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Papanicolau, A.

Publications and source records attributed to Papanicolau, A..

2 recordsLinked to original sources
bioRxiv2026

Apollo 3: Multi-Species Genome Curation

We present Apollo 3, a new manual genome annotation tool that integrates with the JBrowse 2 genome browser. Its functionality is inspired by existing manual genome annotation tools such as Apollo, Artemis, and Otter, but uses an updated and more scalable architecture and technology stack. It allows the simultaneous editing of multiple genomes, including the visualization of synteny to inform those annotations. Apollo 3 can be used as a standalone annotation editor, or it can be installed on a server and used collaboratively. We describe the application's design, features, and use cases.

genomics↗
bioRxiv2017

Data-driven Topological Filtering based on Orthogonal Minimal Spanning Trees: Application to Multi-Group MEG Resting-State Connectivity

In the present study a novel data-driven topological filtering technique is introduced to derive the backbone of functional brain networks relying on orthogonal minimal spanning trees (OMST). The method aims to identify the essential functional connections to ensure optimal information flow via the objective criterion of global efficiency minus the cost of surviving connections. The OMST technique was applied to multichannel, resting-state neuromagnetic recordings from four groups of participants: healthy adults (n=50), adults who have suffered mild traumatic brain injury (n=30), typically developing children (n=27), and reading-disabled children (n=25). Weighted interactions between network nodes (sensors) were computed using an integrated approach of dominant intrinsic coupling modes based on two alternative metrics (symbolic mutual information and phase lag index), resulting in excellent discrimination of individual cases according to their group membership. Classification results using OMST-derived functional networks were clearly superior to results using either relative power spectrum features or functional networks derived through the conventional minimal spanning trees algorithm.

neuroscience↗