MAVID: constrained ancestral alignment of multiple sequences.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08

VISTA: computational tools for comparative genomics. Nucleic Acids Res (2004) 13.52

Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res (2008) 7.35

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05

microRNA target predictions across seven Drosophila species and comparison to mammalian targets. PLoS Comput Biol (2005) 6.77

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol (2007) 6.18

Fast statistical alignment. PLoS Comput Biol (2009) 5.92

Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res (2008) 5.12

Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res (2007) 4.73

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res (2007) 4.33

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82

The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes. J Bacteriol (2007) 3.55

Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet (2006) 3.53

Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol (2005) 3.39

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput Biol (2005) 3.35

Uncertainty in homology inferences: assessing and improving genomic sequence alignment. Genome Res (2007) 3.16

Graemlin: general and robust alignment of multiple large interaction networks. Genome Res (2006) 2.92

Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. PLoS Comput Biol (2008) 2.70

Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res (2006) 2.64

Phylo: a citizen science approach for improving multiple sequence alignment. PLoS One (2012) 2.64

The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol (2014) 2.44

Multiple whole-genome alignments without a reference organism. Genome Res (2009) 2.31

MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. Plant Cell (2010) 2.22

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res (2011) 2.21

Computational analysis identifies human adenovirus type 55 as a re-emergent acute respiratory disease pathogen. J Clin Microbiol (2009) 2.11

Cactus: Algorithms for genome multiple sequence alignment. Genome Res (2011) 2.03

M-GCAT: interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species. BMC Bioinformatics (2006) 1.92

Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res (2006) 1.88

RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics (2011) 1.83

Using the Generic Synteny Browser (GBrowse_syn). Curr Protoc Bioinformatics (2010) 1.77

Subtree power analysis and species selection for comparative genomics. Proc Natl Acad Sci U S A (2005) 1.69

Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over. Genome Biol (2007) 1.68

GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinformatics (2005) 1.66

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion. PLoS Biol (2004) 1.54

Evolutionary constraints in conserved nongenic sequences of mammals. Genome Res (2005) 1.50

Whole-genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes. J Bacteriol (2006) 1.48

Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments. BMC Bioinformatics (2006) 1.44

Circular sequence comparison: algorithms and applications. Algorithms Mol Biol (2016) 1.42

Divergence between the Drosophila pseudoobscura and D. persimilis genome sequences in relation to chromosomal inversions. Genetics (2007) 1.41

Evidence for pervasive adaptive protein evolution in wild mice. PLoS Genet (2010) 1.39

Assessing computational methods of cis-regulatory module prediction. PLoS Comput Biol (2010) 1.27

Computational challenges in the analysis of ancient DNA. Genome Biol (2010) 1.27

Compensatory relationship between splice sites and exonic splicing signals depending on the length of vertebrate introns. BMC Genomics (2006) 1.26

The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol (2013) 1.26

CONREAL web server: identification and visualization of conserved transcription factor binding sites. Nucleic Acids Res (2005) 1.25

Finding regulatory elements and regulatory motifs: a general probabilistic framework. BMC Bioinformatics (2007) 1.22

Identification of evolutionary hotspots in the rodent genomes. Genome Res (2004) 1.21

Identification of transposable elements using multiple alignments of related genomes. Genome Res (2005) 1.17

Comparative genomics and transcriptomics of lineages I, II, and III strains of Listeria monocytogenes. BMC Genomics (2012) 1.16

A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays. Bioinformatics (2009) 1.16

Computational RNomics of drosophilids. BMC Genomics (2007) 1.15

The genomic landscape of short insertion and deletion polymorphisms in the chicken (Gallus gallus) Genome: a high frequency of deletions in tandem duplicates. Genetics (2007) 1.13

Alternative splicing of Alu exons--two arms are better than one. Nucleic Acids Res (2008) 1.11

Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome Biol Evol (2010) 1.06

Visualization of multiple genome annotations and alignments with the K-BROWSER. Genome Res (2004) 1.05

