Published in Trends Genet on April 01, 2005
Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol (2007) 3.53
Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep (2006) 2.96
Transcriptional interferences in cis natural antisense transcripts of humans and mice. Genetics (2007) 1.79
Origin and evolution of spliceosomal introns. Biol Direct (2012) 1.65
Regulation of chromatin structure by long noncoding RNAs: focus on natural antisense transcripts. Trends Genet (2012) 1.46
Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts. Nucleic Acids Res (2005) 1.37
Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. Genome Res (2006) 1.35
"Genome design" model: evidence from conserved intronic sequence in human-mouse comparison. Genome Res (2006) 1.34
Sense-antisense pairs in mammals: functional and evolutionary considerations. Genome Biol (2007) 1.26
Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. Genome Biol Evol (2011) 1.23
Genome-wide functional analysis of human 5' untranslated region introns. Genome Biol (2010) 1.14
Expression breadth and expression abundance behave differently in correlations with evolutionary rates. BMC Evol Biol (2010) 1.03
'Genome design' model and multicellular complexity: golden middle. Nucleic Acids Res (2006) 1.01
Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Res (2013) 0.99
A universal nonmonotonic relationship between gene compactness and expression levels in multicellular eukaryotes. Genome Biol Evol (2009) 0.97
Purifying selection on splice-related motifs, not expression level nor RNA folding, explains nearly all constraint on human lincRNAs. Mol Biol Evol (2014) 0.93
The small introns of antisense genes are better explained by selection for rapid transcription than by "genomic design". Genetics (2005) 0.90
In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure. Biol Direct (2009) 0.89
Association of intron loss with high mutation rate in Arabidopsis: implications for genome size evolution. Genome Biol Evol (2013) 0.88
Evidence against the energetic cost hypothesis for the short introns in highly expressed genes. BMC Evol Biol (2008) 0.87
Protecting exons from deleterious R-loops: a potential advantage of having introns. Biol Direct (2007) 0.87
Selection for the compactness of highly expressed genes in Gallus gallus. Biol Direct (2010) 0.86
Synergistic upregulation of erythropoietin receptor (EPO-R) expression by sense and antisense EPO-R transcripts in the canine lung. Proc Natl Acad Sci U S A (2008) 0.84
Exon definition as a potential negative force against intron losses in evolution. Biol Direct (2008) 0.82
Why eukaryotic cells use introns to enhance gene expression: splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity. Biol Direct (2011) 0.82
Effect of the transposable element environment of human genes on gene length and expression. Genome Biol Evol (2011) 0.82
Expression profile and 5'-terminal structure of Arabidopsis antisense transcripts expressed in seeds. Plant Signal Behav (2011) 0.79
Transposable Element Insertions in Long Intergenic Non-Coding RNA Genes. Front Bioeng Biotechnol (2015) 0.79
Circadian genomics reveal a role for post-transcriptional regulation in mammals. Biochemistry (2014) 0.79
Higher frequency of intron loss from the promoter proximally paused genes of Drosophila melanogaster. Fly (Austin) (2014) 0.75
Functional and evolutionary correlates of gene constellations in the Drosophila melanogaster genome that deviate from the stereotypical gene architecture. BMC Genomics (2010) 0.75
Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet (2002) 6.89
Dosage sensitivity and the evolution of gene families in yeast. Nature (2003) 6.77
Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat Rev Genet (2006) 5.97
Comparisons of dN/dS are time dependent for closely related bacterial genomes. J Theor Biol (2005) 5.20
Altered nuclear retention of mRNAs containing inverted repeats in human embryonic stem cells: functional role of a nuclear noncoding RNA. Mol Cell (2009) 4.54
Clinical-cytogenetic associations in 306 patients with therapy-related myelodysplasia and myeloid leukemia: the University of Chicago series. Blood (2003) 4.15
Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature (2004) 4.06
Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res (2004) 3.45
Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol (2006) 3.44
Alu element-mediated gene silencing. EMBO J (2008) 3.22
Distinct microRNA expression profiles in acute myeloid leukemia with common translocations. Proc Natl Acad Sci U S A (2008) 3.13
Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet (2002) 3.11
Positively charged residues are the major determinants of ribosomal velocity. PLoS Biol (2013) 3.11
Coexpression of neighboring genes in Caenorhabditis elegans is mostly due to operons and duplicate genes. Genome Res (2003) 3.10
MicroRNA expression signatures accurately discriminate acute lymphoblastic leukemia from acute myeloid leukemia. Proc Natl Acad Sci U S A (2007) 3.00
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol (2005) 2.94
Genomewide characterization of non-polyadenylated RNAs. Genome Biol (2011) 2.92
Identifying novel transcripts and novel genes in the human genome by using novel SAGE tags. Proc Natl Acad Sci U S A (2002) 2.87
Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Mol Biol Evol (2005) 2.85
Long noncoding RNAs with snoRNA ends. Mol Cell (2012) 2.71
The signature of selection mediated by expression on human genes. Genome Res (2003) 2.56
Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet (2007) 2.55
Chance and necessity in the evolution of minimal metabolic networks. Nature (2006) 2.48
Genomic function: Rate of evolution and gene dispensability. Nature (2003) 2.40
MicroRNA and cancer: Current status and prospective. Int J Cancer (2007) 2.36
A previously unidentified alternatively spliced isoform of t(8;21) transcript promotes leukemogenesis. Nat Med (2006) 2.36
Evolutionary and physiological importance of hub proteins. PLoS Comput Biol (2006) 2.34
Splicing and the evolution of proteins in mammals. PLoS Biol (2007) 2.32
Gamma-secretase gene mutations in familial acne inversa. Science (2010) 2.30
Leukaemogenesis: more than mutant genes. Nat Rev Cancer (2010) 2.16
Regulation of mir-196b by MLL and its overexpression by MLL fusions contributes to immortalization. Blood (2009) 2.11
Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts. Trends Genet (2005) 2.04
Chromatin structural elements and chromosomal translocations in leukemia. DNA Repair (Amst) (2006) 2.01
Genome-wide studies reveal that Lin28 enhances the translation of genes important for growth and survival of human embryonic stem cells. Stem Cells (2011) 1.90
Evidence for co-evolution of gene order and recombination rate. Nat Genet (2003) 1.84
Still stratus not altocumulus: further evidence against the date/party hub distinction. PLoS Biol (2007) 1.84
Metabolic trade-offs and the maintenance of the fittest and the flattest. Nature (2011) 1.82
A unification of mosaic structures in the human genome. Hum Mol Genet (2003) 1.79
The t(8;21) fusion protein, AML1 ETO, specifically represses the transcription of the p14(ARF) tumor suppressor in acute myeloid leukemia. Nat Med (2002) 1.75
Molecular basis for an attenuated cytoplasmic dsRNA response in human embryonic stem cells. Cell Cycle (2010) 1.71
Oligo(dT) primer generates a high frequency of truncated cDNAs through internal poly(A) priming during reverse transcription. Proc Natl Acad Sci U S A (2002) 1.71
How do synonymous mutations affect fitness? Bioessays (2007) 1.63
Genes that escape X-inactivation in humans have high intraspecific variability in expression, are associated with mental impairment but are not slow evolving. Mol Biol Evol (2013) 1.61
Effects of length and location on the cellular response to double-stranded RNA. Microbiol Mol Biol Rev (2004) 1.57
Similar rates but different modes of sequence evolution in introns and at exonic silent sites in rodents: evidence for selectively driven codon usage. Mol Biol Evol (2004) 1.55
Chromatin remodelling is a major source of coexpression of linked genes in yeast. Trends Genet (2007) 1.55
Decoding the function of nuclear long non-coding RNAs. Curr Opin Cell Biol (2010) 1.54
