Search Results - "Facciotti, Marc T."

Evaluation of algorithm performance in ChIP-seq peak detection by Wilbanks, Elizabeth G, Facciotti, Marc T

“…Next-generation DNA sequencing coupled with chromatin immunoprecipitation (ChIP-seq) is revolutionizing our ability to interrogate whole genome protein-DNA…”
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An integrated pipeline for de novo assembly of microbial genomes by Tritt, Andrew, Eisen, Jonathan A, Facciotti, Marc T, Darling, Aaron E

“…Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types…”
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Phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response by Becker, Erin A, Seitzer, Phillip M, Tritt, Andrew, Larsen, David, Krusor, Megan, Yao, Andrew I, Wu, Dongying, Madern, Dominique, Eisen, Jonathan A, Darling, Aaron E, Facciotti, Marc T

“…Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. Cellular response mechanisms…”
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Thermodynamically inspired classifier for molecular phenotypes of health and disease by Facciotti, Marc T.

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Microscale sulfur cycling in the phototrophic pink berry consortia of the Sippewissett Salt Marsh by Wilbanks, Elizabeth G., Jaekel, Ulrike, Salman, Verena, Humphrey, Parris T., Eisen, Jonathan A., Facciotti, Marc T., Buckley, Daniel H., Zinder, Stephen H., Druschel, Gregory K., Fike, David A., Orphan, Victoria J.

“…Summary Microbial metabolism is the engine that drives global biogeochemical cycles, yet many key transformations are carried out by microbial consortia over…”
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Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant by Persson, Tomas, Battenberg, Kai, Demina, Irina V, Vigil-Stenman, Theoden, Vanden Heuvel, Brian, Pujic, Petar, Facciotti, Marc T, Wilbanks, Elizabeth G, O'Brien, Anna, Fournier, Pascale, Cruz Hernandez, Maria Antonia, Mendoza Herrera, Alberto, Médigue, Claudine, Normand, Philippe, Pawlowski, Katharina, Berry, Alison M

“…Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. Phylogenetically, symbiotic frankiae can be…”
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IRF-1 and miRNA126 Modulate VCAM-1 Expression in Response to a High-Fat Meal by Sun, Chongxiu, Alkhoury, Kenan, Wang, Ying I, Foster, Greg A, Radecke, Christopher E, Tam, Kayan, Edwards, Christina M, Facciotti, Marc T, Armstrong, Ehrin J, Knowlton, Anne A, Newman, John W, Passerini, Anthony G, Simon, Scott I

“…RATIONALE:A high-fat diet accompanied by hypertriglyceridemia increases an individual’s risk for development of atherosclerosis. An early event in this process…”
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Deprotonation of D96 in Bacteriorhodopsin Opens the Proton Uptake Pathway by Wang, Ting, Sessions, Ayla O., Lunde, Christopher S., Rouhani, Shahab, Glaeser, Robert M., Duan, Yong, Facciotti, Marc T.

“…Despite extensive investigation, the precise mechanism controlling the opening of the cytoplasmic proton uptake pathway in bacteriorhodopsin (bR) has remained…”
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A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell by Bonneau, Richard, Facciotti, Marc T., Reiss, David J., Schmid, Amy K., Pan, Min, Kaur, Amardeep, Thorsson, Vesteinn, Shannon, Paul, Johnson, Michael H., Bare, J. Christopher, Longabaugh, William, Vuthoori, Madhavi, Whitehead, Kenia, Madar, Aviv, Suzuki, Lena, Mori, Tetsuya, Chang, Dong-Eun, DiRuggiero, Jocelyne, Johnson, Carl H., Hood, Leroy, Baliga, Nitin S.

