My name is Federico Baldini and I am a Senior Bioinformatician at The Bioinformatics for Next Generation Sequencing (BiNGS) core facility of the Ichan School of Medicine at Mount Sinai (New York City). I am very passionate about computational biology, and I like to combine different bioinformatic approaches to process and analyze human and human-derived data aiming at solving complex biological problems.

Scientific Path

Before joining BiNGS in April 2024, I obtained a MSc in Cellular and Molecular Biology from The University of Florence in 2015, followed by a PhD in Systems Biology from LCSB at the University of Luxembourg in 2019. My PhD dissertation focused on developing new computational modeling methods integrating metabolic modeling and microbial genomics analysis to understand the role of the human gut microbiome in complex diseases (Baldini et al. Bioinformatics 2019; Baldini et al. JOSS 2024). I applied these methods to study Parkinson’s Disease (Baldini et al. BMC Biology 2020; Hertel et al. Cell Reports 2019), and gastrointestinal diseases such as Coeliac Disease, and Inflammatory Bowel Disease (Heinken et al. Microbiome 2019).

After my PhD, I held a Postdoctoral Research Scientist position in the Department of Systems Biology at Columbia University for four years (2020-2024). During my postdoc, I used genome-scale metabolic models, statistical and machine learning methods to explore multi-omics data from human samples elucidating the role of the human microbiome in various human conditions and cancer therapy response. Specifically, I have been studying metabolic and microbial alterations in Preterm Birth (Baldini et al., Nature Microbiology 2024), Adenocarcinoma (Solfisburg et al. Cancer Epidemiol Biomarkers Prev 2024) as well as microbiome and gut metabolome associations with lymphoma patients’ survival and treatment response (Baldini et al., in preparation).

During my PhD and Postdoctoral training, I acquired a deep expertise in microbial genomics analysis (16S rRNA gene sequencing, metagenomics), metabolic modeling (Flux Balance Analysis), metabolomics, data analysis, and machine learning.

Currently, at BiNGS, I am building a strong foundation in human genomics analysis such as transcriptomics (i.e., Bulk RNA-seq, Single Cell RNA-seq) and epigenomics (i.e., ATAC sequencing, Micro-C) analysis. I apply these tools to study different cancer and cancer-related conditions such as human melanoma.

Scientific Vision

I am a firm believer in equal opportunities, and I am convinced that science should be accessible to everyone. If you are studying biology or bioinformatics, and maybe thinking about a possible career in science, please don’t hesitate to reach out! I am still everyday learning something new about this beautiful scientific world, but I love to share my experience and network.

Non-scientific Interests

Outside science I have many other interests. I spend my free time hanging out with friends as well as cooking, practicing sports, reading books, and playing music. I love skiing and playing volleyball as well as playing the clarinet. I also like motorcycles which I have been riding for long and short distance trips. After exploring the beatuful region of Tuscany during my studies in Italy riding my 650 cc motorcycle, currently, with the help of my partner, I am exploring the New York State region!

Getting in Touch

As mentioned before, I love to network and meet other scientists. If you want to get in touch feel free to send me an email at federico.baldini@mssm.edu or to connect and send me a message on LinkedIn.