Ken Sugino

The Phantom of the PCR: detection and consequences of spurious UMIs in mainstream RNA sequencing

The paper identifies and quantifies spurious UMIs generated during PCR in RNA sequencing, showing they inflate counts and distort fold-changes, and proposes experimental prevention.

Omega-seq: ultra-low-background RNA sequencing with faithful molecular counting and precise transcript-end capture

USER-excisable uracil TSOs, a uracil-intolerant polymerase and excess primer confine UMI incorporation to reverse transcription, minimizing background and UMI inflation; a separate Omega-shaped dT primer captures stranded transcript ends.

Dense reconstruction of elongated cell lineages: overcoming suboptimum lineage encoding and sparse cell sampling

The paper develops a method to reconstruct dense neuronal lineages in Drosophila despite sparse sampling and suboptimal lineage encoding.

Conservation and Divergence of Related Neuronal Lineages in the Drosophila Central Brain

The paper maps Drosophila central brain lineages to show how lineage identity and temporal patterning drive neuronal diversity and complexity.

CAMIO for deletion analysis of endogenous DNA sequences in multicellular organisms

CAMIO enables high-throughput deletion analysis of native DNA sequences in multicellular organisms by using CRISPR to generate diverse mutations in offspring.

Robust Reconstruction of CRISPR and Tumor Lineage Using Depth Metrics

The paper introduces a robust method for reconstructing CRISPR and tumor lineages using depth metrics and improves upon existing metrics for lineage reconstruction.

Theoretical modeling on CRISPR-coded cell lineages: efficient encoding and optimal reconstruction

This paper analyzes CRISPR-based cell lineage encoding and reconstruction, finding hierarchical clustering with shared edits is optimal and proposing improved encoding methods to increase trackable depth.

The Transcriptional Logic of Mammalian Neuronal Diversity

The paper identifies homeobox transcription factors as key drivers of neuronal diversity through improved expression metrics and links long genes to regulatory elements and mobile elements.

Stem cell intrinsic, Seven-up-triggered temporal factor gradients diversify intermediate neural progenitors

The paper identifies temporal RNA-binding protein gradients in Drosophila neuroblasts that regulate intermediate neural progenitor fate.