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2,186 results on '"A Baker"'

1. Fisheries rely on threatened salt marshes

Author

Baker, Ronald, Taylor, Matthew D, Able, Kenneth W, Beck, Michael W, Cebrian, Just, Colombano, Denise D, Connolly, Rod M, Currin, Carolyn, Deegan, Linda A, Feller, Ilka C, Gilby, Ben L, Kimball, Matthew E, Minello, Thomas J, Rozas, Lawrence P, Simenstad, Charles, Turner, R Eugene, Waltham, Nathan J, Weinstein, Michael P, Ziegler, Shelby L, Zu Ermgassen, Philine SE, Alcott, Caitlin, Alford, Scott B, Barbeau, Myriam A, Crosby, Sarah C, Dodds, Kate, Frank, Alyssa, Goeke, Janelle, Goodridge Gaines, Lucy A, Hardcastle, Felicity E, Henderson, Christopher J, James, W Ryan, Kenworthy, Matthew D, Lesser, Justin, Mallick, Debbrota, Martin, Charles W, McDonald, Ashley E, McLuckie, Catherine, Morrison, Blair H, Nelson, James A, Norris, Gregory S, Ollerhead, Jeff, Pahl, James W, Ramsden, Sarah, Rehage, Jennifer S, Reinhardt, James F, Rezek, Ryan J, Risse, L Mark, Smith, Joseph AM, Sparks, Eric L, and Staver, Lorie W

Subjects
Environmental Restoration and Remediation, Fisheries, United States, Wetlands, General Science & Technology
Published
2020

3. Multiple sclerosis genomic map implicates peripheral immune cells and microglia in susceptibility

Author

Patsopoulos, Nikolaos A, Baranzini, Sergio E, Santaniello, Adam, Shoostari, Parisa, Cotsapas, Chris, Wong, Garrett, Beecham, Ashley H, James, Tojo, Replogle, Joseph, Vlachos, Ioannis S, McCabe, Cristin, Pers, Tune H, Brandes, Aaron, White, Charles, Keenan, Brendan, Cimpean, Maria, Winn, Phoebe, Panteliadis, Ioannis-Pavlos, Robbins, Allison, Andlauer, Till FM, Zarzycki, Onigiusz, Dubois, Bénédicte, Goris, An, Søndergaard, Helle Bach, Sellebjerg, Finn, Sorensen, Per Soelberg, Ullum, Henrik, Thørner, Lise Wegner, Saarela, Janna, Cournu-Rebeix, Isabelle, Damotte, Vincent, Fontaine, Bertrand, Guillot-Noel, Lena, Lathrop, Mark, Vukusic, Sandra, Berthele, Achim, Pongratz, Viola, Buck, Dorothea, Gasperi, Christiane, Graetz, Christiane, Grummel, Verena, Hemmer, Bernhard, Hoshi, Muni, Knier, Benjamin, Korn, Thomas, Lill, Christina M, Luessi, Felix, Mühlau, Mark, Zipp, Frauke, Dardiotis, Efthimios, Agliardi, Cristina, Amoroso, Antonio, Barizzone, Nadia, Benedetti, Maria D, Bernardinelli, Luisa, Cavalla, Paola, Clarelli, Ferdinando, Comi, Giancarlo, Cusi, Daniele, Esposito, Federica, Ferrè, Laura, Galimberti, Daniela, Guaschino, Clara, Leone, Maurizio A, Martinelli, Vittorio, Moiola, Lucia, Salvetti, Marco, Sorosina, Melissa, Vecchio, Domizia, Zauli, Andrea, Santoro, Silvia, Mancini, Nicasio, Zuccalà, Miriam, Mescheriakova, Julia, van Duijn, Cornelia, Bos, Steffan D, Celius, Elisabeth G, Spurkland, Anne, Comabella, Manuel, Montalban, Xavier, Alfredsson, Lars, Bomfim, Izaura L, Gomez-Cabrero, David, Hillert, Jan, Jagodic, Maja, Lindén, Magdalena, Piehl, Fredrik, Jelčić, Ilijas, Martin, Roland, Sospedra, Mirela, Baker, Amie, Ban, Maria, Hawkins, Clive, Hysi, Pirro, Kalra, Seema, Karpe, Fredrik, Khadake, Jyoti, Lachance, Genevieve, Molyneux, Paul, and Neville, Matthew

Subjects
Neurosciences, Brain Disorders, Multiple Sclerosis, Human Genome, Autoimmune Disease, Clinical Research, Genetics, Neurodegenerative, Aetiology, 2.1 Biological and endogenous factors, Inflammatory and immune system, Neurological, Case-Control Studies, Cell Cycle Proteins, Chromosome Mapping, Chromosomes, Human, X, GTPase-Activating Proteins, Gene Frequency, Genetic Loci, Genome-Wide Association Study, Genomics, Humans, Inheritance Patterns, Major Histocompatibility Complex, Microglia, Polymorphism, Single Nucleotide, Quantitative Trait Loci, RNA-Seq, Transcriptome, International Multiple Sclerosis Genetics Consortium, General Science & Technology
Abstract

We analyzed genetic data of 47,429 multiple sclerosis (MS) and 68,374 control subjects and established a reference map of the genetic architecture of MS that includes 200 autosomal susceptibility variants outside the major histocompatibility complex (MHC), one chromosome X variant, and 32 variants within the extended MHC. We used an ensemble of methods to prioritize 551 putative susceptibility genes that implicate multiple innate and adaptive pathways distributed across the cellular components of the immune system. Using expression profiles from purified human microglia, we observed enrichment for MS genes in these brain-resident immune cells, suggesting that these may have a role in targeting an autoimmune process to the central nervous system, although MS is most likely initially triggered by perturbation of peripheral immune responses.

Published
2019

4. De novo design of tunable, pH-driven conformational changes

Author

Boyken, Scott E, Benhaim, Mark A, Busch, Florian, Jia, Mengxuan, Bick, Matthew J, Choi, Heejun, Klima, Jason C, Chen, Zibo, Walkey, Carl, Mileant, Alexander, Sahasrabuddhe, Aniruddha, Wei, Kathy Y, Hodge, Edgar A, Byron, Sarah, Quijano-Rubio, Alfredo, Sankaran, Banumathi, King, Neil P, Lippincott-Schwartz, Jennifer, Wysocki, Vicki H, Lee, Kelly K, and Baker, David

Subjects
Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, Generic health relevance, Hydrogen-Ion Concentration, Protein Conformation, Protein Engineering, Protein Multimerization, Protein Stability, General Science & Technology
Abstract

The ability of naturally occurring proteins to change conformation in response to environmental changes is critical to biological function. Although there have been advances in the de novo design of stable proteins with a single, deep free-energy minimum, the design of conformational switches remains challenging. We present a general strategy to design pH-responsive protein conformational changes by precisely preorganizing histidine residues in buried hydrogen-bond networks. We design homotrimers and heterodimers that are stable above pH 6.5 but undergo cooperative, large-scale conformational changes when the pH is lowered and electrostatic and steric repulsion builds up as the network histidine residues become protonated. The transition pH and cooperativity can be controlled through the number of histidine-containing networks and the strength of the surrounding hydrophobic interactions. Upon disassembly, the designed proteins disrupt lipid membranes both in vitro and after being endocytosed in mammalian cells. Our results demonstrate that environmentally triggered conformational changes can now be programmed by de novo protein design.

Published
2019

5. The pace of life for forest trees.

Author

Bialic-Murphy, Lalasia, McElderry, Robert M., Esquivel-Muelbert, Adriane, Hoogen, Johan van den, Zuidema, Pieter A., Phillips, Oliver L., Oliveira, Edmar Almeida de, Loayza, Patricia Alvarez, Alvarez-Davila, Esteban, Alves, Luciana F., Maia, Vinícius Andrade, Vieira, Simone Aparecida, Silva, Lidiany Carolina Arantes da, Araujo-Murakami, Alejandro, Arets, Eric, Astigarraga, Julen, Baccaro, Fabrício, Baker, Timothy, Banki, Olaf, and Barroso, Jorcely

Published
2024
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6. Four decades of Hawaiian monk seal entanglement data reveal the benefits of plastic debris removal.

