The Rat Genome Database (RGD): developments towards a phenome database. - Norberto de la Cruz; Susan Bromberg; Dean Pasko; Mary Shimoyama; Simon N. Twigger; Jiali Chen; Chin-Fu Chen; Chunyu Fan; Cindy Foote; Gopal R. Gopinath; Glenn Harris; Aubrey Hughes; et al. (Nucleic Acids Res., 2005)

TF-Cluster: A pipeline for identifying functionally coordinated transcription factors via network decomposition of the shared coexpression connectivity matrix (SCCM). - Jeff Nie; Ron M. Stewart; Hang Zhang; James A. Thomson; Fang Ruan; Xiaoqi Cui; Hairong Wei (BMC Syst. Biol., 2011)

Comparative RNA-seq Analysis in the Unsequenced Axolotl: The Oncogene Burst Highlights Early Gene Expression in the Blastema. - Ron M. Stewart; Cynthia Alexander Rascón; Shulan Tian; Jeff Nie; Chris Barry; Li-Fang Chu; Hamisha Ardalani; Ryan J. Wagner; Mitchell D. Probasco; Jennifer M. Bolin; Ning Leng; Srikumar Sengupta; et al. (PLoS Comput. Biol., 2013)

Bioinformatics Strategies for Identifying Regions of Epigenetic Deregulation Associated with Aberrant Transcript Splicing and RNA-editing. - Mia D. Champion; Ryan A. Hlady; Huihuang Yan; Jared Evans; Jeff Nie; Jeong-Heon Lee; James M. Bogenberger; Kannabiran Nandakumar; Jaime I. Dávila; Raymond M. Moore; Asha A. Nair; Daniel R. O'Brien; et al. (BIOINFORMATICS, 2015)