Institution
United States Department of Energy
Government•Washington D.C., District of Columbia, United States•
About: United States Department of Energy is a government organization based out in Washington D.C., District of Columbia, United States. It is known for research contribution in the topics: Coal & Catalysis. The organization has 13656 authors who have published 14177 publications receiving 556962 citations. The organization is also known as: DOE & Department of Energy.
Topics: Coal, Catalysis, Combustion, Oxide, Hydrogen
Papers published on a yearly basis
Papers
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Jacobs University Bremen1, Max Planck Society2, Howard Hughes Medical Institute3, University of Colorado Boulder4, Michigan State University5, Marine Biological Laboratory6, University of Chicago7, Plymouth Marine Laboratory8, Argonne National Laboratory9, National Institutes of Health10, Yonsei University11, University of Manchester12, University of Oxford13, Harvard University14, New York University15, University of Pennsylvania16, Los Alamos National Laboratory17, United States Department of Energy18, University of Maryland, Baltimore19, Ghent University20, Lawrence Berkeley National Laboratory21, University of Southern California22, National Ecological Observatory Network23, Baylor College of Medicine24, University of New Mexico25, Washington University in St. Louis26, University of Queensland27, San Diego State University28, Cornell University29, Technische Universität München30, J. Craig Venter Institute31, University of Waterloo32, Oak Ridge National Laboratory33, Vrije Universiteit Brussel34, University of Guelph35, Stanford University36, United States Department of Veterans Affairs37
TL;DR: To establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, the minimum information about any (x) sequence is presented (MIxS).
Abstract: Here we present a standard developed by the Genomic Standards Consortium (GSC) for reporting marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The ‘environmental packages’ apply to any genome sequence of known origin and can be used in combination with MIMARKS and other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we present the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
600 citations
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TL;DR: Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosYmbionT evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease.
Abstract: Complete genome DNA sequence and analysis is presented for Wolbachia, the obligate alpha-proteobacterial endosymbiont required for fertility and survival of the human filarial parasitic nematode Brugia malayi. Although, quantitatively, the genome is even more degraded than those of closely related Rickettsia species, Wolbachia has retained more intact metabolic pathways. The ability to provide riboflavin, flavin adenine dinucleotide, heme, and nucleotides is likely to be Wolbachia's principal contribution to the mutualistic relationship, whereas the host nematode likely supplies amino acids required for Wolbachia growth. Genome comparison of the Wolbachia endosymbiont of B. malayi (wBm) with the Wolbachia endosymbiont of Drosophila melanogaster (wMel) shows that they share similar metabolic trends, although their genomes show a high degree of genome shuffling. In contrast to wMel, wBm contains no prophage and has a reduced level of repeated DNA. Both Wolbachia have lost a considerable number of membrane biogenesis genes that apparently make them unable to synthesize lipid A, the usual component of proteobacterial membranes. However, differences in their peptidoglycan structures may reflect the mutualistic lifestyle of wBm in contrast to the parasitic lifestyle of wMel. The smaller genome size of wBm, relative to wMel, may reflect the loss of genes required for infecting host cells and avoiding host defense systems. Analysis of this first sequenced endosymbiont genome from a filarial nematode provides insight into endosymbiont evolution and additionally provides new potential targets for elimination of cutaneous and lymphatic human filarial disease.
590 citations
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United States Department of Energy1, United States Department of Agriculture2, Clark University3, University of Minnesota4, Aix-Marseille University5, Institut national de la recherche agronomique6, Michigan State University7, Pacific Northwest National Laboratory8, Universidad Pública de Navarra9, Great Lakes Bioenergy Research Center10
TL;DR: The results indicate that the prevailing paradigm of white rot vs. brown rot does not capture the diversity of fungal wood decay mechanisms, and suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay.
Abstract: Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillacea can degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.
588 citations
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TL;DR: The detection of emission up to ∼31 GeV from the distant and short GRB, and no evidence for the violation of Lorentz invariance is found, which disfavour quantum-gravity theories in which the quantum nature of space–time on a very small scale linearly alters the speed of light.
Abstract: A cornerstone of Einstein's special relativity is Lorentz invariance-the postulate that all observers measure exactly the same speed of light in vacuum, independent of photon-energy. While special relativity assumes that there is no fundamental length-scale associated with such invariance, there is a fundamental scale (the Planck scale, l(Planck) approximate to 1.62 x 10(-33) cm or E(Planck) = M(Planck)c(2) approximate to 1.22 x 10(19) GeV), at which quantum effects are expected to strongly affect the nature of space-time. There is great interest in the (not yet validated) idea that Lorentz invariance might break near the Planck scale. A key test of such violation of Lorentz invariance is a possible variation of photon speed with energy(1-7). Even a tiny variation in photon speed, when accumulated over cosmological light-travel times, may be revealed by observing sharp features in gamma-ray burst (GRB) light-curves(2). Here we report the detection of emission up to similar to 31GeV from the distant and short GRB090510. We find no evidence for the violation of Lorentz invariance, and place a lower limit of 1.2E(Planck) on the scale of a linear energy dependence (or an inverse wavelength dependence), subject to reasonable assumptions about the emission (equivalently we have an upper limit of l(Planck)/1.2 on the length scale of the effect). Our results disfavour quantum-gravity theories(3,6,7) in which the quantum nature of space-time on a very small scale linearly alters the speed of light.
586 citations
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TL;DR: This work highlights the importance of SOPs for genome annotation and endorse an online repository of Sops and highlights the need for a central repository to store and disseminate procedures and protocols for annotation.
Abstract: The methodologies used to generate genome and metagenome annotations are diverse and vary between groups and laboratories. Descriptions of the annotation process are helpful in interpreting genome annotation data. Some groups have produced Standard Operating Procedures (SOPs) that describe the annotation process, but standards are lacking for structure and content of these descriptions. In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse an online repository of SOPs.
585 citations
Authors
Showing all 13660 results
Name | H-index | Papers | Citations |
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Martin White | 196 | 2038 | 232387 |
Paul G. Richardson | 183 | 1533 | 155912 |
Jie Zhang | 178 | 4857 | 221720 |
Krzysztof Matyjaszewski | 169 | 1431 | 128585 |
Yang Gao | 168 | 2047 | 146301 |
David Eisenberg | 156 | 697 | 112460 |
Marvin Johnson | 149 | 1827 | 119520 |
Carlos Escobar | 148 | 1184 | 95346 |
Joshua A. Frieman | 144 | 609 | 109562 |
Paul Jackson | 141 | 1372 | 93464 |
Greg Landsberg | 141 | 1709 | 109814 |
J. Conway | 140 | 1692 | 105213 |
Pushpalatha C Bhat | 139 | 1587 | 105044 |
Julian Borrill | 139 | 387 | 102906 |
Cecilia Elena Gerber | 138 | 1727 | 106984 |