Global properties of regulatory sequences are predicted by transcription factor recognition mechanisms by Zain M. Patel, Timothy R. Hughes

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Poly-dA:dT tracts form an in vivo nucleosomal turnstile. by Carl G de Boer, Timothy R Hughes

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Comparison of ChIP-Seq Data and a Reference Motif Set for Human KRAB C2H2 Zinc Finger Proteins by Marjan Barazandeh, Samuel A. Lambert, Mihai Albu, Timothy R. Hughes

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RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. by Hilal Kazan, Debashish Ray, Esther T Chan, Timothy R Hughes, Quaid Morris

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Response to “The Reality of Pervasive Transcription”. by Harm van Bakel, Corey Nislow, Benjamin J. Blencowe, Timothy R. Hughes

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Most "dark matter" transcripts are associated with known genes. by Harm van Bakel, Corey Nislow, Benjamin J Blencowe, Timothy R Hughes

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A compendium of nucleosome and transcript profiles reveals determinants of chromatin architecture and transcription. by Harm van Bakel, Kyle Tsui, Marinella Gebbia, Sanie Mnaimneh, Timothy R Hughes, Corey Nislow

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Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function by Nguyen N. T. Vo, Ally Yang, Wiphawee Leesutthiphonchai, Yulong Liu, Timothy R. Hughes, Howard S. Judelson

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Non-base-contacting residues enable kaleidoscopic evolution of metazoan C2H2 zinc finger DNA binding by Hamed S. Najafabadi, Michael Garton, Matthew T. Weirauch, Sanie Mnaimneh, Ally Yang, Philip M. Kim, Timothy R. Hughes

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Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints. by Sarah A Smith, Debashish Ray, Kate B Cook, Michael J Mallory, Timothy R Hughes, Kristen W Lynch

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Chromatin- and transcription-related factors repress transcription from within coding regions throughout the Saccharomyces cerevisiae genome. by Vanessa Cheung, Gordon Chua, Nizar N Batada, Christian R Landry, Stephen W Michnick, Timothy R Hughes, Fred Winston

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Genetic interactions of MAF1 identify a role for Med20 in transcriptional repression of ribosomal protein genes. by Ian M Willis, Gordon Chua, Amy H Tong, Renee L Brost, Timothy R Hughes, Charles Boone, Robyn D Moir

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A novel C2H2 transcription factor that regulates gliA expression interdependently with GliZ in Aspergillus fumigatus. by Taylor J Schoberle, C Kim Nguyen-Coleman, Jennifer Herold, Ally Yang, Matt Weirauch, Timothy R Hughes, John S McMurray, Gregory S May

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Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes. by H Charlotte van der Does, Like Fokkens, Ally Yang, Sarah M Schmidt, Léon Langereis, Joanna M Lukasiewicz, Timothy R Hughes, Martijn Rep

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Parasite burden and CD36-mediated sequestration are determinants of acute lung injury in an experimental malaria model. by Fiona E Lovegrove, Sina A Gharib, Lourdes Peña-Castillo, Samir N Patel, John T Ruzinski, Timothy R Hughes, W Conrad Liles, Kevin C Kain

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The Impact of Probiotic Supplementation on Cognitive, Pathological and Metabolic Markers in a Transgenic Mouse Model of Alzheimer’s Disease by Thomas S. Webberley, Thomas S. Webberley, Giulia Masetti, Ryan J. Bevan, Ryan J. Bevan, Joshua Kerry-Smith, Alison A. Jack, Daryn R. Michael, Sophie Thomas, Maria Glymenaki, Jia Li, Julie A. K. McDonald, Daniel John, James E. Morgan, Julian R. Marchesi, Mark A. Good, Sue F. Plummer, Timothy R. Hughes, Timothy R. Hughes

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High nucleosome occupancy is encoded at human regulatory sequences. by Desiree Tillo, Noam Kaplan, Irene K Moore, Yvonne Fondufe-Mittendorf, Andrea J Gossett, Yair Field, Jason D Lieb, Jonathan Widom, Eran Segal, Timothy R Hughes

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Complement mediated signaling on pulmonary CD103(+) dendritic cells is critical for their migratory function in response to influenza infection. by Matheswaran Kandasamy, Poon C Ying, Adrian W S Ho, Hermi R Sumatoh, Andreas Schlitzer, Timothy R Hughes, David M Kemeny, B Paul Morgan, Florent Ginhoux, Baalasubramanian Sivasankar

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Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians by Jordi Solana, Manuel Irimia, Salah Ayoub, Marta Rodriguez Orejuela, Vera Zywitza, Marvin Jens, Javier Tapial, Debashish Ray, Quaid Morris, Timothy R Hughes, Benjamin J Blencowe, Nikolaus Rajewsky

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The Impact of Lab4 Probiotic Supplementation in a 90-Day Study in Wistar Rats by Thomas S. Webberley, Giulia Masetti, Laura M. Baker, Jordanna Dally, Timothy R. Hughes, Julian R. Marchesi, Alison A. Jack, Sue F. Plummer, Guru Ramanathan, Paul D. Facey, Daryn R. Michael

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