NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction (2009)
Nguyen Ba, Alex N, Pogoutse, Anastassia, Provart, Nicholas, Moses, Alan M
Abstract Background Nuclear localization signals (NLSs) are stretches of residues within a protein that are important for the regulated nuclear import of the protein. Of the many import pathways that...
Inferring Selection on Amino Acid Preference in Protein Domains (2009)
Moses, Alan M., Durbin, Richard
Models that explicitly account for the effect of selection on new mutations have been proposed to account for “codon bias” or the excess of “preferred” codons that results from selection for...
Shultzaberger, Ryan K., Chiang, Derek Y., Moses, Alan M., Eisen, Michael B.
Eukaryotic gene expression is often under the control of cooperatively acting transcription factors whose binding is limited by structural constraints. By determining these structural constraints, we...
Population genomics of domestic and wild yeasts (2008)
David M. Carter, Gianni Liti, Alan M. Moses, Leopold Parts, Stephen A. James, Robert P. Davey, ...
The natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy...
Moses, Alan M, Hériché, Jean-Karim, Durbin, Richard
Abstract Protein kinases are critical to cellular signalling and post-translational gene regulation, but their biological substrates are difficult to identify. We show that cyclin-dependent kinase...
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila (2006)
Alan M. Moses, Daniel A. Pollard, David A. Nix, Venky N. Iyer, Xiao-Yong Li, Mark D. Biggin, ...
The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Daniel A. Pollard, Venky N. Iyer, Alan M. Moses, Michael B. Eisen
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three...
Pollard, Daniel A., Iyer, Venky N., Moses, Alan M., Eisen, Michael B.
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three...
Pollard, Daniel A, Moses, Alan M, Iyer, Venky N, Eisen, Michael B
Abstract Background Molecular evolutionary studies of noncoding sequences rely on multiple alignments. Yet how multiple alignment accuracy varies across sequence types, tree topologies, divergences...
Pollard, Daniel A., Moses, Alan M., Iyer, Venky N., Eisen, Michael B.
Background: Molecular evolutionary studies of noncoding sequences rely on multiple alignments. Yet how multiple alignment accuracy varies across sequence types, tree topologies, divergences and...
Primate-specific evolution of an LDLR enhancer (2006)
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, ...
Background Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. Results In this...
Large-scale turnover of functional transcription factor binding sites in Drosophila (2006)
Alan M. Moses, Daniel Pollard, David A Nix, Venky N. Iyer, Xiao-Yong Li, Mark D Biggin, ...
The gain and loss of functional transcription-factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Daniel Pollard, Venky N. Iyer, Alan M. Moses, Michael B. Eisen
Understanding the basis for incongruence of phylogenies constructed from different genes or loci and how to properly handle such disaccord is an important challenge to evolutionary biology. To...
Large-scale turnover of functional transcription factor binding sites in Drosophila (2006)
Moses, Alan M., Pollard, Daniel A., Nix, David A., Iyer, Venky N., Li, Xiao-Yong, Biggin, Mark D., ...
The gain and loss of functional transcription-factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Primate-Specific Evolution of an LDLR Enhancer (2006)
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M., Chanan, Sumita, Brown, Myles, ...
Sequence changes in regulatory regions have often been invoked to explain phenotypic divergence among species, but molecular examples of this have been difficult to obtain. In this study, we...
In Vivo Enhancer Analysis Chromosome 16 Conserved Noncoding Sequences (2006)
Pennacchio, Len A., Ahituv, Nadav, Moses, Alan M., Nobrega, Marcelo, Prabhakar, Shyam, Shoukry, Malak, ...
The identification of enhancers with predicted specificities in vertebrate genomes remains a significant challenge that is hampered by a lack of experimentally validated training sets. In this study,...
Bmc Bioinformatics, Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen, Michael B Eisen
Research article Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
Large-scale turnover of functional transcription factor binding sites in Drosophila (2006)
Alan M. Moses, Daniel A. Pollard, David A. Nix, Venky N. Iyer, Xiao-yong Li, Mark D. Biggin, ...
The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Bmc Bioinformatics, Daniel A Pollard, Alan M Moses, Venky N Iyer, Michael B Eisen, Michael B Eisen
Research article Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments
Primate-specific evolution of an LDLR enhancer (2005)
Wang, Qian-Fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M., Chanan, Sumita, Brown, Myles, ...
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
A systematic examination of the gene regulatory elements in ascomycete fungi reveals striking conservation along with some examples of the ways in which regulatory systems can evolve.
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Moses, Alan M, Chiang, Derek Y, Pollard, Daniel A, Iyer, Venky N, Eisen, Michael B
Abstract We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding-site...
Alan M Moses, Derek Y Chiang, Daniel A Pollard, Venky N Iyer, Michael B Eisen
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
Conservation and evolution of cis-regulatory systems in ascomycete fungi (2004)
Audrey P. Gasch, Alan M. Moses, Derek Y. Chiang, Hunter B. Fraser, Mark Berardini, Michael B. Eisen
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Position specific variation in the rate of evolution in transcription factor binding sites (2003)
Moses, Alan M., Chiang, Derek Y., Kellis, Manolis, Lander, Eric S., Eisen, Michael B.
