Search Results - "Elkon, Ran"

Characterization of noncoding regulatory DNA in the human genome by Elkon, Ran, Agami, Reuven

“…Genome-wide mapping of regulatory elements will improve our understanding of how genetic variation in the noncoding genome affects disease phenotypes. Genetic…”
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Alternative cleavage and polyadenylation: extent, regulation and function by Elkon, Ran, Ugalde, Alejandro P., Agami, Reuven

“…Key Points Recent advances in technologies for global mapping of alternative polyadenylation (APA) have allowed unprecedented investigation of alternative…”
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DOMINO: a network‐based active module identification algorithm with reduced rate of false calls by Levi, Hagai, Elkon, Ran, Shamir, Ron

“…Algorithms for active module identification (AMI) are central to analysis of omics data. Such algorithms receive a gene network and nodes' activity scores as…”
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Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9 by Korkmaz, Gozde, Lopes, Rui, Ugalde, Alejandro P, Nevedomskaya, Ekaterina, Han, Ruiqi, Myacheva, Ksenia, Zwart, Wilbert, Elkon, Ran, Agami, Reuven

“…CRISPR-Cas9 is used for both enrichment and dropout screens of functional enhancers in human cells. Systematic identification of noncoding regulatory elements…”
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Transcription Impacts the Efficiency of mRNA Translation via Co-transcriptional N6-adenosine Methylation by Slobodin, Boris, Han, Ruiqi, Calderone, Vittorio, Vrielink, Joachim A.F. Oude, Loayza-Puch, Fabricio, Elkon, Ran, Agami, Reuven

“…Transcription and translation are two main pillars of gene expression. Due to the different timings, spots of action, and mechanisms of regulation, these…”
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FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer-promoter map by Hait, Tom Aharon, Amar, David, Shamir, Ron, Elkon, Ran

“…Recent sequencing technologies enable joint quantification of promoters and their enhancer regions, allowing inference of enhancer-promoter links. We show that…”
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Recurrent functional misinterpretation of RNA-seq data caused by sample-specific gene length bias by Mandelboum, Shir, Manber, Zohar, Elroy-Stein, Orna, Elkon, Ran

“…Data normalization is a critical step in RNA sequencing (RNA-seq) analysis, aiming to remove systematic effects from the data to ensure that technical biases…”
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Systematic identification of functional SNPs interrupting 3’UTR polyadenylation signals by Shulman, Eldad David, Elkon, Ran, Barsh, Gregory S, Gruber, Andreas

“…Alternative polyadenylation (APA) is emerging as a widespread regulatory layer since the majority of human protein-coding genes contain several polyadenylation…”
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Incorporating regulatory interactions into gene-set analyses for GWAS data: A controlled analysis with the MAGMA tool by Groenewoud, David, Shye, Avinoam, Elkon, Ran

“…To date, genome-wide association studies have identified thousands of statistically-significant associations between genetic variants, and phenotypes related…”
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Transcription Dynamics Regulate Poly(A) Tails and Expression of the RNA Degradation Machinery to Balance mRNA Levels by Slobodin, Boris, Bahat, Anat, Sehrawat, Urmila, Becker-Herman, Shirly, Zuckerman, Binyamin, Weiss, Amanda N., Han, Ruiqi, Elkon, Ran, Agami, Reuven, Ulitsky, Igor, Shachar, Idit, Dikstein, Rivka

“…Gene expression is regulated by the rates of synthesis and degradation of mRNAs, but how these processes are coordinated is poorly understood. Here, we show…”
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p53 induces transcriptional and translational programs to suppress cell proliferation and growth by Loayza-Puch, Fabricio, Drost, Jarno, Rooijers, Koos, Lopes, Rui, Elkon, Ran, Agami, Reuven

