Author

José Antonio Ramírez-Rafael

Centro de Investigación y de Estudios Avanzados del Instituto Politécnico NacionalORCID 0000-0003-3800-2434Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Bioinformatics· 2 Genomics· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:statistical model· 3 Research Focus:benchmarking· 2 Research Focus:gene regulatory network inference· 2 Assay:bulk RNA-seq· 1 Research Focus:cell-cell communication· 1 Research Focus:differential expression· 1 Approach:experimental assay· 1 Organism:human· 1

Frequent Co-Authors

Annachiara KorchmarosiD· 2 shared Katia Aviña‐PadillaiD· 2 shared Marc HellmuthiD· 2 shared Maribel Hernández-RosalesiD· 2 shared Peter Florian StadleriD· 2 shared Alfredo José Hernández-ÁlvareziD· 1 shared Alitzel López SáncheziD· 1 shared Bruno Schmidt· 1 shared

Activity by Year

2022-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 33 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersBioinformatics

Annachiara KorchmarosORCID

Mutual co-authors in cluster

Author profile →

3 papers

Recent·Most cited

BioinformaticsPLoS Computational BiologyPeer-reviewedAug 12, 2026

REvolutionH-tl: A Fast and Robust Tool for Decoding Evolutionary Gene Histories

José Antonio Ramírez-Rafael, Annachiara Korchmaros, Katia Aviña‐Padilla…·Maribel Hernández-Rosales

REvolutionH-tl automates evolutionary gene history analysis from sequence data, outperforming existing tools in speed and accuracy with integrated visualization.

1 citation

protein sequencestatistical model

𝕏 PostBluesky

BioinformaticsJournal of Combinatorial OptimizationPeer-reviewedAug 1, 2026

Partial Fitch Graphs: Characterization, Satisfiability and Complexity

Marc Hellmuth, Annachiara Korchmaros, José Antonio Ramírez-Rafael…·Sandhya Thekkumpadan Puthiyaveedu

The paper characterizes partial Fitch graphs, shows their satisfiability, and proves NP-hardness of recovering full Fitch graphs from partial data.

DOI 10.1007/s10878-026-01452-1

statistical modelbenchmarking

𝕏 PostBluesky

GenomicsLecture notes in computer sciencePeer-reviewedJan 1, 2022

Deciphering the tissue-specific regulatory role of intronless genes across cancers

Katia Aviña‐Padilla, José Antonio Ramírez-Rafael, Octavio Zambada-Moreno…·Maribel Hernández-Rosales

This study identifies intronless genes differentially expressed across eight cancers, highlighting their role in epigenetic regulation and interactome rewiring in specific tumor types.

2 citationstop 4%

humanbulk RNA-seq

𝕏 PostBluesky