Sequential PAttern mining using a bitmap representation. - Jay Ayres; Jason Flannick; Johannes Gehrke; Tomi Yiu (KDD, 2002)

MAFIA: A Performance Study of Mining Maximal Frequent Itemsets. - Douglas Burdick; Manuel Calimlim; Jason Flannick; Johannes Gehrke; Tomi Yiu (FIMI, 2003)

MAFIA: A Maximal Frequent Itemset Algorithm. - Douglas Burdick; Manuel Calimlim; Jason Flannick; Johannes Gehrke; Tomi Yiu (IEEE Trans. Knowl. Data Eng., 2005)

Integrated Protein Interaction Networks for 11 Microbes. - Balaji S. Srinivasan; Antal F. Novak; Jason Flannick; Serafim Batzoglou; Harley H. McAdams (RECOMB, 2006)

Current progress in network research: toward reference networks for key model organisms. - Balaji S. Srinivasan; Nigam H. Shah; Jason Flannick; Eduardo Abeliuk; Antal F. Novak; Serafim Batzoglou (Briefings Bioinform., 2007)

Automatic Parameter Learning for Multiple Network Alignment. - Jason Flannick; Antal F. Novak; Chuong B. Do; Balaji S. Srinivasan; Serafim Batzoglou (RECOMB, 2008)

Automatic Parameter Learning for Multiple Local Network Alignment. - Jason Flannick; Antal F. Novak; Chuong B. Do; Balaji S. Srinivasan; Serafim Batzoglou (J. Comput. Biol., 2009)

Algorithms for biological network alignment. - Jason Flannick (2009)

Efficiency and Power as a Function of Sequence Coverage, SNP Array Density, and Imputation. - Jason Flannick; Joshua M. Korn; Pierre Fontanillas; George B. Grant; Eric Banks; Mark A. DePristo; David Altshuler (PLoS Comput. Biol., 2012)