E. Carvalho, Charles E. Lawrence
in biology
Sean P. Conlan, Lee Ann, Mccue Lee, A. Newberg, Thomas M. Smith, William Thompson, ...
Use of ensemble centroid helps What We’re Looking For Seeking elements that are short: 6–30 bp Only partial conserved Isolated elements or multiple elements per module Single or multiple...
Structural bioinformatics Structure clustering features on the Sfold Web server (2008)
Chi Yu Chan, Charles E. Lawrence, Ye Ding
Summary: The energy landscape of RNA secondary structures is often complex, and the Boltzmann-weighted ensemble usually contains distinct clusters. Furthermore, the minimum free energy structure...
J. M. Bernardo, M. J. Bayarri, J. O. Berger, A. P. Dawid, D. Heckerman, ...
The clustering problem has attracted much attention from both statisticians and computer scientists in the past fifty years. Methods such as hierarchical clustering and the K-means method are...
Automated mapping of large-scale chromatin structure in ENCODE (2008)
Lian, Heng, Thompson, William A., Thurman, Robert, Stamatoyannopoulos, John A., Noble, William Stafford, Lawrence, Charles E.
Motivation: A recently developed DNaseI assay has given us our first genome-wide view of chromatin structure. In addition to cataloging DNaseI hypersensitive sites, these data allows us to more...
,C.StevenCarmack 1,MichaelP.Ryan (2007)
Lee Ann Mccue, William Thompson, Charles E. Lawrence
Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks,...
Effect of target secondary structure on RNAi efficiency (2007)
Shao, Yu, Chan, Chi Yu, Maliyekkel, Anil, Lawrence, Charles E., Roninson, Igor B., Ding, Ye
RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful tool for gene knockdown studies. However, the levels of knockdown vary...
Newberg, Lee A., Thompson, William A., Conlan, Sean, Smith, Thomas M., McCue, Lee Ann, Lawrence, Charles E.
Motivation: Identification of functionally conserved regulatory elements in sequence data from closely related organisms is becoming feasible, due to the rapid growth of public sequence databases....
The Gibbs Centroid Sampler (2007)
Thompson, William A., Newberg, Lee A., Conlan, Sean, McCue, Lee Ann, Lawrence, Charles E.
The Gibbs Centroid Sampler is a software package designed for locating conserved elements in biopolymer sequences. The Gibbs Centroid Sampler reports a centroid alignment, i.e. an alignment that has...
PhyloScan: identification of transcription factor binding sites using cross-species evidence (2007)
Carmack, C Steven, McCue, Lee, Newberg, Lee A, Lawrence, Charles E
Abstract Background When transcription factor binding sites are known for a particular transcription factor, it is possible to construct a motif model that can be used to scan sequences for...
The Gibbs Centroid Sampler Nucleic Acids Research, 2007, 1–6 doi:10.1093/nar/gkm265 (2007)
William A. Thompson, Lee A. Newberg, Sean Conlan, Lee Ann Mccue, Charles E. Lawrence
The Gibbs Centroid Sampler is a software package designed for locating conserved elements in biopolymer sequences. The Gibbs Centroid Sampler reports a centroid alignment, i.e. an alignment that has...
for cis-regulatory site prediction (2007)
Lee A. Newberg, William A. Thompson, Sean Conlan, Thomas M. Smith, Lee Ann Mccue, Charles E. Lawrence, ...
Motivation: Identification of functionally conserved regulatory elements in sequence data from closely related organisms is becoming feasible, due to the rapid growth of public sequence databases....
for cis-regulatory site prediction (2007)
Lee A. Newberg, William A. Thompson, Sean Conlan, Thomas M. Smith, Lee Ann Mccue, Charles E. Lawrence, ...
Motivation: Identification of functionally conserved regulatory elements in sequence data from closely related organisms is becoming feasible, due to the rapid growth of public sequence databases....
Newberg, Lee A, McCue, Lee Ann, Lawrence, Charles E
Approaches based upon sequence weights, to construct a position weight matrix of nucleotides from aligned inputs, are popular but little effort has been expended to measure their quality.We derive...
Newberg, Lee A, McCue, Lee Ann, Lawrence, Charles E
Approaches based upon sequence weights, to construct a position weight matrix of nucleotides from aligned inputs, are popular but little effort has been expended to measure their quality.We derive...
Newberg, Lee A, McCue, Lee Ann, Lawrence, Charles E
Approaches based upon sequence weights, to construct a position weight matrix of nucleotides from aligned inputs, are popular but little effort has been expended to measure their quality.We derive...
