Search Results - "Badis, Gwenael"

Antisense transcriptional interference mediates condition-specific gene repression in budding yeast by Nevers, Alicia, Doyen, Antonia, Malabat, Christophe, Néron, Bertrand, Kergrohen, Thomas, Jacquier, Alain, Badis, Gwenael

“…Abstract Pervasive transcription generates many unstable non-coding transcripts in budding yeast. The transcription of such noncoding RNAs, in particular…”
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RNA degradation triggered by decapping is largely independent of initial deadenylation by Audebert, Léna, Feuerbach, Frank, Zedan, Mostafa, Schürch, Alexandra P, Decourty, Laurence, Namane, Abdelkader, Permal, Emmanuelle, Weis, Karsten, Badis, Gwenaël, Saveanu, Cosmin

“…RNA stability, important for eukaryotic gene expression, is thought to depend on deadenylation rates, with shortened poly(A) tails triggering decapping and 5'…”
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eIF2A represses cell wall biogenesis gene expression in Saccharomyces cerevisiae by Meyer, Laura, Courtin, Baptiste, Gomard, Maïté, Namane, Abdelkader, Permal, Emmanuelle, Badis, Gwenael, Jacquier, Alain, Fromont-Racine, Micheline

“…Translation initiation is a complex and highly regulated process that represents an important mechanism, controlling gene expression. eIF2A was proposed as an…”
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Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo by Wei, Gong-Hong, Badis, Gwenael, Berger, Michael F, Kivioja, Teemu, Palin, Kimmo, Enge, Martin, Bonke, Martin, Jolma, Arttu, Varjosalo, Markku, Gehrke, Andrew R, Yan, Jian, Talukder, Shaheynoor, Turunen, Mikko, Taipale, Mikko, Stunnenberg, Hendrik G, Ukkonen, Esko, Hughes, Timothy R, Bulyk, Martha L, Taipale, Jussi

“…Members of the large ETS family of transcription factors (TFs) have highly similar DNA‐binding domains (DBDs)—yet they have diverse functions and activities in…”
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A Library of Yeast Transcription Factor Motifs Reveals a Widespread Function for Rsc3 in Targeting Nucleosome Exclusion at Promoters by Badis, Gwenael, Chan, Esther T., van Bakel, Harm, Pena-Castillo, Lourdes, Tillo, Desiree, Tsui, Kyle, Carlson, Clayton D., Gossett, Andrea J., Hasinoff, Michael J., Warren, Christopher L., Gebbia, Marinella, Talukder, Shaheynoor, Yang, Ally, Mnaimneh, Sanie, Terterov, Dimitri, Coburn, David, Li Yeo, Ai, Yeo, Zhen Xuan, Clarke, Neil D., Lieb, Jason D., Ansari, Aseem Z., Nislow, Corey, Hughes, Timothy R.

“…The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we describe systematic…”
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TFCat: the curated catalog of mouse and human transcription factors by Fulton, Debra L, Sundararajan, Saravanan, Badis, Gwenael, Hughes, Timothy R, Wasserman, Wyeth W, Roach, Jared C, Sladek, Rob

“…Unravelling regulatory programs governed by transcription factors (TFs) is fundamental to understanding biological systems. TFCat is a catalog of mouse and…”
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Diversity and Complexity in DNA Recognition by Transcription Factors by Badis, Gwenael, Berger, Michael F, Philippakis, Anthony A, Talukder, Shaheynoor, Gehrke, Andrew R, Jaeger, Savina A, Chan, Esther T, Metzler, Genita, Vedenko, Anastasia, Chen, Xiaoyu, Kuznetsov, Hanna, Wang, Chi-Fong, Coburn, David, Newburger, Daniel E, Morris, Quaid, Hughes, Timothy R, Bulyk, Martha L

“…Sequence preferences of DNA binding proteins are a primary mechanism by which cells interpret the genome. Despite the central importance of these proteins in…”
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YLR419W is the homolog of the mammalian translation initiation factor DHX29 by Fromont-Racine, Micheline, Khanna, Varun, Jacquier, Alain, Badis, Gwenael

“…27 years after the yeast genome sequencing, the function of many ORFs remain unknown. Despite the evolutionary distance between human and yeast, homology with…”
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Hmo1 Is Required for TOR-Dependent Regulation of Ribosomal Protein Gene Transcription by Berger, Axel B., Decourty, Laurence, Badis, Gwenaël, Nehrbass, Ulf, Jacquier, Alain, Gadal, Olivier

“…Article Usage Stats Services MCB Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley…”
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Systematic Determination of Transcription Factor DNA-Binding Specificities in Yeast by Peña-Castillo, Lourdes, Badis, Gwenael

“…Understanding how genes are regulated, decoding their "regulome", is one of the main challenges of the post-genomic era. Here, we describe the in vitro method…”
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Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences by Berger, Michael F., Badis, Gwenael, Gehrke, Andrew R., Talukder, Shaheynoor, Philippakis, Anthony A., Peña-Castillo, Lourdes, Alleyne, Trevis M., Mnaimneh, Sanie, Botvinnik, Olga B., Chan, Esther T., Khalid, Faiqua, Zhang, Wen, Newburger, Daniel, Jaeger, Savina A., Morris, Quaid D., Bulyk, Martha L., Hughes, Timothy R.

