Published in PLoS One on May 14, 2010
The gene YALI0E20207g from Yarrowia lipolytica encodes an N-acetylglucosamine kinase implicated in the regulated expression of the genes from the N-acetylglucosamine assimilatory pathway. PLoS One (2015) 1.37
Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome Res (2012) 1.11
Assessment of de novo assemblers for draft genomes: a case study with fungal genomes. BMC Genomics (2014) 0.95
LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes. Evol Bioinform Online (2011) 0.91
Constructing de novo biosynthetic pathways for chemical synthesis inside living cells. Biochemistry (2011) 0.91
Neighboring Genes Show Correlated Evolution in Gene Expression. Mol Biol Evol (2015) 0.89
Genome evolution in trypanosomatid parasites. Parasitology (2014) 0.85
Functional networking of human divergently paired genes (DPGs). PLoS One (2013) 0.83
Plastid-LCGbase: a collection of evolutionarily conserved plastid-associated gene pairs. Nucleic Acids Res (2014) 0.82
Disruption of Yarrowia lipolytica TPS1 gene encoding trehalose-6-P synthase does not affect growth in glucose but impairs growth at high temperature. PLoS One (2011) 0.78
Identification of host-microbe interaction factors in the genomes of soft rot-associated pathogens Dickeya dadantii 3937 and Pectobacterium carotovorum WPP14 with supervised machine learning. BMC Genomics (2014) 0.75
Co-regulation of translation in protein complexes. Biol Direct (2015) 0.75
Cancer specificity of promoters of the genes involved in cell proliferation control. Acta Naturae (2013) 0.75
The impact of the protein interactome on the syntenic structure of mammalian genomes. PLoS One (2017) 0.75
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
Profile hidden Markov models. Bioinformatics (1998) 56.04
Pfam: the protein families database. Nucleic Acids Res (2013) 22.48
A genome-wide transcriptional analysis of the mitotic cell cycle. Mol Cell (1998) 19.67
GeneWise and Genomewise. Genome Res (2004) 17.87
A gene expression map of Arabidopsis thaliana development. Nat Genet (2005) 17.39
The universal protein resource (UniProt). Nucleic Acids Res (2007) 16.33
Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol (1997) 12.21
OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res (2006) 11.43
A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression. Nat Genet (2000) 9.47
Reconstructing the early evolution of Fungi using a six-gene phylogeny. Nature (2006) 8.94
Iterated profile searches with PSI-BLAST--a tool for discovery in protein databases. Trends Biochem Sci (1998) 8.01
Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol (1996) 6.99
Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nat Genet (2002) 6.89
A kingdom-level phylogeny of eukaryotes based on combined protein data. Science (2000) 6.34
An abundance of bidirectional promoters in the human genome. Genome Res (2004) 5.90
The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet (2004) 5.79
The tree of eukaryotes. Trends Ecol Evol (2005) 3.98
Large clusters of co-expressed genes in the Drosophila genome. Nature (2002) 3.76
The evolution of stramenopiles and alveolates as derived by "substitution rate calibration" of small ribosomal subunit RNA. J Mol Evol (1996) 3.52
Bidirectional gene organization: a common architectural feature of the human genome. Cell (2002) 3.47
Genomic gene clustering analysis of pathways in eukaryotes. Genome Res (2003) 2.89
Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs. Nat Biotechnol (2004) 2.83
The origin of red algae and the evolution of chloroplasts. Nature (2000) 2.83
Systematic analysis of head-to-head gene organization: evolutionary conservation and potential biological relevance. PLoS Comput Biol (2006) 2.11
Identification of the maturation factor for dual oxidase. Evolution of an eukaryotic operon equivalent. J Biol Chem (2006) 2.08
Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nat Genet (2005) 1.86
Genomic structure of the human mitochondrial chaperonin genes: HSP60 and HSP10 are localised head to head on chromosome 2 separated by a bidirectional promoter. Hum Genet (2002) 1.69
Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PLoS Comput Biol (2007) 1.69
Long-range gene control and genetic disease. Adv Genet (2008) 1.48
Coordinate regulation of the human TAP1 and LMP2 genes from a shared bidirectional promoter. J Exp Med (1995) 1.46
Silencing of bidirectional promoters by DNA methylation in tumorigenesis. Cancer Res (2006) 1.46
Alpha 1(IV) and alpha 2(IV) collagen genes are regulated by a bidirectional promoter and a shared enhancer. Proc Natl Acad Sci U S A (1988) 1.44
A bidirectional promoter connects the poly(ADP-ribose) polymerase 2 (PARP-2) gene to the gene for RNase P RNA. structure and expression of the mouse PARP-2 gene. J Biol Chem (2000) 1.24
Epigenetic disruption of two proapoptotic genes MAPK10/JNK3 and PTPN13/FAP-1 in multiple lymphomas and carcinomas through hypermethylation of a common bidirectional promoter. Leukemia (2006) 1.12
GS2: an efficiently computable measure of GO-based similarity of gene sets. Bioinformatics (2009) 1.11
Comparative analyses of bidirectional promoters in vertebrates. BMC Bioinformatics (2008) 1.10
Analysis of the chicken GPAT/AIRC bidirectional promoter for de novo purine nucleotide synthesis. J Biol Chem (1995) 1.08
The determinants of gene order conservation in yeasts. Genome Biol (2007) 1.05
