Search Results - "Bailey, L"

STREME: accurate and versatile sequence motif discovery by Bailey, Timothy L

“…Sequence motif discovery algorithms can identify novel sequence patterns that perform biological functions in DNA, RNA and protein sequences-for example, the…”
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DREME: motif discovery in transcription factor ChIP-seq data by BAILEY, Timothy L

“…Transcription factor (TF) ChIP-seq datasets have particular characteristics that provide unique challenges and opportunities for motif discovery. Most existing…”
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MEME-ChIP: motif analysis of large DNA datasets by MACHANICK, Philip, BAILEY, Timothy L

“…Advances in high-throughput sequencing have resulted in rapid growth in large, high-quality datasets including those arising from transcription factor (TF)…”
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Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts by Ay, Ferhat, Bailey, Timothy L, Noble, William Stafford

“…Our current understanding of how DNA is packed in the nucleus is most accurate at the fine scale of individual nucleosomes and at the large scale of chromosome…”
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Globally rising soil heterotrophic respiration over recent decades by Bond-Lamberty, Ben, Bailey, Vanessa L., Chen, Min, Gough, Christopher M., Vargas, Rodrigo

“…Global soils store at least twice as much carbon as Earth’s atmosphere 1 , 2 . The global soil-to-atmosphere (or total soil respiration, R S ) carbon dioxide…”
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FIMO: scanning for occurrences of a given motif by GRANT, Charles E, BAILEY, Timothy L, STAFFORD NOBLE, William

“…A motif is a short DNA or protein sequence that contributes to the biological function of the sequence in which it resides. Over the past several decades, many…”
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Motif Enrichment Analysis: a unified framework and an evaluation on ChIP data by McLeay, Robert C, Bailey, Timothy L

“…A major goal of molecular biology is determining the mechanisms that control the transcription of genes. Motif Enrichment Analysis (MEA) seeks to determine…”
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An evidence-based review of quantitative SPECT imaging and potential clinical applications by Bailey, Dale L, Willowson, Kathy P

“…SPECT has traditionally been regarded as nonquantitative. Advances in multimodality γ-cameras (SPECT/CT), algorithms for image reconstruction, and…”
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Defining the RGG/RG Motif by Thandapani, Palaniraja, O’Connor, Timothy R., Bailey, Timothy L., Richard, Stéphane

“…Motifs rich in arginines and glycines were recognized several decades ago to play functional roles and were termed glycine-arginine-rich (GAR) domains and/or…”
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Developing a molecular picture of soil organic matter–mineral interactions by quantifying organo–mineral binding by Newcomb, C. J., Qafoku, N. P., Grate, J. W., Bailey, V. L., De Yoreo, J. J.

“…Long residence times of soil organic matter have been attributed to reactive mineral surface sites that sorb organic species and cause inaccessibility due to…”
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GT-Scan: identifying unique genomic targets by O'Brien, Aidan, Bailey, Timothy L

“…A number of technologies, including CRISPR/Cas, transcription activator-like effector nucleases and zinc-finger nucleases, allow the user to target a chosen…”
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What do we know about soil carbon destabilization? by Bailey, Vanessa L, Pries, Caitlin Hicks, Lajtha, Kate

“…Most empirical and modeling research on soil carbon (C) dynamics has focused on those processes that control and promote C stabilization. However, we lack a…”
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Improving occupancy estimation when two types of observational error occur: non-detection and species misidentification by Miller, David A, Nichols, James D, McClintock, Brett T, Grant, Evan H. Campbell, Bailey, Larissa L, Weir, Linda A

“…Efforts to draw inferences about species occurrence frequently account for false negatives, the common situation when individuals of a species are not detected…”
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Polymer mimics of biomacromolecular antifreezes by Biggs, Caroline I., Bailey, Trisha L., Ben Graham, Stubbs, Christopher, Fayter, Alice, Gibson, Matthew I.

“…Antifreeze proteins from polar fish species are remarkable biomacromolecules which prevent the growth of ice crystals. Ice crystal growth is a major problem in…”
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A Crisp(r) New Perspective on SARS-CoV-2 Biology by Bailey, Adam L., Diamond, Michael S.

“…Complementary genome-wide CRISPR-Cas9 screens performed by multiple groups reveal new insights into SARS-CoV-2 biology including aspects of viral entry,…”
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SARS-CoV-2 infection of human ACE2-transgenic mice causes severe lung inflammation and impaired function by Winkler, Emma S., Bailey, Adam L., Kafai, Natasha M., Nair, Sharmila, McCune, Broc T., Yu, Jinsheng, Fox, Julie M., Chen, Rita E., Earnest, James T., Keeler, Shamus P., Ritter, Jon H., Kang, Liang-I, Dort, Sarah, Robichaud, Annette, Head, Richard, Holtzman, Michael J., Diamond, Michael S.

“…Although animal models have been evaluated for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, none have fully recapitulated the lung…”
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Growth, detection, quantification, and inactivation of SARS-CoV-2 by Case, James Brett, Bailey, Adam L., Kim, Arthur S., Chen, Rita E., Diamond, Michael S.

“…Severe acute respiratory syndrome coronavirus (SARS-CoV)-2 is the agent responsible for the coronavirus disease 2019 (COVID-19) global pandemic. SARS-CoV-2 is…”
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Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis by Johnson, Bryan A., Xie, Xuping, Bailey, Adam L., Kalveram, Birte, Lokugamage, Kumari G., Muruato, Antonio, Zou, Jing, Zhang, Xianwen, Juelich, Terry, Smith, Jennifer K., Zhang, Lihong, Bopp, Nathen, Schindewolf, Craig, Vu, Michelle, Vanderheiden, Abigail, Winkler, Emma S., Swetnam, Daniele, Plante, Jessica A., Aguilar, Patricia, Plante, Kenneth S., Popov, Vsevolod, Lee, Benhur, Weaver, Scott C., Suthar, Mehul S., Routh, Andrew L., Ren, Ping, Ku, Zhiqiang, An, Zhiqiang, Debbink, Kari, Diamond, Michael S., Shi, Pei-Yong, Freiberg, Alexander N., Menachery, Vineet D.

“…Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)—a new coronavirus that has led to a worldwide pandemic 1 —has a furin cleavage site (PRRAR) in its…”
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Development and Initial Validation of the Risk Analysis Index for Measuring Frailty in Surgical Populations by Hall, Daniel E, Arya, Shipra, Schmid, Kendra K, Blaser, Casey, Carlson, Mark A, Bailey, Travis L, Purviance, Georgia, Bockman, Tammy, Lynch, Thomas G, Johanning, Jason

“…Growing consensus suggests that frailty-associated risks should inform shared surgical decision making. However, it is not clear how best to screen for frailty…”
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Fruits, vegetables, and health: A comprehensive narrative, umbrella review of the science and recommendations for enhanced public policy to improve intake by Wallace, Taylor C., Bailey, Regan L., Blumberg, Jeffrey B., Burton-Freeman, Britt, Chen, C-y. Oliver, Crowe-White, Kristi M., Drewnowski, Adam, Hooshmand, Shirin, Johnson, Elizabeth, Lewis, Richard, Murray, Robert, Shapses, Sue A., Wang, Ding Ding

“…Fruit and vegetables (F&V) have been a cornerstone of healthy dietary recommendations; the 2015-2020 U.S. Dietary Guidelines for Americans recommend that F&V…”
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