The TIGR rice genome annotation resource: annotating the rice genome and creating resources for plant biologists. - Qiaoping Yuan; Shu Ouyang; Jia Liu; Bernard B. Suh; Foo Cheung; Razvan Sultana; Daniel Lee; John Quackenbush; C. Robin Buell (Nucleic Acids Res., 2003)

DUPCAR: Reconstructing Contiguous Ancestral Regions with Duplications. - Jian Ma 004; Aakrosh Ratan; Brian J. Raney; Bernard B. Suh; Louxin Zhang; Webb Miller; David Haussler (J. Comput. Biol., 2008)

The infinite sites model of genome evolution. - Jian Ma 004; Aakrosh Ratan; Brian J. Raney; Bernard B. Suh; Webb Miller; David Haussler (Proc. Natl. Acad. Sci. USA, 2008)

Cactus Graphs for Genome Comparisons. - Benedict Paten; Mark Diekhans; Dent Earl; John St. John; Jian Ma 004; Bernard B. Suh; David Haussler (J. Comput. Biol., 2011)

ENCODE whole-genome data in the UCSC genome browser (2011 update). - Brian J. Raney; Melissa S. Cline; Kate R. Rosenbloom; Timothy R. Dreszer; Katrina Learned; Galt P. Barber; Laurence R. Meyer; Cricket A. Sloan; Venkat S. Malladi; Krishna M. Roskin; Bernard B. Suh; Angie S. Hinrichs; et al. (Nucleic Acids Res., 2011)