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Nucleotide sequence ofCoxiella burnetiisuperoxide dismutase

Robert A. Heinzen, Marvin E. Frazier, Louis P. Mallavia
1990 Nucleic Acids Research  
doi:10.1093/nar/18.21.6437 pmid:2243797 pmcid:PMC332550 fatcat:m2thwudvvbggtp6uqsmemtb4ue

CAMERA: A Community Resource for Metagenomics

Rekha Seshadri, Saul A Kravitz, Larry Smarr, Paul Gilna, Marvin Frazier
2007 PLoS Biology  
Citation: Seshadri R, Kravitz SA, Smarr L, Gilna P, Frazier M (2007) CAMERA: A community resource for metagenomics. PLoS Biol 5(3): e75.  ...  Kravitz, and Marvin Frazier are at the J. Craig Venter Institute (JCVI) in Rockville, Maryland, United States of America.  ... 
doi:10.1371/journal.pbio.0050075 pmid:17355175 pmcid:PMC1821059 fatcat:c323majirzdljpjvlpri7iqaui

Race Relations and the Race Problem

George E. Simpson, Edgar T. Thompson, E. Franklin Frazier, Horace R. Cayton, George S. Mitchell, Ira D. Reid, W. E. B. Du Bois, Marvin E. Porch, Herbert Aptheker
1940 American Sociological Review  
By Marvin E. Porcu. Pottstown, Pa.: Feroe Printing Co., 1938. Pp. 125. $1.50 (cloth), $1.00 (pap.). Negro Slave Revolts in the United States, 1526-1860. By HERBERT APTHEKER.  ... 
doi:10.2307/2084063 fatcat:sw4uppbgrvfd3pckrxn32yq264

The HuRef Browser: a web resource for individual human genomics

Nelson Axelrod, Yuan Lin, Pauline C. Ng, Timothy B. Stockwell, Jonathan Crabtree, Jiaqi Huang, Ewen Kirkness, Robert L. Strausberg, Marvin E. Frazier, J. Craig Venter, Saul Kravitz, Samuel Levy
2008 Nucleic Acids Research  
The HuRef Genome Browser is a web application for the navigation and analysis of the previously published genome of a human individual, termed HuRef. The browser provides a comparative view between the NCBI human reference sequence and the HuRef assembly, and it enables the navigation of the HuRef genome in the context of HuRef, NCBI and Ensembl annotations. Single nucleotide polymorphisms, indels, inversions, structural and copy-number variations are shown in the context of existing functional
more » ... annotations on either genome in the comparative view. Demonstrated here are some potential uses of the browser to enable a better understanding of individual human genetic variation. The browser provides full access to the underlying reads with sequence and quality information, the genome assembly and the evidence supporting the identification of DNA polymorphisms. The HuRef Browser is a unique and versatile tool for browsing genome assemblies and studying individual human sequence variation in a diploid context. The browser is available online at
doi:10.1093/nar/gkn939 pmid:19036787 pmcid:PMC2686481 fatcat:zevaguxaz5gefax4beu3gadggy

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

Dongying Wu, Martin Wu, Aaron Halpern, Douglas B. Rusch, Shibu Yooseph, Marvin Frazier, J. Craig Venter, Jonathan A. Eisen, Robert Fleischer
2011 PLoS ONE  
Most of our knowledge about the ancient evolutionary history of organisms has been derived from data associated with specific known organisms (i.e., organisms that we can study directly such as plants, metazoans, and culturable microbes). Recently, however, a new source of data for such studies has arrived: DNA sequence data generated directly from environmental samples. Such metagenomic data has enormous potential in a variety of areas including, as we argue here, in studies of very early
more » ... s in the evolution of gene families and of species. Methodology/Principal Findings: We designed and implemented new methods for analyzing metagenomic data and used them to search the Global Ocean Sampling (GOS) Expedition data set for novel lineages in three gene families commonly used in phylogenetic studies of known and unknown organisms: small subunit rRNA and the recA and rpoB superfamilies. Though the methods available could not accurately identify very deeply branched ss-rRNAs (largely due to difficulties in making robust sequence alignments for novel rRNA fragments), our analysis revealed the existence of multiple novel branches in the recA and rpoB gene families. Analysis of available sequence data likely from the same genomes as these novel recA and rpoB homologs was then used to further characterize the possible organismal source of the novel sequences. Conclusions/Significance: Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism. A third possibility is that some come from novel cellular lineages that are only distantly related to any organisms for which sequence data is currently available. If there exist any major, but so-far-undiscovered, deeply branching lineages in the tree of life, we suggest that methods such as those described herein currently offer the best way to search for them.
doi:10.1371/journal.pone.0018011 pmid:21437252 pmcid:PMC3060911 fatcat:w22b7b6ewjhmbpiupqan56r3si

