Search Results - "Colwell, J."

Comparative analysis of nanobody sequence and structure data by Mitchell, Laura S., Colwell, Lucy J.

“…Nanobodies are a class of antigen‐binding protein derived from camelids that achieve comparable binding affinities and specificities to classical antibodies,…”
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Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing by Hopf, Thomas A., Colwell, Lucy J., Sheridan, Robert, Rost, Burkhard, Sander, Chris, Marks, Debora S.

“…We show that amino acid covariation in proteins, extracted from the evolutionary sequence record, can be used to fold transmembrane proteins. We use this…”
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Protein 3D structure computed from evolutionary sequence variation by Marks, Debora S, Colwell, Lucy J, Sheridan, Robert, Hopf, Thomas A, Pagnani, Andrea, Zecchina, Riccardo, Sander, Chris

“…The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of…”
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Analysis of nanobody paratopes reveals greater diversity than classical antibodies by Mitchell, Laura S, Colwell, Lucy J

“…Abstract Nanobodies (Nbs) are a class of antigen-binding protein derived from camelid immune systems, which achieve equivalent binding affinities and…”
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Deep diversification of an AAV capsid protein by machine learning by Bryant, Drew H., Bashir, Ali, Sinai, Sam, Jain, Nina K., Ogden, Pierce J., Riley, Patrick F., Church, George M., Colwell, Lucy J., Kelsic, Eric D.

“…Modern experimental technologies can assay large numbers of biological sequences, but engineered protein libraries rarely exceed the sequence diversity of…”
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ProteInfer, deep neural networks for protein functional inference by Sanderson, Theo, Bileschi, Maxwell L, Belanger, David, Colwell, Lucy J

“…Predicting the function of a protein from its amino acid sequence is a long-standing challenge in bioinformatics. Traditional approaches use sequence alignment…”
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Computational approaches to therapeutic antibody design: established methods and emerging trends by Norman, Richard A, Ambrosetti, Francesco, Bonvin, Alexandre M J J, Colwell, Lucy J, Kelm, Sebastian, Kumar, Sandeep, Krawczyk, Konrad

“…Abstract Antibodies are proteins that recognize the molecular surfaces of potentially noxious molecules to mount an adaptive immune response or, in the case of…”
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MGnify: the microbiome sequence data analysis resource in 2023 by Richardson, Lorna, Allen, Ben, Baldi, Germana, Beracochea, Martin, Bileschi, Maxwell L, Burdett, Tony, Burgin, Josephine, Caballero-Pérez, Juan, Cochrane, Guy, Colwell, Lucy J, Curtis, Tom, Escobar-Zepeda, Alejandra, Gurbich, Tatiana A, Kale, Varsha, Korobeynikov, Anton, Raj, Shriya, Rogers, Alexander B, Sakharova, Ekaterina, Sanchez, Santiago, Wilkinson, Darren J, Finn, Robert D

“…The MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences. The…”
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The composition and structure of the Enceladus plume by Hansen, C. J., Shemansky, D. E., Esposito, L. W., Stewart, A. I. F., Lewis, B. R., Colwell, J. E., Hendrix, A. R., West, R. A., Waite Jr, J. H., Teolis, B., Magee, B. A.

“…The Cassini Ultraviolet Imaging Spectrograph (UVIS) observed an occultation of the Sun by the water vapor plume at the south polar region of Saturn's moon…”
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Protein sectors: statistical coupling analysis versus conservation by Teşileanu, Tiberiu, Colwell, Lucy J, Leibler, Stanislas

“…Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed…”
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core subunit of Polycomb repressive complex 1 is broadly conserved in function but not primary sequence by Beh, Leslie Y, Colwell, Lucy J, Francis, Nicole J

“…Polycomb Group (PcG) proteins mediate heritable gene silencing by modifying chromatin structure. An essential PcG complex, PRC1, compacts chromatin and…”
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An enhanced target-enrichment bait set for Hexacorallia provides phylogenomic resolution of the staghorn corals (Acroporidae) and close relatives by Cowman, Peter F., Quattrini, Andrea M., Bridge, Tom C.L., Watkins-Colwell, Gregory J., Fadli, Nur, Grinblat, Mila, Roberts, T. Edward, McFadden, Catherine S., Miller, David J., Baird, Andrew H.

“…[Display omitted] •Genomic capture methods can resolve clades that lack decades of molecular marker development.•An enhanced bait setfor Hexacorallia recovers…”
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Direct serotonin release in humans shapes aversive learning and inhibition by Colwell, Michael J., Tagomori, Hosana, Shang, Fei, Cheng, Hoi Iao, Wigg, Chloe E., Browning, Michael, Cowen, Philip J., Murphy, Susannah E., Harmer, Catherine J.

“…The role of serotonin in human behaviour is informed by approaches which allow in vivo modification of synaptic serotonin. However, characterising the effects…”
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Enceladus' Water Vapor Plume by Hansen, Candice J, Esposito, L, Stewart, A. I. F, Colwell, J, Hendrix, A, Pryor, W, Shemansky, D, West, R

“…The Cassini spacecraft flew close to Saturn's small moon Enceladus three times in 2005. Cassini's UltraViolet Imaging Spectrograph observed stellar…”
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Glycation changes molecular organization and charge distribution in type I collagen fibrils by Bansode, Sneha, Bashtanova, Uliana, Li, Rui, Clark, Jonathan, Müller, Karin H., Puszkarska, Anna, Goldberga, Ieva, Chetwood, Holly H., Reid, David G., Colwell, Lucy J., Skepper, Jeremy N., Shanahan, Catherine M., Schitter, Georg, Mesquida, Patrick, Duer, Melinda J.

“…Collagen fibrils are central to the molecular organization of the extracellular matrix (ECM) and to defining the cellular microenvironment. Glycation of…”
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Lunar surface: Dust dynamics and regolith mechanics by Colwell, J. E., Batiste, S., Horányi, M., Robertson, S., Sture, S.

“…The lunar surface is characterized by a collisionally evolved regolith resulting from meteoroid bombardment. This lunar soil consists of highly angular…”
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Pharmacological targeting of cognitive impairment in depression: recent developments and challenges in human clinical research by Colwell, Michael J., Tagomori, Hosana, Chapman, Sarah, Gillespie, Amy L., Cowen, Philip J., Harmer, Catherine J., Murphy, Susannah E.

“…Impaired cognition is often overlooked in the clinical management of depression, despite its association with poor psychosocial functioning and reduced…”
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Pretend and Physical Play: Links to Preschoolers' Affective Social Competence by Lindsey, Eric W, Colwell, Malinda J

“…This study investigated different forms of pretend and physical play as predictors of preschool children'saffective social competence(ASC). Data were collected…”
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Honey bee‐collected pollen in agro‐ecosystems reveals diet diversity, diet quality, and pesticide exposure by Colwell, Megan J., Williams, Geoffrey R., Evans, Rodger C., Shutler, Dave

“…European honey bees Apis mellifera are important commercial pollinators that have suffered greater than normal overwintering losses since 2007 in North America…”
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Self-gravity wakes in Saturn's A ring measured by stellar occultations from Cassini by Colwell, J. E., Esposito, L. W., Sremčević, M.

“…An azimuthal brightness asymmetry in Saturn's A ring is caused by ephemeral agglomerations that continually form under the mutual gravity of the ring particles…”
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