Whole-genome annotation by using evidence integration in functional-linkage networks.

By U. Karaoz, T. Murali, S. Letovsky, Yu Zheng, Chunming Ding, C. Cantor, Simon Kasif. Proceedings of the National Academy of Sciences of the United States of America, 2004

336 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/f01e826bd1b2e0e2cd56eafa59b4133b4f3b7432

How researchers see this paper

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In Molecular Biology

1. Roded Sharan
2. Bonnie Berger
3. Trey Ideker
4. Mona Singh
5. Igor Ulitsky
6. Ron Shamir
7. Jinbo Xu
8. Rohit Singh

Citations in the corpus

• Using PPI network autocorrelation in hierarchical multi-label classification trees for gene function prediction (2013, background): “However, the above approaches [29,30,45-47] do not consider the hierarchy of categories.”
• Graph theory and networks in Biology. (2006, background): “Two more sophisticated approaches to protein function prediction that avoid the above mentioned difficulty were described in [189, 190].”
• Global alignment of multiple protein interaction networks with application to functional orthology detection (2008, background): “Also, previous work has explored an integrative approach to predicting protein function (23); the FO predictions made by IsoRank can be incorporated in such a framework.”
• Efficient Algorithms for Detecting Signaling Pathways in Protein Interaction Networks (2005, background): “We have also conducted a related study (Kelley et al., 2003) aimed at identifying pathways that are conserved across two species.”
• Network-based prediction of protein function (2007, methodology): “Interestingly, as pointed out by Deng et al (2004), setting a to 0 and b to 1 yields the exact optimization criterion used by Karaoz et al (2004).”
• Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps (2005, methodology): “In the process, we reformulate the computational problem given by the objective function of Vazquez et al. (2003) and Karaoz et al. (2004) as an integer linear program (ILP), and as opposed to the previous two studies, we find optimal (not heuristic) solutions to the problem using ILP.”