title: Heavy path mining of protein-protein associations in the malaria parasite.
abstract: Annotating and understanding the function of proteins and other elements in a genome can be difficult in the absence of a well-studied and evolutionarily close relative. The causative agent of malaria, one of the oldest and most deadly global infectious diseases, is a good example of this problem. The burden of malaria is huge and there is a pressing need for new, more effective antimalarial strategies. However, techniques such as homology-dependent annotation transfer are severely impaired in this parasite because there are no well-understood close relatives. To circumvent this approach we developed a network-based method that uses a heavy path network-mining algorithm. We uncovered the protein-protein associations that are implicated in important cellular processes including genome integrity, DNA repair, transcriptional regulation, invasion, and pathogenesis, thus demonstrating the utility of this method. The URL of the source code for super-sequence mining method is http://www.cs.utsa.edu/~korkmaz/research/heavy-path-mining/.
authors: Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA. Electronic address: xinran.yu@utsa.edu.
authors: Xinran
authors: X
authors: Yu
authors: Department of Computer Science, University of Texas at San Antonio, San Antonio, TX 78249, USA. Electronic address: turgay.korkmaz@utsa.edu.
authors: Turgay
authors: T
authors: Korkmaz
authors: Novozymes NA, Durham, NC 27709, USA. Electronic address: tglilburn@gmail.com.
authors: Timothy G
authors: TG
authors: Lilburn
authors: Department of Biology, South Texas for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA. Electronic address: hong.cai@utsa.edu.
authors: Hong
authors: H
authors: Cai
authors: Department of Biology, College of Staten Island, City University of New York, Staten Island, NY 10314, USA. Electronic address: jianying.gu@csi.cuny.edu.
authors: Jianying
authors: J
authors: Gu
authors: Department of Biology, South Texas for Emerging Infectious Diseases, University of Texas at San Antonio, San Antonio, TX 78249, USA. Electronic address: yufeng.wang@utsa.edu.
authors: Yufeng
authors: Y
authors: Wang
mesh_terms: D000818:Animals; D019295:Computational Biology; D004260:DNA Repair / Q000235:genetics; D005786:Gene Expression Regulation; D016678:Genome; D008288:Malaria / Q000235:genetics* / Q000469:parasitology; D010963:Plasmodium falciparum / Q000235:genetics* / Q000472:pathogenicity; D049490:Systems Biology
keywords: Bioinformatics; Drug target; Genomics; Heavy path mining; Malaria; Systems biology