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Wannes Mores

dblp:337/6546 · DBLP profile ↗
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1ranked-venue papers
1as first author
1since 2021 · last 2025
—ORCID · unresolved

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author · 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 2 heaviest of 2, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › systems biology › metabolic network analysis
elementary flux modes
0.912025
Accelerated enumeration of extreme rays through a positive-definite elementarity test · Bioinform. 2025
Bioinformatics and computational biology › systems biology
metabolic network analysis
0.912025
Accelerated enumeration of extreme rays through a positive-definite elementarity test · Bioinform. 2025

Methods — techniques the papers use, named apart from their topics

positive-definite elementarity test · 0.9nullspace approach · 0.9canonical basis approach · 0.9
YearPublicationVenuePosition
2025 Accelerated enumeration of extreme rays through a positive-definite elementarity test
abstract
MOTIVATION: Analysis of metabolic networks through extreme rays such as extreme pathways and elementary flux modes has been shown to be effective for many applications. However, due to the combinatorial explosion of candidate vectors, their enumeration is currently limited to small- and medium-scale networks (typically <200 reactions). Partial enumeration of the extreme rays is shown to be possible, but either relies on generating them one-by-one or by implementing a sampling step in the enumeration algorithms. Sampling-based enumeration can be achieved through the canonical basis approach (CBA) or the nullspace approach (NSA). Both algorithms are very efficient in medium-scale networks, but struggle with elementarity testing in sampling-based enumeration of larger networks. RESULTS: In this paper, a novel elementarity test is defined and exploited, resulting in significant speedup of the enumeration. Even though NSA is currently considered more effective, the novel elementarity test allows CBA to significantly outpace NSA. This is shown through two case studies, ranging from a medium-scale network to a genome-scale metabolic network with over 600 reactions. In this study, extreme pathways are chosen as the extreme rays, but the novel elementarity test and CBA are equally applicable to the other types. With the increasing complexity of metabolic networks in recent years, CBA with the novel elementarity test shows even more promise as its advantages grows with increased network complexity. Given this scaling aspect, CBA is now the faster method for enumerating extreme rays in genome-scale metabolic networks. AVAILABILITY AND IMPLEMENTATION: All case studies are implemented in Python. The codebase used to generate extreme pathways using the different approaches is available at https://gitlab.kuleuven.be/biotec-plus/pos-def-ep.
Wannes Mores, Satyajeet S. Bhonsale, Filip Logist, Jan F. M. Van Impe
Bioinform.1