StandEnA: a customizable workflow for standardized annotation and generating a presence--absence matrix of proteins. Bioinformatics Advances, (3)1:vbad069, Oxford University Press, 2023. [PUMA: imported zno]
Complete edge-colored permutation graphs. Advances in Applied Mathematics, (139):102377, Elsevier BV, August 2022. [PUMA: edge-colored graphs permutation zno] URL
Sorting signed permutations by tandem duplication random loss and inverse tandem duplication random loss. Advances in Applied Mathematics, (161):102757, Elsevier, 2024. [PUMA: imported zno]
Compatibility of partitions with trees, hierarchies and split systems. Discrete Applied Mathematics, (314):265–283, Elsevier BV, June 2022. [PUMA: hierarchies partitions trees with zno] URL
RNA interaction format: a general data format for RNA interactions. Bioinformatics, (39)11:btad665, Oxford University Press, 2023. [PUMA: imported zno]
Clusters and Unique Least Common Ancestors in Directed Acyclic Graphs. Research Square Platform LLC, March 2024. [PUMA: Acyclic Ancestors Common Directed Least zno graphs] URL
RNA design principles for riboswitches that regulate RNase P-mediated tRNA processing. Riboregulator Design and Analysis, 179--202, Springer, 2022. [PUMA: imported zno]
REvolutionH-tl: Reconstruction of Evolutionary Histories tool. RECOMB International Workshop on Comparative Genomics, 89--109, 2024. [PUMA: imported zno]
Reaction rebalancing: a novel approach to curating reaction databases. Journal of Cheminformatics, (16)1:82, Springer, 2024. [PUMA: imported zno]
Clustering systems of phylogenetic networks. Theory in Biosciences, (142)4:301–358, Springer Science and Business Media LLC, August 2023. [PUMA: Clustering networks phylogenetic systems zno] URL
Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-) orthologs. Frontiers in Bioinformatics, (3):1322477, Frontiers Media SA, 2023. [PUMA: imported zno]
Chemically inspired Erdős–Rényi hypergraphs. Journal of Mathematical Chemistry, (62)6:1357–1383, Springer Science and Business Media LLC, April 2024. [PUMA: Erdős–Rényi hypergraphs zno] URL
Phylogenetic information as soft constraints in RNA secondary structure prediction. International Symposium on Bioinformatics Research and Applications, 267--279, 2023. [PUMA: imported zno]
BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification. RNA Biology, (21)1:410–421, Informa UK Limited, March 2024. [PUMA: BioDeepfuse RNA classification deep extraction feature learning non-coding zno] URL
Periodic system converges and is affected by wars. 2022. [PUMA: imported zno]
BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria. Briefings in Bioinformatics, (23)4Oxford University Press (OUP), June 2022. [PUMA: BioAutoML RNAs automated bacteria engineering metalearning noncoding predict zno] URL
Optimisation via encodings: a renormalisation group perspective. Journal of Physics A: Mathematical and Theoretical, (56)48:485001, IOP Publishing, 2023. [PUMA: imported zno]
Multiomics reveal unique signatures of human epiploic adipose tissue related to systemic insulin resistance. Gut, (71)11:2179--2193, BMJ Publishing Group, 2022. [PUMA: imported zno]
Best Match Graphs With Binary Trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics, (20)3:1679–1690, Institute of Electrical and Electronics Engineers (IEEE), May 2023. [PUMA: Best Binary Match Trees zno graphs] URL
AsymmeTree: A Flexible Python Package for the Simulation of Complex Gene Family Histories. Software, (1)3:276–298, MDPI AG, August 2022. [PUMA: AsymmeTree Family Gene Histories Package Python Simulation zno] URL