ZmDB, an integrated database for maize genome research. - Qunfeng Dong; Laura Roy; Michael Freeling; Virginia Walbot; Volker Brendel (Nucleic Acids Res., 2003)

Gobe: an interactive, web-based tool for comparative genomic visualization. - Brent S. Pedersen; Haibao Tang; Michael Freeling (Bioinform., 2011)

Screening synteny blocks in pairwise genome comparisons through integer programming. - Haibao Tang; Eric Lyons 002; Brent S. Pedersen; James C. Schnable; Andrew H. Paterson; Michael Freeling (BMC Bioinform., 2011)

qTeller: a tool for comparative multi-genomic gene expression analysis. - Margaret Woodhouse; Shatabdi Sen; David A. Schott; John L. Portwood II; Michael Freeling; Justin W. Walley; Carson M. Andorf; James C. Schnable (Bioinform., 2021)