Author

Baker, Jason D., Johanos, Thea C., Ronco, Hope, Becker, Brenda L., Morioka, James, OÕBrien2, Kevin, and Donohue, Mary J.

Subjects
*CLEANUP of marine debris, *PLASTIC scrap, *MARINE ecology, *MARINE debris, *HAWAIIANS, *OCEAN
Abstract

Abandoned, lost, or otherwise discarded fishing gear causes harm to marine species and ecosystems. To mitigate the destruction wrought by this ocean plastic debris, various cleanup programs have been established, though to our knowledge the benefits of such efforts to marine species and ecosystems have not yet been empirically demonstrated. We examined more than 40 years of Hawaiian monk seal marine debris entanglement records before and after large-scale marine debris removal efforts were initiated in the Northwestern Hawaiian Islands, demonstrating a substantial reduction in entanglement rates where debris removal effort was most concentrated. Large-scale and sustained removal of abandoned, lost, or otherwise discarded fishing gear meaningfully benefits marine ecosystems and has the potential to be transformational in restoration efforts. [ABSTRACT FROM AUTHOR]

Published
2024
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8. High-resolution comparative analysis of great ape genomes

Author

Kronenberg, Zev N, Fiddes, Ian T, Gordon, David, Murali, Shwetha, Cantsilieris, Stuart, Meyerson, Olivia S, Underwood, Jason G, Nelson, Bradley J, Chaisson, Mark JP, Dougherty, Max L, Munson, Katherine M, Hastie, Alex R, Diekhans, Mark, Hormozdiari, Fereydoun, Lorusso, Nicola, Hoekzema, Kendra, Qiu, Ruolan, Clark, Karen, Raja, Archana, Welch, AnneMarie E, Sorensen, Melanie, Baker, Carl, Fulton, Robert S, Armstrong, Joel, Graves-Lindsay, Tina A, Denli, Ahmet M, Hoppe, Emma R, Hsieh, PingHsun, Hill, Christopher M, Pang, Andy Wing Chun, Lee, Joyce, Lam, Ernest T, Dutcher, Susan K, Gage, Fred H, Warren, Wesley C, Shendure, Jay, Haussler, David, Schneider, Valerie A, Cao, Han, Ventura, Mario, Wilson, Richard K, Paten, Benedict, Pollen, Alex, and Eichler, Evan E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Stem Cell Research, Human Genome, Biotechnology, Aetiology, Underpinning research, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Generic health relevance, Animals, Contig Mapping, Evolution, Molecular, Genetic Variation, Genome, Human, Hominidae, Humans, Molecular Sequence Annotation, Sequence Analysis, DNA, General Science & Technology
Abstract

Genetic studies of human evolution require high-quality contiguous ape genome assemblies that are not guided by the human reference. We coupled long-read sequence assembly and full-length complementary DNA sequencing with a multiplatform scaffolding approach to produce ab initio chimpanzee and orangutan genome assemblies. By comparing these with two long-read de novo human genome assemblies and a gorilla genome assembly, we characterized lineage-specific and shared great ape genetic variation ranging from single- to mega-base pair-sized variants. We identified ~17,000 fixed human-specific structural variants identifying genic and putative regulatory changes that have emerged in humans since divergence from nonhuman apes. Interestingly, these variants are enriched near genes that are down-regulated in human compared to chimpanzee cerebral organoids, particularly in cells analogous to radial glial neural progenitors.

Published
2018

9. Accurate computational design of multipass transmembrane proteins

Author

Lu, Peilong, Min, Duyoung, DiMaio, Frank, Wei, Kathy Y, Vahey, Michael D, Boyken, Scott E, Chen, Zibo, Fallas, Jorge A, Ueda, George, Sheffler, William, Mulligan, Vikram Khipple, Xu, Wenqing, Bowie, James U, and Baker, David

Subjects
1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Bioengineering, Computer Simulation, Crystallography, X-Ray, Cytoplasm, Detergents, HEK293 Cells, Humans, Membrane Proteins, Models, Chemical, Protein Engineering, Protein Folding, Protein Multimerization, Protein Stability, Protein Structure, Secondary, Protein Unfolding, General Science & Technology
Abstract

The computational design of transmembrane proteins with more than one membrane-spanning region remains a major challenge. We report the design of transmembrane monomers, homodimers, trimers, and tetramers with 76 to 215 residue subunits containing two to four membrane-spanning regions and up to 860 total residues that adopt the target oligomerization state in detergent solution. The designed proteins localize to the plasma membrane in bacteria and in mammalian cells, and magnetic tweezer unfolding experiments in the membrane indicate that they are very stable. Crystal structures of the designed dimer and tetramer-a rocket-shaped structure with a wide cytoplasmic base that funnels into eight transmembrane helices-are very close to the design models. Our results pave the way for the design of multispan membrane proteins with new functions.

Published
2018

10. Selective targeting of engineered T cells using orthogonal IL-2 cytokine-receptor complexes

Author

Sockolosky, Jonathan T, Trotta, Eleonora, Parisi, Giulia, Picton, Lora, Su, Leon L, Le, Alan C, Chhabra, Akanksha, Silveria, Stephanie L, George, Benson M, King, Indigo C, Tiffany, Matthew R, Jude, Kevin, Sibener, Leah V, Baker, David, Shizuru, Judith A, Ribas, Antoni, Bluestone, Jeffrey A, and Garcia, K Christopher

Subjects
Biotechnology, Vaccine Related, Cancer, Bioengineering, Immunization, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, 5.2 Cellular and gene therapies, Good Health and Well Being, Animals, CD4-Positive T-Lymphocytes, CD8-Positive T-Lymphocytes, Cell Engineering, HEK293 Cells, Humans, Immunotherapy, Adoptive, Melanoma, Experimental, Mice, Neoplasms, Receptors, Interleukin-2, General Science & Technology
Abstract

Interleukin-2 (IL-2) is a cytokine required for effector T cell expansion, survival, and function, especially for engineered T cells in adoptive cell immunotherapy, but its pleiotropy leads to simultaneous stimulation and suppression of immune responses as well as systemic toxicity, limiting its therapeutic use. We engineered IL-2 cytokine-receptor orthogonal (ortho) pairs that interact with one another, transmitting native IL-2 signals, but do not interact with their natural cytokine and receptor counterparts. Introduction of orthoIL-2Rβ into T cells enabled the selective cellular targeting of orthoIL-2 to engineered CD4+ and CD8+ T cells in vitro and in vivo, with limited off-target effects and negligible toxicity. OrthoIL-2 pairs were efficacious in a preclinical mouse cancer model of adoptive cell therapy and may therefore represent a synthetic approach to achieving selective potentiation of engineered cells.

