Ye, Chun Jimmie

Assessing computational tools for the discovery of transcription factor binding sites

Tompa, M., Li, N., Bailey, T. L., Church, G. M., De Moor, B., Eskin, E., Favorov, A. V., Frith, M. C., Fu, Y., Kent, W. J., et al. (2005) · Nature Biotechnology

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 1,268

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

Kang, H. M., Subramaniam, M., Targ, S., Nguyen, M., Maliskova, L., McCarthy, E., Wan, E., Wong, S., Byrnes, L., Lanata, C. M., et al. (2018) · Nature Biotechnology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 1,101

CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells

Rupp, L. J., Schumann, K., Roybal, K. T., Gate, R. E., Ye, C. J., Lim, W. A., & Marson, A. (2017) · Scientific Reports

CAR-T cell therapy researchCancer Immunotherapy and Biomarkers

Cited by 757

Intratumoral CD4+ T Cells Mediate Anti-tumor Cytotoxicity in Human Bladder Cancer

Oh, D. Y., Kwek, S. S., Raju, S. S., Li, T., McCarthy, E., Chow, E., Aran, D., Ilano, A., Pai, C.-C. S., Rancan, C., et al. (2020) · Cell

Cancer Immunotherapy and BiomarkersT-cell and B-cell Immunology

Cited by 734

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins

Schumann, K., Lin, S., Boyer, E., Simeonov, D. R., Subramaniam, M., Gate, R. E., Haliburton, G. E., Ye, C. J., Bluestone, J. A., Doudna, J. A., et al. (2015) · Proceedings of the National Academy of Sciences

CRISPR and Genetic EngineeringCAR-T cell therapy research

Cited by 702

Single-cell eQTL mapping identifies cell type–specific genetic control of autoimmune disease

Yazar, S., Alquicira-Hernandez, J., Wing, K., Senabouth, A., Gordon, M. G., Andersen, S., Lu, Q., Rowson, A., Taylor, T. R. P., Clarke, L., et al. (2022) · Science

Genetic Associations and EpidemiologySingle-cell and spatial transcriptomics

Cited by 682

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

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Parnas, O., Jovanovic, M., Eisenhaure, T. M., Herbst, R. H., Dixit, A., Ye, C. J., Przybylski, D., Platt, R. J., Tirosh, I., Sanjana, N. E., et al. (2015) · Cell

Immune Response and InflammationCRISPR and Genetic Engineering

Cited by 440

Transethnic Genetic-Correlation Estimates from Summary Statistics

Brown, B. C., Ye, C. J., Price, A. L., & Zaitlen, N. (2016) · The American Journal of Human Genetics

Genetic Associations and EpidemiologyGenetic Mapping and Diversity in Plants and Animals

Cited by 340

Parsing the interferon transcriptional network and its disease associations

Mostafavi, S., Yoshida, H., Moodley, D., LeBoité, H., Rothamel, K., Raj, T., Ye, C. J., Chevrier, N., Zhang, S.-Y., Feng, T., et al. (2016) · Cell

interferon and immune responsesCytokine Signaling Pathways and Interactions

Cited by 337

Discovery of stimulation-responsive immune enhancers with CRISPR activation

Simeonov, D. R., Gowen, B. G., Boontanrart, M., Roth, T. L., Gagnon, J. D., Mumbach, M. R., Satpathy, A. T., Lee, Y., Bray, N. L., Chan, A. Y., et al. (2017) · Nature

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 297

Intersection of population variation and autoimmunity genetics in human T cell activation

Ye, C. J., Feng, T., Kwon, H.-K., Raj, T., Wilson, M. T., Asinovski, N., McCabe, C., Lee, M. H., Frohlich, I., Paik, H.-I., et al. (2014) · Science

T-cell and B-cell ImmunologyGenetic Associations and Epidemiology

Cited by 236

Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies

Roth, T. L., Li, P. J., Blaeschke, F., Nies, J. F., Apathy, R., Mowery, C., Yu, R., Nguyen, M. L. T., Lee, Y., Truong, A., et al. (2020) · Cell

