Evolution and comparative analysis of the MHC Class III inflammatory region

[1]  Eric D Green,et al.  Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[2]  R. Arceci,et al.  Cloning and characterization of allograft inflammatory factor-1: a novel macrophage factor identified in rat cardiac allografts with chronic rejection. , 1995, The Journal of clinical investigation.

[3]  S. Sims,et al.  Analysis of the genomic region containing the tammar wallaby (Macropus eugenii) orthologues of MHC class III genes , 2005, Cytogenetic and Genome Research.

[4]  L. Pachter,et al.  Strategies and tools for whole-genome alignments. , 2002, Genome research.

[5]  R. Campbell,et al.  NKp30 (NCR3) is a pseudogene in 12 inbred and wild mouse strains, but an expressed gene in Mus caroli. , 2005, Molecular biology and evolution.

[6]  S. Lewis,et al.  The generic genome browser: a building block for a model organism system database. , 2002, Genome research.

[7]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[8]  P Green,et al.  Base-calling of automated sequencer traces using phred. II. Error probabilities. , 1998, Genome research.

[9]  M. Wakefield,et al.  Marsupials and monotremes sort genome treasures from junk , 2005, Genome Biology.

[10]  R. Gibbs,et al.  PipMaker--a web server for aligning two genomic DNA sequences. , 2000, Genome research.

[11]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[12]  Klaus Pfeffer,et al.  Biological functions of tumor necrosis factor cytokines and their receptors. , 2003, Cytokine & growth factor reviews.

[13]  G. Ribas,et al.  A novel gene encoding a coiled-coil mitochondrial protein located at the telomeric end of the human MHC Class III region. , 2003, Gene.

[14]  C. Carbone,et al.  Expression of allograft inflammatory factor-1 is a marker of activated human vascular smooth muscle cells and arterial injury. , 2000, Arteriosclerosis, thrombosis, and vascular biology.

[15]  C. Heiner,et al.  New dye-labeled terminators for improved DNA sequencing patterns. , 1997, Nucleic acids research.

[16]  W. H. Stone,et al.  Cellular immune response of a marsupial, Monodelphis domestica. , 1991, Developmental and comparative immunology.

[17]  C. Auffray,et al.  The chicken B locus is a minimal essential major histocompatibility complex , 1999, Nature.

[18]  I. Ovcharenko,et al.  eShadow: a tool for comparing closely related sequences. , 2004, Genome research.

[19]  Jon D. McAuliffe,et al.  Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome , 2003, Science.

[20]  A. Bankier,et al.  Random cloning and sequencing by the M13/dideoxynucleotide chain termination method. , 1987, Methods in enzymology.

[21]  F. O'Gara,et al.  LST1 and NCR3 expression in autoimmune inflammation and in response to IFN-γ, LPS and microbial infection , 2005, Immunogenetics.

[22]  D. Haussler,et al.  Article Identification and Characterization of Multi-Species Conserved Sequences , 2022 .

[23]  W. H. Stone,et al.  Absence of a significant mixed lymphocyte reaction in a marsupial (Monodelphis domestica). , 1998, Laboratory animal science.

[24]  R. Biassoni,et al.  Receptors for HLA class-I molecules in human natural killer cells. , 1996, Annual review of immunology.

[25]  C. Ware Network communications: lymphotoxins, LIGHT, and TNF. , 2005, Annual review of immunology.

[26]  David Haussler,et al.  New Methods for Detecting Lineage-Specific Selection , 2006, RECOMB.

[27]  P. Green,et al.  Base-calling of automated sequencer traces using phred. I. Accuracy assessment. , 1998, Genome research.

[28]  Kazuaki Takahashi,et al.  Molecular cloning and functional characterizations of chicken TL1A. , 2005, Developmental and comparative immunology.

[29]  R. Savan,et al.  A novel tumor necrosis factor (TNF) gene present in tandem with theTNF-α gene on the same chromosome in teleosts , 2005, Immunogenetics.

