Prabhakar, Shyam

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

Li, H., Courtois, E. T., Sengupta, D., Tan, Y., Chen, K. H., Goh, J. J. L., Kong, S. L., Chua, C., Hon, L. K., Tan, W. S., et al. (2017) · Nature Genetics

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 1,080

The PsychENCODE project

Akbarian, S., Liu, C., Knowles, J. A., Vaccarino, F. M., Farnham, P. J., Crawford, G. E., Jaffe, A. E., Pinto, D., Dracheva, S., Geschwind, D. H., et al. (2015) · Nature Neuroscience

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 451

Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development

Utz, S. G., See, P., Mildenberger, W., Thion, M. S., Silvin, A., Lutz, M., Ingelfinger, F., Rayan, N. A., Lelios, I., Buttgereit, A., et al. (2020) · Cell

Neuroinflammation and Neurodegeneration MechanismsNeurogenesis and neuroplasticity mechanisms

Cited by 436

Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

Joanito, I., Wirapati, P., Zhao, N., Nawaz, Z., Yeo, G., Lee, F., Eng, C. L. P., Macalinao, D. C., Kahraman, M., Srinivasan, H., et al. (2022) · Nature Genetics

Single-cell and spatial transcriptomicsGenetic factors in colorectal cancer

Cited by 434

Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations

Loh, K. M., Ang, L. T., Zhang, J., Kumar, V., Ang, J., Auyeong, J. Q., Lee, K. L., Choo, S. H., Lim, C. Y. Y., Nichane, M., et al. (2014) · Cell Stem Cell

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 418

Histone Acetylome-wide Association Study of Autism Spectrum Disorder

Sun, W., Poschmann, J., Cruz-Herrera del Rosario, R., Parikshak, N. N., Hajan, H. S., Kumar, V., Ramasamy, R., Belgard, T. G., Elanggovan, B., Wong, C. C. Y., et al. (2016) · Cell

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 306

BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis

Singhal, V., Chou, N., Lee, J., Yue, Y., Liu, J., Chock, W. K., Lin, L., Chang, Y.-C., Teo, E. M. L., Aow, J., et al. (2024) · Nature Genetics

Single-cell and spatial transcriptomicsCell Image Analysis Techniques

Cited by 282

Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism

Ramaswami, G., Won, H., Gandal, M. J., Haney, J., Wang, J. C., Wong, C. C. Y., Sun, W., Prabhakar, S., Mill, J., & Geschwind, D. H. (2020) · Nature Communications

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 113

Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue

Wong, C. C. Y., Smith, R. G., Hannon, E., Ramaswami, G., Parikshak, N. N., Assary, E., Troakes, C., Poschmann, J., Schalkwyk, L. C., Sun, W., et al. (2019) · Human Molecular Genetics

Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental Disorders

Cited by 98

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

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

Huang, Y.-H., Jankowski, A., Cheah, K. S. E., Prabhakar, S., & Jauch, R. (2015) · Scientific Reports

Genomics and Chromatin DynamicsDevelopmental Biology and Gene Regulation

Cited by 86

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms

del Rosario, R. C.-H., Poschmann, J., Rouam, S. L., Png, E., Khor, C. C., Hibberd, M. L., & Prabhakar, S. (2015) · Nature Methods

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 58

A Single-Cell Atlas Identifies Pretreatment Features of Primary Imatinib Resistance in Chronic Myeloid Leukemia

Krishnan, V., Schmidt, F., Nawaz, Z., Lee, K. L., Nori Venkatesh, P., Makheja, M., Chan, Z. E., Yu, M., Arul Rayan, N., Gek Liang Lim, M., et al. (2022) · Blood

Chronic Myeloid Leukemia TreatmentsChronic Lymphocytic Leukemia Research

Cited by 15