Distinct physiological and behavioural functions for parental alleles of imprinted Grb10. Nature (2011) 1.52
Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet (2003) 1.49
ISCN (2005) is not acceptable for describing clonal evolution in cancer. Genes Chromosomes Cancer (2007) 1.44
Aberrant overexpression and function of the miR-17-92 cluster in MLL-rearranged acute leukemia. Proc Natl Acad Sci U S A (2010) 1.43
GroEL dependency affects codon usage--support for a critical role of misfolding in gene evolution. Mol Syst Biol (2010) 1.43
Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Mol Biol Evol (2007) 1.43
Gene regulation by SINES and inosines: biological consequences of A-to-I editing of Alu element inverted repeats. Cell Cycle (2008) 1.42
Leukocyte tyrosine kinase functions in pigment cell development. PLoS Genet (2008) 1.41
Substitution effect on the geometry and electronic structure of the ferrocene. J Comput Chem (2007) 1.39
Evidence against the selfish operon theory. Trends Genet (2004) 1.38
Evidence for a preferential targeting of 3'-UTRs by cis-encoded natural antisense transcripts. Nucleic Acids Res (2005) 1.37
Evidence for a trade-off between translational efficiency and splicing regulation in determining synonymous codon usage in Drosophila melanogaster. Mol Biol Evol (2007) 1.36
Evidence for variation in abundance of antisense transcripts between multicellular animals but no relationship between antisense transcriptionand organismic complexity. Genome Res (2006) 1.35
Consistent deregulation of gene expression between human and murine MLL rearrangement leukemias. Cancer Res (2009) 1.35
Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin. Curr Biol (2005) 1.34
The impact of the nucleosome code on protein-coding sequence evolution in yeast. PLoS Genet (2008) 1.34
Antisense starts making more sense. Nat Biotechnol (2003) 1.34
Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else? Trends Genet (2005) 1.33
Evidence that the human X chromosome is enriched for male-specific but not female-specific genes. Mol Biol Evol (2003) 1.32
Molecular portraits of B cell lineage commitment. Proc Natl Acad Sci U S A (2002) 1.32
Loss-of-function mutations of an inhibitory upstream ORF in the human hairless transcript cause Marie Unna hereditary hypotrichosis. Nat Genet (2009) 1.31
PBX3 is an important cofactor of HOXA9 in leukemogenesis. Blood (2012) 1.30
The evolution of isochores: evidence from SNP frequency distributions. Genetics (2002) 1.29
Medicine: silencing viruses with RNA. Nature (2002) 1.27
A mixture of "cheats" and "co-operators" can enable maximal group benefit. PLoS Biol (2010) 1.27
Predicting the virulence of MRSA from its genome sequence. Genome Res (2014) 1.23
The leukemic fusion gene AML1-MDS1-EVI1 suppresses CEBPA in acute myeloid leukemia by activation of Calreticulin. Proc Natl Acad Sci U S A (2004) 1.22
How biologically relevant are interaction-based modules in protein networks? Genome Biol (2004) 1.22
Gametophytic selection in Arabidopsis thaliana supports the selective model of intron length reduction. PLoS Genet (2005) 1.20
Long noncoding RNAs in mammalian cells: what, where, and why? Wiley Interdiscip Rev RNA (2010) 1.19
TET1 plays an essential oncogenic role in MLL-rearranged leukemia. Proc Natl Acad Sci U S A (2013) 1.19
Genomic DNA breakpoints in AML1/RUNX1 and ETO cluster with topoisomerase II DNA cleavage and DNase I hypersensitive sites in t(8;21) leukemia. Proc Natl Acad Sci U S A (2002) 1.16
Imprinted chromosomal regions of the human genome have unusually high recombination rates. Genetics (2003) 1.15
Identification of a 24-gene prognostic signature that improves the European LeukemiaNet risk classification of acute myeloid leukemia: an international collaborative study. J Clin Oncol (2013) 1.15
The price of silent mutations. Sci Am (2009) 1.14
Maternally-inherited Grb10 reduces placental size and efficiency. Dev Biol (2009) 1.14
Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res (2004) 1.14
Direct and indirect consequences of meiotic recombination: implications for genome evolution. Trends Genet (2011) 1.13