Published in Proc Natl Acad Sci U S A on February 13, 2006
Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet (2008) 9.52
The impact of retrotransposons on human genome evolution. Nat Rev Genet (2009) 8.08
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Transposable elements and the evolution of regulatory networks. Nat Rev Genet (2008) 6.11
Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics (2009) 4.30
Expanding the microRNA targeting code: functional sites with centered pairing. Mol Cell (2010) 4.20
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A (2007) 4.11
Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res (2008) 3.76
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Origin and evolution of human microRNAs from transposable elements. Genetics (2007) 2.39
Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res (2007) 1.79
A family of conserved noncoding elements derived from an ancient transposable element. Proc Natl Acad Sci U S A (2006) 1.68
Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene. PLoS Genet (2007) 1.67
Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Rep (2015) 1.65
Genomic selective constraints in murid noncoding DNA. PLoS Genet (2006) 1.46
The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genet (2013) 1.41
Genomic gems: SINE RNAs regulate mRNA production. Curr Opin Genet Dev (2010) 1.39
Evolutionary history of mammalian transposons determined by genome-wide defragmentation. PLoS Comput Biol (2007) 1.38
An abundant evolutionarily conserved CSB-PiggyBac fusion protein expressed in Cockayne syndrome. PLoS Genet (2008) 1.29
The "domestication syndrome" in mammals: a unified explanation based on neural crest cell behavior and genetics. Genetics (2014) 1.28
Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. Genome Biol (2006) 1.07
Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics (2008) 1.02
The effect of transposable element insertions on gene expression evolution in rodents. PLoS One (2009) 0.96
Convergent evolution of two mammalian neuronal enhancers by sequential exaptation of unrelated retroposons. Proc Natl Acad Sci U S A (2011) 0.96
The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci (2013) 0.94
The opossum genome: insights and opportunities from an alternative mammal. Genome Res (2008) 0.94
A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons. PLoS One (2011) 0.93
Consequences of normalizing transcriptomic and genomic libraries of plant genomes using a duplex-specific nuclease and tetramethylammonium chloride. PLoS One (2013) 0.93
The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. PLoS Genet (2013) 0.91
A c-Myc regulatory subnetwork from human transposable element sequences. Mol Biosyst (2009) 0.85
The role of Transposable Elements in shaping the combinatorial interaction of Transcription Factors. BMC Genomics (2012) 0.83
Distinct groups of repetitive families preserved in mammals correspond to different periods of regulatory innovations in vertebrates. Biol Direct (2012) 0.81
DISCOVER: a feature-based discriminative method for motif search in complex genomes. Bioinformatics (2009) 0.81
Weak preservation of local neutral substitution rates across mammalian genomes. BMC Evol Biol (2009) 0.80
ANRIL/CDKN2B-AS shows two-stage clade-specific evolution and becomes conserved after transposon insertions in simians. BMC Evol Biol (2013) 0.79
The limits of de novo DNA motif discovery. PLoS One (2012) 0.79
Noncoding origins of anthropoid traits and a new null model of transposon functionalization. Genome Res (2014) 0.78
Evolution of conserved secondary structures and their function in transcriptional regulation networks. BMC Genomics (2008) 0.76
Sequence composition similarities with the 7SL RNA are highly predictive of functional genomic features. Nucleic Acids Res (2010) 0.75
Local conservation scores without a priori assumptions on neutral substitution rates. BMC Bioinformatics (2008) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
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
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
Human-mouse alignments with BLASTZ. Genome Res (2003) 35.49
Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res (2004) 24.52
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
Distribution and intensity of constraint in mammalian genomic sequence. Genome Res (2005) 18.85
Repbase update: a database and an electronic journal of repetitive elements. Trends Genet (2000) 16.94
Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol (2004) 10.59
Identification and characterization of multi-species conserved sequences. Genome Res (2003) 10.18
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol (2005) 4.68
Origin of a substantial fraction of human regulatory sequences from transposable elements. Trends Genet (2003) 4.39
Mammalian microRNAs derived from genomic repeats. Trends Genet (2005) 3.60
Mobile elements inserted in the distant past have taken on important functions. Gene (1997) 2.51
Into the heart of darkness: large-scale clustering of human non-coding DNA. Bioinformatics (2004) 2.50
Genetic and molecular analysis of the gypsy chromatin insulator of Drosophila. Proc Natl Acad Sci U S A (1996) 1.94
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
The structure of haplotype blocks in the human genome. Science (2002) 50.88
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72
Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00
A molecular signature of metastasis in primary solid tumors. Nat Genet (2002) 21.36
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
International network of cancer genome projects. Nature (2010) 20.35
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
The mammalian epigenome. Cell (2007) 18.13
Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet (2003) 16.51
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47
Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28
Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
Genetic mapping in human disease. Science (2008) 15.12
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med (2002) 14.01
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet (2001) 13.79
A landscape of driver mutations in melanoma. Cell (2012) 12.61
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature (2004) 12.32
Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell (2012) 11.69
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature (2009) 11.46
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A (2012) 11.23
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol (2012) 10.87
Genetic screens in human cells using the CRISPR-Cas9 system. Science (2013) 10.75
Detecting novel associations in large data sets. Science (2011) 10.60
Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res (2008) 10.49
Reactive oxygen species have a causal role in multiple forms of insulin resistance. Nature (2006) 10.07
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet (2012) 9.93
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell (2013) 9.24
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res (2005) 8.69
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
Lessons from the cancer genome. Cell (2013) 8.12
Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A (2007) 8.00
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Loss of E-cadherin promotes metastasis via multiple downstream transcriptional pathways. Cancer Res (2008) 7.91
Melanoma genome sequencing reveals frequent PREX2 mutations. Nature (2012) 7.77
Sequence analysis of mutations and translocations across breast cancer subtypes. Nature (2012) 7.76
Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell (2007) 7.60
Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A (2008) 7.45
Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell (2011) 7.30
Punctuated evolution of prostate cancer genomes. Cell (2013) 7.23
Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A (2012) 7.14
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N Engl J Med (2014) 6.89
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A (2003) 6.87
Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell (2003) 6.77
Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol (2006) 6.73
Genetic evidence for complex speciation of humans and chimpanzees. Nature (2006) 6.66
Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell (2002) 6.64
The mosaic structure of variation in the laboratory mouse genome. Nature (2002) 6.54
Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle. Proc Natl Acad Sci U S A (2004) 6.53