Core Potentials: The Consensus Segmentation Conjecture. Mathematics in Computer Science, (18)4Springer Science and Business Media LLC, October 2024. [PUMA: Conjecture Consensus Core Potentials Segmentation] URL
Synthetic riboswitches for the analysis of tRNA processing by eukaryotic RNase P enzymes. RNA, (28)4:551--567, Cold Spring Harbor Lab, 2022. [PUMA: imported]
Computational History: Challenges and Opportunities of Formal Approaches. Journal of Social Computing, (4)3:232–242, Institute of Electrical and Electronics Engineers (IEEE), September 2023. [PUMA: Challenges Computational History Opportunities] URL
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]
Complete edge-colored permutation graphs. Advances in Applied Mathematics, (139):102377, Elsevier BV, August 2022. [PUMA: edge-colored graphs permutation] 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]
Salt corrections for RNA secondary structures in the ViennaRNA package. bioRxiv, 2023--04, Cold Spring Harbor Laboratory, 2023. [PUMA: imported]
Compatibility of partitions with trees, hierarchies and split systems. Discrete Applied Mathematics, (314):265–283, Elsevier BV, June 2022. [PUMA: hierarchies partitions trees with] URL
RNA interaction format: a general data format for RNA interactions. Bioinformatics, (39)11:btad665, Oxford University Press, 2023. [PUMA: imported]
Clusters and Unique Least Common Ancestors in Directed Acyclic Graphs. Research Square Platform LLC, March 2024. [PUMA: Acyclic Ancestors Common Directed Graphs Least] URL
RNA design principles for riboswitches that regulate RNase P-mediated tRNA processing. Riboregulator Design and Analysis, 179--202, Springer, 2022. [PUMA: imported]
REvolutionH-tl: R econstruction of Evolution ary H istories t oo l. RECOMB International Workshop on Comparative Genomics, 89--109, 2024. [PUMA: imported]
Reaction rebalancing: a novel approach to curating reaction databases. Journal of Cheminformatics, (16)1:82, Springer, 2024. [PUMA: imported]
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] 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]
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] URL
Phylogenetic information as soft constraints in RNA secondary structure prediction. International Symposium on Bioinformatics Research and Applications, 267--279, 2023. [PUMA: imported]
Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction. Journal of Computational Biology, (31)6:549--563, Mary Ann Liebert, Inc., publishers 140 Huguenot Street, 3rd Floor New~…, 2024. [PUMA: imported]
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] URL
Periodic system converges and is affected by wars. 2022. [PUMA: imported]