“…BACKGROUND: Cell growth and proliferation are tightly connected to ensure that appropriately sized daughter cells are generated following mitosis. Energy…”
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A Pumilio-induced RNA structure switch in p27-3′ UTR controls miR-221 and miR-222 accessibility by Agami, Reuven, Kedde, Martijn, van Kouwenhove, Marieke, Zwart, Wilbert, Oude Vrielink, Joachim A. F, Elkon, Ran

“…Key regulators of 3′ untranslated regions (3′ UTRs) are microRNAs and RNA-binding proteins (RBPs). The p27 tumour suppressor is highly expressed in quiescent…”
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The Poly(A)-Binding Protein Nuclear 1 Suppresses Alternative Cleavage and Polyadenylation Sites by Jenal, Mathias, Elkon, Ran, Loayza-Puch, Fabricio, van Haaften, Gijs, Kühn, Uwe, Menzies, Fiona M., Vrielink, Joachim A.F. Oude, Bos, Arnold J., Drost, Jarno, Rooijers, Koos, Rubinsztein, David C., Agami, Reuven

“…Alternative cleavage and polyadenylation (APA) is emerging as an important layer of gene regulation. Factors controlling APA are largely unknown. We developed…”
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GFI1 functions to repress neuronal gene expression in the developing inner ear hair cells by Matern, Maggie S, Milon, Beatrice, Lipford, Erika L, McMurray, Mark, Ogawa, Yoko, Tkaczuk, Andrew, Song, Yang, Elkon, Ran, Hertzano, Ronna

“…Despite the known importance of the transcription factors ATOH1, POU4F3 and GFI1 in hair cell development and regeneration, their downstream transcriptional…”
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Genetic mapping of developmental trajectories for complex traits and diseases by Shulman, Eldad David, Elkon, Ran

“…[Display omitted] Genome-wide association studies (GWAS) have identified numerous common genetic variants associated with complex human traits and diseases…”
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Matrin 3 binds and stabilizes mRNA by Salton, Maayan, Elkon, Ran, Borodina, Tatiana, Davydov, Aleksey, Yaspo, Marie-Laure, Halperin, Eran, Shiloh, Yosef

“…Matrin 3 (MATR3) is a highly conserved, inner nuclear matrix protein with two zinc finger domains and two RNA recognition motifs (RRM), whose function is…”
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ATM-dependent and -independent dynamics of the nuclear phosphoproteome after DNA damage by Bensimon, Ariel, Schmidt, Alexander, Ziv, Yael, Elkon, Ran, Wang, Shih-Ya, Chen, David J, Aebersold, Ruedi, Shiloh, Yosef

“…The double-strand break (DSB) is a cytotoxic DNA lesion caused by oxygen radicals, ionizing radiation, and radiomimetic chemicals. Cells cope with DNA damage…”
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3'UTR Shortening Potentiates MicroRNA-Based Repression of Pro-differentiation Genes in Proliferating Human Cells by Hoffman, Yonit, Bublik, Debora Rosa, Ugalde, Alejandro P, Elkon, Ran, Biniashvili, Tammy, Agami, Reuven, Oren, Moshe, Pilpel, Yitzhak

“…Most mammalian genes often feature alternative polyadenylation (APA) sites and hence diverse 3'UTR lengths. Proliferating cells were reported to favor APA…”
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EXPANDER--an integrative program suite for microarray data analysis by Shamir, Ron, Maron-Katz, Adi, Tanay, Amos, Linhart, Chaim, Steinfeld, Israel, Sharan, Roded, Shiloh, Yosef, Elkon, Ran

“…Gene expression microarrays are a prominent experimental tool in functional genomics which has opened the opportunity for gaining global, systems-level…”
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Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence by Han, Ruiqi, Li, Li, Ugalde, Alejandro Piñeiro, Tal, Arieh, Manber, Zohar, Barbera, Eric Pinto, Chiara, Veronica Della, Elkon, Ran, Agami, Reuven

“…Functional characterization of non-coding elements in the human genome is a major genomic challenge and the maturation of genome-editing technologies is…”
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