profile picture of Rodolfo Aramayo
  • Associate Professor
Research Areas
  • Biological Timing
  • Biological Resilience
  • Evolution
  • Synthetic Biology

Biography

Joined the Department in 1997

Associations:

Faculty of Genetics

The Master of Biotechnology Program

Research Interests

My current research primarily focuses on understanding the organization, distribution, interconnection, and comparison of information in Biological Systems. At the moment, I am trying to address the following questions:

Can we Develop computational algorithms to address the complexities of genome data?

We are currently studying different ways to correct Transcriptional Profiling estimation errors due to the presence of repetitive sequences in Eukaryotic genomes. We are also developing computational algorithms to identify different regions present in highly related genomes.

Can Digitalization of Genomic Information Simplify Genomic Analysis?

We are particularly intrigued by the prospect of simplifying (i.e., digitizing) the information present in DNA, RNA, and Proteins so as to simplify its manipulation and analysis. We are currently developing novel computational pipelines dedicated to detecting sequence variations within related genomes. We think that digitizing emerging genomic data will not only enable us to use this data effectively but also to integrate it into Artificial Intelligence, Data Clustering, and Image Recognition Algorithms, in ways not done before. We posit that this process of converting biological features into digital equivalents has the potential to simplify genomic information, making it easier to uncover previously unnoticed patterns through complex computational comparisons. This approach has already yielded promising results by revealing unexpected informational patterns across various organisms' chromosomes. We believe that it will streamline and enhance our ability to comprehend different cellular and organismal states. Moreover, it holds significant promise in revolutionizing our understanding of diseases, particularly Cancer and Metagenomics. This informational perspective also contributes to our comprehension of genome evolution, especially in the field of comparative genomics and microbial metagenomics.

Do Non-Coding RNAs regulate the interaction of Ribosomal RNAs and Ribosomal proteins?

Using Homo sapiens Next Generation Sequencing RNA data, we have recently detected the presence of a set on non-coding RNAs with homology to Ribosomal RNAs. We hypothesize that this set of non-coding RNAs interact with segments of Ribosomal RNAs so as to participate (by interfering or enhancing), the interaction of ribosomal proteins with the Ribosomal RNAs. If confirmed, this observation would reveal yet another level of translational regulation. It would also assign function to a large set of non-coding RNAs. In our view, this is a very important, and yet undisclosed, observation that has the potential of changing our current view of translational regulation in all organisms.

How are Sequence Variations Detected and Targeted for Silencing in Fungal Meiosis?

We employ the filamentous fungus Neurospora crassa as a model organism to uncover and comprehend the intricate molecular components responsible for sequence-based comparisons between homologous chromosomes, leading to the initiation of Meiotic Silencing, a phenomenon driven by RNA-mediated processes. Currently, our primary focus centers on the exploration of whether genes recognized for their significance in Meiotic Transvection/Silencing also contribute to the occurrence of Repeat Induced Point Mutation (RIP) phenomena.

Educational Background

  • B.Sc., 1982, University of Brasilia (Brasilia, Brazil), Molecular Biology
  • M.Sc., 1986, University of Brasilia (Brasilia, Brazil), Molecular Biology
  • Ph.D., 1992, University of Georgia, Genetics
  • Postdoctoral research, University of Wisconsin, Stanford University, Genetics.

