Replogle, Joseph M.

Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility

International Multiple Sclerosis Genetics Consortium, Patsopoulos, N. A., Baranzini, S. E., Santaniello, A., Shoostari, P., Cotsapas, C., Wong, G., Beecham, A. H., James, T., Replogle, J., et al. (2019) · Science

Multiple Sclerosis Research StudiesGenetic Associations and Epidemiology

Cited by 1,471

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

De Jager, P. L., Srivastava, G., Lunnon, K., Burgess, J., Schalkwyk, L. C., Yu, L., Eaton, M. L., Keenan, B. T., Ernst, J., McCabe, C., et al. (2014) · Nature Neuroscience

Epigenetics and DNA MethylationDementia and Cognitive Impairment Research

Cited by 956

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

Replogle, J. M., Saunders, R. A., Pogson, A. N., Hussmann, J. A., Lenail, A., Guna, A., Mascibroda, L., Wagner, E. J., Adelman, K., Lithwick-Yanai, G., et al. (2022) · Cell

CRISPR and Genetic EngineeringSingle-cell and spatial transcriptomics

Cited by 795

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

Nuñez, J. K., Chen, J., Pommier, G. C., Cogan, J. Z., Replogle, J. M., Adriaens, C., Ramadoss, G. N., Shi, Q., Hung, K. L., Samelson, A. J., et al. (2021) · Cell

CRISPR and Genetic EngineeringEpigenetics and DNA Methylation

Cited by 760

Polarization of the Effects of Autoimmune and Neurodegenerative Risk Alleles in Leukocytes

Raj, T., Rothamel, K., Mostafavi, S., Ye, C., Lee, M. N., Replogle, J. M., Feng, T., Lee, M., Asinovski, N., Frohlich, I., et al. (2014) · Science

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Cited by 506

Direct capture of CRISPR guides enables scalable, multiplexed, and multi-omic Perturb-seq

Replogle, J. M., Xu, A., Norman, T. M., Meer, E. J., Terry, J. M., Riordan, D., Srinivas, N., Mikkelsen, T. S., Weissman, J. S., & Adamson, B. (2018) · Nature Biotechnology

CRISPR and Genetic EngineeringSingle-cell and spatial transcriptomics

Cited by 465

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

Replogle, J. M., Norman, T. M., Xu, A., Hussmann, J. A., Chen, J., Cogan, J. Z., Meer, E. J., Terry, J. M., Riordan, D. P., Srinivas, N., et al. (2020) · Nature Biotechnology

CRISPR and Genetic EngineeringSingle-cell and spatial transcriptomics

Cited by 465

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

Norman, T. M., Horlbeck, M. A., Replogle, J. M., Ge, A. Y., Xu, A., Jost, M., Gilbert, L. A., & Weissman, J. S. (2019) · Science

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

Cited by 392

CD33 modulates TREM2: convergence of Alzheimer loci

Chan, G., White, C. C., Winn, P. A., Cimpean, M., Replogle, J. M., Glick, L. R., Cuerdon, N. E., Ryan, K. J., Johnson, K. A., Schneider, J. A., et al. (2015) · Nature Neuroscience

Alzheimer's disease research and treatmentsNeuroinflammation and Neurodegeneration Mechanisms

Cited by 162

CD33: increased inclusion of exon 2 implicates the Ig V-set domain in Alzheimer’s disease susceptibility

Raj, T., Ryan, K. J., Replogle, J. M., Chibnik, L. B., Rosenkrantz, L., Tang, A., Rothamel, K., Stranger, B. E., Bennett, D. A., Evans, D. A., et al. (2014) · Human Molecular Genetics

Alzheimer's disease research and treatmentsNeuroinflammation and Neurodegeneration Mechanisms

Cited by 144

Transcriptome-wide analysis of differential expression in perturbation atlases

Nadig, A., Replogle, J. M., Pogson, A. N., Murthy, M., McCarroll, S. A., Weissman, J. S., Robinson, E. B., & O’Connor, L. J. (2025) · Nature Genetics

Single-cell and spatial transcriptomicsCRISPR and Genetic Engineering

Cited by 70