Clara Isabel Bermudez Santana

2011 – Associate Professor , Universidad Nacional de Colombia, Bogotá Colombia
2005 – 2011 Assistant Professor, Universidad Nacional de Colombia, Bogotá Colombia
Academic Distintios
2019- Researcher of CEMarin, Corporation Center of Excellence in Marine Sciences
2010 Magna Cum Laude Doctorate Thesis
2007 – 2010 DAAD Scholar
2004 Meritorious Thesis, Magister in Human Genetics
1997 Laureate Undergraduate Thesis, Biologist
Affiliation to Societies
SOLBIO

EDUCATION

1997
Undergraduate in Biology
Universidad Nacional de Colombia, Faculty of Sciences, Bogotá Colombia
2004
Magister in Human Genetics
Universidad Nacional de Colombia, Faculty of Medicine, Bogotá Colombia
2007-2010
Doctorate
Leipzig University, Faculty of Informatics and Mathematics

RESEARCH INTERESTS

Comparative genomics of ncRNAs in animals and plants
Viromics
Transcriptomics
ncRNA modelling

RECENT SCHOLAR PUBLICATIONS

Physiological and transcriptional dynamics of Passiflora edulis f. edulis under early water deficit reveal joint mRNAs-lncRNAs regulation of key drought response traits
F Rojas-Bautista, PA Lozano-Montaña, E Parra-Rincon, LM Melgarejo, ...
Scientia Horticulturae 361, 114814 , 2026
2026
Complexity of Molecular Analysis by New Generation Sequencing in the Study of Sudden Cardiac Death Within the Forensic Context
J Alape-Ariza, CI Bermudez-Santana
Advances in Forensic Biology and Genetics, 239-265 , 2025
2025
Citations: 1
Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus
CI Bermudez-Santana, JC Gallego-Gómez
Viruses 16 (5), 804 , 2024
2024
Citations: 4
Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells
A Gutierrez-Diaz, S Hoffmann, JC Gallego-Gómez, CI Bermudez-Santana
Frontiers in Bioinformatics 4, 1293412 , 2024
2024
Citations: 3
CASE REPORT: MOLECULAR COMPLEMENT TO THE MEDICO-LEGAL AUTOPSY IN A CASE OF UNEXPLAINED DEATH
JA ARIZA, YAX DURAN-TELLEZ, CI BERMUDEZ-SANTANA
ARC JOURNAL OF FORENSIC SCIENCE Учредители: ARC Publications 8 (1), 17-22 , 2024
2024
Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus. Viruses 2024, 16, 804
CI Bermudez-Santana, JC Gallego-Gómez
2024
Citations: 1
Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus
JC Gallego Gómez, CI Bermudez Santana
MDPI , 2024
2024
Computational Prediction of RNA–RNA Interactions between Small RNA Tracks from Betacoronavirus Nonstructural Protein 3 and Neurotrophin Genes during …
AF Rojas-Cruz, CI Bermúdez-Santana
Viruses 15 (8), 1647 , 2023
2023
Citations: 3
Prevalence of genetic variants associated with sudden cardiac death in a population sample in Colombia
J Alape-Ariza, AH Medina-Rocha, R Cabrera-Pérez, ...
J Clin Anat Pathol 8 (1), 126 , 2023
2023
Citations: 1
RNA structure-altering mutations underlying positive selection on Spike protein reveal novel putative signatures to trace crossing host-species barriers in Betacoronavirus
AF Rojas-Cruz, JC Gallego-Gómez, CI Bermúdez-Santana
RNA biology 19 (1), 1019-1044 , 2022
2022
Citations: 7
Structural Analysis of the Spike Protein of SARS‐CoV‐2 Variants and Other Betacoronaviruses Using Molecular Dynamics
J Bolivar‐Muñoz, S Vits, CI Bermudez‐Santana, JF Galindo
ChemPhysChem 23 (23), e202200382 , 2022
2022
Citations: 1
Next-generation sequencing of postmortem molecular markers to support for medicolegal autopsy
JA Ariza, AHM Rocha, RC Pérez, CI Bermudez-Santana
Forensic Science International: Reports 6, 100300 , 2022
2022
Citations: 5
Next-generation sequencing of postmortem molecular markers to support for medicolegal autopsy
J Alape Ariza, AH Medina Rocha, R Cabrera Perez, ...
2022
RNA structure-altering mutations underlying positive selection on Spike protein reveal novel putative signatures to trace crossing host-species barriers in Betacoronavirus
JC Gallego Gómez, AF Rojas Cruz, CI Bermudez Santana
Taylor and Francis , 2022
2022
The Genome of the “Sea Vomit” Didemnum vexillum
E Parra-Rincón, CA Velandia-Huerto, A Gittenberger, J Fallmann, T Gatter, ...
Life 11 (12), 1377 , 2021
2021
Citations: 4
Toward a taxonomy of virus-NcRNAs Interactions in an RNA world for disentangling some tiny secrets of dengue virus
CI Bermudez-Santana, JC Gallego-Gómez
2021
Citations: 1
Evaluation of conserved RNA secondary structures within and between geographic lineages of Zika virus
K Nicolas Calderon, J Fabian Galindo, CI Bermudez-Santana
Life 11 (4), 344 , 2021
2021
Citations: 10
Evaluation of Conserved RNA Secondary Structures within and between Geographic Lineages of Zika Virus
KC Gallegos, JF Galindo, CI Bermudez-Santana
Preprints , 2021
2021
Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean
T Garcia, J Duitama, SS Zullo, J Gil, A Ariani, S Dohle, A Palkovic, ...
Nature Communications 12 (1), 702 , 2021
2021
Citations: 102
Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nat Commun 12 (1): 702
T Garcia, J Duitama, SS Zullo, J Gil, A Ariani, S Dohle, A Palkovic, ...
2021
Citations: 6

