David Feldman

A Pooled Cell Painting CRISPR Screening Platform Enables de novo Inference of Gene Function by Self-supervised Deep Learning

This paper introduces a pooled CRISPR screening platform combined with self-supervised deep learning to infer gene function from morphological phenotypes without target-specific biomarkers.

Targeting peptide-MHC complexes with designed T cell receptors and antibodies

This paper introduces ADAPT, a deep learning framework for designing TCRs and antibodies that bind to specific pMHC targets, validated through cryo-EM structures and functional testing.

De novo design of miniprotein agonists and antagonists targeting G protein-coupled receptors

This paper presents computational methods for designing GPCR-binding miniproteins and validates them through high-throughput screening, producing agonists and antagonists for multiple GPCRs.

Massively parallel assessment of designed protein solution properties using mass spectrometry and peptide barcoding

The paper develops a method to assess solution properties of designed proteins using mass spectrometry and peptide barcoding, enabling analysis of large protein libraries.

LAMP-Seq: Population-Scale COVID-19 Diagnostics Using Combinatorial Barcoding

LAMP-Seq combines three-step isothermal RT-LAMP amplification with combinatorial barcoding to pool and sequence SARS-CoV-2 clinical samples en masse for scalable diagnostics.

Shuffle-Seq: En masse combinatorial encoding for n-way genetic interaction screens

Shuffle-Seq enables large-scale genetic interaction screens by leveraging barcode co-inheritance in dividing cells, applied to study drug resistance mechanisms in melanoma.

Pooled optical screens in human cells

The paper introduces an optical method to link genetic perturbations with phenotypic outcomes in a pooled setting, identifying novel regulators of immune responses.

CloneRetriever: retrieval of rare clones from heterogeneous cell populations

CloneRetriever identifies and retrieves rare clones from heterogeneous populations to study clonal fitness and selection mechanisms.

Mass Mortality of Wood Frogs (Rana sylvatica) in the Ozark National Forest: Is it Acid Rain?

The paper reports a mass mortality event of wood frogs and other amphibians in the Ozark National Forest without identifying a definitive cause.

Lentiviral co-packaging mitigates the effects of intermolecular recombination and multiple integrations in pooled genetic screens

Diluting lentiviral perturbation libraries with a carrier plasmid during packaging prevents intermolecular recombination and multiple integrations in pooled screens, although viral titer drops by 100-fold.