THE UNIVERSITY OF TEXAS AT EL PASO
We study how genes, noncoding RNAs, and chromatin shape cancer. Our lab brings together computational biology and experimental research to identify mechanisms, biomarkers, and potential therapeutic targets.
Based in El Paso.
Connected through science.
We investigate breast and liver cancer, with an interest in the molecular differences that contribute to disease progression and disparities in patient outcomes.
01 / RESEARCH
We connect molecular measurements with biological function, using multi-omics analysis to guide experiments and interpret disease.
CANCER GENOMICS
Understanding tumor and immune cell diversity in triple-negative breast cancer, including tumors from Hispanic patients.
We combine transcriptomic and chromatin accessibility analyses with functional studies to investigate regulatory programs, treatment response, and the role of ZMYND8 in tumor biology.
RNA & CHROMATIN
Studying how long noncoding RNAs influence gene expression, hormone response, and cancer cell behavior.
Our work includes LINC01016 in estrogen-responsive breast cancer and noncoding RNA networks in liver disease. We use RNA perturbations and sequencing to examine their functions and regulatory relationships.
COMPUTATIONAL BIOLOGY
Combining RNA, protein, chromatin, and tissue imaging to examine disease across molecular and spatial scales.
We develop and apply computational methods for spatial transcriptomics, multi-omics integration, and prediction of gene expression from tissue images. These approaches support studies of cancer and collaborative projects in lung fibrosis and neurodegeneration.
TUMOR GENOMICS
Combining exome, transcriptome, copy-number and clinical data from patient cohorts to find driver genes and markers that predict survival.
We mine large cohorts such as TCGA and PCAWG alongside our own sequencing to connect somatic mutations and copy-number changes with outcomes in breast, uterine and brain cancers, then test the strongest candidates in the lab.
CANCER EPIGENOMICS
How DNA methylation, chromatin accessibility and chromatin readers rewire gene regulation in endocrine-resistant breast cancer.
We profile methylation and chromatin accessibility, and study how X-linked genes and readers such as ZMYND8 reshape the epigenetic landscape of tumors that stop responding to hormone therapy.
Transcriptomics
Proteomics
Chromatin profiling
Exome & targeted sequencing
Single-cell & spatial transcriptomics
DNA methylation
Machine learning
Functional validation
02 / FROM TISSUE TO GENOME
We follow a tumor from the tissue a pathologist sees, to the rearranged genome inside each cell, to the single-cell ecosystem around it and the expression programs that set it apart.
FIG. A · TISSUE
Nests of invasive carcinoma cells with enlarged, irregular nuclei, surrounded by collagen stroma and infiltrating lymphocytes (H&E).
FIG. B · GENOME
Chromosomes around the ring, copy-number gains (orange) and losses (blue), mutation density, and rearrangements joining distant loci.
FIG. C · SINGLE CELL
Single-cell RNA-seq separates tumor cells from the immune and stromal cells around them, including exhausted cytotoxic T cells.
FIG. D · TRANSCRIPTOME
Clustering RNA-seq profiles separates tumors from matched normal tissue by proliferation, hormone-response and noncoding RNA programs.
03 / SELECTED PUBLICATIONS
REVIEW ARTICLE · SIGNAL TRANSDUCTION AND TARGETED THERAPY
Yang B, Sedano MJ, Perez K, et al. · Ramos EI, Gadad SS
RESEARCH ARTICLE · LIVER INTERNATIONAL COMMUNICATIONS
Delgadillo F, Perez K, Yang B, et al. · Ramos E, Gadad S
CONFERENCE ABSTRACT · CANCER RESEARCH
Sanchez R, Chaib Lozano E, Yang B, Gadad S, Ramos E
RESEARCH ARTICLE · MOLECULAR PSYCHIATRY
Kumar S, Ramos E, Hidalgo A, et al. · 30:5121–5136
RESEARCH ARTICLE · BRITISH JOURNAL OF BIOMEDICAL SCIENCE
Reid VA, Yang B, Russo K, et al. · Ramos EI, Gadad SS
RESEARCH ARTICLE · JOURNAL OF THE ENDOCRINE SOCIETY
Ramos E, Yang B, Vasquez Y, Lin K, Choudhari R, Gadad S
Selected recent work is shown above. Explore additional peer-reviewed articles.
