Analyzing genomes with cumulative skew diagrams.

PubWeight™: 3.71‹?› | Rank: Top 1%

🔗 View Article (PMC 147580)

Published in Nucleic Acids Res on May 15, 1998

Authors

A Grigoriev1

Author Affiliations

1: Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany. andy@rag3.rz-berlin.mpg.de

Articles citing this

(truncated to the top 100)

Bacteriophage T4 genome. Microbiol Mol Biol Rev (2003) 5.20

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res (2008) 4.78

The genome of M. acetivorans reveals extensive metabolic and physiological diversity. Genome Res (2002) 4.58

The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol (2005) 4.28

Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev (2007) 4.13

Pathogenicity islands in bacterial pathogenesis. Clin Microbiol Rev (2004) 3.77

Ori-Finder: a web-based system for finding oriCs in unannotated bacterial genomes. BMC Bioinformatics (2008) 3.65

The complete genome and proteome of Mycoplasma mobile. Genome Res (2004) 3.36

Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res (2004) 2.75

A complete sequence of the T. tengcongensis genome. Genome Res (2002) 2.60

The genome sequence of Mycoplasma mycoides subsp. mycoides SC type strain PG1T, the causative agent of contagious bovine pleuropneumonia (CBPP). Genome Res (2004) 2.33

Where does bacterial replication start? Rules for predicting the oriC region. Nucleic Acids Res (2004) 2.09

PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res (2012) 1.91

Strikingly bacteria-like and gene-rich mitochondrial genomes throughout jakobid protists. Genome Biol Evol (2013) 1.90

Identification of replication origins in archaeal genomes based on the Z-curve method. Archaea (2005) 1.83

Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism. Nucleic Acids Res (2004) 1.82

The Methanosarcina barkeri genome: comparative analysis with Methanosarcina acetivorans and Methanosarcina mazei reveals extensive rearrangement within methanosarcinal genomes. J Bacteriol (2006) 1.79

The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One (2010) 1.78

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia. Biol Direct (2008) 1.78

Asymmetric directional mutation pressures in bacteria. Genome Biol (2002) 1.77

Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora. J Bacteriol (2005) 1.77

Insights into corn genes derived from large-scale cDNA sequencing. Plant Mol Biol (2008) 1.69

An archaeal chromosomal autonomously replicating sequence element from an extreme halophile, Halobacterium sp. strain NRC-1. J Bacteriol (2003) 1.67

Construction of an Enterococcus faecalis Tn917-mediated-gene-disruption library offers insight into Tn917 insertion patterns. J Bacteriol (2004) 1.65

In vivo interactions of archaeal Cdc6/Orc1 and minichromosome maintenance proteins with the replication origin. Proc Natl Acad Sci U S A (2001) 1.60

The Whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution. DNA Res (2008) 1.59

Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res (2002) 1.58

Chromosome evolution in the Thermotogales: large-scale inversions and strain diversification of CRISPR sequences. J Bacteriol (2006) 1.57

The sequence of a 1.8-mb bacterial linear plasmid reveals a rich evolutionary reservoir of secondary metabolic pathways. Genome Biol Evol (2010) 1.57

The genome sequence of Psychrobacter arcticus 273-4, a psychroactive Siberian permafrost bacterium, reveals mechanisms for adaptation to low-temperature growth. Appl Environ Microbiol (2010) 1.44

Similar compositional biases are caused by very different mutational effects. Genome Res (2006) 1.41

Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus. Nucleic Acids Res (2009) 1.41

Transcription-coupled and splicing-coupled strand asymmetries in eukaryotic genomes. Nucleic Acids Res (2004) 1.38

Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiol (2006) 1.35

Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent. Nucleic Acids Res (2005) 1.34

Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids. Genome Res (2000) 1.31

The complete plastid genome sequence of the parasitic green alga Helicosporidium sp. is highly reduced and structured. BMC Biol (2006) 1.31

The genome sequence of Clostridium botulinum type C neurotoxin-converting phage and the molecular mechanisms of unstable lysogeny. Proc Natl Acad Sci U S A (2005) 1.28

Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J Bacteriol (2008) 1.27

Sulfolobus tengchongensis spindle-shaped virus STSV1: virus-host interactions and genomic features. J Virol (2005) 1.26

Comparative genomic analysis of three strains of Ehrlichia ruminantium reveals an active process of genome size plasticity. J Bacteriol (2006) 1.23

Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication. Nucleic Acids Res (2005) 1.22

A genomic island present along the bacterial chromosome of the Parachlamydiaceae UWE25, an obligate amoebal endosymbiont, encodes a potentially functional F-like conjugative DNA transfer system. BMC Microbiol (2004) 1.21

Complete genome sequence and lifestyle of black-pigmented Corynebacterium aurimucosum ATCC 700975 (formerly C. nigricans CN-1) isolated from a vaginal swab of a woman with spontaneous abortion. BMC Genomics (2010) 1.20