Newberg, Lee A, McCue, Lee Ann, Lawrence, Charles E
Approaches based upon sequence weights, to construct a position weight matrix of nucleotides from aligned inputs, are popular but little effort has been expended to measure their quality.We derive...
Structure clustering features on the Sfold Web server (2005)
Chan, Chi Yu, Lawrence, Charles E., Ding, Ye
Summary: The energy landscape of RNA secondary structures is often complex, and the Boltzmann-weighted ensemble usually contains distinct clusters. Furthermore, the minimum free energy structure...
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble (2005)
DING, YE, CHAN, CHI YU, LAWRENCE, CHARLES E.
Prediction of RNA secondary structure by free energy minimization has been the standard for over two decades. Here we describe a novel method that forsakes this paradigm for predictions based on...
Structure clustering features on the Sfold Web server (2005)
Chan, Chi Yu, Lawrence, Charles E., Ding, Ye
Summary: The energy landscape of RNA secondary structures is often complex, and the Boltzmann-weighted ensemble usually contains distinct clusters. Furthermore, the minimum free energy structure...
Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description (2004)
Newberg, Lee A, Lawrence, Charles E
Under the assumption that a significant motivation for sequencing the genomes of mammals is the resulting ability to help us locate and characterize functional DNA segments shared with humans, we...
Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description (2004)
Newberg, Lee A, Lawrence, Charles E
Under the assumption that a significant motivation for sequencing the genomes of mammals is the resulting ability to help us locate and characterize functional DNA segments shared with humans, we...
Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description (2004)
Newberg, Lee A, Lawrence, Charles E
Under the assumption that a significant motivation for sequencing the genomes of mammals is the resulting ability to help us locate and characterize functional DNA segments shared with humans, we...
Mammalian Genomes Ease Location of Human DNA Functional Segments but Not Their Description (2004)
Newberg, Lee A, Lawrence, Charles E
Under the assumption that a significant motivation for sequencing the genomes of mammals is the resulting ability to help us locate and characterize functional DNA segments shared with humans, we...
Sfold web server for statistical folding and rational design of nucleic acids (2004)
Ye Ding, Chi Yu Chan, Charles E. Lawrence
nucleic acids
Decoding Human Regulatory Circuits (2004)
Thompson, William, Palumbo, Michael J., Wasserman, Wyeth W., Liu, Jun S., Lawrence, Charles E.
Clusters of transcription factor binding sites (TFBSs) which direct gene expression constitute cis-regulatory modules (CRMs). We present a novel algorithm, based on Gibbs sampling, which locates, de...
Sfold web server for statistical folding and rational design of nucleic acids (2004)
Ding, Ye, Chan, Chi Yu, Lawrence, Charles E.
The Sfold web server provides user-friendly access to Sfold, a recently developed nucleic acid folding software package, via the World Wide Web (WWW). The software is based on a new statistical...
Gibbs recursive sampler: finding transcription factor binding sites (2003)
William Thompson, Eric C. Rouchka, Charles E. Lawrence
The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs...
Gibbs Recursive Sampler: finding transcription factor binding sites (2003)
Thompson, William, Rouchka, Eric C., Lawrence, Charles E.
The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs...
A statistical sampling algorithm for RNA secondary structure prediction (2003)
Ding, Ye, Lawrence, Charles E.
An RNA molecule, particularly a long‐chain mRNA, may exist as a population of structures. Further more, multiple structures have been demonstrated to play important functional roles. Thus, a...
BALSA: Bayesian algorithm for local sequence alignment (2002)
Jun S. Liu, Charles E. Lawrence
The Smith–Waterman algorithm yields a single alignment, which, albeit optimal, can be strongly affected by the choice of the scoring matrix and the gap penalties. Additionally, the scores obtained...
BALSA: Bayesian algorithm for local sequence alignment (2002)
Webb, Bobbie-Jo M., Liu, Jun S., Lawrence, Charles E.
The Smith–Waterman algorithm yields a single alignment, which, albeit optimal, can be strongly affected by the choice of the scoring matrix and the gap penalties. Additionally, the scores obtained...
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes (2001)
McCue, Lee Ann, Thompson, William, Carmack, C. Steven, Ryan, Michael P., Liu, Jun S., Derbyshire, Victoria, ...
Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks,...
Ding, Ye, Lawrence, Charles E.
