Nature Search

Transcriptome-wide analysis of differential expression in perturbation atlases

Transcriptome-wide analysis of differential expression (TRADE) is a broadly applicable tool for characterizing patterns of differential expression across the genome.

Ajay Nadig
Joseph M. Replogle
Luke J. O’Connor
Research21 Apr 2025
Nature Genetics

Volume: 57, P: 1228-1237
Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

Sunshine et al. use Perturb-seq to study host dependencies of SARS-CoV-2 by inactivating host factors genetically and monitoring the course of infection by single-cell sequencing, characterizing global host phenotypes. They identified NFKBIA, EIF4E2 and EIF4H as strong host dependency factors.

Sara Sunshine
Andreas S. Puschnik
Marco Y. Hein
ResearchOpen Access06 Oct 2023
Nature Communications

Volume: 14, P: 1-13
Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

Aging can lead to cognitive decline associated with neural pathology and Alzheimer's disease (AD). Here the authors scan the methylation status of CpGs across the entire genome of brain samples from aged subjects in an epigenome-wide association study (EWAS). Several loci, including ANK1, were associated with AD pathology, gene expression and AD genetic risk networks.

Philip L De Jager
Gyan Srivastava
David A Bennett
Research17 Aug 2014
Nature Neuroscience

Volume: 17, P: 1156-1163
Author Correction: Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning

Luke W. Koblan
Mandana Arbab
David R. Liu
Amendments and Corrections18 Oct 2023
Nature Biotechnology

Volume: 41, P: 1655
scPerturb: harmonized single-cell perturbation data

scPerturb is an information resource for single-cell perturbation data analysis and comparison.

Stefan Peidli
Tessa D. Green
Chris Sander
Research26 Jan 2024
Nature Methods

Volume: 21, P: 531-540
Microfluidics-free single-cell genomics with templated emulsification

A microfluidics-free, scalable single-cell RNA-sequencing method produces high-quality transcriptomes.

Iain C. Clark
Kristina M. Fontanez
Adam R. Abate
ResearchOpen Access06 Mar 2023
Nature Biotechnology

Volume: 41, P: 1557-1566
Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning

Efficiency of transversion base editing is increased by matching a set of base editors to target sequences.

Luke W. Koblan
Mandana Arbab
David R. Liu
Research28 Jun 2021
Nature Biotechnology

Volume: 39, P: 1414-1425
Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

Single-cell CRISPR screens are readily multiplexed and scaled with an improved version of Perturb-seq.

Joseph M. Replogle
Thomas M. Norman
Britt Adamson
Research30 Mar 2020
Nature Biotechnology

Volume: 38, P: 954-961
CD33 modulates TREM2: convergence of Alzheimer loci

This protein quantitative trait analysis in monocytes evaluates cross-talk between Alzheimer risk loci and finds that the NME8 locus influences PTK2B, the CD33 risk allele leads to greater TREM2 expression, and the TREM1 risk allele is associated with a decreased TREM1/TREM2 ratio.

Gail Chan
Charles C White
Philip L De Jager
Research28 Sept 2015
Nature Neuroscience

Volume: 18, P: 1556-1558
Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

Timothy Vyse and colleagues report the results of a large-scale association study of systemic lupus erythematosus (SLE). They identify ten new susceptibility loci and implicate aberrant regulation of innate and adaptive immunity genes in disease pathogenesis.

James Bentham
David L Morris
Timothy J Vyse
Research26 Oct 2015
Nature Genetics

Volume: 47, P: 1457-1464

Search

Transcriptome-wide analysis of differential expression in perturbation atlases

Systematic functional interrogation of SARS-CoV-2 host factors using Perturb-seq

Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci

Author Correction: Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning

scPerturb: harmonized single-cell perturbation data

Microfluidics-free single-cell genomics with templated emulsification

Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

CD33 modulates TREM2: convergence of Alzheimer loci

Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus

Search

Quick links

Search

Filter By:

Search

Quick links