Julia Montague at GalSeq, Milan
- Post by: fantom
- 29 April 2025
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Introduction
Ciao, I’m Julia! I’m originally from Philadelphia, USA, but my academic journey has taken me across the globe. I earned a Bachelor of Science in Biology from The Evergreen State College in Olympia, WA. Later, I completed a Master of Science in Molecular Biology and Evolution from Kiel University in Germany, where my thesis focused on the role of epigenetics in inflammatory disease. Now, I’m an MSCA fellow in the FANTOM doctoral network at the University of Milano-Bicocca in Monza, Italy. My local PhD program is called DIMET—Doctorate in Molecular and Translational Medicine.
My doctoral research focuses on drug-tolerant persister cells (DTPs) and drug resistance mechanisms in ALK+ anaplastic large cell lymphoma (ALCL) and other ALK+ malignancies, such as non-small cell lung cancer (NSCLC). By modeling drug persistence in vitro and using a multiomics approach—integrating RNA sequencing (RNA-seq) with epigenomic data—I aim to characterize the regulatory mechanisms of DTPs. Additionally, I am utilizing whole-genome CRISPR knockout screening to profile the “Resistome” of ALK-driven cancers. With these methodologies, I hope to discover new mechanisms of tyrosine kinase inhibitor (TKI) therapy resistance and contribute to the improvement of patient outcomes. I’m especially interested in cancer evolution and how bioinformatics approaches can help uncover hidden patterns in complex datasets.
Outside of the lab, I love hiking and biking through the beautiful landscape of Northern Italy. I also enjoy cooking and often experiment with a variety of cuisines inspired by the places I’ve lived in and traveled to. With the rest of my free time, I’m learning Italian and enjoy unwinding with a good book.
Galseq Secondment
During my secondment at GalSeq, a genomics company in Milan that specializes in next-generation sequencing (NGS) technologies, I learned how to prepare and sequence RNA-seq and PCR amplicon libraries. It was a great hands-on opportunity to learn about Illumina-based NGS workflows and pick up library prep best practices. Furthermore, I developed skills in nucleic acid purification and analytical steps using automated electrophoresis. I gained a solid understanding of how high-quality sequencing data is generated, which has helped me to bridge my understanding between the wet lab side of an omics-project and the downstream computational analysis. Back in the lab at UNIMIB, I analyzed the data mostly using open-source bioinformatics tools, but also did some custom scripting for quality control and visualization. I wrote pipelines for genome alignment and read counting, and performed downstream analyses including differential gene expression (DGE), gene set enrichment (GSEA), ligand-receptor binding, gene module, and negative/positive CRISPR screening enrichment using popular tools like DESeq2, clusterProfiler, BulkSignalR, WGCNA, MAGeCK, and others. Along the way, I refined my coding abilities in R and Python. The output of this secondment will directly contribute to the progress of my FANTOM projects on drug-tolerant persister cells in ALK+ ALCL and whole-genome CRISPR knockout screening of other ALK+ malignancies.
