Now showing items 1-20 of 28

    • Bioinformatic and Molecular Investigation of Sirt3 Expression 

      Satterstrom, F. Kyle Kyle; Swindell, William R; Bulyk, Martha Leonia; Haigis, Marcia C. (BioMed Central, 2012)
    • Biological Code Breaking in the 21st Century 

      Michelson, Alan M.; Bulyk, Martha Leonia (EMBO and Nature Publishing Group, 2006)
    • CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types 

      Nelms, Bradlee D.; Waldron, Levi; Barrera, Luis A.; Weflen, Andrew W.; Goettel, Jeremy A.; Guo, Guoji; Montgomery, Robert K.; Neutra, Marian R.; Breault, David T.; Snapper, Scott B.; Orkin, Stuart H.; Bulyk, Martha L.; Huttenhower, Curtis; Lencer, Wayne I. (BioMed Central, 2016)
      We present a sensitive approach to predict genes expressed selectively in specific cell types, by searching publicly available expression data for genes with a similar expression profile to known cell-specific markers. Our ...
    • Computational Prediction of Transcription-Factor Binding Site Locations 

      Bulyk, Martha Leonia (BioMed Central, 2003)
      Identifying genomic locations of transcription-factor binding sites, particularly in higher eukaryotic genomes, has been an enormous challenge. Various experimental and computational approaches have been used to detect ...
    • Context influences on TALE–DNA binding revealed by quantitative profiling 

      Rogers, Julia M.; Barrera, Luis A.; Reyon, Deepak; Sander, Jeffry D.; Kellis, Manolis; Joung, J Keith; Bulyk, Martha L. (Nature Pub. Group, 2015)
      Transcription activator-like effector (TALE) proteins recognize DNA using a seemingly simple DNA-binding code, which makes them attractive for use in genome engineering technologies that require precise targeting. Although ...
    • Contribution of Distinct Homeodomain DNA Binding Specificities to Drosophila Embryonic Mesodermal Cell-Specific Gene Expression Programs 

      Busser, Brian W.; Gisselbrecht, Stephen S.; Shokri, Leila; Tansey, Terese R.; Gamble, Caitlin E.; Bulyk, Martha L.; Michelson, Alan M. (Public Library of Science, 2013)
      Homeodomain (HD) proteins are a large family of evolutionarily conserved transcription factors (TFs) having diverse developmental functions, often acting within the same cell types, yet many members of this family paradoxically ...
    • DNA-Binding Specificity Changes in the Evolution of Forkhead Transcription Factors 

      Nakagawa, So; Gisselbrecht, Stephen; Rogers, Julia Maria; Hartl, Daniel L.; Bulyk, Martha Leonia (Proceedings of the National Academy of Sciences, 2013)
      The evolution of transcriptional regulatory networks entails the expansion and diversification of transcription factor (TF) families. The forkhead family of TFs, defined by a highly conserved winged helix DNA-binding domain ...
    • An Evolutionarily Conserved Enhancer Regulates Bmp4 Expression in Developing Incisor and Limb Bud 

      Lachke, Salil A.; O’Connell, Daniel J.; Aboukhalil, Anton; Choe, Sung E.; Turbe-Doan, Annick; Robertson, Erin A.; Amendt, Brad A.; Jumlongras, Dolrudee; Li, Xiao; Ho, Joshua Wing Kei; Olsen, Bjorn Reino; Bulyk, Martha Leonia; Maas, Richard Louis (Public Library of Science, 2012)
      To elucidate the transcriptional regulation of Bmp4 expression during organogenesis, we used phylogenetic footprinting and transgenic reporter analyses to identify Bmp4 cis-regulatory modules (CRMs). These analyses identified ...
    • Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation 

      Kuzu, Guray; Kaye, Emily G.; Chery, Jessica; Siggers, Trevor; Yang, Lin; Dobson, Jason R.; Boor, Sonia; Bliss, Jacob; Liu, Wei; Jogl, Gerwald; Rohs, Remo; Singh, Nadia D.; Bulyk, Martha L.; Tolstorukov, Michael Y.; Larschan, Erica (Public Library of Science, 2016)
      Dosage compensation is an essential process that equalizes transcript levels of X-linked genes between sexes by forming a domain of coordinated gene expression. Throughout the evolution of Diptera, many different X-chromosomes ...
    • Expression-Guided in Silico Evaluation of Candidate Cis Regulatory Codes for Drosophila Muscle Founder Cells 