Chauhan, V., Kumar, R., Veerapandian, R., Ramos, E. I., Jagannath, C., Gadad, S. S., & Dhandayuthapani, S. (2026). BCG overexpressing Ag85B reprograms host immune response through coordinated transcriptional networks. Frontiers in Immunology. https://doi.org/10.3389/fimmu.2026.1876830
Read articleGarnica, O., Veerapandian, R., Das, K., Mishra, A., Rawat, V., Carmona, A., Chauhan, V., Kumar, R., Chacon, J., Khan, A., Ramos, E. I., Gadad, S. S., Jagannath, C., & Dhandayuthapani, S. (2026). Construction and characterization of novel Mycobacterium tuberculosis-derived triple and quadruple knockout vaccines against tuberculosis. Infection and Immunity. https://doi.org/10.1128/iai.00500-25
Read articleVera, D. L., Griffin, P. T., Leigh, D., Kras, J., Ramos, E., Bishof, I., Butler, A., Chwalek, K., Vogel, D. S., Kane, A. E., & Sinclair, D. A. (2025). Multiomic clocks to predict phenotypic age in mice. The Journals of Gerontology, Series A: Biological Sciences and Medical Sciences. Advance online publication. https://doi.org/10.1093/gerona/glaf188
Read articleVeerapandian, R., Yang, B., Carmona, A., Sedano, M. J., Reid, V., Jimenez, R., Chacon, J., Jagannath, C., Ramos, E. I., Gadad, S. S., & Dhandayuthapani, S. (2025). Comparative transcriptomic analysis of mouse macrophages infected with live attenuated vaccine strains of Mycobacterium tuberculosis. Frontiers in Immunology, 16, 1583439. https://doi.org/10.3389/fimmu.2025.1583439
Read articleButler, A. A., Kras, J. J., Chwalek, K. P., Ramos, E. I., Bishof, I. J., Vogel, D. S., & Vera, D. L. (2025). Measuring technical variability in Illumina DNA methylation microarrays. PLOS ONE, 20(7), e0326337.
Yang, B., Sedano, M. J., Diwa, K., Dominguez, J., Boisselier, G., Harrison, A. L., Reid, V. A., Ramos, E. I., Jimenez, M. V., Sanchez-Michael, L. A., Kolli, S., Patel, J., Lee, D., Vijayaraghavan, M., Chacon, J., Dhandayuthapani, S., & Gadad, S. S. (2025). A snapshot of the role of estrogen-regulated divergent non-coding transcripts. Clinical and Translational Discovery, 5(3), e70055. https://doi.org/10.1002/ctd2.70055
Read articleGuha, D., Singh, V., Nandi, S., Ramos, E. I., Gadad, S. S., & Das, C. (2024). ZMYND8 is a regulator of Sonic Hedgehog signaling in ATRA-mediated differentiation of neuroblastoma cells. Biochemistry, 63(12), 1534–1542. https://doi.org/10.1021/acs.biochem.4c00145
Read articleReid, VA*; Ramos, EI*; Veerapandian, R; Carmona, A; Gadad, SS; Dhandayuthapani, S. Differential expression of lncRNAs in HIV patients with TB and HIV-TB with Anti-retroviral treatment. Noncoding RNA. 2024 Jul 13;10(4):40. doi: 10.3390/ncrna10040040. PMID: 39051374. *Contributed equally
Read articleHidalgo, AM; Singh, Vipin, S; Mangadu, T; Guha, D; Ramos, EI*; Das, C*; Gadad, SS*. Characterization and Expression of the Microtubule Associated Protein Tau Gene Isoforms and their Impact on Clinical Outcomes in Glioma Patients. Computational and Structural Biotechnology Reports. May 2024. https://doi.org/10.1016/j.csbr.2024.100002. *Corresponding authors
