Max Frank

The paper presents a multimodal perturbation atlas using CRISPR knockouts in A549 cells, combining microscopy, phase imaging, and scRNA-seq to assess phenotypic resolution.

RNAquarium integrates zebrafish and metatranscriptomic data to identify viral drivers of transcriptomic states and support foundation-model training.

DanioDecima improves gene expression prediction in zebrafish by transferring knowledge from human and mouse models, enhancing correlations and generating synthetic promoters with expected lineage-specific motifs.

The paper presents Zebrahub-Multiome, a single-cell multiomic atlas of zebrafish embryogenesis, revealing gene regulatory network dynamics and cis-regulatory elements across developmental stages.

This paper introduces a data-driven method to detect functional proteoform groups from bottom-up proteomic datasets, identifying state-specific proteoform groups linked to molecular mechanisms.

The paper introduces a new DIA scan mode that improves peptide precursor ion sampling and identification specificity using ion mobility, achieving high proteome coverage and accuracy.

The paper quantifies proteome assembly state changes during mitosis using SEC-SWATH-MS and identifies new mitotic complex disassembly events.

The paper introduces a method to quantify protein complexes using SEC-SWATH-MS and identifies 462 complexes from HEK293 cells.

This study quantifies genomic, proteomic, and phenotypic variability in HeLa cells across laboratories and passages, revealing implications for research reproducibility.