Multiple whole genome alignments and novel biomedical applications at the VISTA portal. Nucleic Acids Res (2007) 1.04

Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27. Genome Res (2005) 1.04

Comparative assessment of methods for aligning multiple genome sequences. Nat Biotechnol (2010) 1.03

Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res (2004) 1.03

Evolutionary diversification of SPANX-N sperm protein gene structure and expression. PLoS One (2007) 1.02

Multiple genome alignment for identifying the core structure among moderately related microbial genomes. BMC Genomics (2008) 1.02

Both selective and neutral processes drive GC content evolution in the human genome. BMC Evol Biol (2008) 1.02

Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc Natl Acad Sci U S A (2014) 1.01

Evolutionary mechanisms shaping the genomic structure of the Williams-Beuren syndrome chromosomal region at human 7q11.23. Genome Res (2005) 1.00

CSA: an efficient algorithm to improve circular DNA multiple alignment. BMC Bioinformatics (2009) 0.99

Orthopoxvirus genome evolution: the role of gene loss. Viruses (2010) 0.98

Phylogenetics of modern birds in the era of genomics. Proc Biol Sci (2005) 0.98

Complete genome sequence of Listeria seeligeri, a nonpathogenic member of the genus Listeria. J Bacteriol (2010) 0.96

Evolutionary conservation of plant gibberellin signalling pathway components. BMC Plant Biol (2007) 0.96

Global analysis of alternative splicing regulation by insulin and wingless signaling in Drosophila cells. Genome Biol (2009) 0.96

Choosing the best heuristic for seeded alignment of DNA sequences. BMC Bioinformatics (2006) 0.96

Traffic of genetic information between segmental duplications flanking the typical 22q11.2 deletion in velo-cardio-facial syndrome/DiGeorge syndrome. Genome Res (2005) 0.95

Towards realistic benchmarks for multiple alignments of non-coding sequences. BMC Bioinformatics (2010) 0.94

Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites. J Mol Evol (2007) 0.93

Applying genomic and bioinformatic resources to human adenovirus genomes for use in vaccine development and for applications in vector development for gene delivery. Viruses (2010) 0.92

SinicView: a visualization environment for comparisons of multiple nucleotide sequence alignment tools. BMC Bioinformatics (2006) 0.90

MicroRNA enrichment among short 'ultraconserved' sequences in insects. Nucleic Acids Res (2006) 0.89

Evolution and comparative analysis of the MHC Class III inflammatory region. BMC Genomics (2006) 0.87

Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation. Genetics (2011) 0.87

Long- and short-term selective forces on malaria parasite genomes. PLoS Genet (2010) 0.86

cisMEP: an integrated repository of genomic epigenetic profiles and cis-regulatory modules in Drosophila. BMC Syst Biol (2014) 0.85

Phylogenetic incongruence in the Drosophila melanogaster species group. Mol Phylogenet Evol (2006) 0.85

Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura. J Mol Evol (2009) 0.84

Unravelling cis-regulatory elements in the genome of the smallest photosynthetic eukaryote: phylogenetic footprinting in Ostreococcus. J Mol Evol (2009) 0.84

Olfactory Receptor-Related Duplicons Mediate a Microdeletion at 11q13.2q13.4 Associated with a Syndromic Phenotype. Mol Syndromol (2010) 0.84

A novel approach to identifying regulatory motifs in distantly related genomes. Genome Biol (2005) 0.83

Evolutionary modeling and prediction of non-coding RNAs in Drosophila. PLoS One (2009) 0.81

Statistical power of phylo-HMM for evolutionarily conserved element detection. BMC Bioinformatics (2007) 0.81

MapToGenome: a comparative genomic tool that aligns transcript maps to sequenced genomes. Evol Bioinform Online (2007) 0.79

ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences. BMC Bioinformatics (2008) 0.78

Manipulating multiple sequence alignments via MaM and WebMaM. Nucleic Acids Res (2005) 0.78

Complexity reduction in context-dependent DNA substitution models. Bioinformatics (2008) 0.78

