Our most prominent achievement was determination and evolutionary analysis of chimpanzee chromosome 22 long arm genomic sequences, published in Nature in 2004. Saitou and Fujiyama were both corresponding authors of this paper. Detailed difference on amino acid sequences and genomic sequences were delineated. In particular, clear difference between insertion and deletion was discovered. We also used chimpanzee genome sequence as outgroup to infer direction of mutations that created human SNP, and estimated nucleotide substitution patterns. Another large scale study was determination of BAC-end sequences of chimpanzee BAC library, and human-chimpanzee difference in terms of nucleotide substitution was determined to be 1.23% (Fujiyama et al., Science, 2002). Gorilla fosmid library was also constructed (Kim et al., Genomics,2003).
We also compared 103 protein coding gene sequences for human, chimpanzee, gorilla, and orangutan (Kitano et al., Molecular Biology and Evolution, 2004). Various statistical tests were used to detect human specific changes, but each test picked up different set of genes. Other results include various types of human and ape comparison on SCA triplet repeat polymorphism (Andres et al, Journal of Molecular Evolution) and polyubiquitin (Tachikui et al., Journal of Molecular Evolution), as well as mitochondrial DNA polymorphism study on African wild chimpanzees (Shimada et al., American Journal of Primatology).