Trade-Offs in Detecting Evolutionarily Constrained Sequence by Comparative Genomics
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journal
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September 2005 |
Comparison of genomic DNA sequences: solved and unsolved problems
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journal
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May 2001 |
Comparative Genomics
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journal
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September 2004 |
The many faces of sequence alignment
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journal
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January 2005 |
Benchmarking tools for the alignment of functional noncoding DNA
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January 2004 |
Evolutionary distance estimation and fidelity of pair wise sequence alignment
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January 2005 |
Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner
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journal
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April 2004 |
Multiple sequence alignment accuracy and evolutionary distance estimation
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journal
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November 2005 |
A Model of the Statistical Power of Comparative Genome Sequence Analysis
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January 2005 |
Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution
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March 2001 |
Phylogenies from Molecular Sequences: Inference and Reliability
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journal
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December 1988 |
Application and Accuracy of Molecular Phylogenies
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journal
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April 1994 |
A comprehensive comparison of multiple sequence alignment programs
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July 1999 |
MCALIGN: Stochastic Alignment of Noncoding DNA Sequences Based on an Evolutionary Model of Sequence Evolution
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March 2004 |
Human-mouse genome comparisons to locate regulatory sites
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journal
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October 2000 |
Factors Influencing the Identification of Transcription Factor Binding Sites by Cross-Species Comparison
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journal
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September 2002 |
Embryonic enhancers in the dpp disk region regulate a second round of Dpp signaling from the dorsal ectoderm to the mesoderm that represses Zfh-1 expression in a subset of pericardial cells
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journal
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October 2003 |
Combining phylogenetic data with co-regulated genes to identify regulatory motifs
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December 2003 |
Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D.pseudoobscura
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May 2004 |
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
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journal
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January 2004 |
Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila
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January 2004 |
MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
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journal
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November 2004 |
Identification of functional transcription factor binding sites using closely related Saccharomyces species
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journal
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April 2005 |
Discovery, validation, and genetic dissection of transcription factor binding sites by comparative and functional genomics
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journal
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August 2005 |
Computational screening of conserved genomic DNA in search of functional noncoding elements
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journal
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July 2005 |
De novo discovery of a tissue-specific gene regulatory module in a chordate
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journal
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September 2005 |
Identifying the conserved network of cis-regulatory sites of a eukaryotic genome
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journal
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November 2005 |
Conservation of regulatory elements between two species of Drosophila
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journal
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January 2003 |
Evidence for stabilizing selection in a eukaryotic enhancer element
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journal
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February 2000 |
Evolution of Transcription Factor Binding Sites in Mammalian Gene Regulatory Regions: Conservation and Turnover
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journal
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July 2002 |
Tracing the Evolutionary History of Drosophila Regulatory Regions with Models that Identify Transcription Factor Binding Sites
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journal
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April 2003 |
Dynamics and function of intron sequences of the wingless gene during the evolution of the Drosophila genus
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journal
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September 2004 |
Sequence Turnover and Tandem Repeats in cis-Regulatory Modules in Drosophila
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journal
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January 2005 |
Conserved noncoding sequences are reliable guides to regulatory elements
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journal
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September 2000 |
Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes
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May 2003 |
Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents
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journal
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November 2003 |
The Share of Human Genomic DNA under Selection Estimated from Human-Mouse Genomic Alignments
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journal
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January 2003 |
Distinguishing Regulatory DNA From Neutral Sites
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journal
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January 2003 |
Patterns of Evolutionary Constraints in Intronic and Intergenic DNA of Drosophila
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journal
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February 2004 |
Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat
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journal
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April 2004 |
Evolutionary constraints in conserved nongenic sequences of mammals
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journal
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September 2005 |
Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
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journal
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July 2005 |
Generation Time and Genomic Evolution in Primates
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journal
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March 1973 |
Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests
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journal
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July 2004 |
The Correlation Between Intron Length and Recombination in Drosophila: Dynamic Equilibrium Between Mutational and Selective Forces
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journal
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November 2000 |
Evolutionary distances for protein-coding sequences: modeling site- specific residue frequencies
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journal
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July 1998 |
Information content of binding sites on nucleotide sequences
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journal
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April 1986 |
Transcriptional Control in the Segmentation Gene Network of Drosophila
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journal
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August 2004 |
Extraction of Functional Binding Sites from Unique Regulatory Regions: The Drosophila Early Developmental Enhancers
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journal
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February 2002 |
Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster
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journal
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November 2004 |
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
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journal
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January 1994 |
MAVID: Constrained Ancestral Alignment of Multiple Sequences
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journal
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April 2004 |
LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA
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journal
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March 2003 |
PipMaker---A Web Server for Aligning Two Genomic DNA Sequences
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journal
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April 2000 |
Human-Mouse Alignments with BLASTZ
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journal
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January 2003 |
Aligning alignments exactly
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conference
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January 2004 |
Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
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journal
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September 1994 |
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
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journal
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April 2006 |
Chromosome evolution in eukaryotes: a multi-kingdom perspective
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journal
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December 2005 |
Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex
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journal
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April 2005 |
Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
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journal
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January 2005 |
Transcriptional regulatory code of a eukaryotic genome
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journal
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September 2004 |
Chromosomal organization is shaped by the transcription regulatory network
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journal
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March 2005 |
Twilight zone of protein sequence alignments
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journal
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February 1999 |
Analysis of Conserved Noncoding DNA in Drosophila Reveals Similar Constraints in Intergenic and Intronic Sequences
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journal
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August 2001 |
High intrinsic rate of DNA loss in Drosophila
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journal
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November 1996 |
High rate of DNA loss in the Drosophila melanogaster and Drosophila virilis species groups
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journal
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March 1998 |
BLAT---The BLAST-Like Alignment Tool
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journal
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March 2002 |
R: A Language for Data Analysis and Graphics
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journal
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September 1996 |
Estimation of evolutionary distances between nucleotide sequences
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journal
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September 1994 |
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
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journal
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October 1985 |
Decoding cis-regulatory DNAs in the Drosophila genome
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journal
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October 2002 |
Functional evolution of noncoding DNA
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journal
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December 2002 |
Pattern of selective constraint in C. elegans and C. briggsae genomes
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journal
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August 1999 |
The CICERO system for CAD/CAM fabrication of full-ceramic crowns
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journal
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March 2001 |
R: A Language for Data Analysis and Graphics
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journal
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September 1996 |
PAML: a program package for phylogenetic analysis by maximum likelihood
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journal
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January 1997 |
Identification of consensus patterns in unaligned DNA sequences known to be functionally related
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journal
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January 1990 |
Accurate anchoring alignment of divergent sequences
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journal
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November 2005 |
Expected Rates and Modes of Evolution of Enhancer Sequences
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journal
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February 2004 |
Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site.
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journal
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March 1994 |
Comparative analysis of multiple protein-sequence alignment methods.
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journal
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July 1994 |
Relative efficiencies of the maximum-parsimony and distance-matrix methods of phylogeny construction for restriction data.
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journal
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May 1991 |
Extraction of Functional Binding Sites from Unique Regulatory Regions: The Drosophila Early Developmental Enhancers
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journal
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February 2002 |
rVistafor Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites
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journal
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April 2002 |
BLAT---The BLAST-Like Alignment Tool
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journal
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March 2002 |
Identification and Classification of Conserved RNA Secondary Structures in the Human Genome
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journal
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January 2005 |