Demo Data from EDBT 2026 / reviewers in the wild / expert
Bram Weytjens
dblp:180/7908
· DBLP profile ↗
1ranked-venue papers
0as first author
1since 2021 · last 2022
—ORCID · none
Domains — the database's venue-derived domains; a paper can count in several
Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021
Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.
| Interdisciplinary, comprehensive, and emerging computing
1 paper |
Bioinformatics and computational biology · 100% |
Topics — the 3 heaviest of 3, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › cancer genomics
cancer driver gene identification |
0.6 | 1 | 2022 | OMEN: network-based driver gene identification using mutual exclusivity · Bioinform. 2022 |
Bioinformatics and computational biology
cancer genomics |
0.6 | 1 | 2022 | OMEN: network-based driver gene identification using mutual exclusivity · Bioinform. 2022 |
Bioinformatics and computational biology › cancer genomics
mutual exclusivity analysis |
0.6 | 1 | 2022 | OMEN: network-based driver gene identification using mutual exclusivity · Bioinform. 2022 |
Methods — techniques the papers use, named apart from their topics
random walk · 0.6logic programming · 0.6
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2022 | OMEN: network-based driver gene identification using mutual exclusivityabstractMOTIVATION: Network-based driver identification methods that can exploit mutual exclusivity typically fail to detect rare drivers because of their statistical rigor. Propagation-based methods in contrast allow recovering rare driver genes, but the interplay between network topology and high-scoring nodes often results in spurious predictions. The specificity of driver gene detection can be improved by taking into account both gene-specific and gene-set properties. Combining these requires a formalism that can adjust gene-set properties depending on the exact network context within which a gene is analyzed. RESULTS: We developed OMEN: a logic programming framework based on random walk semantics. OMEN presents a number of novel concepts. In particular, its design is unique in that it presents an effective approach to combine both gene-specific driver properties and gene-set properties, and includes a novel method to avoid restrictive, a priori filtering of genes by exploiting the gene-set property of mutual exclusivity, expressed in terms of the functional impact scores of mutations, rather than in terms of simple binary mutation calls. Applying OMEN to a benchmark dataset derived from TCGA illustrates how OMEN is able to robustly identify driver genes and modules of driver genes as proxies of driver pathways. AVAILABILITY AND IMPLEMENTATION: The source code is freely available for download at www.github.com/DriesVanDaele/OMEN. The dataset is archived at https://doi.org/10.5281/zenodo.6419097 and the code at https://doi.org/10.5281/zenodo.6419764. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Dries Van Daele, Bram Weytjens, Luc De Raedt, Kathleen Marchal |
Bioinform. | 2 |