The unconventional Xer recombination machinery of Streptococci/Lactococci. PLoS Genet (2007) 1.11

Single-stranded DNA transposition is coupled to host replication. Cell (2010) 1.09

Identification of a putative chromosomal replication origin from Helicobacter pylori and its interaction with the initiator protein DnaA. Nucleic Acids Res (2001) 1.08

The abundant extrachromosomal DNA content of the Spiroplasma citri GII3-3X genome. BMC Genomics (2008) 1.07

Analysis of the lambdoid prophage element e14 in the E. coli K-12 genome. BMC Microbiol (2004) 1.07

Comparative Genometrics (CG): a database dedicated to biometric comparisons of whole genomes. Nucleic Acids Res (2002) 1.06

The genome of epsilon15, a serotype-converting, Group E1 Salmonella enterica-specific bacteriophage. Virology (2007) 1.06

Wavelet to predict bacterial ori and ter: a tendency towards a physical balance. BMC Genomics (2003) 1.06

How does replication-associated mutational pressure influence amino acid composition of proteins? Genome Res (1999) 1.06

The unusual gene organization of Leishmania major chromosome 1 may reflect novel transcription processes. Nucleic Acids Res (2000) 1.05

Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. ISME J (2015) 1.05

Distinctive architecture of the chloroplast genome in the chlorophycean green alga Stigeoclonium helveticum. Mol Genet Genomics (2006) 1.04

Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins. Nucleic Acids Res (2010) 1.04

The host-range, genomics and proteomics of Escherichia coli O157:H7 bacteriophage rV5. Virol J (2013) 1.02

The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection. Evol Bioinform Online (2007) 1.02

In silico and in vivo evaluation of bacteriophage phiEF24C, a candidate for treatment of Enterococcus faecalis infections. Appl Environ Microbiol (2008) 0.99

The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA. BMC Plant Biol (2010) 0.99

Peaks cloaked in the mist: the landscape of mammalian replication origins. J Cell Biol (2015) 0.98

Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes. BMC Genomics (2011) 0.97

The genome sequence of the crenarchaeon Acidilobus saccharovorans supports a new order, Acidilobales, and suggests an important ecological role in terrestrial acidic hot springs. Appl Environ Microbiol (2010) 0.96

Replication landscape of the human genome. Nat Commun (2016) 0.96

Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index. BMC Genomics (2009) 0.95

Genomic and functional analysis of Vibrio phage SIO-2 reveals novel insights into ecology and evolution of marine siphoviruses. Environ Microbiol (2012) 0.95

Evolutionary rates and gene dispensability associate with replication timing in the archaeon Sulfolobus islandicus. Genome Biol Evol (2010) 0.94

The complete genome sequence of Pantoea ananatis AJ13355, an organism with great biotechnological potential. Appl Microbiol Biotechnol (2011) 0.94

Defining components of the chromosomal origin of replication of the hyperthermophilic archaeon Pyrococcus furiosus needed for construction of a stable replicating shuttle vector. Appl Environ Microbiol (2011) 0.94

Recent Advances in the Identification of Replication Origins Based on the Z-curve Method. Curr Genomics (2014) 0.94

The mitochondrial genome of the pathogenic yeast Candida subhashii: GC-rich linear DNA with a protein covalently attached to the 5' termini. Microbiology (2010) 0.93

Evolutionary paths of streptococcal and staphylococcal superantigens. BMC Genomics (2012) 0.93

The complete plastid genome sequence of the secondarily nonphotosynthetic alga Cryptomonas paramecium: reduction, compaction, and accelerated evolutionary rate. Genome Biol Evol (2009) 0.93

The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region. Nucleic Acids Res (2005) 0.93

Strand compositional asymmetries of nuclear DNA in eukaryotes. J Mol Evol (2003) 0.92

High correlation between the turnover of nucleotides under mutational pressure and the DNA composition. BMC Evol Biol (2001) 0.92

Genomic and functional characterization of the modular broad-host-range RA3 plasmid, the archetype of the IncU group. Appl Environ Microbiol (2008) 0.92

A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis. BMC Res Notes (2009) 0.92

Identification and autonomous replication capability of a chromosomal replication origin from the archaeon Sulfolobus solfataricus. Extremophiles (2004) 0.91

Two-parameter characterization of chromosome-scale recombination rate. Genome Res (2009) 0.91

M-protein and other intrinsic virulence factors of Streptococcus pyogenes are encoded on an ancient pathogenicity island. BMC Genomics (2009) 0.91

New criteria for selecting the origin of DNA replication in Wolbachia and closely related bacteria. BMC Genomics (2007) 0.90

DNA replication and strand asymmetry in prokaryotic and mitochondrial genomes. Curr Genomics (2012) 0.89