Published
2018

12. Generalized biomolecular modeling and design with RoseTTAFold All-Atom

Author

Krishna, Rohith, primary, Wang, Jue, additional, Ahern, Woody, additional, Sturmfels, Pascal, additional, Venkatesh, Preetham, additional, Kalvet, Indrek, additional, Lee, Gyu Rie, additional, Morey-Burrows, Felix S., additional, Anishchenko, Ivan, additional, Humphreys, Ian R., additional, McHugh, Ryan, additional, Vafeados, Dionne, additional, Li, Xinting, additional, Sutherland, George A., additional, Hitchcock, Andrew, additional, Hunter, C. Neil, additional, Kang, Alex, additional, Brackenbrough, Evans, additional, Bera, Asim K., additional, Baek, Minkyung, additional, DiMaio, Frank, additional, and Baker, David, additional

Published
2024
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13. Protein structure determination using metagenome sequence data

Author

Ovchinnikov, Sergey, Park, Hahnbeom, Varghese, Neha, Huang, Po-Ssu, Pavlopoulos, Georgios A, Kim, David E, Kamisetty, Hetunandan, Kyrpides, Nikos C, and Baker, David

Subjects
Biochemistry and Cell Biology, Bioinformatics and Computational Biology, Biological Sciences, Generic health relevance, Algorithms, Amino Acid Sequence, Computational Biology, Crystallography, X-Ray, Databases, Protein, Evolution, Molecular, Metagenome, Models, Molecular, Protein Conformation, Protein Folding, Proteins, Sequence Analysis, Protein, Software, General Science & Technology
Abstract

Despite decades of work by structural biologists, there are still ~5200 protein families with unknown structure outside the range of comparative modeling. We show that Rosetta structure prediction guided by residue-residue contacts inferred from evolutionary information can accurately model proteins that belong to large families and that metagenome sequence data more than triple the number of protein families with sufficient sequences for accurate modeling. We then integrate metagenome data, contact-based structure matching, and Rosetta structure calculations to generate models for 614 protein families with currently unknown structures; 206 are membrane proteins and 137 have folds not represented in the Protein Data Bank. This approach provides the representative models for large protein families originally envisioned as the goal of the Protein Structure Initiative at a fraction of the cost.

Published
2017

15. Senescent intimal foam cells are deleterious at all stages of atherosclerosis

Author

Childs, Bennett G, Baker, Darren J, Wijshake, Tobias, Conover, Cheryl A, Campisi, Judith, and van Deursen, Jan M

Subjects
Aging, Cardiovascular, Atherosclerosis, Aetiology, 2.1 Biological and endogenous factors, Animals, Cellular Senescence, Chemokines, Cyclin-Dependent Kinase Inhibitor p16, Cytokines, Foam Cells, Mice, Mice, Transgenic, Plaque, Atherosclerotic, Receptors, LDL, Tunica Intima, General Science & Technology
Abstract

Advanced atherosclerotic lesions contain senescent cells, but the role of these cells in atherogenesis remains unclear. Using transgenic and pharmacological approaches to eliminate senescent cells in atherosclerosis-prone low-density lipoprotein receptor-deficient (Ldlr-/-) mice, we show that these cells are detrimental throughout disease pathogenesis. We find that foamy macrophages with senescence markers accumulate in the subendothelial space at the onset of atherosclerosis, where they drive pathology by increasing expression of key atherogenic and inflammatory cytokines and chemokines. In advanced lesions, senescent cells promote features of plaque instability, including elastic fiber degradation and fibrous cap thinning, by heightening metalloprotease production. Together, these results demonstrate that senescent cells are key drivers of atheroma formation and maturation and suggest that selective clearance of these cells by senolytic agents holds promise for the treatment of atherosclerosis.

Published
2016

16. Accurate design of megadalton-scale two-component icosahedral protein complexes.

Author

Bale, Jacob, Gonen, Shane, Liu, Yuxi, Sheffler, William, Ellis, Daniel, Thomas, Chantz, Cascio, Duilio, Yeates, Todd, King, Neil, Baker, David, and Gonen, Tamir

Subjects
Capsid, Crystallography, X-Ray, Genome, Viral, Microscopy, Electron, Models, Molecular, Molecular Weight, Multiprotein Complexes, Nanostructures, Protein Engineering, Protein Subunits, Scattering, Small Angle, Viral Proteins, X-Ray Diffraction
Abstract

Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1.8 to 2.8 megadaltons) and dimensions (24 to 40 nanometers in diameter) comparable to those of small viral capsids. Electron microscopy, small-angle x-ray scattering, and x-ray crystallography show that 10 designs spanning three distinct icosahedral architectures form materials closely matching the design models. In vitro assembly of icosahedral complexes from independently purified components occurs rapidly, at rates comparable to those of viral capsids, and enables controlled packaging of molecular cargo through charge complementarity. The ability to design megadalton-scale materials with atomic-level accuracy and controllable assembly opens the door to a new generation of genetically programmable protein-based molecular machines.

Published
2016

17. De novo design of protein homo-oligomers with modular hydrogen-bond network–mediated specificity

Author

Boyken, Scott E, Chen, Zibo, Groves, Benjamin, Langan, Robert A, Oberdorfer, Gustav, Ford, Alex, Gilmore, Jason M, Xu, Chunfu, DiMaio, Frank, Pereira, Jose Henrique, Sankaran, Banumathi, Seelig, Georg, Zwart, Peter H, and Baker, David

Subjects
Inorganic Chemistry, Biochemistry and Cell Biology, Chemical Sciences, Biological Sciences, Generic health relevance, Crystallography, X-Ray, Hydrogen Bonding, Hydrophobic and Hydrophilic Interactions, Models, Chemical, Protein Engineering, Protein Interaction Mapping, Protein Interaction Maps, Protein Multimerization, Protein Stability, Protein Structure, Secondary, Proteins, General Science & Technology
Abstract

In nature, structural specificity in DNA and proteins is encoded differently: In DNA, specificity arises from modular hydrogen bonds in the core of the double helix, whereas in proteins, specificity arises largely from buried hydrophobic packing complemented by irregular peripheral polar interactions. Here, we describe a general approach for designing a wide range of protein homo-oligomers with specificity determined by modular arrays of central hydrogen-bond networks. We use the approach to design dimers, trimers, and tetramers consisting of two concentric rings of helices, including previously not seen triangular, square, and supercoiled topologies. X-ray crystallography confirms that the structures overall, and the hydrogen-bond networks in particular, are nearly identical to the design models, and the networks confer interaction specificity in vivo. The ability to design extensive hydrogen-bond networks with atomic accuracy enables the programming of protein interaction specificity for a broad range of synthetic biology applications; more generally, our results demonstrate that, even with the tremendous diversity observed in nature, there are fundamentally new modes of interaction to be discovered in proteins.

Published
2016

18. Opportunities for advances in climate change economics

Author

Burke, M, Craxton, M, Kolstad, CD, Onda, C, Allcott, H, Baker, E, Barrage, L, Carson, R, Gillingham, K, Graff-Zivin, J, Greenstone, M, Hallegatte, S, Hanemann, WM, Heal, G, Hsiang, S, Jones, B, Kelly, DL, Kopp, R, Kotchen, M, Mendelsohn, R, Meng, K, Metcalf, G, Moreno-Cruz, J, Pindyck, R, Rose, S, Rudik, I, Stock, J, and Tol, RSJ

Subjects
Climate Action, General Science & Technology
Abstract

Target carbon's costs, policy designs, and developing countries

Published
2016

19. Long-read sequence assembly of the gorilla genome

Author

Gordon, David, Huddleston, John, Chaisson, Mark JP, Hill, Christopher M, Kronenberg, Zev N, Munson, Katherine M, Malig, Maika, Raja, Archana, Fiddes, Ian, Hillier, LaDeana W, Dunn, Christopher, Baker, Carl, Armstrong, Joel, Diekhans, Mark, Paten, Benedict, Shendure, Jay, Wilson, Richard K, Haussler, David, Chin, Chen-Shan, and Eichler, Evan E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Animals, Contig Mapping, Evolution, Molecular, Expressed Sequence Tags, Female, Genetic Variation, Genome, Human, Genomics, Gorilla gorilla, Humans, Sequence Alignment, Sequence Analysis, DNA, General Science & Technology
Abstract

Accurate sequence and assembly of genomes is a critical first step for studies of genetic variation. We generated a high-quality assembly of the gorilla genome using single-molecule, real-time sequence technology and a string graph de novo assembly algorithm. The new assembly improves contiguity by two to three orders of magnitude with respect to previously released assemblies, recovering 87% of missing reference exons and incomplete gene models. Although regions of large, high-identity segmental duplications remain largely unresolved, this comprehensive assembly provides new biological insight into genetic diversity, structural variation, gene loss, and representation of repeat structures within the gorilla genome. The approach provides a path forward for the routine assembly of mammalian genomes at a level approaching that of the current quality of the human genome.

