Kellis, Manolis

Analysis of variation at transcription factor binding sites in Drosophila and humans

Spivakov, M., Akhtar, J., Kheradpour, P., Beal, K., Girardot, C., Koscielny, G., Herrero, J., Kellis, M., Furlong, E. E., & Birney, E. (2012) · Genome Biology

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 94

Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration

Welch, G. M., Boix, C. A., Schmauch, E., Davila-Velderrain, J., Victor, M. B., Dileep, V., Bozzelli, P. L., Su, Q., Cheng, J. D., Lee, A., et al. (2022) · Science Advances

Neuroinflammation and Neurodegeneration MechanismsNeurological Disease Mechanisms and Treatments

Cited by 84

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

Mudge, J. M., Jungreis, I., Hunt, T., Gonzalez, J. M., Wright, J. C., Kay, M., Davidson, C., Fitzgerald, S., Seal, R., Tweedie, S., et al. (2019) · Genome Research

Genomics and Phylogenetic StudiesGenomics and Rare Diseases

Cited by 80

A partnership of the lipid scramblase XK and of the lipid transfer protein VPS13A at the plasma membrane

Samander, A. G., Wu, Y., Pineda, S. S., García, F. J., Eisen, J. N., Leonzino, M., Uğur, B., Kellis, M., Heiman, M., & De Camilli, P. (2022) · Proceedings of the National Academy of Sciences

Cellular transport and secretionLipid Membrane Structure and Behavior

Cited by 79

Evolutionary principles of modular gene regulation in yeasts

Thompson, D. A., Roy, S., Chan, M., Styczynsky, M. P., Pfiffner, J., French, C., Socha, A., Thielke, A., Napolitano, S., Muller, P., et al. (2013) · eLife

Fungal and yeast genetics researchGene Regulatory Network Analysis

Cited by 78

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

Wu, Y.-C., Rasmussen, M. D., Bansal, M. S., & Kellis, M. (2014) · Genome Research

Genomics and Phylogenetic StudiesGenome Rearrangement Algorithms

Cited by 77

Reconstruction of Cell-type-Specific Interactomes at Single-Cell Resolution

Mohammadi, S., Davila-Velderrain, J., & Kellis, M. (2019) · Cell Systems

Bioinformatics and Genomic NetworksGene Regulatory Network Analysis

Cited by 73

Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics

Barbeira, A. N., Dickinson, S. P., Bonazzola, R., Zheng, J., Wheeler, H. E., Torres, J. M., Torstenson, E. S., Shah, K. P., Garcia, T., Edwards, T. L., et al. (2018) · Nature Communications

Genetic Associations and EpidemiologyBioinformatics and Genomic Networks

Cited by 69

Systematic chromatin state comparison of epigenomes associated with diverse properties including sex and tissue type

Yen, A., & Kellis, M. (2015) · Nature Communications

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 67

Alzheimer's loci: epigenetic associations and interaction with genetic factors

Chibnik, L. B., Yu, L., Eaton, M. L., Srivastava, G., Schneider, J. A., Kellis, M., Bennett, D. A., & De Jager, P. L. (2015) · Annals of Clinical and Translational Neurology

Alzheimer's disease research and treatmentsEpigenetics and DNA Methylation

Cited by 60

Leveraging single-cell ATAC-seq and RNA-seq to identify disease-critical fetal and adult brain cell types

Kim, S. S., Truong, B., Jagadeesh, K., Dey, K. K., Shen, A. Z., Raychaudhuri, S., Kellis, M., & Price, A. L. (2024) · Nature Communications

Single-cell and spatial transcriptomicsGenetic Associations and Epidemiology

Cited by 56

Token Reduction Should Go Beyond Efficiency in Generative Models -- From Vision, Language to Multimodality

Kong, Z., Li, Y., Zeng, F., Xin, L., Messica, S., Lin, X., Zhao, P., Kellis, M., Tang, H., & Zitnik, M. (2025) · arXiv

Multimodal Machine Learning ApplicationsTopic Modeling

Cited by 51

ABCA7 variants impact phosphatidylcholine and mitochondria in neurons

von Maydell, D., Wright, S. E., Pao, P.-C., Staab, C., King, O., Spitaleri, A., Bonner, J. M., Liu, L., Yu, C. J., Chiu, C.-C., et al. (2025) · Nature

Alzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

Cited by 35

Single-cell mosaicism analysis reveals cell-type-specific somatic mutational burden in Alzheimer’s Dementia

Kousi, M., Boix, C., Park, Y. P., Mathys, H., Sledzieski, S., Peng, Z., Bennett, D. A., Tsai, L.-H., & Kellis, M. (2022) · bioRxiv (Cold Spring Harbor Laboratory)

Alzheimer's disease research and treatmentsSingle-cell and spatial transcriptomics

Cited by 7

Interpreting noncoding genetic variation in complex traits and human disease

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

Genetic Associations and EpidemiologyGenomics and Rare Diseases

Cited by 6

Biophysical characterization of high-confidence, small human proteins

Whited, A. M., Jungreis, I., Allen, J., Cleveland, C., Mudge, J. M., Kellis, M., Rinn, J., & Hough, L. E. (2024) · Biophysical Reports

Protein Structure and DynamicsGenomics and Phylogenetic Studies

Cited by 5

Biophysical characterization of high-confidence, small human proteins

Whited, A. M., Jungreis, I., Allen, J., Cleveland, C. L., Mudge, J. M., Kellis, M., Rinn, J. L., & Hough, L. E. (2024) · Biophysical Reports

Protein Structure and DynamicsGenomics and Phylogenetic Studies

Cited by 5

Proteogenomics in cerebrospinal fluid and plasma reveals new biological fingerprint of cerebral small vessel disease

Debette, S., Caro, I., Western, D., Namba, S., Sun, N., Kawaguchi, S., He, Y., Fujita, M., Roshchupkin, G., D'Aoust, T., et al. (2024) · Research Square

Cerebrovascular and genetic disordersMultiple Sclerosis Research Studies

Cited by 5