Using multiple alignments to improve seeded local alignment algorithms. Nucleic Acids Res (2005) 0.78

Conserved PCR primer set designing for closely-related species to complete mitochondrial genome sequencing using a sliding window-based PSO algorithm. PLoS One (2011) 0.78

Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages. PLoS Genet (2016) 0.77

Multiple organism algorithm for finding ultraconserved elements. BMC Bioinformatics (2008) 0.77

Ancestral sequence alignment under optimal conditions. BMC Bioinformatics (2005) 0.77

Meta-alignment with crumble and prune: partitioning very large alignment problems for performance and parallelization. BMC Bioinformatics (2011) 0.76

Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model. BMC Bioinformatics (2010) 0.76

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47

BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78

Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol (1981) 67.56

Prediction of complete gene structures in human genomic DNA. J Mol Biol (1997) 58.76

Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol (1987) 41.41

fastDNAmL: a tool for construction of phylogenetic trees of DNA sequences using maximum likelihood. Comput Appl Biosci (1994) 24.63

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res (2003) 23.03

Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol (1996) 15.98

Optimal alignment between groups of sequences and its application to multiple sequence alignment. Comput Appl Biosci (1993) 15.69

Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31

AVID: A global alignment program. Genome Res (2003) 10.06

Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (2003) 9.93

Recent progress in multiple sequence alignment: a survey. Pharmacogenomics (2002) 7.69

Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups. Am J Hum Genet (2002) 6.02

An evolutionary model for maximum likelihood alignment of DNA sequences. J Mol Evol (1991) 5.84

DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics (1998) 5.11

MAVID multiple alignment server. Nucleic Acids Res (2003) 3.53

Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics (2001) 3.36

Inching toward reality: an improved likelihood model of sequence evolution. J Mol Evol (1992) 2.86

A structural EM algorithm for phylogenetic inference. J Comput Biol (2002) 2.67

A hidden Markov model for progressive multiple alignment. Bioinformatics (2003) 1.67

Positive and negative regulatory elements of the rabbit embryonic epsilon-globin gene revealed by an improved multiple alignment program and functional analysis. DNA Seq (1993) 1.66

Statistical alignment: computational properties, homology testing and goodness-of-fit. J Mol Biol (2000) 1.59

An algorithm for statistical alignment of sequences related by a binary tree. Pac Symp Biocomput (2001) 1.57

Using guide trees to construct multiple-sequence evolutionary HMMs. Bioinformatics (2003) 1.46

Identification of evolutionary hotspots in the rodent genomes. Genome Res (2004) 1.21

Visualization of multiple genome annotations and alignments with the K-BROWSER. Genome Res (2004) 1.05

The number of multiple alignments. Mol Phylogenet Evol (1998) 0.92

Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15

TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75

Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol (2012) 14.01

VISTA: computational tools for comparative genomics. Nucleic Acids Res (2004) 13.52

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66

Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol (2011) 10.63

A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol (2006) 10.14

AVID: A global alignment program. Genome Res (2003) 10.06

Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (2003) 9.93

Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics (2011) 8.05

rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res (2002) 7.33

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05

Disordered microbial communities in asthmatic airways. PLoS One (2010) 6.35

Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol (2007) 6.18

Fast statistical alignment. PLoS Comput Biol (2009) 5.92

Viral population estimation using pyrosequencing. PLoS Comput Biol (2008) 5.89

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71

Strategies and tools for whole-genome alignments. Genome Res (2003) 4.86

Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods (2012) 4.43

SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res (2003) 4.17

MAVID multiple alignment server. Nucleic Acids Res (2003) 3.53

Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput Biol (2005) 3.39

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc Natl Acad Sci U S A (2011) 3.30

Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics (2011) 2.98

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol (2010) 2.32

Exon-level microarray analyses identify alternative splicing programs in breast cancer. Mol Cancer Res (2010) 1.84

Mapping and identification of essential gene functions on the X chromosome of Drosophila. EMBO Rep (2001) 1.83

Subtree power analysis and species selection for comparative genomics. Proc Natl Acad Sci U S A (2005) 1.69

