PROPER: global protein interaction network alignment through percolation matching

Background The alignment of protein-protein interaction (PPI) networks enables us to uncover the relationships between different species, which leads to a deeper understanding of biological systems. Network alignment can be used to transfer biological knowledge between species. Although different PI-network alignment algorithms were introduced during the last decade, developing an accurate and scalable algorithm that can find alignments with high biological and structural similarities among PPI networks is still challenging. Results In this paper, we introduce a new global network alignment algorithm for PPI networks called PROPER. Compared to other global network alignment methods, our algorithm shows higher accuracy and speed over real PPI datasets and synthetic networks. We show that the PROPER algorithm can detect large portions of conserved biological pathways between species. Also, using a simple parsimonious evolutionary model, we explain why PROPER performs well based on several different comparison criteria. Conclusions We highlight that PROPER has high potential in further applications such as detecting biological pathways, finding protein complexes and PPI prediction. The PROPER algorithm is available at http://proper.epfl.ch

Genetic analyses of diverse populations improves discovery for complex traits

Genome-wide association studies (GWAS) have laid the foundation for investigations into the biology of complex traits, drug development and clinical guidelines. However, the majority of discovery efforts are based on data from populations of European ancestry1–3. In light of the differential genetic architecture that is known to exist between populations, bias in representation can exacerbate existing disease and healthcare disparities. Critical variants may be missed if they have a low frequency or are completely absent in European populations, especially as the field shifts its attention towards rare variants, which are more likely to be population-specific4–10. Additionally, effect sizes and their derived risk prediction scores derived in one population may not accurately extrapolate to other populations11,12. Here we demonstrate the value of diverse, multi-ethnic participants in large-scale genomic studies. The Population Architecture using Genomics and Epidemiology (PAGE) study conducted a GWAS of 26 clinical and behavioural phenotypes in 49,839 non-European individuals. Using strategies tailored for analysis of multi-ethnic and admixed populations, we describe a framework for analysing diverse populations, identify 27 novel loci and 38 secondary signals at known loci, as well as replicate 1,444 GWAS catalogue associations across these traits. Our data show evidence of effect-size heterogeneity across ancestries for published GWAS associations, substantial benefits for fine-mapping using diverse cohorts and insights into clinical implications. In the United States—where minority populations have a disproportionately higher burden of chronic conditions13—the lack of representation of diverse populations in genetic research will result in inequitable access to precision medicine for those with the highest burden of disease. We strongly advocate for continued, large genome-wide efforts in diverse populations to maximize genetic discovery and reduce health disparities. © 2019, The Author(s), under exclusive licence to Springer Nature Limited

Restricted Composition Deletion Correcting Codes

We investigate deletion correcting codes and restricted composition codes in particular. Restricted composition codes generalize codes on permutations and multipermutations. We use graph theoretic methods to characterize codes, establish bounds on code size, and describe constructions. The substring partial order has a well-known property. For any string, the number of superstrings of a particular length depends only on the length of the original string. We generalize this property to take compositions into account. For any string, the number of superstrings of a particular composition depends only on the composition of the original string. We present a bijective proof of this fact. We apply this result to obtain a lower bound on the size of restricted composition codes. We obtain an upper bound by analyzing deletion errors when the composition of deleted symbols is restricted to a particular worst case composition. We construct binary restricted composition single-deletion correcting codes and show that they are asymptotically optimal and form an optimal coloring. There is a natural distance on compositions that provides a lower bound on deletion distance. Unrestricted deletion correcting codes can be constructed from the union of restricted composition codes as long as the set of compositions used themselves form a code. The nonbinary single-deletion correcting codes constructed by Tenengolts are a special case of our method

Population change of Trillium govanianum (Melanthiaceae) amid altered indigenous harvesting practices in the Indian Himalayas

© 2017 Elsevier B.V. Ethnobotanical relevance Trillium govanianum Wall. ex D. Don (Melanthiaceae) is valued as a traditional medicinal herb in the Himalayan region. Applications include treatment of cancer, hypertension, neurasthenia, giddiness, arthritis, dysentery, inflammation, sepsis and reproductive disorders. Its range is highly specific, and limited to cold, shaded and moist habitats at 2400-3500 m a.s.l. Rhizomes are gathered from wild populations for trade, and this has recently emerged as a significant source of income among indigenous people of the Indian Himalayan region. Aim To assess the impact of changing rhizome prices on T. govanianum in the Indian Himalayan region by observing the status of existing populations and assessing the typical methods used for gathering and trade of rhizomes. Material and methods Ecological attributes were assessed in 17 sites from Tirthan Valley (Himachal Pradesh), Munsiyari and Tunghnath (Uttarakhand). Socio-economic attributes assessed through communal focus groups and interviews with 579 medicinal plants gatherers and 19 traders, using semi-structured open ended questionnaires. Results Population decline was highest in Munsiyari, followed by Tirthan Valley and Tunghnath, indicating that the species may become locally extinct in some areas. Methods used for gathering did not consider regeneration. Conclusion Gathering of T. govanianum from wild populations is unselective and unmanaged, raising the potential threat of local extinctions. Sustainable utilization and effective conservation is needed to protect the species and maintain community incomes. A status of ‘threatened’ is justified for the species in the Indian Himalayan region, due to its slow life cycle, specific habitat requirement, low population density, and commercial value