Read articleRamos, EI; Veerapandian, R; Das, K; Chacon, J; Gadad, SS; Dhandayuthapani, S. Pathogenic Mycoplasmas of humans dysregulate the long noncoding RNAs in epithelial cells. Non-coding RNA Research. 2023 Mar 8, 8(3):282-293. doi: 10.1016/j.ncrna.2023.03.002 PMID: 36970372
Read articleVeerapandian, R; Ramos, EI; Vijayaraghavan, M; Sedano, MJ; Carmona, A; Chacon, JA; Gadad, SS; Dhandayuthapani, S. Mycobacterium smegmatis secreting methionine sulfoxide reductase A (MsrA) modulates cellular processes in mouse macrophages. Biochimie. 2023 Feb 19, S0300-9084(23)00048-2 doi: 10.1016/j.biochi.2023.02.010. PMID: 36809827
Read articleAdhikary, S; Singh, V; Choudhari, R; Yang, B; Adhikari, S; Ramos, EI; Chaudhuri, S; Roy, S; Gadad, SS; Das, C. ZMYND8 suppresses MAPT213 LncRNA transcription to promote neuronal differentiation. Cell Death & Disease. 2022 Sep 5;13(9);766. doi: 10.1038/s41419-022-05212-x. PMID:36064715; PMCID: PMC9445031.
Read articleRamos, EI*; Das, K*; Harrison, A; Garcia, A; Gadad, S; Dhandayuthapani, S. Mycoplasma genitalium and M. pneumoniae regulate a distinct set of protein-coding genes in epithelial cells. Frontiers in Immunology. 2021 Oct 11;12:738431. doi: 10.3389/fimmu.2021.738431. PMID: 34707609; PMCID: PMC8544821.
Read articleMondal, P*; Gadad, SS*; Ahikari, S; Ramos, EI; Sen, S; Prasad, P; Das, C. TCF19 and p53 Regulate Transcription of TIGAR and SOC2 in HCC for Mitochondrial Energy Metabolism and Stress Adaptation. The FASEB Journal. 2021 Sep;35(9):e21814. doi: 10.1096/fj.202002486RR. PMID: 34369624
Read articleGadad, BS; Vargas-Medrano, J; Ramos, EI; Najera, K; Fagan, M; Forero, A; Thompson, PM. Altered levels of interleukins and neurotrophic growth factors in mood disorders and suicidality: an analysis from periphery to central nervous system. Translational Psychiatry, 2021 Jun;(11)341. doi: 10.1038/s41398-021-01452-1
Read articleSedano, MJ*; Ramos, EI*; Choudhari, R; Harrison, A; Subramani, R; Lakshmanaswamy, R; Zilaie, M; Gadad, SS. Hypoxanthine Phosphoribosyl Transferase 1 is Upregulated, Predicts Clinical Outcome and Controls Gene Expression in Breast Cancer. Cancers (Basel), 2020 Jun;12(6):1522. doi: 10.3390/cancers12061522. PMID: 32532008 2021.03.26.437262
Read articleSedano, MJ; Harrison AL; Zilaie, M; Das, C; Choudhari, R; Ramos, EI; Gadad, SS. Emerging Roles of Estrogen-Regulated Enhancer and Long Non-Coding RNAs. International Journal of Molecular Sciences, 2020 May;21(10):3711. doi: 10.3390/ijms21103711. PMID: 32466143
Read articleChoudhari, R; Sedano, M; Harrison, A; Subramani R; Lin, KY; Ramos, EI; Lakshmanaswamy, R; Gadad, S. Long noncoding RNAs in Cancer: From Discovery to Therapeutic Targets. Advances in Clinical Chemistry, 2020;95:105-147, https://doi.org/10.1016/bs.acc.2019.08.003. PMID: 32122521
Read articleVasquez, YM; Nandu, TS; Kelleher, AM; Ramos, EI; Gadad, S; Kraus WL. Genome-wide analysis and functional prediction of the estrogen-regulated transcriptional response in the mouse uterus. Biology of Reproduction, 2019 Sep; 12:10.1093/biolre/ioz183. PMID: 31511857