Published
2016

20. Electron-scale dynamics of the diffusion region during symmetric magnetic reconnection in space

Author

Torbert, R. B., Burch, J. L., Phan, T. D., Hesse, M., Argall, M. R., Shuster, J., Ergun, R. E., Alm, L., Nakamura, R., Genestreti, K. J., Gershman, D. J., Paterson, W. R., Turner, D. L., Cohen, I., Giles, B. L., Pollock, C. J., Wang, S., Chen, L.-J., Stawarz, J. E., Eastwood, J. P., Hwang, K. J., Farrugia, C., Dors, I., Vaith, H., Mouikis, C., Ardakani, A., Mauk, B. H., Fuselier, S. A., Russell, C. T., Strangeway, R. J., Moore, T. E., Drake, J. F., Shay, M. A., Khotyaintsev, Yuri V., Lindqvist, P.-A., Baumjohann, W., Wilder, F. D., Ahmadi, N., Dorelli, J. C., Avanov, L. A., Oka, M., Baker, D. N., Fennell, J. F., Blake, J. B., Jaynes, A. N., Le Contel, O., Petrinec, S. M., Lavraud, B., and Saito, Y.

Published
2018

22. De novo design of self-assembling helical protein filaments

Author

Shen, Hao, Fallas, Jorge A., Lynch, Eric, Sheffler, William, Parry, Bradley, Jannetty, Nicholas, Decarreau, Justin, Wagenbach, Michael, Vicente, Juan Jesus, Chen, Jiajun, Wang, Lei, Dowling, Quinton, Oberdorfer, Gustav, Stewart, Lance, Wordeman, Linda, De Yoreo, James, Jacobs-Wagner, Christine, Kollman, Justin, and Baker, David

Published
2018

23. Top-down design of protein architectures with reinforcement learning

Author

Isaac D. Lutz, Shunzhi Wang, Christoffer Norn, Alexis Courbet, Andrew J. Borst, Yan Ting Zhao, Annie Dosey, Longxing Cao, Jinwei Xu, Elizabeth M. Leaf, Catherine Treichel, Patrisia Litvicov, Zhe Li, Alexander D. Goodson, Paula Rivera-Sánchez, Ana-Maria Bratovianu, Minkyung Baek, Neil P. King, Hannele Ruohola-Baker, and David Baker

Subjects
Multidisciplinary
Abstract

As a result of evolutionary selection, the subunits of naturally occurring protein assemblies often fit together with substantial shape complementarity to generate architectures optimal for function in a manner not achievable by current design approaches. We describe a “top-down” reinforcement learning–based design approach that solves this problem using Monte Carlo tree search to sample protein conformers in the context of an overall architecture and specified functional constraints. Cryo–electron microscopy structures of the designed disk-shaped nanopores and ultracompact icosahedra are very close to the computational models. The icosohedra enable very-high-density display of immunogens and signaling molecules, which potentiates vaccine response and angiogenesis induction. Our approach enables the top-down design of complex protein nanomaterials with desired system properties and demonstrates the power of reinforcement learning in protein design.

Published
2023

24. Global diversity, population stratification, and selection of human copy-number variation.

Author

Krumm, Niklas, Huddleston, John, Coe, Bradley, Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn, Posukh, Olga, Sahakyan, Hovhannes, Watkins, W, Yepiskoposyan, Levon, Abdullah, M, Bravi, Claudio, Capelli, Cristian, Hervig, Tor, Wee, Joseph, Tyler-Smith, Chris, van Driem, George, Romero, Irene, Jha, Aashish, Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena, Ayodo, George, Beall, Cynthia, Di Rienzo, Anna, Hammer, Michael, Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah, Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, Eichler, Evan, Mallick, Swapan, Nelson, Bradley, Hormozdiari, Fereydoun, Henn, Brenna, and Sudmant, Peter

Subjects
Animals, Black People, DNA Copy Number Variations, Evolution, Molecular, Gene Duplication, Genome, Human, Hominidae, Humans, Native Hawaiian or Other Pacific Islander, Phylogeny, Polymorphism, Single Nucleotide, Population, Selection, Genetic, Sequence Deletion
Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

Published
2015

25. Global diversity, population stratification, and selection of human copy-number variation

Author

Sudmant, Peter H, Mallick, Swapan, Nelson, Bradley J, Hormozdiari, Fereydoun, Krumm, Niklas, Huddleston, John, Coe, Bradley P, Baker, Carl, Nordenfelt, Susanne, Bamshad, Michael, Jorde, Lynn B, Posukh, Olga L, Sahakyan, Hovhannes, Watkins, W Scott, Yepiskoposyan, Levon, Abdullah, M Syafiq, Bravi, Claudio M, Capelli, Cristian, Hervig, Tor, Wee, Joseph TS, Tyler-Smith, Chris, van Driem, George, Romero, Irene Gallego, Jha, Aashish R, Karachanak-Yankova, Sena, Toncheva, Draga, Comas, David, Henn, Brenna, Kivisild, Toomas, Ruiz-Linares, Andres, Sajantila, Antti, Metspalu, Ene, Parik, Jüri, Villems, Richard, Starikovskaya, Elena B, Ayodo, George, Beall, Cynthia M, Di Rienzo, Anna, Hammer, Michael F, Khusainova, Rita, Khusnutdinova, Elza, Klitz, William, Winkler, Cheryl, Labuda, Damian, Metspalu, Mait, Tishkoff, Sarah A, Dryomov, Stanislav, Sukernik, Rem, Patterson, Nick, Reich, David, and Eichler, Evan E

Subjects
Genetics, Human Genome, Animals, Black People, DNA Copy Number Variations, Evolution, Molecular, Gene Duplication, Genome, Human, Hominidae, Humans, Native Hawaiian or Other Pacific Islander, Phylogeny, Polymorphism, Single Nucleotide, Population, Selection, Genetic, Sequence Deletion, General Science & Technology
Abstract

In order to explore the diversity and selective signatures of duplication and deletion human copy-number variants (CNVs), we sequenced 236 individuals from 125 distinct human populations. We observed that duplications exhibit fundamentally different population genetic and selective signatures than deletions and are more likely to be stratified between human populations. Through reconstruction of the ancestral human genome, we identify megabases of DNA lost in different human lineages and pinpoint large duplications that introgressed from the extinct Denisova lineage now found at high frequency exclusively in Oceanic populations. We find that the proportion of CNV base pairs to single-nucleotide-variant base pairs is greater among non-Africans than it is among African populations, but we conclude that this difference is likely due to unique aspects of non-African population history as opposed to differences in CNV load.

Published
2015

26. A Habitable Fluvio-Lacustrine Environment at Yellowknife Bay, Gale Crater, Mars

Author

Grotzinger, JP, Sumner, DY, Kah, LC, Stack, K, Gupta, S, Edgar, L, Rubin, D, Lewis, K, Schieber, J, Mangold, N, Milliken, R, Conrad, PG, DesMarais, D, Farmer, J, Siebach, K, Calef, F, Hurowitz, J, McLennan, SM, Ming, D, Vaniman, D, Crisp, J, Vasavada, A, Edgett, KS, Malin, M, Blake, D, Gellert, R, Mahaffy, P, Wiens, RC, Maurice, S, Grant, JA, Wilson, S, Anderson, RC, Beegle, L, Arvidson, R, Hallet, B, Sletten, RS, Rice, M, Bell, J, Griffes, J, Ehlmann, B, Anderson, RB, Bristow, TF, Dietrich, WE, Dromart, G, Eigenbrode, J, Fraeman, A, Hardgrove, C, Herkenhoff, K, Jandura, L, Kocurek, G, Lee, S, Leshin, LA, Leveille, R, Limonadi, D, Maki, J, McCloskey, S, Meyer, M, Minitti, M, Newsom, H, Oehler, D, Okon, A, Palucis, M, Parker, T, Rowland, S, Schmidt, M, Squyres, S, Steele, A, Stolper, E, Summons, R, Treiman, A, Williams, R, Yingst, A, Team, MSL Science, Kemppinen, Osku, Bridges, Nathan, Johnson, Jeffrey R, Cremers, David, Godber, Austin, Wadhwa, Meenakshi, Wellington, Danika, McEwan, Ian, Newman, Claire, Richardson, Mark, Charpentier, Antoine, Peret, Laurent, King, Penelope, Blank, Jennifer, Weigle, Gerald, Li, Shuai, Robertson, Kevin, Sun, Vivian, Baker, Michael, Edwards, Christopher, Farley, Kenneth, Miller, Hayden, Newcombe, Megan, Pilorget, Cedric, Brunet, Claude, Hipkin, Victoria, and Léveillé, Richard

