Stark, Alexander

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 2,533

Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila

Brennecke, J., Aravin, A. A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., & Hannon, G. J. (2007) · Cell

Chromosomal and Genetic VariationsRNA Interference and Gene Delivery

Cited by 2,524

bantam Encodes a Developmentally Regulated microRNA that Controls Cell Proliferation and Regulates the Proapoptotic Gene hid in Drosophila

Brennecke, J., Hipfner, D. R., Stark, A., Russell, R. B., & Cohen, S. M. (2003) · Cell

MicroRNA in disease regulationDevelopmental Biology and Gene Regulation

Cited by 2,042

Transcriptional enhancers: from properties to genome-wide predictions

Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,356

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

Arnold, C. D., Gerlach, D., Stelzer, C., Boryń, Ł. M., Rath, M., & Stark, A. (2013) · Science

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 1,125

A high-resolution map of human evolutionary constraint using 29 mammals

Broad Institute Sequencing Platform and Whole Genome Assembly Team, Lindblad-Toh, K., Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Genome Institute at Washington University, Garber, M., Zuk, O., Lin, M. F., Parker, B. J., Washietl, S., Kheradpour, P., et al. (2011) · Nature

Genomics and Phylogenetic StudiesChromosomal and Genetic Variations

Cited by 1,108

Animal MicroRNAs Confer Robustness to Gene Expression and Have a Significant Impact on 3′UTR Evolution

Stark, A., Brennecke, J., Bushati, N., Russell, R. B., & Cohen, S. M. (2005) · Cell

MicroRNA in disease regulationRNA Research and Splicing

Cited by 1,080

Enhancer–core-promoter specificity separates developmental and housekeeping gene regulation

Zabidi, M. A., Arnold, C. D., Schernhuber, K., Pagani, M., Rath, M., Frank, O., & Stark, A. (2015) · Nature

Genomics and Chromatin DynamicsDevelopmental Biology and Gene Regulation

Cited by 471

Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks

Neduva, V., Linding, R., Su-Angrand, I., Stark, A., Masi, F. D., Gibson, T. J., Lewis, J., Serrano, L., & Russell, R. B. (2005) · PLoS Biology

Bioinformatics and Genomic NetworksProtein Structure and Dynamics

Cited by 359

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

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of enhancers

de Almeida, B. P., Reiter, F., Pagani, M., & Stark, A. (2021) · Nature Genetics

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 284

DeepSTARR predicts enhancer activity from DNA sequence and enables the de novo design of synthetic enhancers

de Almeida, B. P., Reiter, F., Pagani, M., & Stark, A. (2022) · Nature Genetics

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 283

Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors

Zabidi, M. A., & Stark, A. (2016) · Trends in Genetics

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 228

Resolving systematic errors in widely used enhancer activity assays in human cells

Muerdter, F., Boryń, Ł. M., Woodfin, A. R., Neumayr, C., Rath, M., Zabidi, M. A., Pagani, M., Haberle, V., Kazmar, T., Catarino, R. R., et al. (2018) · Nature Methods

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 208

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

Arnold, C. D., Gerlach, D., Spies, D., Matts, J. A., Sytnikova, Y. A., Pagani, M., Lau, N. C., & Stark, A. (2014) · Nature Genetics

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 175

Transcriptional cofactors display specificity for distinct types of core promoters

Haberle, V., Arnold, C. D., Pagani, M., Rath, M., Schernhuber, K., & Stark, A. (2019) · Nature

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 123

A Histone Deacetylase Adjusts Transcription Kinetics at Coding Sequences during Candida albicans Morphogenesis

Hnisz, D., Bardet, A. F., Nobile, C. J., Petryshyn, A., Glaser, W., Schöck, U., Stark, A., & Kuchler, K. (2012) · PLoS Genetics

Fungal and yeast genetics researchGenomics and Chromatin Dynamics

Cited by 100

Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo

de Almeida, B. P., Schaub, C., Pagani, M., Secchia, S., Furlong, E. E. M., & Stark, A. (2024) · Nature

Genomics and Chromatin DynamicsCRISPR and Genetic Engineering

Cited by 87