[30]  M. Springer,et al.  Relationships among orders and families of marsupials based on 12S ribosomal DNA sequences and the timing of the marsupial radiation , 1994, Journal of Mammalian Evolution.

[31]  L. Hood,et al.  Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. , 2003, Genome research.

[32]  J. Bonfield,et al.  A new DNA sequence assembly program. , 1995, Nucleic acids research.

[33]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[34]  J E Sulston,et al.  Short-insert libraries as a method of problem solving in genome sequencing. , 1998, Genome research.

[35]  D. Cooper,et al.  Low MHC class II variability in a marsupial. , 1994, Reproduction, fertility, and development.

[36]  Robert D. Finn,et al.  Pfam: clans, web tools and services , 2005, Nucleic Acids Res..

[37]  Hiroshi Sato,et al.  Functional SNPs in the lymphotoxin-α gene that are associated with susceptibility to myocardial infarction , 2002, Nature Genetics.

[38]  Lior Pachter,et al.  MAVID: constrained ancestral alignment of multiple sequences. , 2003, Genome research.

[39]  H. Inoko,et al.  The haplotype block, NFKBIL1-ATP6V1G2-BAT1-MICB-MICA, within the class III-class I boundary region of the human major histocompatibility complex may control susceptibility to hepatitis C virus-associated dilated cardiomyopathy. , 2005, Tissue antigens.

[40]  Alina Deshpande,et al.  TNF-alpha promoter polymorphisms and susceptibility to human papillomavirus 16-associated cervical cancer. , 2005, The Journal of infectious diseases.

[41]  R. Allen Polymorphism of the human TNF-α promoter — random variation or functional diversity? , 1999 .

[42]  M. Flajnik,et al.  Ancestral Organization of the MHC Revealed in the Amphibian Xenopus1 , 2006, The Journal of Immunology.

[43]  Greg Elgar,et al.  Fugu orthologues of human major histocompatibility complex genes: a genome survey , 2002, Immunogenetics.

[44]  M. Springer,et al.  The evolution of tribospheny and the antiquity of mammalian clades. , 2003, Molecular phylogenetics and evolution.

[45]  R. Allen Polymorphism of the human TNF-alpha promoter--random variation or functional diversity? , 1999, Molecular immunology.

[46]  S. Weissman,et al.  Evolving views of the major histocompatibility complex. , 1997, Blood.

[47]  F. Hentges,et al.  LST1: A Gene with Extensive Alternative Splicing and Immunomodulatory Function1 , 2000, The Journal of Immunology.

[48]  Robert P. Erickson,et al.  Natural history of the major histocompatibility complex , 1987 .

[49]  B. McManus,et al.  Allograft inflammatory factory-1. A cytokine-responsive macrophage molecule expressed in transplanted human hearts. , 1996, Transplantation.

[50]  M. Feldmann,et al.  Cytokines and anti-cytokine biologicals in autoimmunity: present and future. , 2002, Cytokine & growth factor reviews.

[51]  S. Beck,et al.  A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish , 2005, BMC Genomics.

[52]  S. Beck,et al.  Comparative Genomic Analysis of Two Avian (Quail and Chicken) MHC Regions12 , 2004, The Journal of Immunology.

[53]  Anthony T Papenfuss,et al.  Reconstructing an Ancestral Mammalian Immune Supercomplex from a Marsupial Major Histocompatibility Complex , 2006, PLoS biology.

[54]  T. Kiss,et al.  Characterisation of the U83 and U84 small nucleolar RNAs: two novel 2'-O-ribose methylation guide RNAs that lack complementarities to ribosomal RNAs. , 2000, Nucleic acids research.

[55]  C. Burge,et al.  Computational inference of homologous gene structures in the human genome. , 2001, Genome research.

[56]  K. Pfeffer,et al.  The intriguing biology of the tumour necrosis factor/tumour necrosis factor receptor superfamily: players, rules and the games , 2005, Immunology.

[57]  A. Kondacs,et al.  Lymphotoxin-α gene 252G allelic variant is a risk factor for large-vessel-associated ischemic stroke , 2005, Journal of Molecular Neuroscience.