GC skew and mitochondrial origins of replication.

[1]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[2]  Matthias Bernt,et al.  A comprehensive analysis of bilaterian mitochondrial genomes and phylogeny. , 2013, Molecular phylogenetics and evolution.

[3]  P. Stadler,et al.  Genetic aspects of mitochondrial genome evolution. , 2013, Molecular phylogenetics and evolution.

[4]  P. Stadler,et al.  MITOS: improved de novo metazoan mitochondrial genome annotation. , 2013, Molecular phylogenetics and evolution.

[5]  P. Stadler,et al.  Mitochondrial Genome Evolution , 2013 .

[6]  Marcos T. Oliveira,et al.  Replicating animal mitochondrial DNA , 2013, Genetics and molecular biology.

[7]  H. Jacobs,et al.  Mitochondrial DNA replication proceeds via a ‘bootlace’ mechanism involving the incorporation of processed transcripts , 2013, Nucleic acids research.

[8]  A. Reyes,et al.  Human mitochondrial DNA replication. , 2012, Cold Spring Harbor perspectives in biology.

[9]  Jiao Cheng,et al.  Complete mitochondrial genome sequence of bighead croaker Collichthys niveatus (Perciformes, Sciaenidae): a mitogenomic perspective on the phylogenetic relationships of Pseudosciaeniae. , 2012, Gene.

[10]  Tatiana A. Tatusova,et al.  NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy , 2011, Nucleic Acids Res..

[11]  J. Archibald,et al.  Origins of Mitochondria and Plastids , 2012 .

[12]  D. Secor,et al.  A phylogeny of the temperate seabasses (Moronidae) characterized by a translocation of the mt-nd6 gene. , 2012, Journal of fish biology.

[13]  Matthias Bernt,et al.  A method for computing an inventory of metazoan mitochondrial gene order rearrangements , 2011, BMC Bioinformatics.

[14]  P. Stadler,et al.  The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria , 2011, BMC Evolutionary Biology.

[15]  Tianjun Xu,et al.  The complete mitochondrial genome of bighead croaker, Collichthys niveatus (Perciformes, Sciaenidae): structure of control region and phylogenetic considerations , 2011, Molecular Biology Reports.

[16]  Evgeny M. Zdobnov,et al.  The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell , 2010, Bioinform..

[17]  Graziano Pesole,et al.  Hypervariability of ascidian mitochondrial gene order: exposing the myth of deuterostome organelle genome stability. , 2010, Molecular biology and evolution.

[18]  F. You,et al.  The complete mitochondrial genome of the large yellow croaker, Larimichthys crocea (Perciformes, Sciaenidae): unusual features of its control region and the phylogenetic position of the Sciaenidae. , 2009, Gene.

[19]  Sarah J. Bourlat,et al.  The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida) is ancestral within the deuterostomes , 2009, BMC Evolutionary Biology.

[20]  Matthias Bernt,et al.  An Algorithm for Inferring Mitogenome Rearrangements in a Phylogenetic Tree , 2008, RECOMB-CG.

[21]  D. Posada,et al.  Inverted replication of vertebrate mitochondria. , 2008, Molecular biology and evolution.

[22]  P. Stadler,et al.  Evolution of Mitochondrial Gene Orders in Echinoderms , 2022 .

[23]  L. Podsiadlowski,et al.  The complete mitochondrial genome of Scutigerella causeyae (Myriapoda: Symphyla) and the phylogenetic position of Symphyla. , 2007, Molecular phylogenetics and evolution.

[24]  Joern Pütz,et al.  Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures. , 2007, RNA.

[25]  Peter F. Stadler,et al.  The mitochondrial DNA of Xenoturbella bocki: genomic architecture and phylogenetic analysis , 2007, Theory in Biosciences.

[26]  Ji-Young Kim,et al.  Complete mitochondrial genome of the rock bream Oplegnathus fasciatus (Perciformes, Oplegnathidae) with phylogenetic considerations. , 2007, Gene.

[27]  M. Tomita,et al.  Noise‐reduction filtering for accurate detection of replication termini in bacterial genomes , 2007, FEBS letters.

[28]  C. Saccone,et al.  The complete nucleotide sequence of theRattus norvegicus mitochondrial genome: Cryptic signals revealed by comparative analysis between vertebrates , 1989, Journal of Molecular Evolution.

[29]  H. Jacobs,et al.  Replication of vertebrate mitochondrial DNA entails transient ribonucleotide incorporation throughout the lagging strand , 2006, The EMBO journal.

[30]  B. Rao,et al.  Possible multiple origins of replication in primate mitochondria: Alternative role of tRNA sequences. , 2006, Journal of theoretical biology.

[31]  J. Boore,et al.  Requirements and standards for organelle genome databases. , 2006, Omics : a journal of integrative biology.

[32]  B. Lang,et al.  Poriferan mtDNA and animal phylogeny based on mitochondrial gene arrangements. , 2005, Systematic biology.

[33]  M. Miya,et al.  The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences , 2005 .

[34]  S. Pääbo,et al.  Rearrangements of mitochondrial transfer RNA genes in marsupials , 1991, Journal of Molecular Evolution.

[35]  G. Pesole,et al.  The main regulatory region of mammalian mitochondrial DNA: Structure-function model and evolutionary pattern , 1991, Journal of Molecular Evolution.

[36]  Noboru Sueoka,et al.  Intrastrand parity rules of DNA base composition and usage biases of synonymous codons , 2005, Journal of Molecular Evolution.

