I am from New Jersey. New Yorkers may think they have better bagels and pizza, but they’re wrong.
I graduated from Gettysburg College in 2016 with a B.S. in biochemistry and molecular biology. As a first-generation college student, I got my initial exposure to scientific research in the PhagesRock lab under the mentorship of professors Véronique Delesalle and Greg Krukonis.
After undergrad, I enrolled at Cornell University as a graduate student in the field of Genetics, Genomics & Development, and shortly thereafter joined the Brito Lab in the Meinig School of Biomedical Engineering. My graduate work involved the application of different sequencing techniques to understand the DNA and RNA content of the human gut microbiome.
I defended my thesis in April 2022, titled Metagenomic Methods to Investigate Mobile Element Context and Nascent Transcription in the Human Gut Microbiome.
Currently, I am postdoc with Paul Turner in the Center for Phage Biology and Therapy at Yale.
I am interested in bacterial genomics, host-microbe interactions, and all things bacteriophage. My training is in molecular biology with a focus on DNA and RNA sequencing of microbiomes. While much of my time is spent at the bench, I am proficient in R, Bash, and many Linux-based sequencing analysis tools.
In 2020, I co-authored a paper with Dr. Alyssa Kent on the use of proximity ligation sequencing (commonly called Hi-C) to resolve mobile element carriage in the gut microbiomes of cancer patients. We found that Hi-C could detect the putative transfer of multi-drug resistance genes between commensal microbes and pathogens within individual patients through time. You can read more about it in Ilana’s Behind the Paper highlight or in my Twitter thread:
Excited for the publication of my first paper as a PhD student in the Brito Lab @ilanabrito123 @CornellBME @NatureComms: "Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C" https://t.co/4ZpBtGDA8m— Albert Vill (@_AlbertVill) September 1, 2020
In 2022, I wrote a manuscript on the application of precision run-on sequencing to assess nascent transcription in bacteria. When applied to human stool samples, PRO-seq captures transcription at metagenomic loci that are co-transcriptionally processed, including tRNAs and CRISPR arrays. The manuscript is available as a preprint on bioRxiv.
My favorite result: PRO-seq captures active transcription across #CRISPR arrays, and patterns suggest that endonuclease processing of crRNAs is concurrent with pre-crRNA transcription pic.twitter.com/vS1tbBI94x— Albert Vill (@_AlbertVill) April 28, 2022
The Brito Lab is continuing to innovate in the microbiome mobile gene space with techniques like OIL-PCR and GCN models for HGT prediction.
I love R and I appreciate well-documented bioinformatics tools. When I write a handy piece of code, I like to optimize it for ease-of-use. Please see my code & resources page for descriptions of tools and scripts that I’ve developed as part of my ongoing research in metagenomics and bacterial genetics.
I’m a regular contributor on Biology Stack Exchange. Below are some of my favorite questions I’ve answered. Come ask more!
- What are the limitations of 16S rRNA sequencing?
- Does direction relative to origin of replication matter on small plasmids?
- Which proteins are part of the most different protein complexes?
- What fraction of bacterial proteins are membrane bound?
- What are the reasons for using oligo-dT instead of oligo-U to isolate mRNAs?
- Will all bacteria become resistant against all antibiotics in the long term?
- What are the considerations for studying population genetics of bacterial pan-genomes?