Stamatoyannopoulos, John A.

An encyclopedia of mouse DNA elements (Mouse ENCODE)

Mouse ENCODE Consortium, Stamatoyannopoulos, J. A., Snyder, M., Hardison, R., Ren, B., Gingeras, T., Gilbert, D. M., Groudine, M., Bender, M., Kaul, R., et al. (2012) · Genome Biology

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 446

Global reference mapping of human transcription factor footprints

Vierstra, J., Lazar, J., Sandstrom, R., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Haugen, E., et al. (2020) · Nature

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 386

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

Mayer, A., di Iulio, J., Maleri, S., Eser, U., Vierstra, J., Reynolds, A., Sandstrom, R., Stamatoyannopoulos, J. A., & Churchman, L. S. (2015) · Cell

Genomics and Chromatin DynamicsRNA Research and Splicing

Cited by 367

Index and biological spectrum of human DNase I hypersensitive sites

Meuleman, W., Muratov, A., Rynes, E., Halow, J., Lee, K., Bates, D., Diegel, M., Dunn, D., Neri, F., Teodosiadis, A., et al. (2020) · Nature

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 331

Domains of genome-wide gene expression dysregulation in Down’s syndrome

Letourneau, A., Santoni, F. A., Bonilla, X., Sailani, M. R., Gonzalez, D., Kind, J., Chevalier, C., Thurman, R., Sandstrom, R. S., Hibaoui, Y., et al. (2014) · Nature

Down syndrome and intellectual disability researchGenomics and Chromatin Dynamics

Cited by 319

Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism

Voss, T. C., Schiltz, R. L., Sung, M.-H., Yen, P. M., Stamatoyannopoulos, J. A., Biddie, S. C., Johnson, T. A., Miranda, T. B., John, S., & Hager, G. L. (2011) · Cell

Genomics and Chromatin DynamicsDiffusion and Search Dynamics

Cited by 307

Role of DNA Methylation in Modulating Transcription Factor Occupancy

Maurano, M. T., Wang, H., John, S., Shafer, A., Canfield, T., Lee, K., & Stamatoyannopoulos, J. A. (2015) · Cell Reports

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 281

Single-molecule regulatory architectures captured by chromatin fiber sequencing

Stergachis, A. B., Debo, B. M., Haugen, E., Churchman, L. S., & Stamatoyannopoulos, J. A. (2020) · Science

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 257

DNA methylation status predicts cell type‐specific enhancer activity

Wiench, M., John, S., Baek, S., Johnson, T. A., Sung, M., Escobar, T., Simmons, C. A., Pearce, K. H., Biddie, S. C., Sabo, P. J., et al. (2011) · The EMBO Journal

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 245

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

Li, X.-Y., Thomas, S., Sabo, P. J., Eisen, M. B., Stamatoyannopoulos, J. A., & Biggin, M. D. (2011) · Genome Biology

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 217

Conservation of trans-acting circuitry during mammalian regulatory evolution

Stergachis, A. B., Neph, S., Sandstrom, R., Haugen, E., Reynolds, A. P., Zhang, M., Byron, R., Canfield, T., Stelhing-Sun, S., Lee, K., et al. (2014) · Nature

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 212

Probing DNA shape and methylation state on a genomic scale with DNase I

Lazarovici, A., Zhou, T., Shafer, A., Dantas Machado, A. C., Riley, T. R., Sandstrom, R., Sabo, P. J., Lu, Y., Rohs, R., Stamatoyannopoulos, J. A., et al. (2013) · Proceedings of the National Academy of Sciences

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 162

Positively selected enhancer elements endow osteosarcoma cells with metastatic competence

Morrow, J. J., Bayles, I., Funnell, A. P. W., Miller, T. E., Saiakhova, A., Lizardo, M. M., Bartels, C. F., Kapteijn, M. Y., Hung, S., Mendoza, A., et al. (2018) · Nature Medicine

Genomics and Chromatin DynamicsCancer Cells and Metastasis

Cited by 161

Functional footprinting of regulatory DNA

Vierstra, J., Reik, A., Chang, K.-H., Stehling-Sun, S., Zhou, Y., Hinkley, S. J., Paschon, D. E., Zhang, L., Psatha, N., Bendana, Y. R., et al. (2015) · Nature Methods

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 133

Genomic discovery of potent chromatin insulators for human gene therapy

Liu, M., Maurano, M. T., Wang, H., Qi, H., Song, C.-Z., Navas, P. A., Emery, D. W., Stamatoyannopoulos, J. A., & Stamatoyannopoulos, G. (2015) · Nature Biotechnology

Virus-based gene therapy researchGenomics and Chromatin Dynamics

Cited by 121

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

Rapid empirical discovery of optimal peptides for targeted proteomics

Stergachis, A. B., MacLean, B., Lee, K., Stamatoyannopoulos, J. A., & MacCoss, M. J. (2011) · Nature Methods

Advanced Proteomics Techniques and ApplicationsMass Spectrometry Techniques and Applications

Cited by 110

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

Genetics and Genomics of Longitudinal Lung Function Patterns in Individuals with Asthma

McGeachie, M. J., Yates, K. P., Zhou, X., Guo, F., Sternberg, A. L., Van Natta, M. L., Wise, R. A., Szefler, S. J., Sharma, S., Kho, A. T., et al. (2016) · American Journal of Respiratory and Critical Care Medicine

Asthma and respiratory diseasesGenetic Associations and Epidemiology

Cited by 25