CRISPR and Genetic EngineeringCAR-T cell therapy research

Cited by 186

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

Gate, R. E., Cheng, C. S., Aiden, A. P., Siba, A., Tabaka, M., Lituiev, D., Machol, I., Gordon, M. G., Subramaniam, M., Shamim, M., et al. (2018) · Nature Genetics

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 181

The development and evolution of inhibitory neurons in primate cerebrum

Schmitz, M. T., Sandoval, K., Chen, C. P., Mostajo-Radji, M. A., Seeley, W. W., Nowakowski, T. J., Ye, C. J., Paredes, M. F., & Pollen, A. A. (2022) · Nature

Neurogenesis and neuroplasticity mechanismsDevelopmental Biology and Gene Regulation

Cited by 111

Enhancing droplet-based single-nucleus RNA-seq resolution using the semi-supervised machine learning classifier DIEM

Alvarez, M., Rahmani, E., Jew, B., Garske, K. M., Miao, Z., Benhammou, J. N., Ye, C. J., Pisegna, J. R., Pietiläinen, K. H., Halperin, E., et al. (2020) · Scientific Reports

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 93

Demuxafy: improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Neavin, D., Senabouth, A., Arora, H., Lee, J. T. H., Ripoll-Cladellas, A., sc-eQTLGen Consortium, Franke, L., Prabhakar, S., Ye, C. J., McCarthy, D. J., et al. (2024) · Genome Biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 90

Demuxafy : Improvement in droplet assignment by integrating multiple single-cell demultiplexing and doublet detection methods

Neavin, D., Senabouth, A., Hang Lee, J. T., Ripoll, A., sc-eQTLGen Consortium, Franke, L., Prabhakar, S., Ye, C. J., McCarthy, D. J., Melé, M., et al. (2022) · Genome biology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 90

Functional characterization of Alzheimer’s disease genetic variants in microglia

Yang, X., Wen, J., Yang, H., Jones, I. R., Zhu, X., Liu, W., Li, B., Clelland, C. D., Luo, W., Wong, M. Y., et al. (2023) · Nature Genetics

Alzheimer's disease research and treatmentsNeuroinflammation and Neurodegeneration Mechanisms

Cited by 71

Optimized design of single-cell RNA sequencing experiments for cell-type-specific eQTL analysis

Mandric, I., Schwarz, T., Majumdar, A., Hou, K., Briscoe, L., Perez, R., Subramaniam, M., Hafemeister, C., Satija, R., Ye, C. J., et al. (2020) · Nature Communications

Single-cell and spatial transcriptomicsGenetic Associations and Epidemiology

Cited by 62

Cell-subtype specific effects of genetic variation in the aging and Alzheimer cortex

Fujita, M., Gao, Z., Zeng, L., McCabe, C., White, C. C., Ng, B., Green, G. S., Rozenblatt-Rosen, O., Phillips, D., Amir-Zilberstein, L., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Genetic Associations and EpidemiologySingle-cell and spatial transcriptomics

Cited by 36

Multi-Modal Single-Cell Sequencing Identifies Cellular Immunophenotypes Associated With Juvenile Dermatomyositis Disease Activity

Neely, J., Hartoularos, G., Bunis, D., Sun, Y., Lee, D., Kim, S., Ye, C. J., & Sirota, M. (2022) · Frontiers in Immunology

Inflammatory Myopathies and DermatomyositisSystemic Sclerosis and Related Diseases

Cited by 26

Genome-wide prediction of disease variants with a deep protein language model

Brandes, N., Goldman, G., Wang, C. H., Ye, C. J., & Ntranos, V. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Genomics and Rare DiseasesMachine Learning in Bioinformatics

Cited by 24

Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis

Wang, V. E., Blaser, B. W., Patel, R. K., Behbehani, G. K., Rao, A. A., Durbin-Johnson, B., Jiang, T., Logan, A. C., Settles, M., Mannis, G. N., et al. (2021) · Blood Cancer Discovery

Acute Myeloid Leukemia ResearchRetinoids in leukemia and cellular processes

Cited by 11