Multiple alignment by sequence annealing. Bioinformatics (2007) 1.63

CGAL: computing genome assembly likelihoods. Genome Biol (2013) 1.53

HMM sampling and applications to gene finding and alternative splicing. Bioinformatics (2003) 1.49

Modeling and automation of sequencing-based characterization of RNA structure. Proc Natl Acad Sci U S A (2011) 1.49

Multiple-sequence functional annotation and the generalized hidden Markov phylogeny. Bioinformatics (2004) 1.46

Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Hum Mol Genet (2006) 1.43

Shape-based peak identification for ChIP-Seq. BMC Bioinformatics (2011) 1.38

Analysis of epistatic interactions and fitness landscapes using a new geometric approach. BMC Evol Biol (2007) 1.30

Development of a low bias method for characterizing viral populations using next generation sequencing technology. PLoS One (2010) 1.25

Reference based annotation with GeneMapper. Genome Biol (2006) 1.24

Identification of evolutionary hotspots in the rodent genomes. Genome Res (2004) 1.21

Identification of transposable elements using multiple alignments of related genomes. Genome Res (2005) 1.17

The computational challenges of applying comparative-based computational methods to whole genomes. Brief Bioinform (2002) 1.17

Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics (2008) 1.16

Intraspecies sequence comparisons for annotating genomes. Genome Res (2004) 1.15

SLAM web server for comparative gene finding and alignment. Nucleic Acids Res (2003) 1.15

A dynamic alternative splicing program regulates gene expression during terminal erythropoiesis. Nucleic Acids Res (2014) 1.13

Parametric alignment of Drosophila genomes. PLoS Comput Biol (2006) 1.12

Genome methylation in D. melanogaster is found at specific short motifs and is independent of DNMT2 activity. Genome Res (2014) 1.12

Coverage statistics for sequence census methods. BMC Bioinformatics (2010) 1.07

SHAPE-Seq: High-Throughput RNA Structure Analysis. Curr Protoc Chem Biol (2012) 1.06

Visualization of multiple genome annotations and alignments with the K-BROWSER. Genome Res (2004) 1.05

Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Res (2004) 1.03

Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One (2008) 0.99

Interpreting the unculturable majority. Nat Methods (2007) 0.95

On the optimality of the neighbor-joining algorithm. Algorithms Mol Biol (2008) 0.92

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states. Genome Res (2011) 0.91

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics (2008) 0.90

Large multiple organism gene finding by collapsed Gibbs sampling. J Comput Biol (2005) 0.89

MetMap enables genome-scale Methyltyping for determining methylation states in populations. PLoS Comput Biol (2010) 0.89

RNA-Seq and find: entering the RNA deep field. Genome Med (2011) 0.87

Updating RNA-Seq analyses after re-annotation. Bioinformatics (2013) 0.84

Beyond pairwise distances: neighbor-joining with phylogenetic diversity estimates. Mol Biol Evol (2005) 0.84

Combinatorics of least-squares trees. Proc Natl Acad Sci U S A (2008) 0.83

A closer look at RNA editing. Nat Biotechnol (2012) 0.80

The cyclohedron test for finding periodic genes in time course expression studies. Stat Appl Genet Mol Biol (2007) 0.78

Toward the human genotope. Bull Math Biol (2007) 0.78

Erratum: Near-optimal probabilistic RNA-seq quantification. Nat Biotechnol (2016) 0.77

Quantifying uniformity of mapped reads. Bioinformatics (2012) 0.76

Tracing the most parsimonious indel history. J Comput Biol (2011) 0.76

Estimating intrinsic and extrinsic noise from single-cell gene expression measurements. Stat Appl Genet Mol Biol (2016) 0.76

Exploring the genetic basis of variation in gene predictions with a synthetic association study. PLoS One (2010) 0.75

Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor. Genomics (2007) 0.75

Picking alignments from (Steiner) trees. J Comput Biol (2003) 0.75

Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains. Stat Appl Genet Mol Biol (2011) 0.75