Gutierrez-Diaz A, Hoffmann S, Gallego-Gómez JC and Bermudez-Santana CI:
Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells. Front. Bioinform.(2024) 4:1293412. doi: 10.3389/fbinf.2024.1293412
Rojas-Cruz, A. F., Gallego-Gómez, J. C., & Bermúdez-Santana, C. I.:
RNA structure-altering mutations underly-ing positive selection on Spike protein re-veal novel putative signatures to trace crossing host-species barriers in Betacoronavirus. RNA biology, 2022, 19(1), 1019¿1044. https://doi.org/10.1080/15476286.2022.2115750
Bermudez-Santana CI, Gallego-Gómez JC.:
Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus. Viruses. 2024 May 18;16(5):804. doi: 10.3390/v16050804. PMID: 38793685; PMCID: PMC11125801.
Ariza, J.A., Medina-Rocha, A.H., Cabrera-Pérez, R., & Bermúdez-Santana, C.I.:
Prevalence of Genetic Variants Associated with Sudden Cardiac Death in a Population Sample in Colombia. Journal of Clinical & Anatomic Pathology. (2023) DOI:10.47275/2332-4864-126
Alape Ariza J, Medina Rocha AH, Cabrera Pérez R and Bermúdez- Santana CI:
Retrospective Molecular Analysis in Five Cases Probably Associated with Sudden Death the National Institute of Legal Med-icine and Forensic Sciences of Colombia, In-ternational Journal of Forensic Sciences (2023) DOI: 10.23880/ijfsc-16000304
Rojas-Cruz, A. F., & Bermúdez-Santana, C. I.:
Computational Prediction of RNA-RNA In-teractions between Small RNA Tracks from Betacoronavirus Nonstructural Pro-tein 3 and Neurotrophin Genes during In-fection of an Epithelial Lung Cancer Cell Line: Potential Role of Novel Small Regula-tory RNA. Viruses, 2023, 15(8), 1647. https://doi.org/10.3390/v15081647
Ariza, J.A., Pinzón Reyes, A, Medina-Rocha, A.H., Cabrera-Pérez, R., & Bermúdez-Santana, C.I.:
In silico Functional Analysis of Variants in Genes Associated with Sudden Cardiac Death in Cases of the National Institute of Legal Medicine of Colombia Journal of Fo-rensic Research Volume 14:03, 2023 DOI: 10.37421/2157- 7145.2023.14.555
Joseph Alape Ariza, Arbey Hernán Medina Rocha, Rodrigo Cabrera Pérez, Clara Isabel Bermudez-Santana,:
Next-generation sequencing of postmor-tem molecular markers to support for medicolegal autopsy, Forensic Science In-ternational: Reports, Volume 6, 2022, 100300 https://doi.org/10.1016/j.fsir.2022.100300
Bolivar-Muñoz, J., Vits, S., Bermudez-Santana, C. I., & Galindo, J. F.:
Structural Analysis of the Spike Protein of SARS-CoV-2 Variants and Other Betacoro-naviruses Using Molecular Dynam-ics. Chemphyschem : a European journal of chemical physics and physical chemis-try, 2022 23(23), e202200382. https://doi.org/10.1002/cphc.202200382
Nicolas Calderon K, Fabian Galindo J, Ber-mudez-Santana CI.:
Evaluation of Conserved RNA Secondary Structures within and between Geograph-ic Lineages of Zika Virus. Life (Basel). 2021 Apr 14;11(4):344. doi: 10.3390/life11040344. PMID: 33919874; PMCID: PMC8070784.
