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Nikolic, V.

Publications and source records attributed to Nikolic, V..

2 recordsLinked to original sources

Overlapping Pathogenic Signalling Pathways and Biomarkers in Preeclampsia and Cardiovascular Disease

ObjectivesPreeclampsia is a cardiovascular pregnancy complication which occurs in 5-10% of pregnancies that can lead to a number of pregnancy complications including maternal and foetal death. Long-term, preeclampsia is associated with up to 8-fold increased risk of cardiovascular disease (CVD) for both mothers and their offspring. The lack of mechanistic data in relation to the causes or consequences of preeclampsia has prevented the development of effective therapeutic or monitoring strategies. Study designThis study investigates common underlying mechanisms of preeclampsia and CVD, specifically hypertension and heart failure with preserved ejection fraction (HFpEF) using "in silico" approach of publicly available datasets. Integrated techniques were designed to mine data repositories and identify relevant biomarkers associated with these three conditions. Main outcomes measuresThe knowledge base tools were employed that enabled the analysis of these biomarkers to discover potential molecular and biological links between these three conditions. ResultsOur bioinformatics "in silico" analyses of the publically available datasets identified 76 common biomarkers between preeclampsia, hypertension and HFpEF. These biomarkers were representative of 29 pathways commonly enriched across the three conditions which were largely related to inflammation, metabolism, angiogenesis, remodelling, haemostasis, apoptosis, endoplasmic reticulum (ER) stress signalling and the renin-angiotensin-aldosterone (RAAS) system. ConclusionsThis bioinformatics approach which uses the wealth of scientific data available in public repositories can be helpful to gain a deeper understanding of the overlapping pathogenic mechanisms of associated diseases, which could be explored as biomarkers or targets to prevent long-term cardiovascular complications such as hypertension and HFpEF following preeclampsia. HighlightsO_LIWomen with preeclampsia have increased risk of cardiovascular disease later in life but the mechanism is poorly understood. C_LIO_LI"In silico" analyses of publically available datasets provided overlapping biomarkers and pathogenic pathways between preeclampsia, hypertension and heart failure with preserved ejection fraction (HFpEF). C_LIO_LIThese data could be utilised in the future studies that may lead to the development of better risk stratification strategies or preventative treatments for women post preeclampsia. C_LI

bioinformatics

ntJoin: Fast and lightweight assembly-guided scaffolding using minimizer graphs

SummaryThe ability to generate high-quality genome sequences is cornerstone to modern biological research. Even with recent advancements in sequencing technologies, many genome assemblies are still not achieving reference-grade. Here, we introduce ntJoin, a tool that leverages structural synteny between a draft assembly and reference sequence(s) to contiguate and correct the former with respect to the latter. Instead of alignments, ntJoin uses a lightweight mapping approach based on a graph data structure generated from ordered minimizer sketches. The tool can be used in a variety of different applications, including improving a draft assembly with a reference-grade genome, a short read assembly with a draft long read assembly, and a draft assembly with an assembly from a closely-related species. When scaffolding a human short read assembly using the reference human genome or a long read assembly, ntJoin improves the NGA50 length 23- and 13-fold, respectively, in under 13 m, using less than 11 GB of RAM. Compared to existing reference-guided assemblers, ntJoin generates highly contiguous assemblies faster and using less memory. Availability and implementationntJoin is written in C++ and Python, and is freely available at https://github.com/bcgsc/ntjoin. Contactlcoombe@bcgsc.ca

bioinformatics