Read articleUli, N; Michelen-Gomez, E; Ramos, EI; Druley, TE. Age-specific changes in genome-wide methylation enrich for Foxa2 and estrogen receptor alpha binding sites. PLoS One, 2018 Sep; 13(9):e0203147. PMID: 30256791
Read articleDruley, TE; Wang, L; Lin, SJ; Lee, JH; Zhang, Q; Daw, EW; Abel, HJ; Chasnoff, SE; Ramos, EI; Levinson, BT; Thyagaraja, B; Newman, AB; Christensen, K; Mayeux, R; Province MA. Candidate gene resequencing to identify rare, pedigree-specific variants influencing healthy aging phenotypes in the long life family study. BMC Geriatrics, 2016 Apr;16:80. PMID: 27060904
Read articleHing, B; Ramos, E; Braun, P; Mckane, M Jancic, D; Tamashiro, KL; Lee, RS; Michaelson, JJ; Druley, TE; Potash, JB. Adaptation of the targeted capture Methyl-Seq platform for the mouse genome identifies novel tissue-specific DNA methylation patterns of genes involved in neurodevelopment. Epigenetics, 2015. 10(7):581-96. PMID: 25985232
Read articleRamos, EI; Bien-Willner, GA; Li, J; Hughes, AE; Giacalone, J; Chasnoff, S; Kulkarni, S; Parmacek, M; Cole, FS; Druley, TE. Genetic variation in MKL2 and decreased downstream PCTAIRE1 expression in extreme, fatal primary human microcephaly. Clin Genet, 2014 May; 85(5):423-32 PMID: 23692340
Read articleRamos, E*; Levinson, BT*; Chasnoff, S; Hughes, A; Young, AL; Thornton, K; Li, A; Vallania, FL; Province, M; Druley, TE. Population-based rare variant detection via pooled exome or custom hybridization capture with or without individual indexing. BMC Genomics, 2012 Dec;13:683. PMID: 23216810
Read articleChatterjee, R; Ramos, E; Hoffman, M; VanWinkle, J; Martin, DR; Davis, TK; Hoshi, M; Hmiel, SP; Beck, A; Hruska, K; Coplen, D; Liapis, H; Mitra, R; Druley, T; Austin, P; Jain, S. Traditional and targeted exome sequencing reveals common, rare and novel functional deleterious variants in RET-signaling complex in a cohort of living US patients with urinary tract malformations. Human Genet. 2012 Nov;131(11):1725-38. PMID: 22729463
Read articleVallania, F; Ramos, E; Cresci, S; Mitra, RD; Druley, TE. Detection of rare genomic variants from pooled sequencing using SPLINTER. J Vis Exp. 2012 Jun;(64). pii: 3943. doi: 10.3791/3943. PMID: 22760212
Read articleVallania, FL; Druley, TE; Ramos, E; Wang, J; Borecki, I; Province, M; Mitra, RD. High-throughput discovery of rare insertions and deletions in large cohorts. Genome Res. 2010 Dec; 20(12):1711-1718. PMID: 21041413
Read articleRamos, EI; Garza, KM; Krauth-Siegel, RL; Bader, JO; Martinez, LE; Maldonado, RA. 2,3-Diphenyl-1,4-naphthoquinone: A Potential Chemotherapeutic Agent Against Trypanosoma cruzi. J Parasitology. 2009 Apr; 95(2):461-6. PMID: 18788881
Read article04 / PEOPLE & TRAINING
Assistant Professor
Department of Biological Sciences · UTEP
Dr. Ramos’ research combines cancer genomics, epigenetics, and bioinformatics. He trained in molecular genetics and genomics at Washington University in St. Louis, followed by postdoctoral work in cancer genomics at Baylor College of Medicine and genomics at TTUHSC El Paso.
