The vTR preprint is out!
On September 2, 2025, a study investigating the functions of viral transcriptional regulators (vTRs) was posted on bioRxiv. This large-scale effort, spearheaded by Jaice, systematically explores how vTRs reprogram host gene expression across multiple modalities, including transcriptomics, protein–DNA interactions, protein–protein interactions, and transcriptional activity assays. Read the full preprint here: https://www.biorxiv.org/content/10.64898/2025.12.01.691387v1
The dsDNA virus preprint is out!
On July 20, 2025, work by Tommy H. Taslim and Joseph A. Finkelberg was published on bioRxiv. This study expands the known landscape of cis-regulatory elements (CREs) in human-infecting dsDNA viruses by approximately 13-fold and provides new insights into how CREs function within compact viral genomes. Read the full preprint here: https://doi.org/10.1101/2025.07.20.665756
The lab presents research at Cold Spring Harbor Laboratory!
Benedetta, Berkay, Yousry and Tommy spent three days in Cold Spring Harbor Laboratory, where they attended the Systems Biology: Global regulation of gene expression meeting in March 2026, where they presented posters on their work characterizing viral cis-regulatory elements and silencers. Juan also gave a talk titled “Viral transcriptional regulators extensively rewire host pathways through diverse mechanisms”.
Benedetta wins Genome Science Institute Grand Research Pilot Prize!
After being selected for a Trainee Lightning Talk at the GSI 17th Annual Research Symposium, Benedetta was awarded the Grand Research Pilot Prize, which supports her research through genomic research reagents. Berkay, Jaice, Yousry, and Tommy also presented posters showcasing their work.
Mohamed Yousry ElSadec Awarded NIH T32 Fellowship in Synthetic Biology & Biotechnology (SB2)
Mohamed Yousry ElSadec has been awarded an NIH T32 training grant through the Synthetic Biology and Biotechnology (SB2) program at Boston University. This competitive fellowship will support his research for 21 months and includes a full-time industry internship.
Devlin publishes paper "MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models" in Genome Biology!
Genome-scale metabolic models (GSMMs) are used to predict metabolic fluxes, with applications ranging from identifying novel drug targets...
Clarissa and Anna publish a paper titled "Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms" in Molecular Cell!
Most human TF genes encode multiple isoforms differing in DNA-binding domains, effector domains, or other protein regions. The extent to...
Congratulations Dr. Patalano!
Sam successfully defended her dissertation titled, “Use of High-throughput Screening Approaches to Delineate Immune and Pluripotency Gene...
Benedetta publishes a review “Applications of high-throughput reporter assays to gene regulation studies” in Current Opinion in Structural Biology!
In this review, we discuss the different ways that high-throughput reporter assays, such as MPRAs and STARR-seq, can be employed to...
ICARus: a pipeline to extract robust gene expression signatures from transcriptome datasets
We developed the R package ICARus, designed to streamline the application of independent component analysis (ICA) and extraction of...