Integrative classification of human coding and noncoding genes through RNA metabolism profiles von Mukherjee, Neelanjan, Calviello, Lorenzo, Hirsekorn, Antje, de Pretis, Stefano, Pelizzola, Mattia, Ohler, Uwe

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Detecting actively translated open reading frames in ribosome profiling data von Calviello, Lorenzo, Mukherjee, Neelanjan, Wyler, Emanuel, Zauber, Henrik, Hirsekorn, Antje, Selbach, Matthias, Landthaler, Markus, Obermayer, Benedikt, Ohler, Uwe

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Global identification of functional microRNA-mRNA interactions in Drosophila von Wessels, Hans-Hermann, Lebedeva, Svetlana, Hirsekorn, Antje, Wurmus, Ricardo, Akalin, Altuna, Mukherjee, Neelanjan, Ohler, Uwe

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PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data von Corcoran, David L, Georgiev, Stoyan, Mukherjee, Neelanjan, Gottwein, Eva, Skalsky, Rebecca L, Keene, Jack D, Ohler, Uwe

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Global target mRNA specification and regulation by the RNA-binding protein ZFP36 von Mukherjee, Neelanjan, Jacobs, Nicholas C, Hafner, Markus, Kennington, Elizabeth A, Nusbaum, Jeffrey D, Tuschl, Thomas, Blackshear, Perry J, Ohler, Uwe

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Deciphering human ribonucleoprotein regulatory networks von Mukherjee, Neelanjan, Wessels, Hans-Hermann, Lebedeva, Svetlana, Sajek, Marcin, Ghanbari, Mahsa, Garzia, Aitor, Munteanu, Alina, Yusuf, Dilmurat, Farazi, Thalia, Hoell, Jessica I, Akat, Kemal M, Akalin, Altuna, Tuschl, Thomas, Ohler, Uwe

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PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking von Forman, Thomas E, Sajek, Marcin P, Larson, Eric D, Mukherjee, Neelanjan, Fantauzzo, Katherine A

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Viral MicroRNA Targetome of KSHV-Infected Primary Effusion Lymphoma Cell Lines von Gottwein, Eva, Corcoran, David L., Mukherjee, Neelanjan, Skalsky, Rebecca L., Hafner, Markus, Nusbaum, Jeffrey D., Shamulailatpam, Priscilla, Love, Cassandra L., Dave, Sandeep S., Tuschl, Thomas, Ohler, Uwe, Cullen, Bryan R.

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Ribonomic Analysis of Human Pum1 Reveals cis-trans Conservation across Species despite Evolution of Diverse mRNA Target Sets von Morris, Adam R., Mukherjee, Neelanjan, Keene, Jack D.

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Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data von Li, Song, Liberman, Louisa M, Mukherjee, Neelanjan, Benfey, Philip N, Ohler, Uwe

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Coordinated posttranscriptional mRNA population dynamics during T-cell activation von Keene, Jack D, Mukherjee, Neelanjan, Lager, Patrick J, Friedersdorf, Matthew B, Thompson, Marshall A

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Transcriptomic Response Dynamics of Human Primary and Immortalized Adrenocortical Cells to Steroidogenic Stimuli von Wellman, Kimberly, Fu, Rui, Baldwin, Amber, Rege, Juilee, Murphy, Elisabeth, Rainey, William E., Mukherjee, Neelanjan

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Tissue type-specific expression of the dsRNA-binding protein 76 and genome-wide elucidation of its target mRNAs von Neplioueva, Valentina, Dobrikova, Elena Y, Mukherjee, Neelanjan, Keene, Jack D, Gromeier, Matthias

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Radiation enhances the invasive potential of primary glioblastoma cells via activation of the Rho signaling pathway von Zhai, Gary G, Malhotra, Rajeev, Delaney, Meaghan, Latham, Douglas, Nestler, Ulf, Zhang, Min, Mukherjee, Neelanjan, Song, Qinhui, Robe, Pierre, Chakravarti, Arnab

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ELAVL1 primarily couples mRNA stability with the 3′ UTRs of interferon-stimulated genes von Rothamel, Katherine, Arcos, Sarah, Kim, Byungil, Reasoner, Clara, Lisy, Samantha, Mukherjee, Neelanjan, Ascano, Manuel

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SSMART: sequence-structure motif identification for RNA-binding proteins von Munteanu, Alina, Mukherjee, Neelanjan, Ohler, Uwe

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Adenovirus-mediated inhibition of survivin expression sensitizes human prostate cancer cells to paclitaxel in vitro and in vivo von Zhang, Min, Mukherjee, Neelanjan, Bermudez, R. Scott, Latham, Douglas E., Delaney, Meaghan A., Zietman, Anthony L., Shipley, William U., Chakravarti, Arnab

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FMRP targets distinct mRNA sequence elements to regulate protein expression von Ascano, Manuel, Mukherjee, Neelanjan, Bandaru, Pradeep, Miller, Jason B., Nusbaum, Jeffrey D., Corcoran, David L., Langlois, Christine, Munschauer, Mathias, Dewell, Scott, Hafner, Markus, Williams, Zev, Ohler, Uwe, Tuschl, Thomas

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PDGFR[alpha] signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking von Forman, Thomas E, Sajek, Marcin P, Larson, Eric D, Mukherjee, Neelanjan, Fantauzzo, Katherine A

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Integrative Regulatory Mapping Indicates that the RNA-Binding Protein HuR Couples Pre-mRNA Processing and mRNA Stability von Mukherjee, Neelanjan, Corcoran, David L., Nusbaum, Jeffrey D., Reid, David W., Georgiev, Stoyan, Hafner, Markus, Ascano, Manuel, Tuschl, Thomas, Ohler, Uwe, Keene, Jack D.

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