Parra-Rincón, E., Velandia-Huerto, C. A., Gittenberger, A., Fallmann, J., Gatter, T., Brown, F. D., Stadler, P. F., & Bermúdez-Santana, C. I.:
The Genome of the "Sea Vom-it" Didemnum vexillum. Life (Basel, Swit-zerland), 2021, 11(12), 1377. https://doi.org/10.3390/life11121377
Garcia, T., Duitama, J., Zullo, S. S., Gil, J., Ariani, A., Dohle, S., Palkovic, A., Skeen, P., Bermudez-Santana, C. I., Debouck, D. G., Martínez-Castillo, J., Gepts, P., & Cha-cón-Sánchez, M. I.:
Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nature communica-tions, 2021, 12(1), 702. https://doi.org/10.1038/s41467-021-20921-1
Álvarez-Díaz, D. A., Gutiérrez-Díaz, A. A., Orozco-García, E., Puerta-González, A., Bermúdez-Santana, C. I., & Gallego-Gómez, J. C.:
Dengue virus potentially promotes migra-tory responses on endothelial cells by en-hancing pro-migratory soluble factors and miRNAs. Virus research, 2019, 259, 68¿76. https://doi.org/10.1016/j.virusres.2018.10.018
Rui Faria, Deborah Triant4, Alvaro Per-domo¿Sabogal, Bert Overduin8, Christoph Bleidorn,Clara Isabel Bermudez Santana, David Langenberger, Giovanni Marco Dall¿Olio, Henrike Indrischek,Jan Aerts, Jan Engelhardt, Johannes Engelken2, Katja Liebal, Mario Fasold, Sofia Robb,Sonja Grath, Sree Rohit Raj Kolora, Tiago Car-valho, Walter Salzburger, Vladimir Jo-vanovic and Katja Nowick,:
Introducing evolutionary biologists to the analysis of big data: guidelines to organize extended bioinformatics training courses. Evolution: Education and Out-reach volume 11, Article number: 8 (2018)
Velandia-Huerto CA, Gittenberger AA, Brown FD, Stadler PF, Bermúdez-Santana CI.:
Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum. BMC Genomics. 2016 Aug 30;17(1):691. doi: 10.1186/s12864-016-2934-5. PMID: 27576499; PMCID: PMC5006418.
Velandia-Huerto CA, Berkemer SJ, Hoffmann A, Retzlaff N, Romero Marroquín LC, Hernández-Rosales M, Stadler PF, Bermúdez-Santana CI.:
Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies. BMC Genomics. 2016 Aug 11;17(1):617. doi: 10.1186/s12864-016-2927-4. PMID: 27515907; PMCID: PMC4981973.
Bermudez-Santana C, Attolini CS, Kirsten T, Engelhardt J, Prohaska SJ, Steigele S, Stadler PF.:
Genomic organization of eukaryotic tRNAs. BMC Genomics. 2010 Apr 28;11:270. doi: 10.1186/1471-2164-11-270. PMID: 20426822; PMCID: PMC2888827.
Langenberger D, Bermudez-Santana CI, Stadler PF, Hoffmann S.:
Identification and classification of small RNAs in transcriptome sequence data. Pac Symp Biocomput. 2010:80-7. doi: 10.1142/9789814295291_0010. PMID: 19908360.
Langenberger D, Bermudez-Santana C, Hertel J, Hoffmann S, Khaitovich P, Stadler PF.:
Evidence for human microRNA-offset RNAs in small RNA sequencing data. Bioinformatics. 2009 Sep 15;25(18):2298-301. doi: 10.1093/bioinformatics/btp419. Epub 2009 Jul 6. PMID: 19584066.
Copeland CS, Marz M, Rose D, Hertel J, Brindley PJ, Bermudez Santana CB, Kehr S, Attolini CS, Stadler PF.:
Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum. BMC Genomics. 2009 Oct 8;10:464. doi: 10.1186/1471-2164-10-464. PMID: 19814823; PMCID: PMC2770079.
Galindo, J F, Bermúdez, C I, Daza, EE:
tRNA structure from a graph and quantum theoretical perspective,
Journal of Theoretical Biology, Volume 240, Issue 4, 2006,
Pages 574-582, ISSN 0022-5193, https://doi.org/10.1016/j.jtbi.2005.10.017.
Galindo, J F, Bermúdez, C I, Daza, EE:
A classification of central nucleotides induced by the influence of neighboring nucleotides in triplets, Journal of Molecular Structure: THEOCHEM, Volume 769, Issues 1¿3, 2006, Pages 103-109, ISSN 0166-1280, https://doi.org/10.1016/j.theochem.2006.04.015.
Bermúdez CI, Daza EE, Andrade E.:
Characterization and comparison of Escherichia coli transfer RNAs by graph theory based on secondary structure. J Theor Biol. 1999 Mar 21;197(2):193-205. doi: 10.1006/jtbi.1998.0866. PMID: 10074393.