Jafar S. Jabbari

The paper identifies SCAF4-CPA and KHDRBS1/SAM68 as key regulators of RNAPII termination under CDK12 inactivation, showing termination dynamics influence elongation rate and response to inhibition.

The paper uses long-read sequencing to map Drp1 transcript variants in human and mouse tissues, revealing tissue-specific expression and isoform-dependent mitochondrial fission activity.

TIRE-seq streamlines RNA-seq workflows by integrating mRNA purification into library preparation, improving efficiency and data quality in perturbation studies.

The paper introduces scRaCH-seq, a method for single-cell long-read sequencing that improves detection of isoform usage and mutations in targeted genes, demonstrating its application in CLL samples.

scPipe provides a preprocessing pipeline for single-cell ATAC-Seq and multi-modal data in R/Bioconductor, enabling quality control and downstream analysis.

The paper benchmarks long-read RNA-sequencing tools using synthetic data to evaluate isoform detection and differential expression analysis performance.

The paper presents a draft genome assembly of the Australian black tiger shrimp, revealing a fragmented IHHNV EVE sequence with implications for viral detection and RNAi mechanisms.

The paper develops FLT-seq and FLAMES to characterize full-length isoforms in single cells of human and mouse, identifying thousands of unannotated isoforms and linking them to functional modules and drug resistance mutations.

This study benchmarks 9 scRNA-seq preprocessing workflows, finding that while they vary in gene detection and quantification, downstream analysis with effective normalization and clustering methods leads to consistent clustering results.

The paper generates a human neural retina transcriptome atlas using single-cell RNA sequencing, identifying 18 cell types and revealing a novel role for MALAT1 in rod degeneration.

The paper benchmarks scRNA-seq analysis methods using synthetic datasets generated from mixed cancer cell lines, identifying methods that perform well across tasks like normalization, clustering, and integration.

The paper characterizes the transcriptome of human stem cell-derived retinal ganglion cells using single-cell RNA sequencing, identifying three subpopulations with varying maturity levels.