Assistant Professor Ph.D. (2018) California Institute of Technology For an organism to exist and persist, it must robustly execute cellular and developmental programs despite routine genetic and environmental stressors. All metazoans use the highly conserved small RNA pathways, also called RNA interference (RNAi), to regulate their genomes in a precise, temporal, and cell-specific manner. Defects in RNAi can cause catastrophic gene mis-regulation, allow de-repressed transposons to wreak havoc on the genome, and disrupt many essential cellular and physiological processes, manifesting in humans as infertility, cancer & neurodegenerative disorders, amongst other diseases. However, at present, our understanding of the higher order mechanisms governing these complex epigenetic pathways remains rudimentary; despite knowing they are crucial to maintaining cellular homeostasis. My laboratory uses C. elegans as a model system to investigate the higher order molecular mechanisms that maintain appropriate small RNA-mediated gene regulation and heritable epigenetic signals, and we examine how disruption of small RNA pathway homeostasis impacts physiology during normal and stress conditions. Because small RNA pathway-mediated gene regulation is involved in many physiological processes and diseases, such as cancer and neurodegenerative disorders, our research has broad biomedical relevance. Current projects in the laboratory are addressing four core questions: (1) How do small RNA and chromatin modifying pathways work together to maintain genome stability? (2) What are the subcellular and processing fates of small RNA pathway-targeted transcripts, and how are these fates altered by genetic and environmental perturbations? (3) What are the regulatory mechanisms that control small RNA pathways? (4) What are the molecular and physiological consequences of disrupting small RNA pathway homeostasis? Current Grant Support National Science Foundation 2441124: "CAREER: Uncovering small RNA and chromatin modifying pathway interactions that regulate transcriptome homeostasis" NIH R35GM155429: “Understanding what regulates a regulator: the molecular basis for homeostatic small RNA-mediated gene regulation.” Rogers lab website Education Education: B.S. in Informatics with a Minor in Chemistry (2011) Baylor University Ph.D. in Molecular Biology and Biochemistry (2018) California Institute of Technology Research Research Areas: Molecular Genetics Genomics and Bioinformatics Developmental Biology Selected Publications Selected Publications: Saima Akhter*, Favour E. Nwose*, Ha Meem^, Trilotma Sen^, Alicia K. Rogers (2026) Echoes of the past: inheritance of gene silencing across generations. An educational primer for use with "A unified framework governing the establishment and maintenance of transgenerational epigenetic inheritance.". Genetics, iyag173. *co-first authors. ^equal contributors. Ha Meem and Alicia K. Rogers (2026) Sensor-mediated fine-tuning of siRNA levels is required for spermatogenic piRNA pathway function. BioRxiv, DOI: 0.64898/2026.03.20.713214 Neeka Mardani-Kamali and Alicia K. Rogers (2025) Bioinformatic identification of regulatory feedback motifs with RNAi pathways using multi-omics datasets. Methods in Enzymology, ISSN 0076-6879. Trilotma Sen, Cara McCormick, and Alicia K. Rogers (2024) Small RNA-mediated genetic switches coordinate ALG-3/4 small RNA pathway function. Nucleic Acids Research, 9;52(15):9431-9449. Alicia K. Rogers and Carolyn M. Phillips (2020) A small-RNA-mediated feedback loop maintains proper levels of 22G-siRNAs in C. elegans. Cell Reports, 33(3):108279. Alicia K. Rogers and Carolyn M. Phillips (2020) Disruption of the mutator complex triggers a low penetrance larval arrest phenotype. microPublication Biology, 2020:10.17912/micropub.biology.000252. Alicia K. Rogers and Carolyn M. Phillips (2020) RNAi pathways repress reprogramming of C. elegans germ cells during heat stress. Nucleic Acids Research, 48(8):4256-4273. Google Scholar Awards, Honors and Recognitions Of note: Term Member, American Cancer Society PF-Molecular Biology & Biochemistry (PF-MBB) Peer Review Committee (2026 - present) TAMEST Protégé, Texas Academy of Medicine, Engineering, Science and Technology (TAMEST) Annual Conference. (2023). The University of Texas System Rising STARS (Science and Technology Acquisition and Retention) Award, The University of Texas System. (2022-2024). American Cancer Society Postdoctoral Fellowship, American Cancer Society. (2021). National Science Foundation RNA 2021 Conference Award, National Science Foundation. (2021). California Institute of Technology Graduate Leadership Award, California Institute of Technology. (2018). Microsymposium Ph.D. Workshop Travel Award, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna, Austria. (2017). NSF Graduate Research Fellowship (GRFP), National Science Foundation. (2013-2016). NIH Cell and Molecular Biology Training Program (T32) Fellowship, California Institute of Technology. (2012-2013).