“…Most homeodomains are unique within a genome, yet many are highly conserved across vast evolutionary distances, implying strong selection on their precise…”
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Targeted mRNA Degradation by Deadenylation-Independent Decapping by Badis, Gwenael, Saveanu, Cosmin, Fromont-Racine, Micheline, Jacquier, Alain

“…Modulating the rate of mRNA degradation is a fast and efficient way to control gene expression. In a yeast strain deleted of EDC3, a component of the decapping…”
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Yeast ribosomal protein L7 and its homologue Rlp7 are simultaneously present at distinct sites on pre-60S ribosomal particles by Babiano, Reyes, Badis, Gwenael, Saveanu, Cosmin, Namane, Abdelkader, Doyen, Antonia, Díaz-Quintana, Antonio, Jacquier, Alain, Fromont-Racine, Micheline, de la Cruz, Jesús

“…Ribosome biogenesis requires >300 assembly factors in Saccharomyces cerevisiae. Ribosome assembly factors Imp3, Mrt4, Rlp7 and Rlp24 have sequence similarity…”
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Evaluation of Data-Dependent versus Targeted Shotgun Proteomic Approaches for Monitoring Transcription Factor Expression in Breast Cancer by Sandhu, Charanjit, Hewel, Johannes A, Badis, Gwenael, Talukder, Shaheynoor, Liu, Jian, Hughes, Timothy R, Emili, Andrew

“…In breast cancer, there is a significant degree of molecular diversity among tumors. Multiple perturbations in signal transduction pathways impinge on…”
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Objective sequence-based subfamily classifications of mouse homeodomains reflect their in vitro DNA-binding preferences by Santos, Miguel A, Turinsky, Andrei L, Ong, Serene, Tsai, Jennifer, Berger, Michael F, Badis, Gwenael, Talukder, Shaheynoor, Gehrke, Andrew R, Bulyk, Martha L, Hughes, Timothy R, Wodak, Shoshana J

“…Classifying proteins into subgroups with similar molecular function on the basis of sequence is an important step in deriving reliable functional annotations…”
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Cryptic Pol II Transcripts Are Degraded by a Nuclear Quality Control Pathway Involving a New Poly(A) Polymerase by Wyers, Françoise, Rougemaille, Mathieu, Badis, Gwenaël, Rousselle, Jean-Claude, Dufour, Marie-Elisabeth, Boulay, Jocelyne, Régnault, Béatrice, Devaux, Frédéric, Namane, Abdelkader, Séraphin, Bertrand, Libri, Domenico, Jacquier, Alain

“…Since detection of an RNA molecule is the major criterion to define transcriptional activity, the fraction of the genome that is expressed is generally…”
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eIF2A represses cell wall biogenesis gene expression in Saccharomyces cerevisiae by Laura Meyer, Baptiste Courtin, Maïté Gomard, Abdelkader Namane, Emmanuelle Permal, Gwenael Badis, Alain Jacquier, Micheline Fromont-Racine

“…Translation initiation is a complex and highly regulated process that represents an important mechanism, controlling gene expression. eIF2A was proposed as an…”
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A snoRNA that guides the two most conserved pseudouridine modifications within rRNA confers a growth advantage in yeast by Badis, Gwenael, Fromont-Racine, Micheline, Jacquier, Alain

“…Ribosomal RNAs contain a number of modified nucleotides. The most abundant nucleotide modifications found within rRNAs fall into two types: 2'-O-ribose…”
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Predicting the binding preference of transcription factors to individual DNA k-mers by Alleyne, Trevis M., Peña-Castillo, Lourdes, Badis, Gwenael, Talukder, Shaheynoor, Berger, Michael F., Gehrke, Andrew R., Philippakis, Anthony A., Bulyk, Martha L., Morris, Quaid D., Hughes, Timothy R.

“…Motivation: Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding…”
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A new library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters by Badis, Gwenael, Chan, Esther T., van Bakel, Harm, Pena-Castillo, Lourdes, Tillo, Desiree, Tsui, Kyle, Carlson, Clayton D., Gossett, Andrea J., Hasinoff, Michael J., Warren, Christopher L., Gebbia, Marinella, Talukder, Shaheynoor, Yang, Ally, Mnaimneh, Sanie, Terterov, Dimitri, Coburn, David, Yeo, Ai Li, Yeo, Zhen Xuan, Clarke, Neil D., Lieb, Jason D., Ansari, Aseem Z., Nislow, Corey, Hughes, Timothy R.

“…The sequence specificity of DNA-binding proteins is the primary mechanism by which the cell recognizes genomic features. Here, we describe systematic…”
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