Nabeel Ahmed

The paper identifies inherited intergenic lncRNAs in zebrafish embryos that function as enhancer-associated regulators during maternal-to-zygotic transition.

mRNAfold improves mRNA design by co-optimizing stability, local structure, and codon choice, showing better in-solution stability and complex effects on protein production.

The paper introduces MutSigCVsyn, an algorithm to identify synonymous cancer drivers by accounting for mutational heterogeneity, and identifies 30 novel synonymous drivers in cancer whole-genome sequences.

The paper identifies amino acid pairs at the ribosome's P- and A-sites that predictably and causally modulate translation-elongation rates in yeast.

The paper develops chemical kinetic methods to measure translation initiation, elongation, and codon-specific rates from ribosome profiling data, finding significant variability in codon translation rates.

This paper uses Integer Programming to accurately identify A-site locations on ribosome-protected mRNA fragments from Ribo-Seq data, improving signal-to-noise ratio by utilizing a wider range of fragment sizes.