Giacomo Marino

Full Stack Developer & Bioinformatician

I am a full stack developer and bioinformatician with a passion for data science and machine learning. I am currently working as a Bioinformatics Software Engineer at the Ma'ayan Laboratory at the Ichan School of Medicine at Mount Sinai, where I am involved in development of web severs and bioinformatic tools. I graduated from Brown University in 2022 with a ScB in Neuroscience & AB in Computer Science. I am particularily interested in the intersection of neuroscience and computer science, and the use of computational methods to accelerate biological discovery. Here is one of my recent highlighted projects:

Typescript, PL/pgSQL, PostGraphile, Rust, Python, Next.js, TailwindCSS, Docker

Rummageo

Automatically generated signatures from GEO

The Gene Expression Omnibus (GEO) is a major open biomedical research repository for transcriptomics and other omics datasets. It currently contains millions of gene expression samples from tens of thousands of studies collected by many biomedical research laboratories from around the world. While users of the GEO repository can search the metadata describing studies and samples for locating relevant studies, there is currently no method or resource that facilitates global search of GEO at the data level. To address this shortcoming, we developed Rummageo, a webserver application that enables gene expression signature search against all human and mouse RNA-seq studies deposited into GEO. To enable such a search engine, we performed offline automatic identification of conditions from uniformly aligned GEO studies available from ARCHS4, and then computed differential expression signatures to extract gene sets from these signatures. In total, Rummageo currently contains 135,264 human and 158,062 mouse gene sets from 23,395 GEO studies. Overall, Rummagene provides an unprecedented resource for the biomedical research community enabling hypotheses generation for many future studies.