Single-stranded regions in RNA secondary structure are important for RNA–RNA and RNA–protein interactions. We present a probability profile approach for the prediction of these regions based on a...
Markovian Structures in Biological Sequence Alignments (1999)
Jun S. Liu, Andrew F. Neuwald, Charles E. Lawrence
this article, we provide a coherent view of the two recent models used for multiple sequence alignment --- the hidden Markov model (HMM) and the block-based motif model --- in order to develop a set...
Extracting protein alignment models from the sequence database (1997)
Andrew F. Neuwald, Jun S. Liu, David J. Lipman, Charles E. Lawrence
Biologists often gain structural and functional insights into a protein sequence by constructing a multiple alignment model of the family. Here a program called PROBE fully automates this process of...
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...
Auger, Ivan E., Lawrence, Charles E.
Amphipathic helices, which play important roles in protein structure, occur in a wide variety of lengths. Yet existing methods employ fixed window lengths. We present a hierarchical procedure that...
TAYLOR, PHILIP R., STELMA, JEANETTE M., LAWRENCE, CHARLES E.
The authors studied the relation of polychlorinated biphenyls (PCBs) to birth weight and gestational age among the live offspring of women occupationally exposed to PCBs during the manufacture of...
Ding, Ye, Lawrence, Charles E.
Single-stranded regions in RNA secondary structure are important for RNA–RNA and RNA–protein interactions. We present a probability profile approach for the prediction of these regions based on a...
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
McCue, Lee Ann, Thompson, William, Carmack, C. Steven, Ryan, Michael P., Liu, Jun S., Derbyshire, Victoria, ...
Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks,...
BALSA: Bayesian algorithm for local sequence alignment
Webb, Bobbie-Jo M., Liu, Jun S., Lawrence, Charles E.
The Smith–Waterman algorithm yields a single alignment, which, albeit optimal, can be strongly affected by the choice of the scoring matrix and the gap penalties. Additionally, the scores obtained...
Gibbs Recursive Sampler: finding transcription factor binding sites
Thompson, William, Rouchka, Eric C., Lawrence, Charles E.
The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs...
McCue, Lee Ann, Thompson, William, Carmack, C. Steven, Lawrence, Charles E.
As the number of sequenced genomes has grown, the questions of which species are most useful and how many genomes are sufficient for comparison have become increasingly important for comparative...
A statistical sampling algorithm for RNA secondary structure prediction
Ding, Ye, Lawrence, Charles E.
An RNA molecule, particularly a long-chain mRNA, may exist as a population of structures. Further more, multiple structures have been demonstrated to play important functional roles. Thus, a...
Sfold web server for statistical folding and rational design of nucleic acids
Ding, Ye, Chan, Chi Yu, Lawrence, Charles E.
The Sfold web server provides user-friendly access to Sfold, a recently developed nucleic acid folding software package, via the World Wide Web (WWW). The software is based on a new statistical...
Decoding Human Regulatory Circuits
Thompson, William, Palumbo, Michael J., Wasserman, Wyeth W., Liu, Jun S., Lawrence, Charles E.
Clusters of transcription factor binding sites (TFBSs) which direct gene expression constitute cis-regulatory modules (CRMs). We present a novel algorithm, based on Gibbs sampling, which locates, de...
Kolker, Eugene, Picone, Alex F., Galperin, Michael Y., Romine, Margaret F., Higdon, Roger, Makarova, Kira S., ...
The γ-proteobacterium Shewanella oneidensis strain MR-1 is a metabolically versatile organism that can reduce a wide range of organic compounds, metal ions, and radionuclides. Similar to most other...
A test of the negative discriminative stimulus as a reinforcer of observing1
Dinsmoor, James A., Browne, Michael P., Lawrence, Charles E.
Five pigeons were used to test the hypothesis that the source of reinforcement for observing behavior is the information that it provides concerning the schedule of primary reinforcement. On a...
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
DING, YE, CHAN, CHI YU, LAWRENCE, CHARLES E.
Prediction of RNA secondary structure by free energy minimization has been the standard for over two decades. Here we describe a novel method that forsakes this paradigm for predictions based on...
Ding, Ye, Lawrence, Charles E.
Single-stranded regions in RNA secondary structure are important for RNA–RNA and RNA–protein interactions. We present a probability profile approach for the prediction of these regions based on a...
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes
McCue, Lee Ann, Thompson, William, Carmack, C. Steven, Ryan, Michael P., Liu, Jun S., Derbyshire, Victoria, ...
Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks,...