Subjects
Bays, Carbon, Exobiology, Extraterrestrial Environment, Geologic Sediments, Hydrogen, Hydrogen-Ion Concentration, Iron, Mars, Nitrogen, Oxidation-Reduction, Oxygen, Phosphorus, Salinity, Sulfur, Water, MSL Science Team, General Science & Technology
Abstract

The Curiosity rover discovered fine-grained sedimentary rocks, which are inferred to represent an ancient lake and preserve evidence of an environment that would have been suited to support a martian biosphere founded on chemolithoautotrophy. This aqueous environment was characterized by neutral pH, low salinity, and variable redox states of both iron and sulfur species. Carbon, hydrogen, oxygen, sulfur, nitrogen, and phosphorus were measured directly as key biogenic elements; by inference, phosphorus is assumed to have been available. The environment probably had a minimum duration of hundreds to tens of thousands of years. These results highlight the biological viability of fluvial-lacustrine environments in the post-Noachian history of Mars.

Published
2014

27. Signature morphoelectric properties of diverse GABAergic interneurons in the human neocortex

Author

Lee, Brian R., primary, Dalley, Rachel, additional, Miller, Jeremy A., additional, Chartrand, Thomas, additional, Close, Jennie, additional, Mann, Rusty, additional, Mukora, Alice, additional, Ng, Lindsay, additional, Alfiler, Lauren, additional, Baker, Katherine, additional, Bertagnolli, Darren, additional, Brouner, Krissy, additional, Casper, Tamara, additional, Csajbok, Eva, additional, Donadio, Nicholas, additional, Driessens, Stan L.W., additional, Egdorf, Tom, additional, Enstrom, Rachel, additional, Galakhova, Anna A., additional, Gary, Amanda, additional, Gelfand, Emily, additional, Goldy, Jeff, additional, Hadley, Kristen, additional, Heistek, Tim S., additional, Hill, Dijon, additional, Hou, Wen-Hsien, additional, Johansen, Nelson, additional, Jorstad, Nik, additional, Kim, Lisa, additional, Kocsis, Agnes Katalin, additional, Kruse, Lauren, additional, Kunst, Michael, additional, León, Gabriela, additional, Long, Brian, additional, Mallory, Matthew, additional, Maxwell, Michelle, additional, McGraw, Medea, additional, McMillen, Delissa, additional, Melief, Erica J., additional, Molnar, Gabor, additional, Mortrud, Marty T., additional, Newman, Dakota, additional, Nyhus, Julie, additional, Opitz-Araya, Ximena, additional, Ozsvár, Attila, additional, Pham, Trangthanh, additional, Pom, Alice, additional, Potekhina, Lydia, additional, Rajanbabu, Ram, additional, Ruiz, Augustin, additional, Sunkin, Susan M., additional, Szöts, Ildikó, additional, Taskin, Naz, additional, Thyagarajan, Bargavi, additional, Tieu, Michael, additional, Trinh, Jessica, additional, Vargas, Sara, additional, Vumbaco, David, additional, Waleboer, Femke, additional, Walling-Bell, Sarah, additional, Weed, Natalie, additional, Williams, Grace, additional, Wilson, Julia, additional, Yao, Shenqin, additional, Zhou, Thomas, additional, Barzó, Pál, additional, Bakken, Trygve, additional, Cobbs, Charles, additional, Dee, Nick, additional, Ellenbogen, Richard G., additional, Esposito, Luke, additional, Ferreira, Manuel, additional, Gouwens, Nathan W., additional, Grannan, Benjamin, additional, Gwinn, Ryder P., additional, Hauptman, Jason S., additional, Hodge, Rebecca, additional, Jarsky, Tim, additional, Keene, C. Dirk, additional, Ko, Andrew L., additional, Korshoej, Anders Rosendal, additional, Levi, Boaz P., additional, Meier, Kaare, additional, Ojemann, Jeffrey G., additional, Patel, Anoop, additional, Ruzevick, Jacob, additional, Silbergeld, Daniel L., additional, Smith, Kimberly, additional, Sørensen, Jens Christian, additional, Waters, Jack, additional, Zeng, Hongkui, additional, Berg, Jim, additional, Capogna, Marco, additional, Goriounova, Natalia A., additional, Kalmbach, Brian, additional, de Kock, Christiaan P.J., additional, Mansvelder, Huib D., additional, Sorensen, Staci A., additional, Tamas, Gabor, additional, Lein, Ed S., additional, and Ting, Jonathan T., additional

Published
2023
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28. More than 10,000 pre-Columbian earthworks are still hidden throughout Amazonia