Identification and characterization of a bidirectional promoter from the intergenic region between the human DDX13 and RD genes. Mol Cells (2000) 1.04
Temperature sensitivity caused by mutant release factor 1 is suppressed by mutations that affect 16S rRNA maturation. J Bacteriol (2004) 1.03
Prediction-based approaches to characterize bidirectional promoters in the mammalian genome. BMC Genomics (2008) 1.00
The Leishmania genome project: new insights into gene organization and function. Med Microbiol Immunol (2001) 1.00
Abnormal methylation of the common PARK2 and PACRG promoter is associated with downregulation of gene expression in acute lymphoblastic leukemia and chronic myeloid leukemia. Int J Cancer (2006) 0.99
Analysis of human CYP1A1 and CYP1A2 genes and their shared bidirectional promoter in eight world populations. Hum Mutat (2010) 0.98
The human H2A and H2B histone gene complement. Biol Chem (1999) 0.96
Halobacterial S9 operon. Three ribosomal protein genes are cotranscribed with genes encoding a tRNA(Leu), the enolase, and a putative membrane protein in the archaebacterium Haloarcula (Halobacterium) marismortui. J Biol Chem (1991) 0.96
Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts. BMC Genomics (2009) 0.91
Two genes for de novo purine nucleotide synthesis on human chromosome 4 are closely linked and divergently transcribed. J Biol Chem (1994) 0.89
Co-regulated expression of HAND2 and DEIN by a bidirectional promoter with asymmetrical activity in neuroblastoma. BMC Mol Biol (2009) 0.89
The evolution of small gene clusters: evidence for an independent origin of the maltase gene cluster in Drosophila virilis and Drosophila melanogaster. Mol Biol Evol (1997) 0.84
Cooperation between NRF-2 and YY-1 transcription factors is essential for triggering the expression of the PREPL-C2ORF34 bidirectional gene pair. BMC Mol Biol (2009) 0.82
Inferring functional relationships from conservation of gene order. Methods Mol Biol (2008) 0.80
Genes and chromosomes of Leishmania infantum. Mem Inst Oswaldo Cruz (1998) 0.79
An expressed GNRP-like gene shares a bi-directional promoter with SF3A2 (SAP62) immediately upstream of AMH. Gene (2001) 0.77
The landscape of viral expression and host gene fusion and adaptation in human cancer. Nat Commun (2013) 2.17
Gel-forming mucins appeared early in metazoan evolution. Proc Natl Acad Sci U S A (2007) 2.16
SRPDB: Signal Recognition Particle Database. Nucleic Acids Res (2003) 2.16
The tmRDB and SRPDB resources. Nucleic Acids Res (2006) 2.01
RNAcentral: A vision for an international database of RNA sequences. RNA (2011) 1.73
Prediction of signal recognition particle RNA genes. Nucleic Acids Res (2002) 1.72
Large-scale identification of genes implicated in kidney glomerulus development and function. EMBO J (2006) 1.69
Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res (2005) 1.56
A family of putative transcription termination factors shared amongst metazoans and plants. Curr Genet (2005) 1.33
Kinship in the SRP RNA family. RNA Biol (2009) 1.28
Evolution of the iron-responsive element. RNA (2007) 1.27
Early evolution of histone mRNA 3' end processing. RNA (2007) 1.20
A nomenclature for all signal recognition particle RNAs. RNA (2005) 1.20
Bioinformatic identification of polymerizing and transmembrane mucins in the puffer fish Fugu rubripes. Glycobiology (2004) 1.17
Inventory and analysis of the protein subunits of the ribonucleases P and MRP provides further evidence of homology between the yeast and human enzymes. Nucleic Acids Res (2006) 1.17
Conserved and variable domains of RNase MRP RNA. RNA Biol (2009) 1.09
Computational screen for spliceosomal RNA genes aids in defining the phylogenetic distribution of major and minor spliceosomal components. Nucleic Acids Res (2008) 1.09
The glomerular transcriptome and a predicted protein-protein interaction network. J Am Soc Nephrol (2007) 1.07
In vivo mutagenesis reveals that OriL is essential for mitochondrial DNA replication. EMBO Rep (2012) 1.06
eGOB: eukaryotic Gene Order Browser. Bioinformatics (2011) 1.04
LRPPRC is a mitochondrial matrix protein that is conserved in metazoans. Biochem Biophys Res Commun (2010) 1.03
An inventory of mucin genes in the chicken genome shows that the mucin domain of Muc13 is encoded by multiple exons and that ovomucin is part of a locus of related gel-forming mucins. BMC Genomics (2006) 1.01
Identification and comparative analysis of components from the signal recognition particle in protozoa and fungi. BMC Genomics (2004) 0.97
Structure of mitochondrial transcription termination factor 3 reveals a novel nucleic acid-binding domain. Biochem Biophys Res Commun (2010) 0.96
Combination of reverse and chemical genetic screens reveals angiogenesis inhibitors and targets. Chem Biol (2009) 0.92
Conformational variability of the GTPase domain of the signal recognition particle receptor FtsY. J Struct Biol (2005) 0.88
U12 type introns were lost at multiple occasions during evolution. BMC Genomics (2010) 0.87
Identification of chloroplast signal recognition particle RNA genes. Plant Cell Physiol (2004) 0.87
Neural cell adhesion molecule-deficient beta-cell tumorigenesis results in diminished extracellular matrix molecule expression and tumour cell-matrix adhesion. Tumour Biol (2005) 0.83
Cell specific internal translation efficiency of Epstein-Barr virus present in solid organ transplant patients. J Med Virol (2007) 0.76