Research articles:

Qi Y, Missiuro PE, Kapoor A, Hunter CP, Jaakkola TS, Gifford DK, Ge H. Semi-supervised analysis of gene expression profiles for lineage-specific development in the Caenorhabditis elegans embryo. Bioinformatics (In press)

Gunsalus KC*, Ge H*, Schetter AJ*, Goldberg DS*, Han JJ, Hao T, Berriz G, Bertin N, Huang J, Chuang L-S, Li N, Mani R, Hyman AA, Sonnichsen B, Echeverri CJ, Roth FP, Vidal M, Piano F. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature (2005) 436(7052):861-5

*These authors contributed equally to this publication.

Li S^*, Armstrong CM^*, Bertin N^*, Ge H^*, Milstein S^*, Boxem M^*, Vidalain P^*, Han JJ^*,Chesneau A^*, Hao T, Goldberg DS, Berriz GF, Li N, Martinez M, Lamesch P, Wong SL, Zhang LV, Jacotot L, Vaglio P, Reboul J, Rual J, Li Q, Gabel HW, Elewa A, Baumgartner B, Rose DJ, Yu H, Bosak S, Sequerra R, Fraser A, Mango SE, Saxton WM, Strome S, van den Heuvel S, Fabio Piano F, Vandenhaute J, Sardet C, Harper JW, Gerstein M, Doucette-Stamm L, Gunsalus KC, Cusick ME, Roth FP, Hill DE, Vidal M. The C. elegans interactome project: mapping the protein network of a metazoan. Science (2004) 303(5657):540-3

^*These authors contributed equally to this publication.

Walhout AJ, Reboul J, Shtanko O, Bertin N, Vaglio P, Ge H, Lee H, Doucette-Stamm L, Gunsalus KC, Schetter AJ, Morton DG, Kemphues KJ, Reinke V, Kim SK, Piano F, Vidal M. Integration of interactome, phenome and transcriptome mapping data for the C. elegans germline. Current Biology (2002) 12(22):1952-8

Ge H, Liu Z, Church GM, Vidal M.  Correlation between transcriptome and interactome mapping data from S.cerevisiae.  Nature Genetics (2001) 29(4):482-6 (Also see Nature Genetics 2003 33(1):15-7)

Matthews LR, Vaglio P, Reboul J, Ge H, Davis BP, Garrels J, Vincent S, Vidal M. Identification of potential interaction networks using sequence-based searches for conserved protein-protein interactions or "interologs". Genome Research (2001) 11(12):2120-6

Method papers:

Vidalain P-O^*, Boxem M^*, Ge H, Li S and Vidal M. Increasing specificity in high-throughput yeast two-hybrid experiments.Methods (2004) 32(4):363-70.

^*These authors contributed equally to this publication.

Reviews:

Ge H, Player CM, Zou L. Toward a global picture of development: lessons from genome-scale analysis in Caenorhabditis elegans embryonic development. Developmental Dynamics (In press)

Ge H, Walhout AJ, Vidal M. Integrating "omic" information: a bridge between genomics and systems biology. Trends in Genetics (2003) 19(10):551-60