Pardis Christine Sabeti

This study identifies eltrombopag olamine and quercetin as CCHFV entry inhibitors using a BSL-2 pseudotype screening platform validated against authentic CCHFV under BSL-4 conditions.

This study uses spatial transcriptomics to show that aging disrupts spatial and temporal coordination of folliculogenesis in mouse ovaries, leading to tissue disorganization and reproductive decline.

This paper develops a CRISPR-based assay for rapid detection of cefixime resistance in Neisseria gonorrhoeae by analyzing penA gene mosaicism.

This study functionally characterizes 221,412 trait-associated variants using MPRA in 5 cell types, identifying 12,025 regulatory variants and revealing widespread epistasis and non-TF mechanisms.

This paper designs an mRNA-LNP vaccine by integrating RNA, lipid, and antigen engineering to achieve 90% protection in a murine model.

The paper introduces TCAT, a pipeline to annotate T-cell GEPs, identifying 46 reproducible programs across diverse tissues and diseases.

This study uses Massively Parallel Ribosome Profiling to identify thousands of viral ORFs, including non-canonical ones, and shows their impact on HLA-I peptides and protein synthesis regulation.

This study introduces MPAC, a machine learning model that predicts the cis-regulatory impact of non-coding variants, demonstrating its accuracy across diverse applications and datasets.

Delphy provides a fast, scalable Bayesian phylogenetic analysis tool for outbreak tracking, achieving 1,000x speedups while maintaining state-of-the-art accuracy.

This study uses long-read assemblies to show that genetic modules across multiple plasmids organize Borrelia burgdorferi strain variation and influence virulence in Lyme disease.

This paper designs artificial CRISPR-Cas13a guide RNAs using model-directed algorithms, showing improved sensitivity and variant discrimination in nucleic acid detection.

This paper designs synthetic cis-regulatory elements (CREs) that outperform natural ones in driving cell type-specific gene expression using deep learning and experimental validation.

TOGA integrates gene annotation and orthology inference across hundreds of genomes, improving ortholog detection and creating large comparative gene resources.

A machine learning approach identifies enhancer-phenotype associations across mammals, revealing links to brain size and behavior evolution.

The paper curates TE content in 248 mammalian genomes, finding trends in recent TE accumulation and associations with dietary habits.

A 240-species placental mammal alignment resolves constraint to single bases, estimating at least 10.7% of the human genome is constrained, with 48.5% of constrained bases unannotated.

The paper identifies bats as a hotspot for horizontal transfer of DNA transposons, finding over 200 putative elements and shared transposons across mammals and reptiles.

The paper identifies three regulatory variants associated with IVD expression and linked to GWAS signals, showing synergistic and opposing effects through functional experiments.

The paper reports 109 non-coding CRISPR screens analyzing 13.3Mb of the genome, identifies CRE-gene links, and provides guidelines and tools for screening non-coding regulatory elements.

This paper designs viral diagnostics using a model-based optimization approach, achieving higher sensitivity and specificity across viral genomic variation.

This study profiles lncRNA expression in single cells during Ebola virus infection in vivo, revealing cell-type specific changes and potential roles in immune response and viral hijacking.

Fine-mapping 148 complex traits in three biobanks with combined n = 811,261 yields 4,518 causal variant-trait pairs, 285 of them repeating in more than one population.

The paper identifies causal 3'UTR variants linked to human disease and evolution using a new high-throughput assay and functional analysis.

This study uses metagenomic sequencing to detect pathogens in CNS infections, identifying novel pathogens and improving detection methods.

The paper introduces DNA spike-ins to detect contamination in SARS-CoV-2 amplicon-based sequencing and demonstrates their utility in a real-world outbreak investigation.

This study creates a single-cell and spatial atlas of autopsy tissues from COVID-19 patients, revealing altered cellular responses and potential therapeutic targets.

This paper develops CRISPR-Cas13a-based diagnostics for real-time detection of Ebola and Lassa viruses in field settings, demonstrating sensitivity and usability in clinical samples.

HCR-FlowFISH identifies cis-regulatory elements and their target genes by quantifying gene expression changes after CRISPR perturbations, using >270,000 perturbations to detect CREs for multiple genes.

A machine-learning design pipeline produced CRISPR-Cas13 detection assays for 67 viral taxa; the best of 4 screened SARS-CoV-2 designs reached 10 copies/μl on synthetic RNA.

The paper uses metagenomic sequencing to identify a yellow fever outbreak in Edo State, Nigeria, from undiagnosed fever cases.