      Philippakis, Anthony Andrew; Busser, Brian W; Gisselbrecht, Stephen S; He, Fangxue Sherry; Estrada, Beatriz; Michelson, Alan D; Bulyk, Martha Leonia (Public Library of Science, 2006)
      While combinatorial models of transcriptional regulation can be inferred for metazoan systems from a priori biological knowledge, validation requires extensive and time-consuming experimental work. Thus, there is a need ...
    • Genome-Wide Analysis of ETS-Family DNA-Binding In Vitro and In Vivo 

      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; Taipale, Jussi; Bulyk, Martha Leonia (Nature Publishing Group, 2010)
      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 physiology and oncogenesis. Some differences in DNA-binding ...
    • Highly parallel assays of tissue-specific enhancers in whole Drosophila embryos 

      Gisselbrecht, Stephen S.; Barrera, Luis A.; Porsch, Martin; Aboukhalil, Anton; Estep, Preston W.; Vedenko, Anastasia; Palagi, Alexandre; Kim, Yongsok; Zhu, Xianmin; Busser, Brian W.; Gamble, Caitlin E.; Iagovitina, Antonina; Singhania, Aditi; Michelson, Alan M.; Bulyk, Martha L. (2013)
      Transcriptional enhancers are a primary mechanism by which tissue-specific gene expression is achieved. Despite the importance of these regulatory elements in development, responses to environmental stresses, and disease, ...
    • Inferring Condition-Specific Transcription Factor Function from DNA Binding and Gene Expression Data 

      McCord, Rachel Patton; Berger, Michael F; Philippakis, Anthony Andrew; Bulyk, Martha Leonia (2007)
      Numerous genomic and proteomic datasets are permitting the elucidation of transcriptional regulatory networks in the yeast Saccharomyces cerevisiae. However, predicting the condition dependence of regulatory network ...
    • Integrative Functional Genomics 

      Bulyk, Martha Leonia (BioMed Central, 2004)
      A report on the Keystone Symposium 'Biological Discovery Using Diverse High-Throughput Data', Steamboat Springs, USA, 30 March-4 April 2004.
    • Meta-Analysis Discovery of Tissue-Specific DNA Sequence Motifs from Mammalian Gene Expression Data 

      Huber, Bertrand R; Bulyk, Martha Leonia (BioMed Central, 2006)
      Background: A key step in the regulation of gene expression is the sequence-specific binding of transcription factors (TFs) to their DNA recognition sites. However, elucidating TF binding site (TFBS) motifs in higher ...
    • Meta-Profiles of Gene Expression during Aging: Limited Similarities between Mouse and Human and an Unexpectedly Decreased Inflammatory Signature 

      Swindell, William R.; Johnston, Andrew; Sun, Liou; Xing, Xianying; Fisher, Gary J.; Bulyk, Martha Leonia; Elder, James T.; Gudjonsson, Johann E. (Public Library of Science, 2012)
      Background: Skin aging is associated with intrinsic processes that compromise the structure of the extracellular matrix while promoting loss of functional and regenerative capacity. These processes are accompanied by a ...
    • Modular Evolution of DNA-Binding Preference of a Tbrain Transcription Factor Provides a Mechanism for Modifying Gene Regulatory Networks 

      Cheatle Jarvela, Alys M.; Brubaker, Lisa; Vedenko, Anastasia; Gupta, Anisha; Armitage, Bruce A.; Bulyk, Martha L.; Hinman, Veronica F. (Oxford University Press, 2014)
      Gene regulatory networks (GRNs) describe the progression of transcriptional states that take a single-celled zygote to a multicellular organism. It is well documented that GRNs can evolve extensively through mutations to ...
    • Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex 

      Siggers, Trevor; Duyzend, Michael H; Reddy, Jessica; Khan, Sidra; Bulyk, Martha L (Nature Publishing Group, 2011)
      Recruitment of cofactors to specific DNA sites is integral for specificity in gene regulation. As a model system, we examined how targeting and transcriptional control of the sulfur metabolism genes in Saccharomyces ...
    • Nuclear respiratory factor 2 induces SIRT3 expression 

      Satterstrom, F Kyle; Swindell, William R; Laurent, Gaëlle; Vyas, Sejal; Bulyk, Martha L; Haigis, Marcia C (John Wiley & Sons, Ltd, 2015)
      The mitochondrial deacetylase SIRT3 regulates several important metabolic processes. SIRT3 is transcriptionally upregulated in multiple tissues during nutrient stresses such as dietary restriction and fasting, but the ...
    • 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 ...