Jim Kent, a Research Scientist at UCSC, has published two papers in Genome Research.
The first discusses the technical aspects and optimization of Kent's sequence alignment tool, BLAT. Entitled, "BLAT'the BLAST-like alignment tool," it can be found in Genome Research, April 2002; 12(4):656-664.
The second, "The human genome browser at UCSC," describes the conceptual and technical framework of the UCSC Genome Browser, its underlying MYSQL database, and its overall use. It can be found in Genome Research, June 2002; 12(6):996-1006.