ORCID: 0000-0001-9921-7944CURRENT LAB MEMBERS
Postdoctoral Researcher
lncRNA networks in immune cell exhaustion in triple-negative breast cancer
Research Associate
Functional roles of LINC01016 and ZMYND8 in estrogen-responsive breast cancer
Ph.D. student
Noncoding RNAs and cancer-testis antigens in liver disease and HCC
Ph.D. student
Integrative multi-omics of glioblastoma heterogeneity and therapy resistance
Ph.D. student
Single-cell genomic characterization of tumor and immune heterogeneity in triple-negative breast cancer
EDUCATION & ACADEMIC EXPERIENCE
Tenure-track faculty · Department of Biological Sciences
Texas Tech University Health Sciences Center El Paso · Molecular and Translational Medicine
Baylor College of Medicine · Pediatric Oncology
Washington University in St. Louis
University of Texas at El Paso · Minor in Chemistry
METHODS & EXPERTISE
Our work draws on RNA-seq, single-cell RNA-seq, exome and targeted sequencing, ChIP-seq, ATAC-seq, DNA methylation analysis, and multi-omics integration. Statistical analysis and machine learning help us connect molecular profiles with disease mechanisms.
SCIENTIFIC SERVICE
Dr. Enrique Ramos serves as a Review Editor in Epigenomics and Epigenetics and a Topic Editor for “Noncoding RNA-Mediated Chromatin Architecture in Immune Dysfunction” at Frontiers in Genetics. His reviewing experience includes PLOS ONE, BMC Cancer, PNAS NEXUS, Scientific Reports, Human Genomics, and the Computational and Structural Biotechnology Journal, among others.
He served on the Endocrine Society Early Career Special Interest Group Steering Committee from 2021 to 2024.
| Student | Current position |
|---|---|
| Arnav Joshi, Ph.D. | AI Analyst, Constellation |
| Dayo Shittu, M.S. | Computational Biology Researcher, National Institutes of Health |
| Axel Hidalgo, M.S. | MD/PhD student, Mayo Clinic |
| Andrew Parra, M.S. | Professional Research Assistant, University of Colorado Anschutz Medical Campus |
| Mason Bettes, B.S. | Medical student, TTUHSC El Paso |
| Laura A. Sanchez-Michael, M.S. | Ph.D. student in Biological Sciences, UTEP |
| Yifan Wang, Ph.D. | Data Science Analyst, El Paso Electric Company |
| Francis Owusu-Dampare, B.S. | Master’s student in Bioinformatics, UTEP |
| Dristi Adhikari, M.S. | — |
05 / FUNDING & HONORS
Selected funding, fellowships, and distinctions from Dr. Ramos’ academic record.
RESEARCH SUPPORT
Epigenetic Regulation of Spatial Gene Expression and Tumor Microenvironment in Triple-Negative Breast Cancer Among Hispanic Population.
RESEARCH INFRASTRUCTURE
Science and Technology Acquisition and Retention award.
SELECTED AWARDS & HONORS
First-Time Principal Investigator · UTEP Research & Innovation
Award to attend the AACR Annual Meeting
Endocrine Society Committee on Diversity and Inclusion session, and TTUHSC El Paso Research Symposium
Science of Cancer Health Disparities conference
Future Leaders Advancing Research in Endocrinology · Class of 2020
06 / NEWS
SEPTEMBER 2026
Barbara Yang’s review “RNA therapeutics: current status and future directions” is published in Signal Transduction and Targeted Therapy. Read the review
AUGUST 2026
Frida Delgadillo received the Jess Hay Endowment for Chancellor’s Graduate Student Research Fellowship. Congrats, Frida!
JULY 2026
Frida Delgadillo’s noncoding RNA–based molecular phenotyping of liver disease patients appears in Liver International Communications.
APRIL 2026
The lab presented work on lncRNA networks in immune cell exhaustion in TNBC, cancer-testis antigens in hepatocellular carcinoma, and the role of noncoding transcripts in glucose-dependent gene regulation in estrogen receptor-positive breast cancer.
JANUARY 2026
Dr. Enrique Ramos received UTEP Research & Innovation’s award for first-time principal investigators.
07 / CONNECT
Interested in collaborating or learning more about research and training in the lab? Connect with Dr. Ramos through the profiles below.
FIND US AT UTEP
Department of Biological Sciences
The University of Texas at El Paso
El Paso, Texas