Research

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.