BALSA: Bayesian algorithm for local sequence alignment
Webb, Bobbie-Jo M., Liu, Jun S., Lawrence, Charles E.
The Smith–Waterman algorithm yields a single alignment, which, albeit optimal, can be strongly affected by the choice of the scoring matrix and the gap penalties. Additionally, the scores obtained...
Gibbs Recursive Sampler: finding transcription factor binding sites
Thompson, William, Rouchka, Eric C., Lawrence, Charles E.
The Gibbs Motif Sampler is a software package for locating common elements in collections of biopolymer sequences. In this paper we describe a new variation of the Gibbs Motif Sampler, the Gibbs...
McCue, Lee Ann, Thompson, William, Carmack, C. Steven, Lawrence, Charles E.
As the number of sequenced genomes has grown, the questions of which species are most useful and how many genomes are sufficient for comparison have become increasingly important for comparative...
A statistical sampling algorithm for RNA secondary structure prediction
Ding, Ye, Lawrence, Charles E.
An RNA molecule, particularly a long-chain mRNA, may exist as a population of structures. Further more, multiple structures have been demonstrated to play important functional roles. Thus, a...
Sfold web server for statistical folding and rational design of nucleic acids
Ding, Ye, Chan, Chi Yu, Lawrence, Charles E.
The Sfold web server provides user-friendly access to Sfold, a recently developed nucleic acid folding software package, via the World Wide Web (WWW). The software is based on a new statistical...
Decoding Human Regulatory Circuits
Thompson, William, Palumbo, Michael J., Wasserman, Wyeth W., Liu, Jun S., Lawrence, Charles E.
Clusters of transcription factor binding sites (TFBSs) which direct gene expression constitute cis-regulatory modules (CRMs). We present a novel algorithm, based on Gibbs sampling, which locates, de...
Kolker, Eugene, Picone, Alex F., Galperin, Michael Y., Romine, Margaret F., Higdon, Roger, Makarova, Kira S., ...
The γ-proteobacterium Shewanella oneidensis strain MR-1 is a metabolically versatile organism that can reduce a wide range of organic compounds, metal ions, and radionuclides. Similar to most other...
A test of the negative discriminative stimulus as a reinforcer of observing1
Dinsmoor, James A., Browne, Michael P., Lawrence, Charles E.
Five pigeons were used to test the hypothesis that the source of reinforcement for observing behavior is the information that it provides concerning the schedule of primary reinforcement. On a...
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
DING, YE, CHAN, CHI YU, LAWRENCE, CHARLES E.
Prediction of RNA secondary structure by free energy minimization has been the standard for over two decades. Here we describe a novel method that forsakes this paradigm for predictions based on...
PhyloScan: identification of transcription factor binding sites using cross-species evidence
Carmack, C Steven, McCue, Lee Ann, Newberg, Lee A, Lawrence, Charles E
Thompson, William A., Newberg, Lee A., Conlan, Sean, McCue, Lee Ann, Lawrence, Charles E.
The Gibbs Centroid Sampler is a software package designed for locating conserved elements in biopolymer sequences. The Gibbs Centroid Sampler reports a centroid alignment, i.e. an alignment that has...
Effect of target secondary structure on RNAi efficiency
Shao, Yu, Chan, Chi Yu, Maliyekkel, Anil, Lawrence, Charles E., Roninson, Igor B., Ding, Ye
RNA interference (RNAi) mediated by small interfering RNAs (siRNAs) or short hairpin RNAs (shRNAs) has become a powerful tool for gene knockdown studies. However, the levels of knockdown vary...
Measuring Global Credibility with Application to Local Sequence Alignment
McCue, Lee Ann, Lawrence, Charles E.
Computational biology is replete with high-dimensional (high-D) discrete prediction and inference problems, including sequence alignment, RNA structure prediction, phylogenetic inference, motif...
Automated mapping of large-scale chromatin structure in ENCODE
Lian, Heng, Thompson, William A., Thurman, Robert, Stamatoyannopoulos, John A., Noble, William Stafford, Lawrence, Charles E.
Motivation: A recently developed DNaseI assay has given us our first genome-wide view of chromatin structure. In addition to cataloging DNaseI hypersensitive sites, these data allows us to more...
Centroid estimation in discrete high-dimensional spaces with applications in biology
Carvalho, Luis E., Lawrence, Charles E.
Maximum likelihood estimators and other direct optimization-based estimators dominated statistical estimation and prediction for decades. Yet, the principled foundations supporting their dominance do...