Background: The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental...
Position specific variation in the rate of evolution in transcription factor binding sites (2003)
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Abstract Background The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of...
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Abstract Background Transcriptional regulation in eukaryotes often involves multiple transcription factors binding to the same transcription control region, and to understand the regulatory content...
BMC Evolutionary Biology BioMed Central (2003)
Alan M Moses, Derek Y Chiang, Manolis Kellis, Eric S L, Michael B Eisen, Eric S Lander, ...
Research article Position specific variation in the rate of evolution in transcription factor binding sites
2003 Chiang et Volume al. 4, Issue 7, Article R43 Open Access (2003)
Derek Y Chiang, Alan M Moses, Manolis Kellis, Eric S L, Michael B Eisen
Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts
BMC Evolutionary Biology BioMed Central (2003)
Alan M Moses, Derek Y Chiang, Manolis Kellis, Eric S L, Michael B Eisen, Eric S Lander, ...
Research article Position specific variation in the rate of evolution in transcription factor binding sites
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
The determination of conserved sequences has identified individual transcription factor binding sites. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts...
Position specific variation in the rate of evolution in transcription factor binding sites
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
Gasch, Audrey P, Moses, Alan M, Chiang, Derek Y, Fraser, Hunter B, Berardini, Mark, Eisen, Michael B
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Moses, Alan M, Chiang, Derek Y, Pollard, Daniel A, Iyer, Venky N, Eisen, Michael B
MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments.
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
Moses, Alan M, Pollard, Daniel A, Nix, David A, Iyer, Venky N, Li, Xiao-Yong, Biggin, Mark D, ...
The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Pollard, Daniel A, Iyer, Venky N, Moses, Alan M, Eisen, Michael B
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three...
Chiang, Derek Y, Moses, Alan M, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
The determination of conserved sequences has identified individual transcription factor binding sites. The incorporation of both joint conservation and spacing constraints of sequence pairs predicts...
Position specific variation in the rate of evolution in transcription factor binding sites
Moses, Alan M, Chiang, Derek Y, Kellis, Manolis, Lander, Eric S, Eisen, Michael B
Conservation and Evolution of Cis-Regulatory Systems in Ascomycete Fungi
Gasch, Audrey P, Moses, Alan M, Chiang, Derek Y, Fraser, Hunter B, Berardini, Mark, Eisen, Michael B
Relatively little is known about the mechanisms through which gene expression regulation evolves. To investigate this, we systematically explored the conservation of regulatory networks in fungi by...
Moses, Alan M, Chiang, Derek Y, Pollard, Daniel A, Iyer, Venky N, Eisen, Michael B
MONKEY is a new method for identifying conserved transcription-factor binding sites from multiple-sequence alignments.
Large-Scale Turnover of Functional Transcription Factor Binding Sites in Drosophila
Moses, Alan M, Pollard, Daniel A, Nix, David A, Iyer, Venky N, Li, Xiao-Yong, Biggin, Mark D, ...
The gain and loss of functional transcription factor binding sites has been proposed as a major source of evolutionary change in cis-regulatory DNA and gene expression. We have developed an...
Pollard, Daniel A, Iyer, Venky N, Moses, Alan M, Eisen, Michael B
The phylogenetic relationship of the now fully sequenced species Drosophila erecta and D. yakuba with respect to the D. melanogaster species complex has been a subject of controversy. All three...
Primate-specific evolution of an LDLR enhancer
Wang, Qian-fei, Prabhakar, Shyam, Wang, Qianben, Moses, Alan M, Chanan, Sumita, Brown, Myles, ...
Analysis of primate-specific evolution of the LDL receptor enhancer demonstrates a molecular mechanism by which ancestral mammalian regulatory elements can evolve to perform new functions.
Moses, Alan M, Hériché, Jean-Karim, Durbin, Richard
A novel computational strategy is used to predict cyclin-dependent targets by exploiting their propensity for occurring in clusters on substrate proteins.
Determining Physical Constraints in Transcriptional Initiation Complexes Using DNA Sequence Analysis
Shultzaberger, Ryan K., Chiang, Derek Y., Moses, Alan M., Eisen, Michael B.
Eukaryotic gene expression is often under the control of cooperatively acting transcription factors whose binding is limited by structural constraints. By determining these structural constraints, we...
Moses, Alan M., Liku, Muluye E., Li, Joachim J., Durbin, Richard
Evolutionary change in gene regulation is a key mechanism underlying the genetic component of organismal diversity. Here, we study evolution of regulation at the posttranslational level by examining...
NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction
Nguyen Ba, Alex N, Pogoutse, Anastassia, Provart, Nicholas, Moses, Alan M
Inferring Selection on Amino Acid Preference in Protein Domains
Moses, Alan M., Durbin, Richard
Models that explicitly account for the effect of selection on new mutations have been proposed to account for “codon bias” or the excess of “preferred” codons that results from selection for...