Hughes, Timothy R.

The Human Transcription Factors

Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell

Genomics and Chromatin DynamicsGene Regulatory Network Analysis

Cited by 3,399

Expanded encyclopaedias of DNA elements in the human and mouse genomes

The ENCODE Project Consortium, Abascal, F., Acosta, R., Addleman, N. J., Adrian, J., Afzal, V., Ai, R., Aken, B., Akiyama, J. A., Jammal, O. A., et al. (2020) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 2,378

A compendium of RNA-binding motifs for decoding gene regulation

Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., et al. (2013) · Nature

RNA Research and SplicingRNA and protein synthesis mechanisms

Cited by 1,480

Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function

Lécuyer, E., Yoshida, H., Parthasarathy, N., Alm, C., Babak, T., Cerovina, T., Hughes, T. R., Tomancak, P., & Krause, H. M. (2007) · Cell

RNA Research and SplicingRNA and protein synthesis mechanisms

Cited by 967

Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences

Berger, M. F., Badis, G., Gehrke, A. R., Talukder, S., Philippakis, A. A., Peña-Castillo, L., Alleyne, T. M., Mnaimneh, S., Botvinnik, O. B., Chan, E. T., et al. (2008) · Cell

Genomics and Chromatin DynamicsProtein Structure and Dynamics

Cited by 606

Exploration of Essential Gene Functions via Titratable Promoter Alleles

Mnaimneh, S., Davierwala, A. P., Haynes, J., Moffat, J., Peng, W.-T., Zhang, W., Yang, X., Pootoolal, J., Chua, G., Lopez, A., et al. (2004) · Cell

Fungal and yeast genetics researchBioinformatics and Genomic Networks

Cited by 604

The draft genome and transcriptome of Cannabis sativa.

van Bakel, H., Stout, J. M., Cote, A. G., Tallon, C. M., Sharpe, A. G., Hughes, T. R., & Page, J. E. (2011) · Genome Biology

Cannabis and Cannabinoid ResearchGenomics and Phylogenetic Studies

Cited by 575

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo

Wei, G., Badis, G., Berger, M. F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A. R., et al. (2010) · The EMBO Journal

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 568

The Human Transcription Factors

Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., Chen, X., Taipale, J., Hughes, T. R., & Weirauch, M. T. (2018) · Cell

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 550

Global Survey of Organ and Organelle Protein Expression in Mouse: Combined Proteomic and Transcriptomic Profiling

Kislinger, T., Cox, B., Kannan, A., Chung, C., Hu, P., Ignatchenko, A., Scott, M. S., Gramolini, A. O., Morris, Q., Hallett, M. T., et al. (2006) · Cell

Advanced Proteomics Techniques and ApplicationsBioinformatics and Genomic Networks

Cited by 482

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities

Jolma, A., Kivioja, T., Toivonen, J., Cheng, L., Wei, G., Enge, M., Taipale, M., Vaquerizas, J. M., Yan, J., Sillanpää, M. J., et al. (2010) · Genome Research

Genomics and Chromatin DynamicsAdvanced biosensing and bioanalysis techniques

Cited by 441

Probing microRNAs with microarrays: tissue specificity and functional inference

BABAK, T., ZHANG, W., MORRIS, Q., BLENCOWE, B. J., & HUGHES, T. R. (2004) · RNA

MicroRNA in disease regulationPlant Molecular Biology Research

Cited by 385

Evaluation of methods for modeling transcription factor sequence specificity

DREAM5 Consortium, Weirauch, M. T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T. R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., et al. (2013) · Nature Biotechnology

Genomics and Chromatin DynamicsGenomics and Phylogenetic Studies

Cited by 381

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

Najafabadi, H. S., Mnaimneh, S., Schmitges, F. W., Garton, M., Lam, K. N., Yang, A., Albu, M., Weirauch, M. T., Radovani, E., Kim, P. M., et al. (2015) · Nature Biotechnology

Genomics and Chromatin DynamicsChromosomal and Genetic Variations

Cited by 346

SMAUG Is a Major Regulator of Maternal mRNA Destabilization in Drosophila and Its Translation Is Activated by the PAN GU Kinase

Tadros, W., Goldman, A. L., Babak, T., Menzies, F., Vardy, L., Orr-Weaver, T., Hughes, T. R., Westwood, J. T., Smibert, C. A., & Lipshitz, H. D. (2007) · Developmental Cell

RNA Research and SplicingDevelopmental Biology and Gene Regulation

Cited by 330

Revealing global regulatory features of mammalian alternative splicing using a quantitative microarray platform

Pan, Q., Shai, O., Misquitta, C., Zhang, W., Saltzman, A. L., Mohammad, N., Babak, T., Siu, H., Hughes, T. R., Morris, Q. D., et al. (2004) · Molecular Cell

RNA Research and SplicingCancer-related molecular mechanisms research

Cited by 323

A critical assessment of Mus musculusgene function prediction using integrated genomic evidence

Peña-Castillo, L., Tasan, M., Myers, C. L., Lee, H., Joshi, T., Zhang, C., Guan, Y., Leone, M., Pagnani, A., Kim, W. K., et al. (2008) · Genome Biology

Bioinformatics and Genomic NetworksGenomics and Phylogenetic Studies

Cited by 248

Multiparameter functional diversity of human C2H2 zinc finger proteins

Schmitges, F. W., Radovani, E., Najafabadi, H. S., Barazandeh, M., Campitelli, L. F., Yin, Y., Jolma, A., Zhong, G., Guo, H., Kanagalingam, T., et al. (2016) · Genome Research

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 193

Conservation of core gene expression in vertebrate tissues

Chan, E. T., Quon, G. T., Chua, G., Babak, T., Trochesset, M., Zirngibl, R. A., Aubin, J., Ratcliffe, M. J., Wilde, A., Brudno, M., et al. (2009) · Journal of Biology

Developmental Biology and Gene RegulationGenomics and Chromatin Dynamics

Cited by 190

Why Are There Still Over 1000 Uncharacterized Yeast Genes?

Peña-Castillo, L., & Hughes, T. R. (2007) · Genetics

Fungal and yeast genetics researchBioinformatics and Genomic Networks

Cited by 161

CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo

Mann, I. K., Chatterjee, R., Zhao, J., He, X., Weirauch, M. T., Hughes, T. R., & Vinson, C. (2013) · Genome Research

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 126

Functional coordination of alternative splicing in the mammalian central nervous system

Fagnani, M., Barash, Y., Ip, J. Y., Misquitta, C., Pan, Q., Saltzman, A. L., Shai, O., Lee, L., Rozenhek, A., Mohammad, N., et al. (2007) · Genome Biology

RNA Research and SplicingRNA regulation and disease

Cited by 120

Two-Color Cell Array Screen Reveals Interdependent Roles for Histone Chaperones and a Chromatin Boundary Regulator in Histone Gene Repression

Fillingham, J., Kainth, P., Lambert, J.-P., van Bakel, H., Tsui, K., Peña-Castillo, L., Nislow, C., Figeys, D., Hughes, T. R., Greenblatt, J., et al. (2009) · Molecular Cell

Genomics and Chromatin DynamicsChromatin Remodeling and Cancer

Cited by 108

A structural approach reveals how neighbouring C2H2 zinc fingers influence DNA binding specificity

Garton, M., Najafabadi, H. S., Schmitges, F. W., Radovani, E., Hughes, T. R., & Kim, P. M. (2015) · Nucleic Acids Research

Protein Structure and DynamicsGenomics and Chromatin Dynamics

Cited by 48