Complete genome sequence of Archaeoglobus profundus type strain (AV18). Stand Genomic Sci (2010) 0.87

The chloroplast genome of the green alga Schizomeris leibleinii (Chlorophyceae) provides evidence for bidirectional DNA replication from a single origin in the chaetophorales. Genome Biol Evol (2011) 0.86

Biological consequences of ancient gene acquisition and duplication in the large genome of Candidatus Solibacter usitatus Ellin6076. PLoS One (2011) 0.86

Applying Shannon's information theory to bacterial and phage genomes and metagenomes. Sci Rep (2013) 0.86

Mitochondrial genome of the basidiomycetous yeast Jaminaea angkorensis. Curr Genet (2013) 0.85

A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (Chargaff's second parity rule). DNA Res (2009) 0.85

Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes. Biochimie (2015) 0.85

GraphDNA: a Java program for graphical display of DNA composition analyses. BMC Bioinformatics (2007) 0.85

The first complete genome sequence of the class Fimbriimonadia in the phylum Armatimonadetes. PLoS One (2014) 0.85

Replication intermediates of the linear mitochondrial DNA of Candida parapsilosis suggest a common recombination based mechanism for yeast mitochondria. J Biol Chem (2014) 0.84

Genometrics as an essential tool for the assembly of whole genome sequences: the example of the chromosome of Bifidobacterium longum NCC2705. BMC Microbiol (2005) 0.83

Co-evolution of segregation guide DNA motifs and the FtsK translocase in bacteria: identification of the atypical Lactococcus lactis KOPS motif. Nucleic Acids Res (2012) 0.83

Analyses of six homologous proteins of Protochlamydia amoebophila UWE25 encoded by large GC-rich genes (lgr): a model of evolution and concatenation of leucine-rich repeats. BMC Evol Biol (2007) 0.83

Association of purine asymmetry, strand-biased gene distribution and PolC within Firmicutes and beyond: a new appraisal. BMC Genomics (2014) 0.83

The genome of BCJA1c: a bacteriophage active against the alkaliphilic bacterium, Bacillus clarkii. Extremophiles (2004) 0.83

The genomic landscape of the verrucomicrobial methanotroph Methylacidiphilum fumariolicum SolV. BMC Genomics (2014) 0.83

Articles cited by this

The complete genome sequence of Escherichia coli K-12. Science (1997) 84.27

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science (1995) 68.34

Sequence and organization of the human mitochondrial genome. Nature (1981) 57.39

Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science (1996) 41.35

The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature (1997) 34.00

The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature (1997) 33.47

The minimal gene complement of Mycoplasma genitalium. Science (1995) 32.41

Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res (1996) 28.37

Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature (1997) 19.08

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature (1997) 14.38

Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol (1997) 12.21

Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res (1996) 10.46

Replication of animal mitochondrial DNA. Cell (1982) 7.79

Simian virus 40 DNA replication in vitro. Proc Natl Acad Sci U S A (1984) 7.76

Asymmetric substitution patterns in the two DNA strands of bacteria. Mol Biol Evol (1996) 7.18

Mispair specificity of methyl-directed DNA mismatch correction in vitro. J Biol Chem (1988) 4.20

spo0J is required for normal chromosome segregation as well as the initiation of sporulation in Bacillus subtilis. J Bacteriol (1994) 3.87

A sensitive genetic assay for the detection of cytosine deamination: determination of rate constants and the activation energy. Biochemistry (1990) 3.51

Frequency and distribution of DNA uptake signal sequences in the Haemophilus influenzae Rd genome. Science (1995) 3.44

Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes. J Mol Evol (1995) 3.44

The structure and function of yeast ARS elements. Curr Opin Genet Dev (1993) 2.66

Variability of gene order in different Helicobacter pylori strains contributes to genome diversity. Mol Microbiol (1996) 2.35

Strand asymmetries in DNA evolution. Trends Genet (1997) 2.16

A simple vectorial representation of DNA sequences for the detection of replication origins in bacteria. Biochimie (1996) 1.73

Strand asymmetry in human mitochondrial DNA mutations. Genomics (1994) 1.71

Inequality in mutation rates of the two strands of DNA. Nature (1987) 1.47

Mapping of genes on the linear chromosome of the bacterium Borrelia burgdorferi: possible locations for its origin of replication. FEMS Microbiol Lett (1992) 1.42

The DNA sequence of adenovirus type 40. J Mol Biol (1993) 1.41

The bacterial nucleoid visualized by fluorescence microscopy of cells lysed within agarose: comparison of Escherichia coli and spirochetes of the genus Borrelia. J Bacteriol (1997) 1.18

Helicobacter pylori: a surprisingly conserved bacterium. Nat Biotechnol (1998) 1.06

Search for additional replication terminators in the Bacillus subtilis 168 chromosome. J Bacteriol (1997) 0.91