Kellis, Manolis

Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration

Menon, M., Mohammadi, S., Davila-Velderrain, J., Goods, B. A., Cadwell, T. D., Xing, Y., Stemmer-Rachamimov, A., Shalek, A. K., Love, J. C., Kellis, M., et al. (2019) · Nature Communications

Single-cell and spatial transcriptomicsRetinal Development and Disorders

Cited by 331

Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells

Ram, O., Goren, A., Amit, I., Shoresh, N., Yosef, N., Ernst, J., Kellis, M., Gymrek, M., Issner, R., Coyne, M., et al. (2011) · Cell

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 331

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

Marbach, D., Lamparter, D., Quon, G., Kellis, M., Kutalik, Z., & Bergmann, S. (2016) · Nature Methods

Gene Regulatory Network AnalysisGenomics and Chromatin Dynamics

Cited by 326

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

Kheradpour, P., Ernst, J., Melnikov, A., Rogov, P., Wang, L., Zhang, X., Alston, J., Mikkelsen, T. S., & Kellis, M. (2013) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 315

Effect of predicted protein-truncating genetic variants on the human transcriptome

Rivas, M. A., Pirinen, M., Conrad, D. F., Lek, M., Tsang, E. K., Karczewski, K. J., Maller, J. B., Kukurba, K. R., DeLuca, D. S., Fromer, M., et al. (2015) · Science

Genomics and Rare DiseasesRNA Research and Splicing

Cited by 313

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites

Xie, X., Mikkelsen, T. S., Gnirke, A., Lindblad-Toh, K., Kellis, M., & Lander, E. S. (2007) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 305

Whole-genome ChIP–chip analysis of Dorsal, Twist, and Snail suggests integration of diverse patterning processes in the Drosophila embryo

Zeitlinger, J., Zinzen, R. P., Stark, A., Kellis, M., Zhang, H., Young, R. A., & Levine, M. (2007) · Genes & Development

Genomics and Chromatin DynamicsDevelopmental Biology and Gene Regulation

Cited by 286

Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer

Akdemir, K. C., Le, V. T., Chandran, S., Li, Y., Verhaak, R. G., Beroukhim, R., Campbell, P. J., Chin, L., Dixon, J. R., Futreal, P. A., et al. (2020) · Nature Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 283

Reconstruction of the human blood–brain barrier in vitro reveals a pathogenic mechanism of APOE4 in pericytes

Blanchard, J. W., Bula, M., Davila-Velderrain, J., Akay, L. A., Zhu, L., Frank, A., Victor, M. B., Bonner, J. M., Mathys, H., Lin, Y.-T., et al. (2020) · Nature Medicine

Barrier Structure and Function StudiesAlzheimer's disease research and treatments

Cited by 283

Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation

Lee, H., Fenster, R. J., Pineda, S. S., Gibbs, W. S., Mohammadi, S., Davila-Velderrain, J., Garcia, F. J., Therrien, M., Novis, H. S., Gao, F., et al. (2020) · Neuron

Genetic Neurodegenerative DiseasesNeuroinflammation and Neurodegeneration Mechanisms

Cited by 279

The Genotype-Tissue Expression (GTEx) project

Lonsdale, J., Thomas, J., Salvatore, M., Phillips, R., Lo, E., Shad, S., Hasz, R., Walters, G., Garcia, F., Young, N., et al. (2013) · Nature Genetics

Genetic Associations and EpidemiologyGenomics and Chromatin Dynamics

Cited by 263

TrustLLM: Trustworthiness in Large Language Models

Huang, Y., Sun, L., Wang, H., Wu, S., Zhang, Q., Li, Y., Gao, C., Huang, Y., Lyu, W., Zhang, Y., et al. (2024) · arXiv

Ethics and Social Impacts of AIExplainable Artificial Intelligence (XAI)

Cited by 256

Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

Ward, L. D., & Kellis, M. (2012) · Science

Evolution and Genetic DynamicsChromosomal and Genetic Variations

Cited by 209

Epigenomic dissection of Alzheimer’s disease pinpoints causal variants and reveals epigenome erosion

Xiong, X., James, B. T., Boix, C. A., Park, Y. P., Galani, K., Victor, M. B., Sun, N., Hou, L., Ho, L.-L., Mantero, J., et al. (2023) · Cell

Alzheimer's disease research and treatmentsGenomics and Chromatin Dynamics

Cited by 205

NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data

He, L., Davila-Velderrain, J., Sumida, T. S., Hafler, D. A., Kellis, M., & Kulminski, A. M. (2021) · Communications Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 181

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

Ernst, J., Melnikov, A., Zhang, X., Wang, L., Rogov, P., Mikkelsen, T. S., & Kellis, M. (2016) · Nature Biotechnology

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 162

Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble

Marco, A., Meharena, H. S., Dileep, V., Raju, R. M., Davila-Velderrain, J., Zhang, A. L., Adaikkan, C., Young, J. Z., Gao, F., Kellis, M., et al. (2020) · Nature Neuroscience

Memory and Neural MechanismsGenomics and Chromatin Dynamics

Cited by 159

High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human

Wang, X., He, L., Goggin, S. M., Saadat, A., Wang, L., Sinnott-Armstrong, N., Claussnitzer, M., & Kellis, M. (2018) · Nature Communications

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 159

High-throughput 5’ UTR engineering for enhanced protein production in non-viral gene therapies

Cao, J., Novoa, E. M., Zhang, Z., Chen, W. C. W., Liu, D., Choi, G. C. G., Wong, A. S. L., Wehrspaun, C., Kellis, M., & Lu, T. K. (2021) · Nature Communications

Virus-based gene therapy researchRNA and protein synthesis mechanisms

Cited by 159

Neuronal DNA double-strand breaks lead to genome structural variations and 3D genome disruption in neurodegeneration

Dileep, V., Boix, C. A., Mathys, H., Marco, A., Welch, G. M., Meharena, H. S., Loon, A., Jeloka, R., Peng, Z., Bennett, D. A., et al. (2023) · Cell

DNA Repair MechanismsAlzheimer's disease research and treatments

Cited by 130

An encyclopedia of enhancer-gene regulatory interactions in the human genome

Gschwind, A. R., Mualim, K. S., Karbalayghareh, A., Sheth, M. U., Dey, K. K., Jagoda, E., Nurtdinov, R. N., Xi, W., Tan, A. S., Jones, H., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory)

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 119

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Wu, W., Cheng, Y., Keller, C. A., Ernst, J., Kumar, S. A., Mishra, T., Morrissey, C., Dorman, C. M., Chen, K.-B., Drautz, D., et al. (2011) · Genome Research

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 118

A wealth of discovery built on the Human Genome Project — by the numbers

Gates, A. J., Gysi, D. M., Kellis, M., & Barabási, A.-L. (2021) · Nature

Science, Research, and MedicineGenetic Associations and Epidemiology

Cited by 98

MEF2 is a Key Regulator of Cognitive Potential and Confers Resilience to Neurodegeneration

Barker, S. J., Raju, R. M., Milman, N. E. P., Wang, J., Davila-Velderrain, J., Gunter-Rahman, F., Parro, C. C., Bozzelli, P. L., Abdurrob, F., Abdelaal, K., et al. (2021) · Science Translational Medicine

Alzheimer's disease research and treatmentsNeurogenesis and neuroplasticity mechanisms

Cited by 96