About
I'm Fatima, a computational microbiologist at Medical College of Wisconsin. For the past five years I've studied how the gut microbiome can shape host disease or health in a variety of contexts (antipsychotic-induced weight gain, long COVID, bariatric surgery). Along the way I've built open-source bioinformatic tools, contributed to four peer-reviewed publications, and helped identify a weight loss bacterial metabolite. I'm relocating to the NY/NJ area and actively exploring roles in computational biology, bioinformatics, and life sciences consulting.
Skills
Programming Languages:
Amplicon & Metagenomics:
Sequence Alignment & Protein Prediction
R/Github/Bioconductor Packages:
Projects
GERMINATE
HMM-based pipeline for building non-redundant protein gene catalogs from seed sequences. Takes curated seed sequences, builds a statistical fingerprint, and searches it against millions of bacterial proteins to identify functional genes of interest at scale.
Bash & Python
HMMER
CD-HIT
SEEDscraper
Webscraper to automate extracting proteins seed sequences from UniProtKB database using query entries. Stores concatenated sequences into fasta file and SQL database.
Python & SQL
Publications
Published online: 07 Apr 2025
Reutericyclin, a specialized metabolite of Limosilactobacillus reuteri, mitigates risperidone-induced weight gain in mice
Identification of specialized metabolite, reutericyclin, produced by L. reuteri as a potential probiotic to restore energy balance induced by risperidone and to promote leanness.
Published online: 22 May 2025
Reutericyclin mitigates risperidone-induced suppression of anaerobic energy expenditure.
Reutericyclin treatment shown to enhance gut microbial fermentation, deflecting risperidone-induced weight gain through modulation of energy expenditure.
Published online: 07 Apr 2025
Gut Microbiota and Neurovascular Patterns in Amnestic Mild Cognitive Impairment.
Interplay between neurovascular function in neurodegeneration and the gut microbiome.
Published online: 22 Aug 2025
Gut microbiome and bile acid changes after male rodent sleeve gastrectomy: what comes first?
Sleeve gastrectomy-induced alterations in bile acid composition and gut microbiome.