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Comparative Genomics 

  • Linking Yeast Genetics to Mammalian Genomes: Identification and Mapping of the Human Homolog of Cdc27 Via the Expressed Sequence Tag (EST) Data Base (1993) |PubMed|PDF|
  • Genes Conserved in Yeast and Humans (1994) |PubMed|PDF|
  • Comparative Genomics, Genome Cross-Referencing and XREFdb (1995) |PubMed|PDF|
  • Comparative Analysis of 1196 Orthologous Mouse and Human Full-Length mRNA and Protein Sequences (1996) |PubMed|PDF|
  • Genomes and Evolution (1996) |PubMed|PDF|
  • XREFdb: Cross-Referencing Genes, Genetics and Mammalian Genomes (1996) |PubMed|PDF|
  • Yeast Genes and Human Disease (1996) |PubMed|PDF|
  • Genome Cross-Referencing and XREFdb: Implications for the Identification and Analysis of Genes Mutated in Human Disease (1997) |PubMed|PDF| Between 1993 and 2000, we published a series of papers defining a new scientific discipline that we called comparative genomics (Bassett et al., 1995).  Comparative sequence analysis of gene families had been a strong interest of mine since graduate school (e.g. Boguski et al., 1985).  However two developments in the early 1990s took this field to a new level.  First was the realization that significant homologies and strong functional inferences could be detected between human disease genes and genes from model organisms as evolutionarily remote as bacteria and yeast (Boguski, 1995).  Second was the development of genome-scale, transcribed sequence collections and databases and software tools to support large-scale comparative analyses (Boguski et al., 1993, Bassett et al., 1995).  This paper represents the state-of-the-art of comparative genomics in 1997 and describes results obtained from the analysis of the 84 human disease genes that had been positionally cloned as of this date.  This paper also describes the rationale, design and operation of a new public resource, XREFdb, for cross-referencing the genes of model organisms with mammalian phenotypes and the locations of the mammalian homologs of these genes on maps of the mouse and human genomes.  The construction of XREFdb required an enormous amount of data integration: EST sequences and protein sequences from six organisms from yeast to human, phenotypic data on human disease genes from OMIM, correlated syntenic regions of human and mouse chromosomes.  XREFdb had a novel map query function that allowed retrieval of all gene, phenotype and transcript mapping data at user-selected chromosomal loci and, in this sense, represented the first human genome browser.
  • Identifying Human Homologs of Cell Cycle Genes Using dbEST and XREFdb (1997) |PubMed|PDF|
  • Positionally Cloned Human Disease Genes: Patterns of Evolutionary Conservation and Functional Motifs (1997) |PubMed|PDF|
  • Evolutionary Parameters of the Transcribed Mammalian Genome: An Analysis of 2,820 Orthologous Rodent and Human Sequences (1998) |PubMed|PDF|
  • Synonymous and Nonsynonymous Substitution Distances Are Correlated in Mouse and Rat Genes (1998) |PubMed|PDF|
  • Human and Nematode Orthologs--Lessons from the Analysis of 1800 Human Genes and the Proteome of Caenorhabditis elegans (1999) |PubMed|PDF|
  • Classical Oncogenes and Tumor Suppressor Genes: A Comparative Genomics Perspective (2000) |PubMed|PDF|
  • Comparative Genomics of the Eukaryotes (2000) |PubMed|PDF|
  • A Survey of Human Disease Gene Counterparts in the Drosophila Genome (2000) |PubMed|PDF|
  • XREFdb: Cross-Referencing the Genetics and Genes of Mammals and Model Organisms (2000) |PubMed|PDF|
  • Comparative Genomics: The Mouse That Roared (2002) |PubMed|PDF|

Although I didn't coin the term "Comparative Genomics" until the early 1990s, "Comparative Analysis" of genes and sequence data across species was a primary interest and recurring theme of my research since graduate school (see some examples below). 

  • Comparative Analysis of Repeated Sequences in Rat Apolipoproteins A-I, A-IV, and E (1985) |PubMed|PDF|
  • Human Liver Fatty Acid Binding Protein. Isolation of a Full Length cDNA and Comparative Sequence Analyses of Orthologous and Paralogous Proteins (1985) |PubMed|PDF|
  • Primary Structure and Comparative Sequence Analysis of an Insect Apolipoprotein. Apolipophorin-III from Manduca Sexta (1987) |PubMed|PDF|
  • Comparative Analysis of the Beta Transducin Family with Identification of Several New Members Including PWP1, a Nonessential Gene of Saccharomyces cerevisiae That Is Divergently Transcribed from NMT1 (1992) |PubMed|PDF|

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