Paul C. Blainey

Cross-feeding reshapes interactions between antibiotic stressors through metabolic feedbacks

The paper shows that cross-feeding between bacteria changes how antibiotic combinations affect growth, shifting interactions toward antagonism due to metabolic feedbacks.

Live-cell transcriptomics with engineered virus-like particles

This paper develops a live-cell transcriptomics method using engineered virus-like particles to capture dynamic gene expression without destroying cells.

Systematic functional genetic analysis of cell-substrate adhesion

This study identifies gene targets involved in cell-substrate adhesion through functional genetic analyses in human cells, revealing dynamic requirements and novel regulators.

Brieflow: An Integrated Computational Pipeline for High-Throughput Analysis of Optical Pooled Screening Data

Brieflow is a computational pipeline for analyzing optical pooled screening data, demonstrating its ability to recover biological modules missed by existing methods.

Stitch-seq: Scalable CRISPR gene expression response profiling

Stitch-seq enables high-throughput profiling of CRISPR perturbations and gene/protein expression in millions of cells without cell barcoding or extensive sequencing.

The one-week automated genome-wide optical pooled screen

The paper introduces OttoSeq, an automated optical pooled screen platform that completes a genome-wide cell painting screen in eight days, analyzing over 5 million cells across 21,732 gene knockouts.

Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution

The paper introduces LRAA, a framework for accurate isoform discovery and quantification in long-read RNA-seq data, outperforming existing methods across multiple benchmarks.

Deep mapping of the TCR-antigen interface using pMHC-pseudotyped viruses and yeast display

The paper introduces VelociRAPTR, a method to map TCR-antigen interactions by combining yeast-displayed TCR libraries with pMHC-displaying virus-like particles, revealing biased recognition patterns and enabling TCR engineering.

Single-cell image-based genetic screens systematically identify regulators of Ebola virus subcellular infection dynamics

This study uses single-cell image-based CRISPR screens to identify host factors regulating Ebola virus infection, revealing new therapeutic targets like UQCRB and STRAP.

Bacterial peptide deformylase inhibitors induce prophages in competitors

The paper shows that a metabolite from Vibrio ordalii induces prophages in competing Vibrio species by inhibiting peptide deformylase, enhancing competitive advantage through prophage activation.

Massively parallel combination screen reveals small molecule sensitization of antibiotic-resistant Gram-negative ESKAPE pathogens

This study uses high-throughput screening to identify small molecules that enhance antibiotic efficacy against multidrug-resistant Gram-negative bacteria.

Heterochromatin fidelity is a therapeutic vulnerability in lymphoma and other human cancers

The paper identifies KDM4 demethylase inhibition as a therapeutic strategy for lymphoma and other cancers by rewiring heterochromatin and inducing DNA damage.

A genome-wide atlas of human cell morphology

The paper presents a genome-wide perturbation atlas using CRISPR-Cas9 knockouts to link genes to cellular phenotypes, identifying TMEM251/LYSET as a Golgi-resident protein involved in lysosomal enzyme trafficking.

Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening

The paper identifies regulators of STING trafficking through genome-wide screening and characterizes their functional impact on STING signaling.

Systematic deconstruction of myeloid cell signaling in tuberculosis granulomas reveals IFN-γ, TGF-β, and time are associated with conserved myeloid diversity

This study uses multi-omics approaches to analyze myeloid cell diversity in TB granulomas and identifies IFN-γ, TGF-β, and time as factors driving macrophage diversity.

CROPseq-multi: a universal solution for multiplexed perturbation in high-content pooled CRISPR screens

CROPseq-multi enables multiplexed CRISPR perturbations across various screening methods with improved barcode detection and compatibility.

De novo mutations mediate phenotypic switching in an opportunistic human lung pathogen

This study shows that de novo mutations in Burkholderia dolosa cause phenotypic switching, with O-antigen loss increasing immune cell uptake but reducing lung competitiveness, depending on infection duration and tissue localization.

Programmable multi-kilobase RNA editing using CRISPR-mediated trans-splicing

Splice Editing uses CRISPR-mediated trans-splicing to correct large RNA segments in human cells, enabling efficient and specific RNA and protein correction without DNA mutagenesis.

High-throughput RNA isoform sequencing using programmable cDNA concatenation

This paper introduces MAS-ISO-seq, a method to boost throughput of long-read RNA sequencing for isoform discovery, showing improved detection of differentially spliced genes and cell clustering in T cells.

Compressed phenotypic screens for complex multicellular models and high-content assays

The paper introduces a method to compress phenotypic screens using computational deconvolution, demonstrating increased efficiency and applicability to complex multicellular models.

Designing viral diagnostics with model-based optimization

This paper designs viral diagnostics using a model-based optimization approach, achieving higher sensitivity and specificity across viral genomic variation.

NickSeq for genome-wide strand-specific identification of DNA single-strand break sites with single nucleotide resolution

NickSeq identifies DNA single-strand break sites with single nucleotide resolution, enabling analysis of nicking activity in genome editing tools and DNA damage.

Somatic Truth Data from Cell Lineage

The paper introduces a benchmark dataset of validated somatic mutations derived from cell lineage, providing a large collection of true somatic variation for use in mutation discovery pipelines.

Nucleic Acid Cleavage with a Hyperthermophilic Cas9 from an Unculturable Ignavibacterium

The paper identifies IgnaviCas9, a hyperthermophilic Cas9 from an unculturable Ignavibacterium, which functions at higher temperatures than existing Cas9 variants and is applied in RNA-seq library preparation.

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.

A Bayesian model of acquisition and clearance of bacterial colonization incorporating within-host variation

The paper presents a Bayesian model to estimate bacterial acquisition and clearance rates by accounting for within-host genetic variation and sampling intervals, validated using simulations and applied to MRSA isolates.

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.