ORCID Profile
0000-0002-4577-8276
Current Organisations
Athens University Medical School
,
Biomedical Sciences Research Center Alexander Fleming
,
Ancilia Biosciences
,
Ηellenic Army Academy
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Publisher: Springer Science and Business Media LLC
Date: 28-11-2008
Abstract: Complexity is a key problem when visualizing biological networks as the number of entities increases, most graphical views become incomprehensible. Our goal is to enable many thousands of entities to be visualized meaningfully and with high performance. We present a new visualization tool, Arena3D, which introduces a new concept of staggered layers in 3D space. Related data – such as proteins, chemicals, or pathways – can be grouped onto separate layers and arranged via layout algorithms, such as Fruchterman-Reingold, distance geometry, and a novel hierarchical layout. Data on a layer can be clustered via k-means, affinity propagation, Markov clustering, neighbor joining, tree clustering, or UPGMA ('unweighted pair-group method with arithmetic mean'). A simple input format defines the name and URL for each node, and defines connections or similarity scores between pairs of nodes. The use of Arena3D is illustrated with datasets related to Huntington's disease. Arena3D is a user friendly visualization tool that is able to visualize biological or any other network in 3D space. It is free for academic use and runs on any platform. It can be downloaded or lunched directly from arena3d.org . Java3D library and Java 1.5 need to be pre-installed for the software to run.
Publisher: Springer Science and Business Media LLC
Date: 12-06-2017
DOI: 10.1038/NBT.3886
Abstract: We present 1,003 reference genomes that were sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) initiative, selected to maximize sequence coverage of phylogenetic space. These genomes double the number of existing type strains and expand their overall phylogenetic ersity by 25%. Comparative analyses with previously available finished and draft genomes reveal a 10.5% increase in novel protein families as a function of phylogenetic ersity. The GEBA genomes recruit 25 million previously unassigned metagenomic proteins from 4,650 s les, improving their phylogenetic and functional interpretation. We identify numerous biosynthetic clusters and experimentally validate a ergent phenazine cluster with potential new chemical structure and antimicrobial activity. This Resource is the largest single release of reference genomes to date. Bacterial and archaeal isolate sequence space is still far from saturated, and future endeavors in this direction will continue to be a valuable resource for scientific discovery.
Publisher: Springer Science and Business Media LLC
Date: 02-2012
Abstract: Keeping up-to-date with bioscience literature is becoming increasingly challenging. Several recent methods help meet this challenge by allowing literature search to be launched based on lists of abstracts that the user judges to be 'interesting'. Some methods go further by allowing the user to provide a second input set of 'uninteresting' abstracts these two input sets are then used to search and rank literature by relevance. In this work we present the service 'Caipirini' ( caipirini.org ) that also allows two input sets, but takes the novel approach of allowing ranking of literature based on one or more sets of genes. To evaluate the usefulness of Caipirini, we used two test cases, one related to the human cell cycle, and a second related to disease defense mechanisms in Arabidopsis thaliana . In both cases, the new method achieved high precision in finding literature related to the biological mechanisms underlying the input data sets. To our knowledge Caipirini is the first service enabling literature search directly based on biological relevance to gene sets thus, Caipirini gives the research community a new way to unlock hidden knowledge from gene sets derived via high-throughput experiments.
Location: United States of America
Location: Greece
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Georgios Pavlopoulos.