[37]  M. Miya,et al.  Evolution of the Mitochondrial Genome in Cephalochordata as Inferred from Complete Nucleotide Sequences from Two Epigonichthys Species , 2005, Journal of Molecular Evolution.

[38]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology Information: update , 2004, Nucleic acids research.

[39]  M. M. Nass.  Precise sequence assignment of replication origin in the control region of chick mitochondrial DNA relative to 5′ and 3′ D-loop ends, secondary structure, DNA synthesis, and protein binding , 1995, Current Genetics.

[40]  N. Perna,et al.  Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes , 1995, Journal of Molecular Evolution.

[41]  N. Sueoka.  Intrastrand parity rules of DNA base composition and usage biases of synonymous codons , 1995, Journal of Molecular Evolution.

[42]  Nicole T. Perna,et al.  Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes , 2004, Journal of Molecular Evolution.

[43]  H. Jacobs,et al.  Mammalian Mitochondrial DNA Replicates Bidirectionally from an Initiation Zone* , 2003, Journal of Biological Chemistry.

[44]  J. Inoue,et al.  Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. , 2003, Molecular phylogenetics and evolution.

[45]  Gregory D. Schuler,et al.  Database resources of the National Center for Biotechnology , 2003, Nucleic Acids Res..

[46]  P. Janvier,et al.  Complete mitochondrial DNA of the hagfish, Eptatretus burgeri: the comparative analysis of mitochondrial DNA sequences strongly supports the cyclostome monophyly. , 2002, Molecular phylogenetics and evolution.

[47]  B. J. Hinnebusch,et al.  Analyzing DNA strand compositional asymmetry to identify candidate replication origins of Borrelia burgdorferi linear and circular plasmids. , 2000, Genome research.

[48]  D. Clayton.  Transcription and replication of mitochondrial DNA. , 2000, Human reproduction.

[49]  H. Jacobs,et al.  Coupled Leading- and Lagging-Strand Synthesis of Mammalian Mitochondrial DNA , 2000, Cell.

[50]  J. Boore.  The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deu , 2000 .

[51]  J. Boore.  Animal mitochondrial genomes. , 1999, Nucleic acids research.

[52]  J. Boore,et al.  Complete sequence, gene arrangement, and genetic code of mitochondrial DNA of the cephalochordate Branchiostoma floridae (Amphioxus) , 1999, Molecular biology and evolution.

[53]  J. Boore,et al.  Big trees from little genomes: mitochondrial gene order as a phylogenetic tool. , 1998, Current opinion in genetics & development.

[54]  S. Salzberg,et al.  Skewed oligomers and origins of replication. , 1998, Gene.

[55]  C Saccone,et al.  Asymmetrical directional mutation pressure in the mitochondrial genome of mammals. , 1998, Molecular biology and evolution.

[56]  Vincent Laudet,et al.  Complete sequence of the amphioxus (Branchiostoma lanceolatum) mitochondrial genome: relations to vertebrates , 1998, Nucleic Acids Res..

[57]  A Grigoriev,et al.  Analyzing genomes with cumulative skew diagrams. , 1998, Nucleic acids research.

[58]  S. Yoshida,et al.  Mitochondrial DNA Replication , 1998 .

[59]  C Saccone,et al.  Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications. , 1997, Gene.

[60]  H. Ochman,et al.  Strand asymmetries in DNA evolution. , 1997, Trends in genetics : TIG.

[61]  H. Markov,et al.  An algorithm to , 1997 .

[62]  D. Clayton.  39 Mitochondrial DNA Replication , 1996 .

[63]  M. Nishida,et al.  Variations in mitochondrial tRNA gene organization of reptiles as phylogenetic markers. , 1995, Molecular biology and evolution.

[64]  T. Kocher,et al.  Complete sequence of a sea lamprey (Petromyzon marinus) mitochondrial genome: early establishment of the vertebrate genome organization. , 1995, Genetics.

[65]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[66]  T. Ozawa,et al.  Strand asymmetry in human mitochondrial DNA mutations. , 1994, Genomics.

[67]  D. A. Clayton,et al.  Replication and transcription of vertebrate mitochondrial DNA. , 1991, Annual review of cell biology.

[68]  R. Low,et al.  Mapping of control elements in the displacement loop region of bovine mitochondrial DNA. , 1987, The Journal of biological chemistry.

[69]  J. Hixson,et al.  Both the conserved stem-loop and divergent 5'-flanking sequences are required for initiation at the human mitochondrial origin of light-strand DNA replication. , 1986, The Journal of biological chemistry.

[70]  A. Bollon,et al.  The complete nucleotide sequence of the rat 18S ribosomal RNA gene and comparison with the respective yeast and frog genes. , 1983, Nucleic acids research.

[71]  D. A. Clayton,et al.  Replication of animal mitochondrial DNA , 1982, Cell.

[72]  F. Sanger,et al.  Sequence and organization of the human mitochondrial genome , 1981, Nature.

[73]  D. Clayton,et al.  Mechanism of mitochondrial DNA replication in mouse L-cells: localization and sequence of the light-strand origin of replication. , 1979, Journal of molecular biology.

[74]  E. F. Williams,et al.  Is blood protein amide nitrogen a source of urinary ammonia ? 3. On the question of synthesis of protein amides from ammonia. , 1933 .

[75]  The mitochondrial , 2022 .