MOST CITED SCHOLAR PUBLICATIONS

Evidence for human microRNA-offset RNAs in small RNA sequencing data
D Langenberger, C Bermudez-Santana, J Hertel, S Hoffmann, ...
Bioinformatics 25 (18), 2298-2301 , 2009
2009
Citations: 161
Genomic organization of eukaryotic tRNAs
C Bermudez-Santana, CSO Attolini, T Kirsten, J Engelhardt, SJ Prohaska, ...
BMC genomics 11 (1), 270 , 2010
2010
Citations: 131
Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean
T Garcia, J Duitama, SS Zullo, J Gil, A Ariani, S Dohle, A Palkovic, ...
Nature Communications 12 (1), 702 , 2021
2021
Citations: 102
Identification and classification of small RNAs in transcriptome sequence data
D Langenberger, CI Bermudez-Santana, PF Stadler, S Hoffmann
Biocomputing 2010, 80-87 , 2010
2010
Citations: 85
Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies
CA Velandia-Huerto, SJ Berkemer, A Hoffmann, N Retzlaff, ...
BMC genomics 17 (1), 617 , 2016
2016
Citations: 33
Evolutionary genomics of microRNAs and their relatives
A Tanzer, M Riester, J Hertel, CI Bermudez-Santana, J Gorodkin, ...
Evolutionary genomics and systems biology, 295-327 , 2010
2010
Citations: 31
Dengue virus potentially promotes migratory responses on endothelial cells by enhancing pro-migratory soluble factors and miRNAs
DA Álvarez-Díaz, AA Gutiérrez-Díaz, E Orozco-García, A Puerta-González, ...
Virus Research 259, 68-76 , 2019
2019
Citations: 29
Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum
CA Velandia-Huerto, AA Gittenberger, FD Brown, PF Stadler, ...
BMC genomics 17 (1), 691 , 2016
2016
Citations: 19
Evaluation of conserved RNA secondary structures within and between geographic lineages of Zika virus
K Nicolas Calderon, J Fabian Galindo, CI Bermudez-Santana
Life 11 (4), 344 , 2021
2021
Citations: 10
RNA structure-altering mutations underlying positive selection on Spike protein reveal novel putative signatures to trace crossing host-species barriers in Betacoronavirus
AF Rojas-Cruz, JC Gallego-Gómez, CI Bermúdez-Santana
RNA biology 19 (1), 1019-1044 , 2022
2022
Citations: 7
Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nat Commun 12: 702
T Garcia, J Duitama, SS Zullo, J Gil, A Ariani, S Dohle, A Palkovic, ...
2021
Citations: 7
Nonprotein-coding RNAs as regulators of development in tunicates
CA Velandia-Huerto, FD Brown, A Gittenberger, PF Stadler, ...
Marine Organisms as Model Systems in Biology and Medicine, 197-225 , 2018
2018
Citations: 7
Evolutionary genomics and systems biology
A Tanzer, M Riester, J Hertel, CI Bermudez-Santana, J Gorodkin, ...
Wiley-Blackwell , 2010
2010
Citations: 7
Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean. Nat Commun 12 (1): 702
T Garcia, J Duitama, SS Zullo, J Gil, A Ariani, S Dohle, A Palkovic, ...
2021
Citations: 6
Buscando agujas en un pajar: viajes de RNAs pequenos in silico e in vitro
CI Bermudez Santana
Acta Biológica Colombiana 16 (3), 103-114 , 2011
2011
Citations: 6
Next-generation sequencing of postmortem molecular markers to support for medicolegal autopsy
JA Ariza, AHM Rocha, RC Pérez, CI Bermudez-Santana
Forensic Science International: Reports 6, 100300 , 2022
2022
Citations: 5
Toward a Categorization of Virus-ncRNA Interactions in the World of RNA to Disentangle the Tiny Secrets of Dengue Virus
CI Bermudez-Santana, JC Gallego-Gómez
Viruses 16 (5), 804 , 2024
2024
Citations: 4
The Genome of the “Sea Vomit” Didemnum vexillum
E Parra-Rincón, CA Velandia-Huerto, A Gittenberger, J Fallmann, T Gatter, ...
Life 11 (12), 1377 , 2021
2021
Citations: 4
Introducing evolutionary biologists to the analysis of big data: guidelines to organize extended bioinformatics training courses
R Faria, D Triant, A Perdomo-Sabogal, B Overduin, C Bleidorn, ...
Evolution: Education and Outreach 11 (1), 8 , 2018
2018
Citations: 4
Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells
A Gutierrez-Diaz, S Hoffmann, JC Gallego-Gómez, CI Bermudez-Santana
Frontiers in Bioinformatics 4, 1293412 , 2024
2024
Citations: 3

