Welcome to the homepage of Jason Flannick. I am currently a fifth year PhD student at Stanford University. My advisor is Serafim Batzoglou and my research area is computational molecular biology. My main interest is the design of algorithmic or statistical techniques to analyze novel high-throughput biological data. My specific interests include the analysis of biological networks, functional genomics, systems biology, comparative genomics, and population genetics.
View my résumé.
Flannick J, Novak A, Do C B, Srinivasan B S, Batzoglou S. Automatic Parameter Learning for Network Alignment. Proceedings of the Twelfth Annual International Conference on Computational Molecular Biology, (RECOMB 2008), To appear.
Srinivasan B S, Shah N H, Flannick J, Abeliuk E, Novak A, Batzoglou S. Current progress in network research: toward reference networks for key model organisms. Briefings in Bioinformatics, 2007.
Flannick J*, Novak A*, Srinivasan B S, McAdams H H, Batzoglou S. Græmlin: General and Robust Alignment of Multiple Large Interaction Networks. Genome Research 16(9), 2006.
Srinivasan B S, Novak A, Flannick J, Batzoglou S, McAdams H. Integrated Protein Interaction Networks for 11 Microbes. Proceedings of the Tenth Annual International Conference on Computational Molecular Biology, (RECOMB 2006), pp. 1.14.
Flannick J, Batzoglou, S. Using multiple alignments to improve seeded local alignment algorithms. Nucleic Acids Research 33(14): 4563-77, 2005.
Burdick D, Calimlin M, Flannick J, Gehrke J, Yiu T. MAFIA: A Performance Study of Mining Maximal Frequent Itemsets. FIMI 2003.
Ayres J, Flannick J, Gehrke J, Yiu, T. Sequential PAttern Mining using a bitmap representation. KDD 2002: 429-435.Flannick J, Novak A, Batzoglou S. Automatic Parameter Learning for Network Alignment. Cold Spring Harbor Laboratories Conference on Genome Informatics, 2007.
Novak A*, Flannick J*, Srinivasan B S, McAdams H H, Batzoglou S. Scalable and General Pairwise and Multiple Network Alignment. Cold Spring Harbor Laboratories Conference on Genome Informatics, 2005.
Flannick J, Batzoglou S. Using multiple alignments to improve seeded local alignment algorithms (Poster). Cold Spring Harbor Laboratories conference on Genome Informatics, 2005.
* denotes co-first authorship with Tony Novak
Last updated: Februrary 17, 2008