Designing coarse grained-and atom basedpotentials for protein-protein docking
- Protein interaction maps on the fly. Pankratz, Michael J.; Uetz, Peter // Nature Biotechnology;Jan2004, Vol. 22 Issue 1, p43
Presents the protein interaction maps for the fruit fly Drosophila melanogaster. Aspects of protein-protein interaction on a genome-wide level; Estimation of biologically relevant interactions; Benefits of comparing interaction networks; Need for integrating functional genomics data.
- Identification of dysfunctional modules and disease genes in congenital heart disease by a network-based approach. // BMC Genomics;2011 Supplement 2, Vol. 12 Issue Suppl 2, p592
Background: The incidence of congenital heart disease (CHD) is continuously increasing among infants born alive nowadays, making it one of the leading causes of infant morbidity worldwide. Various studies suggest that both genetic and environmental factors lead to CHD, and therefore identifying...
- Toward a Molecular Understanding of Pleiotropy. Xionglei He; Jianzhi Zhang // Genetics;Aug2006, Vol. 173 Issue 4, p1885
Pleiotropy refers to the observation of a single gene influencing multiple phenotypic traits. Although pleiotropy is a common phenomenon with broad implications, its molecular basis is unclear. Using functional genomic data of the yeast Saccharomyces cerevisiae, here we show that, compared with...
- The Gene Interaction Miner: a new tool for data mining contextual information for proteinâ€“protein interaction analysis. Ikin, Aaron; Riveros, Carlos; Moscato, Pablo; Mendes, Alexandre // Bioinformatics;Jan2010, Vol. 26 Issue 2, p283
Motivation: This work was motivated by the need for an automated tool for discovery of genetic networks and the availability of extensive contextual proteinâ€“protein interaction information in the iHOP repository. At the moment, this information cannot be explored to its full potential due...
- Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era. Praneenararat, Thanet; Takagi, Toshihisa; Iwasaki, Wataru // BMC Genomics;2012, Vol. 13 Issue Suppl 7, p1
Background: The overwhelming amount of network data in functional genomics is making its visualization cluttered with jumbling nodes and edges. Such cluttered network visualization, which is known as "hair-balls", is significantly hindering data interpretation and analysis of researchers....
- Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality. Zotenko, Elena; Mestre, Julian; O'Leary, Dianne P.; Przytycka, Teresa M. // PLoS Computational Biology;Aug2009, Vol. 4 Issue 8, p1
The centrality-lethality rule, which notes that high-degree nodes in a protein interaction network tend to correspond to proteins that are essential, suggests that the topological prominence of a protein in a protein interaction network may be a good predictor of its biological importance. Even...
- Genomics: Profiling transcriptional heterogeneity. // Nature Methods;Jul2013, Vol. 10 Issue 7, p607
The article cites a new study that developed transcript isoform sequencing to profile isoform diversity.
- Population genomics: Triallelic sites and demographic history. Flintoft, Louisa // Nature Reviews Genetics;Jan2014, Vol. 15 Issue 1, p2
The article highlights a study on population genetic, which is the site-frequency spectrum, describing the distribution of allele frequencies in the population.
- Network Topologies and Convergent Aetiologies Arising from Deletions and Duplications Observed in Individuals with Autism. Noh, Hyun Ji; Ponting, Chris P.; Boulding, Hannah C.; Meader, Stephen; Betancur, Catalina; Buxbaum, Joseph D.; Pinto, Dalila; Marshall, Christian R.; Lionel, Anath C.; Scherer, Stephen W.; Webber, Caleb // PLoS Genetics;Jun2013, Vol. 9 Issue 6, p1
Autism Spectrum Disorders (ASD) are highly heritable and characterised by impairments in social interaction and communication, and restricted and repetitive behaviours. Considering four sets of de novo copy number variants (CNVs) identified in 181 individuals with autism and exploiting mouse...