Publications

Langenberger, David; Bermudez-Santana, Clara; Hertel, Jana; Hoffmann, Steve; Khaitovich, Philipp; Stadler, Peter F; ,Evidence for human microRNA-offset RNAs in small RNA sequencing data,Bioinformatics,25,18,2298-2301,2009,Oxford University Press (Google Scholar 139)
Langenberger, David; Bermudez-Santana, CI; Stadler, Peter F; Hoffmann, Steve; ,Identification and classification of small RNAs in transcriptome sequence data,Biocomputing 2010,,,80-87,2010,World Scientific (Google Scholar 71)
Bermudez-Santana, Clara; Attolini, Camille Stephan-Otto; Kirsten, Toralf; Engelhardt, Jan; Prohaska, Sonja J; Steigele, Stephan; Stadler, Peter F; ,Genomic organization of eukaryotic tRNAs,BMC genomics,11,1,1-14,2010,Springer (Google Scholar 69)
Tanzer, Andrea; Riester, Markus; Hertel, Jana; Bermudez‐Santana, Clara Isabel; Gorodkin, Jan; Hofacker, Ivo L; Stadler, Peter F; ,Evolutionary genomics of microRNAs and their relatives,Evolutionary genomics and systems biology,,,295-327,2010,Wiley Online Library (Google Scholar 23)
Velandia-Huerto, Cristian A; Berkemer, Sarah J; Hoffmann, Anne; Retzlaff, Nancy; Marroquín, Liliana C Romero; Hernández-Rosales, Maribel; Stadler, Peter F; Bermúdez-Santana, Clara I; ,"Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies",BMC genomics,17,1,1-15,2016,Springer (Google Scholar 14)
Velandia-Huerto, Cristian A; Gittenberger, Adriaan A; Brown, Federico D; Stadler, Peter F; Bermúdez-Santana, Clara I; ,Automated detection of ncRNAs in the draft

GRANT DETAILS

Virological expedition in representative ecosystems of Colombia: tropical humid rainforest of Sierra Nevada
de Santa Martha. Departamento Administrativo de Ciencia, Tecnología e Innovación (Bogotá, 18-01 to present|Grant Part of GRANT_NUMBER: Contract Number 863-2017 Project 210477757671 Co-researcher

Detection of molecular variability in the genome of the SARS-CoV-2 virus and in other betacoronaviruses: Towards a molecular surveillance system in pandemic and post-pandemic Universidad Nacional de Colombia (Bogota) - Principal researcher

Identification Of Mutations In Genes Associated With Hereditary Channel Disease Through Exomic Analysis. Universidad Nacional de Colombia (Bogotá) 2020-09 to 2022-02|Grant Part of GRANT_NUMBER: Hermes Código: 49924 Principal researcher

Characterization of the virome of marine invertebrate holobionts as a basis for ecological studies of marine ecosystems Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS) (Bogota) 2021-01 to 2022-01|Salary award GRANT_NUMBER: Hermes Código: 47367 Co-researcher

Evolutionary Genomics of Specialized Metabolism Departamento Administrativo de Ciencia, Tecnología e Innovación (COLCIENCIAS) (Bogota) 2019-06 to 2024-06|Grant GRANT_NUMBER: Hermes Código Código: 44598- Co-researcher