Author

Peripato, Vinicius, primary, Levis, Carolina, additional, Moreira, Guido A., additional, Gamerman, Dani, additional, ter Steege, Hans, additional, Pitman, Nigel C. A., additional, de Souza, Jonas G., additional, Iriarte, José, additional, Robinson, Mark, additional, Junqueira, André Braga, additional, Trindade, Thiago B., additional, de Almeida, Fernando O., additional, Moraes, Claide de Paula, additional, Lombardo, Umberto, additional, Tamanaha, Eduardo K., additional, Maezumi, Shira Y., additional, Ometto, Jean P. H. B., additional, Braga, José R. G., additional, Campanharo, Wesley A., additional, Cassol, Henrique L. G., additional, Leal, Philipe R., additional, de Assis, Mauro L. R., additional, da Silva, Adriana M., additional, Phillips, Oliver L., additional, Costa, Flávia R. C., additional, Flores, Bernardo Monteiro, additional, Hoffman, Bruce, additional, Henkel, Terry W., additional, Umaña, Maria Natalia, additional, Magnusson, William E., additional, Valderrama Sandoval, Elvis H., additional, Barlow, Jos, additional, Milliken, William, additional, Lopes, Maria Aparecida, additional, Simon, Marcelo Fragomeni, additional, van Andel, Tinde R., additional, Laurance, Susan G. W., additional, Laurance, William F., additional, Torres-Lezama, Armando, additional, Assis, Rafael L., additional, Molino, Jean-François, additional, Mestre, Mickaël, additional, Hamblin, Michelle, additional, Coelho, Luiz de Souza, additional, Lima Filho, Diogenes de Andrade, additional, Wittmann, Florian, additional, Salomão, Rafael P., additional, Amaral, Iêda Leão, additional, Guevara, Juan Ernesto, additional, de Almeida Matos, Francisca Dionízia, additional, Castilho, Carolina V., additional, Carim, Marcelo de Jesus Veiga, additional, Cárdenas López, Dairon, additional, Sabatier, Daniel, additional, Irume, Mariana Victória, additional, Martins, Maria Pires, additional, Guimarães, José Renan da Silva, additional, Bánki, Olaf S., additional, Piedade, Maria Teresa Fernandez, additional, Ramos, José Ferreira, additional, Luize, Bruno Garcia, additional, Novo, Evlyn Márcia Moraes de Leão, additional, Núñez Vargas, Percy, additional, Silva, Thiago Sanna Freire, additional, Venticinque, Eduardo Martins, additional, Manzatto, Angelo Gilberto, additional, Reis, Neidiane Farias Costa, additional, Terborgh, John, additional, Casula, Katia Regina, additional, Demarchi, Layon O., additional, Honorio Coronado, Euridice N., additional, Monteagudo Mendoza, Abel, additional, Montero, Juan Carlos, additional, Schöngart, Jochen, additional, Feldpausch, Ted R., additional, Quaresma, Adriano Costa, additional, Aymard C., Gerardo A., additional, Baraloto, Chris, additional, Castaño Arboleda, Nicolás, additional, Engel, Julien, additional, Petronelli, Pascal, additional, Zartman, Charles Eugene, additional, Killeen, Timothy J., additional, Marimon, Beatriz S., additional, Marimon-Junior, Ben Hur, additional, Schietti, Juliana, additional, Sousa, Thaiane R., additional, Vasquez, Rodolfo, additional, Rincón, Lorena M., additional, Berenguer, Erika, additional, Ferreira, Joice, additional, Mostacedo, Bonifacio, additional, do Amaral, Dário Dantas, additional, Castellanos, Hernán, additional, de Medeiros, Marcelo Brilhante, additional, Andrade, Ana, additional, Camargo, José Luís, additional, Farias, Emanuelle de Sousa, additional, Magalhães, José Leonardo Lima, additional, Mendonça Nascimento, Henrique Eduardo, additional, de Queiroz, Helder Lima, additional, Brienen, Roel, additional, Cardenas Revilla, Juan David, additional, Stevenson, Pablo R., additional, Araujo-Murakami, Alejandro, additional, Barçante Ladvocat Cintra, Bruno, additional, Feitosa, Yuri Oliveira, additional, Barbosa, Flávia Rodrigues, additional, Carpanedo, Rainiellen de Sá, additional, Duivenvoorden, Joost F., additional, de Noronha, Janaína da Costa, additional, Rodrigues, Domingos de Jesus, additional, Mogollón, Hugo F., additional, Ferreira, Leandro Valle, additional, Householder, John Ethan, additional, Lozada, José Rafael, additional, Comiskey, James A., additional, Draper, Freddie C., additional, de Toledo, José Julio, additional, Damasco, Gabriel, additional, Dávila, Nállarett, additional, García-Villacorta, Roosevelt, additional, Lopes, Aline, additional, Cornejo Valverde, Fernando, additional, Alonso, Alfonso, additional, Dallmeier, Francisco, additional, Gomes, Vitor H. F., additional, Jimenez, Eliana M., additional, Neill, David, additional, Peñuela Mora, Maria Cristina, additional, de Aguiar, Daniel P. P., additional, Arroyo, Luzmila, additional, Antunes Carvalho, Fernanda, additional, Coelho de Souza, Fernanda, additional, Feeley, Kenneth J., additional, Gribel, Rogerio, additional, Pansonato, Marcelo Petratti, additional, Ríos Paredes, Marcos, additional, Brasil da Silva, Izaias, additional, Ferreira, Maria Julia, additional, Fine, Paul V. A., additional, Fonty, Émile, additional, Guedes, Marcelino Carneiro, additional, Licona, Juan Carlos, additional, Pennington, Toby, additional, Peres, Carlos A., additional, Villa Zegarra, Boris Eduardo, additional, Parada, Germaine Alexander, additional, Pardo Molina, Guido, additional, Vos, Vincent Antoine, additional, Cerón, Carlos, additional, Maas, Paul, additional, Silveira, Marcos, additional, Stropp, Juliana, additional, Thomas, Raquel, additional, Baker, Tim R., additional, Daly, Doug, additional, Huamantupa-Chuquimaco, Isau, additional, Vieira, Ima Célia Guimarães, additional, Weiss Albuquerque, Bianca, additional, Fuentes, Alfredo, additional, Klitgaard, Bente, additional, Marcelo-Peña, José Luis, additional, Silman, Miles R., additional, Tello, J. Sebastián, additional, Vriesendorp, Corine, additional, Chave, Jerome, additional, Di Fiore, Anthony, additional, Hilário, Renato Richard, additional, Phillips, Juan Fernando, additional, Rivas-Torres, Gonzalo, additional, von Hildebrand, Patricio, additional, Pereira, Luciana de Oliveira, additional, Barbosa, Edelcilio Marques, additional, de Matos Bonates, Luiz Carlos, additional, Doza, Hilda Paulette Dávila, additional, Zárate Gómez, Ricardo, additional, Gallardo Gonzales, George Pepe, additional, Gonzales, Therany, additional, Malhi, Yadvinder, additional, de Andrade Miranda, Ires Paula, additional, Mozombite Pinto, Linder Felipe, additional, Prieto, Adriana, additional, Rudas, Agustín, additional, Ruschel, Ademir R., additional, Silva, Natalino, additional, Vela, César I. A., additional, Zent, Egleé L., additional, Zent, Stanford, additional, Cano, Angela, additional, Carrero Márquez, Yrma Andreina, additional, Correa, Diego F., additional, Costa, Janaina Barbosa Pedrosa, additional, Galbraith, David, additional, Holmgren, Milena, additional, Kalamandeen, Michelle, additional, Lobo, Guilherme, additional, Nascimento, Marcelo Trindade, additional, Oliveira, Alexandre A., additional, Ramirez-Angulo, Hirma, additional, Rocha, Maira, additional, Scudeller, Veridiana Vizoni, additional, Sierra, Rodrigo, additional, Tirado, Milton, additional, van der Heijden, Geertje, additional, Vilanova Torre, Emilio, additional, Ahuite Reategui, Manuel Augusto, additional, Baider, Cláudia, additional, Balslev, Henrik, additional, Cárdenas, Sasha, additional, Casas, Luisa Fernanda, additional, Farfan-Rios, William, additional, Ferreira, Cid, additional, Linares-Palomino, Reynaldo, additional, Mendoza, Casimiro, additional, Mesones, Italo, additional, Urrego Giraldo, Ligia Estela, additional, Villarroel, Daniel, additional, Zagt, Roderick, additional, Alexiades, Miguel N., additional, de Oliveira, Edmar Almeida, additional, Garcia-Cabrera, Karina, additional, Hernandez, Lionel, additional, Palacios Cuenca, Walter, additional, Pansini, Susamar, additional, Pauletto, Daniela, additional, Ramirez Arevalo, Fredy, additional, Sampaio, Adeilza Felipe, additional, Valenzuela Gamarra, Luis, additional, and Aragão, Luiz E. O. C., additional

Published
2023
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29. Design of stimulus-responsive two-state hinge proteins

Author

Praetorius, Florian, primary, Leung, Philip J. Y., additional, Tessmer, Maxx H., additional, Broerman, Adam, additional, Demakis, Cullen, additional, Dishman, Acacia F., additional, Pillai, Arvind, additional, Idris, Abbas, additional, Juergens, David, additional, Dauparas, Justas, additional, Li, Xinting, additional, Levine, Paul M., additional, Lamb, Mila, additional, Ballard, Ryanne K., additional, Gerben, Stacey R., additional, Nguyen, Hannah, additional, Kang, Alex, additional, Sankaran, Banumathi, additional, Bera, Asim K., additional, Volkman, Brian F., additional, Nivala, Jeff, additional, Stoll, Stefan, additional, and Baker, David, additional

Published
2023
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30. DNA methylation networks underlying mammalian traits