Selected Electronic Publications

  1. Aramayo R. Taxonomy_Fasta_Headers_Python. In: https://doi.org/10.5281/zenodo.15216319, editor. Zenodo. v2025-04-14-1.0.1 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2025.
  2. Aramayo R. HeatMap_Tables_Python. In: https://doi.org/10.5281/zenodo.15214452, editor. Zenodo. v2025-04-14-1.0.3 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2025.
  3. Aramayo R. Transcripts_Plots_Python. In: https://doi.org/10.5281/zenodo.14962604, editor. Zenodo. v2025-03-03-1.0.2 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2025.
  4. Aramayo R. PepStats_Tables_Bash. In: https://doi.org/10.5281/zenodo.12209240, editor. Zenodo. v2024-06-21-1.0.5 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  5. Aramayo R. Fasta_Seq_Prepare_Bash. In: https://doi.org/10.5281/zenodo.12209223, editor. Zenodo. v2024-06-21-1.0.5 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  6. Aramayo R. Fasta_Seq_Plot_Bash. In: https://doi.org/10.5281/zenodo.12209220, editor. Zenodo. v2024-06-21-1.0.7 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  7. Aramayo R. Fasta_GFF3_Equalizer_Bash. In: https://doi.org/10.5281/zenodo.12209207, editor. Zenodo. v2024-06-21-1.0.2 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  8. Aramayo R. A re-analysis of an existing Drosophila melanogaster dataset reveals a new set of genes involved in post-mating response. In: https://doi.org/10.5281/zenodo.10928217, editor. Zenodo. v2024-04-04-1.0.4 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  9. Aramayo R. Assessing the Influence of Sequence Duplications and Genome Annotations on Transcriptional Profiling Measurements. In: https://doi.org/10.5281/zenodo.11122398, editor. Zenodo. v2024-05-06-1.0.0 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.
  10. Aramayo R. Busco_Plot. In: https://doi.org/10.5281/zenodo.10945686, editor. Zenodo. v2024-04-08-1.0.0 ed. Zenodo (CERN Data Centre & Invenio): CERN Data Centre & InvenioRDM; 2024.

Selected Peer-Reviewed Publications

  1. Aramayo R, Nan B. De Novo Assembly and Annotation of the Complete Genome Sequence of Myxococcus xanthus DZ2. Microbiol Resour Announc. 2022;11(5):e0107421. Epub 20220406. doi: 10.1128/mra.01074-21. PubMed PMID: 35384715; PMCID: PMC9119067.
  2. Maitra N, He C, Blank HM, Tsuchiya M, Schilling B, Kaeberlein M, Aramayo R, Kennedy BK, Polymenis M. Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity. Elife. 2020;9:e53127. Epub 20200520. doi: 10.7554/eLife.53127. PubMed PMID: 32432546; PMCID: PMC7263821.
  3. Stavrianakou M, Perez R, Wu C, Sachs MS, Aramayo R, Harlow M. Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ. BMC Genomics. 2017;18(1):611. Epub 20170814. doi: 10.1186/s12864-017-3890-4. PubMed PMID: 28806931; PMCID: PMC5557070.
  4. Clanton RM, Wu G, Akabani G, Aramayo R. Control of seizures by ketogenic diet-induced modulation of metabolic pathways. Amino Acids. 2017;49(1):1–20. Epub 20160928. doi: 10.1007/s00726-016-2336-7. PubMed PMID: 27683025.
  5. Aramayo R, Selker EU. Neurospora crassa, a model system for epigenetics research. Cold Spring Harb Perspect Biol. 2013;5(10):a017921. Epub 20131001. doi: 10.1101/cshperspect.a017921. PubMed PMID: 24086046; PMCID: PMC3783048.
  6. Lee DW, Millimaki R, Aramayo R. QIP, a component of the vegetative RNA silencing pathway, is essential for meiosis and suppresses meiotic silencing in Neurospora crassa. Genetics. 2010;186(1):127–33.
  7. Kelly WG, Aramayo R. Meiotic silencing and the epigenetics of sex. Chromosome Res. 2007;15(5):633–51. doi: 10.1007/s10577-007-1143-0. PubMed PMID: 17674151; PMCID: PMC4090689.
  8. Freitag M, Lee DW, Kothe GO, Pratt RJ, Aramayo R, Selker EU. DNA methylation is independent of RNA interference in Neurospora. Science. 2004;304(5679):1939–.
  9. Lee DW, Pratt RJ, McLaughlin M, Aramayo R. An argonaute-like protein is required for meiotic silencing. Genetics. 2003;164(2):821.
  10. Aramayo R, Metzenberg RL. Meiotic transvection in fungi. Cell. 1996;86(1):103–13. doi: 10.1016/s0092-8674(00)80081-1. PubMed PMID: 8689677.