SCDIFF: reconstruct cell differentiation trajectories and underlying regulatory networks from scRNA-seq RNA-seq data
TBSP: Trajectory Inference Based on SNP informationSeveral recent studies focus on the inference of developmental and response trajectories from single cell RNA-Seq (scRNA-Seq) data. A number of computational methods, often referred to as pseudo-time ordering, have been developed for this task. Recently, CRISPR has also been used to reconstruct lineage trees by inserting random mutations. However, both approaches suffer from drawbacks that limit their use. Here we develop a method (named TBSP) to detect significant, cell type specific, sequence mutations from scRNA-Seq data. We show that only a few mutations are enough for reconstructing good branching models. Integrating these mutations with expression data further improves the accuracy of the reconstructed models. Please check here for details.
iDREM: interactive Dynamic Regulatory Events MinerThe Dynamic Regulatory Events Miner (DREM) software was initially developed to integrate static protein-DNA interaction data with time series gene expression data for reconstructing dynamic regulatory networks. In recent years, several additional types of high-throughput time series data have been used to study biological processes including time series miRNA expression, proteomics, epigenomics and single cell RNA-Seq. Integrating all available time series and static datasets in a unified model remains an important challenge and goal. To address this goal, and to enable interactive queries of the resulting learned models we have developed a new version of DREM termed interactive DREM (iDREM). iDREM provides support for all data types mentioned above and more. Importantly, it also allows users to interactively visualize a gene, TF, path or model-centric view of each of these data types, their interactions and their impact on the resulting model. We showcase the functionality of the new tool by applying it to integrate several data types from multiple labs for modeling brain development regulatory networks. Please read here for details.
TarPmiR: a new approach for microRNA target site predictionThe identification of microRNA (miRNA) target sites is fundamentally important for studying gene regulation. There are dozens of computational methods available for miRNA target site prediction. Despite their existence, we still cannot reliably identify miRNA target sites, partially due to our limited understanding of the characteristics of miRNA target sites. The recently published CLASH (cross-linking ligation and sequencing of hybrids) data provide an unprecedented opportunity to study the characteristics of miRNA target sites and improve miRNA target site prediction methods. Applying four different machine learning approaches to the CLASH data, we identified seven new features of miRNA target sites. Combining these new features with those commonly used by existing miRNA target prediction algorithms, we developed an approach called TarPmiR for miRNA target site prediction. Testing on two human and one mouse non-CLASH datasets, we showed that TarPmiR predicted more than 74.2 % of true miRNA target sites in each dataset. Compared with three existing approaches, we demonstrated that TarPmiR is superior to these existing approaches in terms of better recall and better precision. Please read here for details.