Author

Haghani, Amin, primary, Li, Caesar Z., additional, Robeck, Todd R., additional, Zhang, Joshua, additional, Lu, Ake T., additional, Ablaeva, Julia, additional, Acosta-Rodríguez, Victoria A., additional, Adams, Danielle M., additional, Alagaili, Abdulaziz N., additional, Almunia, Javier, additional, Aloysius, Ajoy, additional, Amor, Nabil M.S., additional, Ardehali, Reza, additional, Arneson, Adriana, additional, Baker, C. Scott, additional, Banks, Gareth, additional, Belov, Katherine, additional, Bennett, Nigel C., additional, Black, Peter, additional, Blumstein, Daniel T., additional, Bors, Eleanor K., additional, Breeze, Charles E., additional, Brooke, Robert T., additional, Brown, Janine L., additional, Carter, Gerald, additional, Caulton, Alex, additional, Cavin, Julie M., additional, Chakrabarti, Lisa, additional, Chatzistamou, Ioulia, additional, Chavez, Andreas S., additional, Chen, Hao, additional, Cheng, Kaiyang, additional, Chiavellini, Priscila, additional, Choi, Oi-Wa, additional, Clarke, Shannon, additional, Cook, Joseph A., additional, Cooper, Lisa N., additional, Cossette, Marie-Laurence, additional, Day, Joanna, additional, DeYoung, Joseph, additional, Dirocco, Stacy, additional, Dold, Christopher, additional, Dunnum, Jonathan L., additional, Ehmke, Erin E., additional, Emmons, Candice K., additional, Emmrich, Stephan, additional, Erbay, Ebru, additional, Erlacher-Reid, Claire, additional, Faulkes, Chris G., additional, Fei, Zhe, additional, Ferguson, Steven H., additional, Finno, Carrie J., additional, Flower, Jennifer E., additional, Gaillard, Jean-Michel, additional, Garde, Eva, additional, Gerber, Livia, additional, Gladyshev, Vadim N., additional, Goya, Rodolfo G., additional, Grant, Matthew J, additional, Green, Carla B., additional, Hanson, M. Bradley, additional, Hart, Daniel W., additional, Haulena, Martin, additional, Herrick, Kelsey, additional, Hogan, Andrew N., additional, Hogg, Carolyn J., additional, Hore, Timothy A., additional, Huang, Taosheng, additional, Izpisua Belmonte, Juan Carlos, additional, Jasinska, Anna J., additional, Jones, Gareth, additional, Jourdain, Eve, additional, Kashpur, Olga, additional, Katcher, Harold, additional, Katsumata, Etsuko, additional, Kaza, Vimala, additional, Kiaris, Hippokratis, additional, Kobor, Michael S., additional, Kordowitzki, Pawel, additional, Koski, William R., additional, Krützen, Michael, additional, Kwon, Soo Bin, additional, Larison, Brenda, additional, Lee, Sang-Goo, additional, Lehmann, Marianne, additional, Lemaître, Jean-François, additional, Levine, Andrew J., additional, Li, Xinmin, additional, Li, Cun, additional, Lim, Andrea R., additional, Lin, David T. S., additional, Lindemann, Dana M., additional, Liphardt, Schuyler W., additional, Little, Thomas J., additional, Macoretta, Nicholas, additional, Maddox, Dewey, additional, Matkin, Craig O., additional, Mattison, Julie A., additional, McClure, Matthew, additional, Mergl, June, additional, Meudt, Jennifer J., additional, Montano, Gisele A., additional, Mozhui, Khyobeni, additional, Munshi-South, Jason, additional, Murphy, William J., additional, Naderi, Asieh, additional, Nagy, Martina, additional, Narayan, Pritika, additional, Nathanielsz, Peter W., additional, Nguyen, Ngoc B., additional, Niehrs, Christof, additional, Nyamsuren, Batsaikhan, additional, O’Brien, Justine K., additional, Ginn, Perrie O’Tierney, additional, Odom, Duncan T, additional, Ophir, Alexander G., additional, Osborn, Steve, additional, Ostrander, Elaine A., additional, Parsons, Kim M., additional, Paul, Kimberly C., additional, Pedersen, Amy B., additional, Pellegrini, Matteo, additional, Peters, Katharina J., additional, Petersen, Jessica L., additional, Pietersen, Darren W., additional, Pinho, Gabriela M., additional, Plassais, Jocelyn, additional, Poganik, Jesse R., additional, Prado, Natalia A., additional, Reddy, Pradeep, additional, Rey, Benjamin, additional, Ritz, Beate R., additional, Robbins, Jooke, additional, Rodriguez, Magdalena, additional, Russell, Jennifer, additional, Rydkina, Elena, additional, Sailer, Lindsay L., additional, Salmon, Adam B., additional, Sanghavi, Akshay, additional, Schachtschneider, Kyle M., additional, Schmitt, Dennis, additional, Schmitt, Todd, additional, Schomacher, Lars, additional, Schook, Lawrence B., additional, Sears, Karen E., additional, Seifert, Ashley W., additional, Shafer, Aaron B.A., additional, Shindyapina, Anastasia V., additional, Simmons, Melanie, additional, Singh, Kavita, additional, Sinha, Ishani, additional, Slone, Jesse, additional, Snell, Russel G., additional, Soltanmohammadi, Elham, additional, Spangler, Matthew L., additional, Spriggs, Maria, additional, Staggs, Lydia, additional, Stedman, Nancy, additional, Steinman, Karen J., additional, Stewart, Donald T, additional, Sugrue, Victoria J., additional, Szladovits, Balazs, additional, Takahashi, Joseph S., additional, Takasugi, Masaki, additional, Teeling, Emma C., additional, Thompson, Michael J., additional, Van Bonn, Bill, additional, Vernes, Sonja C., additional, Villar, Diego, additional, Vinters, Harry V., additional, Vu, Ha, additional, Wallingford, Mary C., additional, Wang, Nan, additional, Wilkinson, Gerald S., additional, Williams, Robert W., additional, Yan, Qi, additional, Yao, Mingjia, additional, Young, Brent G., additional, Zhang, Bohan, additional, Zhang, Zhihui, additional, Zhao, Yang, additional, Zhao, Peng, additional, Zhou, Wanding, additional, Zoller, Joseph A., additional, Ernst, Jason, additional, Seluanov, Andrei, additional, Gorbunova, Vera, additional, Yang, X. William, additional, Raj, Ken, additional, and Horvath, Steve, additional

Published
2023
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33. Evidence for High-Energy Extraterrestrial Neutrinos at the IceCube Detector

Author

Aartsen, MG, Abbasi, R, Abdou, Y, Ackermann, M, Adams, J, Aguilar, JA, Ahlers, M, Altmann, D, Auffenberg, J, Bai, X, Baker, M, Barwick, SW, Baum, V, Bay, R, Beatty, JJ, Bechet, S, Becker Tjus, J, Becker, K-H, Benabderrahmane, ML, BenZvi, S, Berghaus, P, Berley, D, Bernardini, E, Bernhard, A, Bertrand, D, Besson, DZ, Binder, G, Bindig, D, Bissok, M, Blaufuss, E, Blumenthal, J, Boersma, DJ, Bohaichuk, S, Bohm, C, Bose, D, Böser, S, Botner, O, Brayeur, L, Bretz, H-P, Brown, AM, Bruijn, R, Brunner, J, Carson, M, Casey, J, Casier, M, Chirkin, D, Christov, A, Christy, B, Clark, K, Clevermann, F, Coenders, S, Cohen, S, Cowen, DF, Cruz Silva, AH, Danninger, M, Daughhetee, J, Davis, JC, Day, M, De Clercq, C, De Ridder, S, Desiati, P, de Vries, KD, de With, M, DeYoung, T, Díaz-Vélez, JC, Dunkman, M, Eagan, R, Eberhardt, B, Eichmann, B, Eisch, J, Ellsworth, RW, Euler, S, Evenson, PA, Fadiran, O, Fazely, AR, Fedynitch, A, Feintzeig, J, Feusels, T, Filimonov, K, Finley, C, Fischer-Wasels, T, Flis, S, Franckowiak, A, Frantzen, K, Fuchs, T, Gaisser, TK, Gallagher, J, Gerhardt, L, Gladstone, L, Glüsenkamp, T, Goldschmidt, A, Golup, G, Gonzalez, JG, Goodman, JA, Góra, D, Grandmont, DT, Grant, D, Groß, A, Ha, C, and Haj Ismail, A

Subjects
Nuclear and Plasma Physics, Particle and High Energy Physics, Physical Sciences, IceCube Collaboration, astro-ph.HE, astro-ph.CO, hep-ex, General Science & Technology
Abstract

We report on results of an all-sky search for high-energy neutrino events interacting within the IceCube neutrino detector conducted between May 2010 and May 2012. The search follows up on the previous detection of two PeV neutrino events, with improved sensitivity and extended energy coverage down to about 30 TeV. Twenty-six additional events were observed, substantially more than expected from atmospheric backgrounds. Combined, both searches reject a purely atmospheric origin for the 28 events at the 4σ level. These 28 events, which include the highest energy neutrinos ever observed, have flavors, directions, and energies inconsistent with those expected from the atmospheric muon and neutrino backgrounds. These properties are, however, consistent with generic predictions for an additional component of extraterrestrial origin.

