Search Results - "Bergman, C. M."

ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation by Montgomery, S. B., Griffith, O. L., Sleumer, M. C., Bergman, C. M., Bilenky, M., Pleasance, E. D., Prychyna, Y., Zhang, X., Jones, S. J. M.

“…Motivation: Our understanding of gene regulation is currently limited by our ability to collectively synthesize and catalogue transcriptional regulatory…”
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Drosophila DNase I footprint database: a systematic genome annotation of transcription factor binding sites in the fruitfly, Drosophila melanogaster by Bergman, Casey M., Carlson, Joseph W., Celniker, Susan E.

“…Despite increasing numbers of computational tools developed to predict cis-regulatory sequences, the availability of high-quality datasets of transcription…”
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Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences by Bergman, C M, Kreitman, M

“…Comparative genomic approaches to gene and cis-regulatory prediction are based on the principle that differential DNA sequence conservation reflects variation…”
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Discovering and detecting transposable elements in genome sequences by Bergman, Casey M., Quesneville, Hadi

“…The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and…”
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An antibody to lymphotoxin and tumor necrosis factor prevents transfer of experimental allergic encephalomyelitis by RUDDLE, N. H, BERGMAN, C. M, MCGRATH, K. M, LINGENHELD, E. G, GRUNNET, M. L, PADULA, S. J, CLARK, R. B

“…Uncertainty regarding pathogenic mechanisms has been a major impediment to effective prevention and treatment for human neurologic diseases such as multiple…”
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REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila by Gallo, Steven M, Gerrard, Dave T, Miner, David, Simich, Michael, Des Soye, Benjamin, Bergman, Casey M, Halfon, Marc S

“…The REDfly database of Drosophila transcriptional cis-regulatory elements provides the broadest and most comprehensive available resource for experimentally…”
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Caribou movement as a correlated random walk by BERGMAN, C. M, SCHAEFER, J. A, LUTTICH, S. N

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The Effect of Tissue Complexity and Sward Height on the Functional Response of Wood Bison by Bergman, C. M., Fryxell, J. M., Gates, C. C.

“…1. Little is known about the interplay between tissue complexity and tissue selection and its effect on the ungulate functional response. Effects of sward…”
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REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila by Halfon, Marc S, Gallo, Steven M, Bergman, Casey M

“…The identification and study of the cis-regulatory elements that control gene expression are important areas of biological research, but few resources exist to…”
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The CD40 ligand expressed by human B cells costimulates B cell responses by Grammer, AC, Bergman, MC, Miura, Y, Fujita, K, Davis, LS, Lipsky, PE

“…The possibility that activated B cells might express a ligand for CD40 that was of functional importance for B cell responses was examined by using highly…”
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Purifying Selection Maintains Highly Conserved Noncoding Sequences in Drosophila by Casillas, Sònia, Barbadilla, Antonio, Bergman, Casey M.

“…The majority of metazoan genomes consist of nonprotein-coding regions, although the functional significance of most noncoding DNA sequences remains unknown…”
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Embryonic enhancers in the dpp disk region regulate a second round of Dpp signaling from the dorsal ectoderm to the mesoderm that represses Zfh-1 expression in a subset of pericardial cells by Johnson, A.N, Bergman, C.M, Kreitman, M, Newfeld, S.J

“…During germ band elongation, widespread decapentaplegic (dpp) expression in the dorsal ectoderm patterns the underlying mesoderm. These Dpp signals specify…”
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Caribou Movement as a Correlated Random Walk by Bergman, Carita M., Schaefer, James A., S. N. Luttich

“…Movement is a primary mechanism coupling animals to their environment, yet there exists little empirical analysis to test our theoretical knowledge of this…”
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Ungulate Foraging Strategies: Energy Maximizing or Time Minimizing? by Bergman, Carita M., Fryxell, John M., Gates, C. Cormack, Fortin, Daniel

“…1. Many classical models of ungulate foraging are premised on energy maximization, yet limited empirical evidence and untested currency assumptions make the…”
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allometry of patch selection in ruminants by Wilmshurst, J.F, Fryxell, J.M, Bergman, C.M

“…An axiomatic feature of food consumption by animals is that intake rate and prey abundance are positively related. While this has been demonstrated rigorously…”
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Kinetics and Cellular Origin of Cytokines in the Central Nervous System: Insight into Mechanisms of Myelin Oligodendrocyte Glycoprotein-Induced Experimental Autoimmune Encephalomyelitis by Juedes, Amy E, Hjelmstrom, Peter, Bergman, Cheryl M, Neild, Annie L, Ruddle, Nancy H

“…Experimental autoimmune encephalomyelitis induced by myelin oligodendrocyte glycoprotein (MOG) in C57BL/6 (H-2b) mice is characterized by early (day 12) acute…”
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Tracing the evolutionary history of Drosophila regulatory regions with models that identify transcription factor binding sites by Dermitzakis, Emmanouil T, Bergman, Casey M, Clark, Andrew G

“…Much of evolutionary change is mediated at the level of gene expression, yet our understanding of regulatory evolution remains unsatisfying. In light of recent…”
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A critical role for lymphotoxin in experimental allergic encephalomyelitis by Suen, W E, Bergman, C M, Hjelmström, P, Ruddle, N H

“…The lymphotoxin (LT)/tumor necrosis factor (TNF) family has been implicated in the neurologic inflammatory diseases multiple sclerosis (MS) and experimental…”
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Site fidelity of female caribou at multiple spatial scales by SCHAEFER, James A, BERGMAN, Carita M, LUTTICH, Stuart N

“…Studies of site fidelity have been hampered by arbitrary designations of spatial scale and the lack of null models for comparison. We generated null…”
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Lymphotoxin alpha 3 Induces Chemokines and Adhesion Molecules: Insight into the Role of LT alpha in Inflammation and Lymphoid Organ Development by Cuff, CA, Schwartz, J, Bergman, C M, Russell, K S, Bender, J R, Ruddle, N H

“…Lymphotoxin (LT) plays an important role in inflammation and lymphoid organ development, though the mechanisms by which it promotes these processes are poorly…”
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