Browsing by Author "Bulyk, Martha"
Now showing items 21-30 of 30
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Nucleotides of Transcription Factor Binding Sites Exert Interdependent Effects on the Binding Affinities of Transcription Factors
Bulyk, Martha; Johnson, Philip; Church, GeorgeWe can determine the effects of many possible sequence variations in transcription factor binding sites using microarray binding experiments. Analysis of wild-type and mutant Zif268 (Egr1) zinc fingers bound to microarrays ... -
Objective Sequence-Based Subfamily Classifications of Mouse Homeodomains Reflect Their In Vitro DNA-Binding Preferences
Santos, Miguel A.; Turinsky, Andrei L.; Ong, Serene; Tsai, Jennifer; Berger, Michael F.; Badis, Gwenael; Talukder, Shaheynoor; Gehrke, Andrew R.; Hughes, Timothy R.; Wodak, Shoshana J.; Bulyk, Martha Leonia (Oxford University Press, 2010)Classifying proteins into subgroups with similar molecular function on the basis of sequence is an important step in deriving reliable functional annotations computationally. So far, however, available classification ... -
Phosphorylation of the chromatin remodeling factor DPF3a induces cardiac hypertrophy through releasing HEY repressors from DNA
Cui, Huanhuan; Schlesinger, Jenny; Schoenhals, Sophia; Tönjes, Martje; Dunkel, Ilona; Meierhofer, David; Cano, Elena; Schulz, Kerstin; Berger, Michael F.; Haack, Timm; Abdelilah-Seyfried, Salim; Bulyk, Martha L.; Sauer, Sascha; Sperling, Silke R. (Oxford University Press, 2016)DPF3 (BAF45c) is a member of the BAF chromatin remodeling complex. Two isoforms have been described, namely DPF3a and DPF3b. The latter binds to acetylated and methylated lysine residues of histones. Here, we elaborate on ... -
Predicting the Binding Preference of Transcription Factors to Individual DNA \(\kappa\)-mers
Alleyne, Trevis M.; Peña-Castillo, Lourdes; Badis, Gwenael; Talukder, Shaheynoor; Berger, Michael F.; Gehrke, Andrew R.; Philippakis, Anthony Andrew; Bulyk, Martha Leonia; Morris, Quaid D.; Hughes, Timothy R. (Oxford University Press, 2008)Motivation: Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding preferences, however, are unknown or poorly characterized, in part due ... -
Short-Term Calorie Restriction in Male Mice Feminizes Gene Expression and Alters Key Regulators of Conserved Aging Regulatory Pathways
Estep, Preston Wayne; Warner, Jason B.; Bulyk, Martha Leonia (Public Library of Science, 2009)Background: Calorie restriction (CR) is the only intervention known to extend lifespan in a wide range of organisms, including mammals. However, the mechanisms by which it regulates mammalian aging remain largely unknown, ... -
UniPROBE, Update 2011: Expanded Content and Search Tools in the Online Database of Protein-Binding Microarray Data on Protein–DNA Interactions
Robasky, Kimberly; Bulyk, Martha Leonia (Oxford University Press, 2010)The Universal PBM Resource for Oligonucleotide-Binding Evaluation (UniPROBE) database is a centralized repository of information on the DNA-binding preferences of proteins as determined by universal protein-binding microarray ... -
UniPROBE: An Online Database of Protein Binding Microarray Data on Protein–DNA Interactions
Newburger, Daniel E.; Bulyk, Martha Leonia (Oxford University Press, 2009)The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA-binding specificities of proteins. ... -
Using a Structural and Logics Systems Approach to Infer bHLH-DNA Binding Specificity Determinants
De Masi, Federico; Grove, Christian A.; Vedenko, Anastasia; Alibés, Andreu; Gisselbrecht, Stephen S.; Serrano, Luis; Bulyk, Martha Leonia; Walhout, Albertha J. M. (Oxford University Press, 2011)Numerous efforts are underway to determine gene regulatory networks that describe physical relationships between transcription factors (TFs) and their target DNA sequences. Members of paralogous TF families typically ... -
Using Protein Design Algorithms to Understand the Molecular Basis of Disease Caused by Protein–DNA Interactions: The Pax6 Example
Alibés, Andreu; Nadra, Alejandro D.; De Masi, Federico; Bulyk, Martha Leonia; Serrano, Luis; Stricher, François (Oxford University Press, 2010)Quite often a single or a combination of protein mutations is linked to specific diseases. However, distinguishing from sequence information which mutations have real effects in the protein’s function is not trivial. Protein ... -
The Vibrio harveyi Master Quorum-sensing Regulator, LuxR, a TetR-type Protein is Both an Activator and a Repressor: DNA Recognition and Binding Specificity at Target Promoters
Pompeani, Audra J; Irgon, Joseph J; Berger, Michael F; Bulyk, Martha Leonia; Wingreen, Ned S; Bassler, Bonnie L (Blackwell Publishing Ltd, 2008)Quorum sensing is the process of cell-to-cell communication by which bacteria communicate via secreted signal molecules called autoinducers. As cell population density increases, the accumulation of autoinducers leads to ...