Published
2013

34. Comprehensive computational design of ordered peptide macrocycles

Author

Hosseinzadeh, Parisa, Bhardwaj, Gaurav, Mulligan, Vikram Khipple, Shortridge, Matthew D., Craven, Timothy W., Pardo-Avila, Fátima, Rettie, Stephen A., Kim, David E., Silva, Daniel-Adriano, Ibrahim, Yehia M., Webb, Ian K., Cort, John R., Adkins, Joshua N., Varani, Gabriele, and Baker, David

Published
2017

35. Natural selection shaped the rise and fall of passenger pigeon genomic diversity

Author

Murray, Gemma G. R., Soares, André E. R., Novak, Ben J., Schaefer, Nathan K., Cahill, James A., Baker, Allan J., Demboski, John R., Doll, Andrew, Da Fonseca, Rute R., Fulton, Tara L., Gilbert, M. Thomas P., Heintzman, Peter D., Letts, Brandon, McIntosh, George, O’Connell, Brendan L., Peck, Mark, Pipes, Marie-Lorraine, Rice, Edward S., Santos, Kathryn M., Sohrweide, A. Gregory, Vohr, Samuel H., Corbett-Detig, Russell B., Green, Richard E., and Shapiro, Beth

Published
2017

36. From pipelines to pathways in the study of academic progress

Author

René F. Kizilcec, Rachel B. Baker, Elizabeth Bruch, Kalena E. Cortes, Laura T. Hamilton, David Nathan Lang, Zachary A. Pardos, Marissa E. Thompson, and Mitchell L. Stevens

Subjects
Multidisciplinary
Abstract

Students and administrators can benefit from new analytics

Published
2023

37. Following Gene Duplication, Paralog Interference Constrains Transcriptional Circuit Evolution

Author

Baker, Christopher R, Hanson-Smith, Victor, and Johnson, Alexander D

Subjects
Genetics, Biotechnology, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Amino Acid Sequence, Arginine, Candida albicans, Evolution, Molecular, Gene Duplication, Gene Regulatory Networks, Kluyveromyces, Minichromosome Maintenance 1 Protein, Molecular Sequence Data, Saccharomyces cerevisiae, Sequence Deletion, Transcription, Genetic, General Science & Technology
Abstract

Most models of gene duplication assume that the ancestral functions of the preduplication gene are independent and can therefore be neatly partitioned between descendant paralogs. However, many gene products, such as transcriptional regulators, are components within cooperative assemblies; here, we show that a natural consequence of duplication and divergence of such proteins can be competitive interference between the paralogs. Our example is based on the duplication of the essential MADS-box transcriptional regulator Mcm1, which is found in all fungi and regulates a large set of genes. We show that a set of historical amino acid sequence substitutions minimized paralog interference in contemporary species and, in doing so, increased the molecular complexity of this gene regulatory network. We propose that paralog interference is a common constraint on gene duplicate evolution, and its resolution, which can generate additional regulatory complexity, is needed to stabilize duplicated genes in the genome.

Published
2013

38. Top-down design of protein architectures with reinforcement learning

Author

Lutz, Isaac D., primary, Wang, Shunzhi, additional, Norn, Christoffer, additional, Courbet, Alexis, additional, Borst, Andrew J., additional, Zhao, Yan Ting, additional, Dosey, Annie, additional, Cao, Longxing, additional, Xu, Jinwei, additional, Leaf, Elizabeth M., additional, Treichel, Catherine, additional, Litvicov, Patrisia, additional, Li, Zhe, additional, Goodson, Alexander D., additional, Rivera-Sánchez, Paula, additional, Bratovianu, Ana-Maria, additional, Baek, Minkyung, additional, King, Neil P., additional, Ruohola-Baker, Hannele, additional, and Baker, David, additional

Published
2023
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39. Iconic CO2 time series at risk

Author

Houweling, S, Badawy, B, Baker, DF, Basu, S, Belikov, D, Bergamaschi, P, Bousquet, P, Broquet, G, Butler, T, Canadell, JG, Chen, J, Chevallier, F, Ciais, P, Collatz, JG, Denning, S, Engelen, R, Enting, IG, Fischer, ML, Fraser, A, Gerbig, C, Gloor, M, Jacobson, AR, Jones, DBA, Heimann, M, Khalil, A, Kaminski, T, Kasibhatla, PS, Krakauer, NY, Krol, M, Maki, T, Maksyutov, S, Manning, A, Meesters, A, Miller, JB, Palmer, PI, Patra, P, Peters, W, Peylin, P, Poussi, Z, Prather, MJ, Randerson, JT, Röckmann, T, Rödenbeck, C, Sarmiento, JL, Schimel, DS, Scholze, M, Schuh, A, Suntharalingam, P, Takahashi, T, Turnbull, J, Yurganov, L, and Vermeulen, A

Published
2012

47. Cassini Imaging Science: Initial Results on Saturn's Atmosphere

Author

Porco, C. C., Baker, E., Barbara, J., Beurle, K., Brahic, A., Burns, J. A., Charnoz, S., Cooper, N., Dawson, D. D., Del Genio, A. D., Denk, T., Dones, L., Dyudina, U., Evans, M. W., Giese, B., Grazier, K., Helfenstein, P., Ingersoll, A. P., Jacobson, R. A., Johnson, T. V., McEwen, A., Murray, C. D., Neukum, G., Owen, W. M., Perry, J., Roatsch, T., Spitale, J., Squyres, S., Thomas, P., Tiscareno, M., Turtle, E., Vasavada, A. R., Veverka, J., Wagner, R., and West, R.

Published
2005

48. Cassini Imaging Science: Initial Results on Phoebe and Iapetus

Author

Porco, C. C., Baker, E., Barbara, J., Beurle, K., Brahic, A., Burns, J. A., Charnoz, S., Cooper, N., Dawson, D. D., Del Genio, A. D., Denk, T., Dones, L., Dyudina, U., Evans, M. W., Giese, B., Grazier, K., Helfenstein, P., Ingersoll, A. P., Jacobson, R. A., Johnson, T. V., McEwen, A., Murray, C. D., Neukum, G., Owen, W. M., Perry, J., Roatsch, T., Spitale, J., Squyres, S., Thomas, P. C., Tiscareno, M., Turtle, E., Vasavada, A. R., Veverka, J., Wagner, R., and West, R.

Published
2005

49. Cassini Imaging Science: Initial Results on Saturn's Rings and Small Satellites

Author

Porco, C. C., Baker, E., Barbara, J., Beurle, K., Brahic, A., Burns, J. A., Charnoz, S., Cooper, N., Dawson, D. D., Del Genio, A. D., Denk, T., Dones, L., Dyudina, U., Evans, M. W., Giese, B., Grazier, K., Helfenstein, P., Ingersoll, A. P., Jacobson, R. A., Johnson, T. V., McEwen, A., Murray, C. D., Neukum, G., Owen, W. M., Perry, J., Roatsch, T., Spitale, J., Squyres, S., Thomas, P., Tiscareno, M., Turtle, E., Vasavada, A. R., Veverka, J., Wagner, R., and West, R.

Published
2005

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