“…The environment significantly influences the dynamic expression and assembly of all components encoded in the genome of an organism into functional biological…”
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A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site by Becker, Erin A, Yao, Andrew I, Seitzer, Phillip M, Kind, Tobias, Wang, Ting, Eigenheer, Rich, Shao, Katie S Y, Yarov-Yarovoy, Vladimir, Facciotti, Marc T

“…Opsins are photosensitive proteins catalyzing light-dependent processes across the tree of life. For both microbial (type 1) and metazoan (type 2) opsins,…”
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Schiff base switch II precedes the retinal thermal isomerization in the photocycle of bacteriorhodopsin by Wang, Ting, Facciotti, Marc T, Duan, Yong

“…In bacteriorhodopsin, the order of molecular events that control the cytoplasmic or extracellular accessibility of the Schiff bases (SB) are not well…”
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Role of Squalene in the Organization of Monolayers Derived from Lipid Extracts of Halobacterium salinarum by Gilmore, Sean F, Yao, Andrew I, Tietel, Zipora, Kind, Tobias, Facciotti, Marc T, Parikh, Atul N

“…We have studied interfacial compressibility and lateral organization in monolayer configurations of total (squalene containing) and polar (squalene-devoid)…”
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Combining Microbial Culturing With Mathematical Modeling in an Introductory Course-Based Undergraduate Research Experience by Furrow, Robert E., Kim, Hyunsoo G., Abdelrazek, Samah M. R., Dahlhausen, Katherine, Yao, Andrew I., Eisen, Jonathan A., Goldman, Mark S., Albeck, John G., Facciotti, Marc T.

“…Quantitative techniques are a critical part of contemporary biology research, but students interested in biology enter college with widely varying quantitative…”
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Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea by Baliga, Nitin S, Bonneau, Richard, Facciotti, Marc T, Pan, Min, Glusman, Gustavo, Deutsch, Eric W, Shannon, Paul, Chiu, Yulun, Weng, Rueyhung Sting, Gan, Rueichi Richie, Hung, Pingliang, Date, Shailesh V, Marcotte, Edward, Hood, Leroy, Ng, Wailap Victor

“…We report the complete sequence of the 4,274,642-bp genome of Haloarcula marismortui, a halophilic archaeal isolate from the Dead Sea. The genome is organized…”
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The Exploration of Novel Regulatory Relationships Drives Haloarchaeal Operon-Like Structural Dynamics over Short Evolutionary Distances by Seitzer, Phillip, Yao, Andrew I, Cisneros, Ariana, Facciotti, Marc T

“…Operons are a dominant feature of bacterial and archaeal genome organization. Numerous investigations have related aspects of operon structure to operon…”
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Prevalence of transcription promoters within archaeal operons and coding sequences by Reiss, David J, Koide, Tie, Baliga, Nitin S, Peterson, Amelia, Pratap, Abhishek, Bare, J Christopher, Pan, Min, Van, Phu T, Schmid, Amy K, Marzolf, Bruz, Deutsch, Eric W, Pang, Wyming Lee, Martin, Dan, Facciotti, Marc T, Lo, Fang-Yin

“…Despite the knowledge of complex prokaryotic‐transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with…”
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Gene Gangs of the Chloroviruses: Conserved Clusters of Collinear Monocistronic Genes by Seitzer, Phillip, Jeanniard, Adrien, Ma, Fangrui, Van Etten, James L, Facciotti, Marc T, Dunigan, David D

“…Chloroviruses (family ) are dsDNA viruses found throughout the world's inland waters. The open reading frames in the genomes of 41 sequenced chloroviruses (330…”
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JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison by Seitzer, Phillip, Huynh, Tu Anh, Facciotti, Marc T

“…Cross-species comparisons of gene neighborhoods (also called genomic contexts) in microbes may provide insight into determining functionally related or…”
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Conserved substitution patterns around nucleosome footprints in eukaryotes and Archaea derive from frequent nucleosome repositioning through evolution by Warnecke, Tobias, Becker, Erin A, Facciotti, Marc T, Nislow, Corey, Lehner, Ben

“…Nucleosomes, the basic repeat units of eukaryotic chromatin, have been suggested to influence the evolution of eukaryotic genomes, both by altering the…”
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General Transcription Factor Specified Global Gene Regulation in Archaea by Facciotti, Marc T., Reiss, David J., Pan, Min, Kaur, Amardeep, Vuthoori, Madhavi, Bonneau, Richard, Shannon, Paul, Srivastava, Alok, Donohoe, Samuel M., Hood, Leroy E., Baliga, Nitin S.

“…Cells responding to dramatic environmental changes or undergoing a developmental switch typically change the expression of numerous genes. In bacteria, σ…”
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