The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples

Shannon J. Williamson, Douglas B. Rusch, Shibu Yooseph, Aaron L. Halpern, Karla B. Heidelberg, John I. Glass, Cynthia Andrews-Pfannkoch, Douglas Fadrosh, Christopher S. Miller, Granger Sutton, Marvin Frazier, J. Craig Venter (+1 others)
2008 PLoS ONE  
doi:10.1371/journal.pone.0001456 pmid:18213365 pmcid:PMC2186209 fatcat:vcw2acnfazg4fcsjt5mzds3jae

Genomic and functional adaptation in surface ocean planktonic prokaryotes

Shibu Yooseph, Kenneth H. Nealson, Douglas B. Rusch, John P. McCrow, Christopher L. Dupont, Maria Kim, Justin Johnson, Robert Montgomery, Steve Ferriera, Karen Beeson, Shannon J. Williamson, Andrey Tovchigrechko (+8 others)
2010 Nature  
The understanding of marine microbial ecology and metabolism has been hampered by the paucity of sequenced reference genomes. To this end, we report the sequencing of 137 diverse marine isolates collected from around the world. We analysed these sequences, along with previously published marine prokaryotic genomes, in the context of marine metagenomic data, to gain insights into the ecology of the surface ocean prokaryotic picoplankton (0.1-3.0 mm size range). The results suggest that the
more » ... ced genomes define two microbial groups: one composed of only a few taxa that are nearly always abundant in picoplanktonic communities, and the other consisting of many microbial taxa that are rarely abundant. The genomic content of the second group suggests that these microbes are capable of slow growth and survival in energy-limited environments, and rapid growth in energy-rich environments. By contrast, the abundant and cosmopolitan picoplanktonic prokaryotes for which there is genomic representation have smaller genomes, are probably capable of only slow growth and seem to be relatively unable to sense or rapidly acclimate to energy-rich conditions. Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass.
doi:10.1038/nature09530 pmid:21048761 fatcat:mlsemudx3vci7kyjr3zaddsq4u

Metagenomes from High-Temperature Chemotrophic Systems Reveal Geochemical Controls on Microbial Community Structure and Function

William P. Inskeep, Douglas B. Rusch, Zackary J. Jay, Markus J. Herrgard, Mark A. Kozubal, Toby H. Richardson, Richard E. Macur, Natsuko Hamamura, Ryan deM. Jennings, Bruce W. Fouke, Anna-Louise Reysenbach, Frank Roberto (+10 others)
2010 PLoS ONE  
The Yellowstone caldera contains the most numerous and diverse geothermal systems on Earth, yielding an extensive array of unique high-temperature environments that host a variety of deeply-rooted and understudied Archaea, Bacteria and Eukarya. The combination of extreme temperature and chemical conditions encountered in geothermal environments often results in considerably less microbial diversity than other terrestrial habitats and offers a tremendous opportunity for studying the structure
more » ... function of indigenous microbial communities and for establishing linkages between putative metabolisms and element cycling. Metagenome sequence (14-15,000 Sanger reads per site) was obtained for five hightemperature (.65uC) chemotrophic microbial communities sampled from geothermal springs (or pools) in Yellowstone National Park (YNP) that exhibit a wide range in geochemistry including pH, dissolved sulfide, dissolved oxygen and ferrous iron. Metagenome data revealed significant differences in the predominant phyla associated with each of these geochemical environments. Novel members of the Sulfolobales are dominant in low pH environments, while other Crenarchaeota including distantly-related Thermoproteales and Desulfurococcales populations dominate in suboxic sulfidic sediments. Several novel archaeal groups are well represented in an acidic (pH 3) Fe-oxyhydroxide mat, where a higher O 2 influx is accompanied with an increase in archaeal diversity. The presence or absence of genes and pathways important in S oxidation-reduction, H 2 -oxidation, and aerobic respiration (terminal oxidation) provide insight regarding the metabolic strategies of indigenous organisms present in geothermal systems. Multiple-pathway and protein-specific functional analysis of metagenome sequence data corroborated results from phylogenetic analyses and clearly demonstrate major differences in metabolic potential across sites. The distribution of functional genes involved in electron transport is consistent with the hypothesis that geochemical parameters (e.g., pH, sulfide, Fe, O 2 ) control microbial community structure and function in YNP geothermal springs.
doi:10.1371/journal.pone.0009773 pmid:20333304 pmcid:PMC2841643 fatcat:2m453kl4n5dwbn4omx64mn3dqm

The Diploid Genome Sequence of an Individual Human

Samuel Levy, Granger Sutton, Pauline C Ng, Lars Feuk, Aaron L Halpern, Brian P Walenz, Nelson Axelrod, Jiaqi Huang, Ewen F Kirkness, Gennady Denisov, Yuan Lin, Jeffrey R MacDonald (+20 others)
2007 PLoS Biology  
Presented here is a genome sequence of an individual human. It was produced from ;32 million random DNA fragments, sequenced by Sanger dideoxy technology and assembled into 4,528 scaffolds, comprising 2,810 million bases (Mb) of contiguous sequence with approximately 7.5-fold coverage for any given region. We developed a modified version of the Celera assembler to facilitate the identification and comparison of alternate alleles within this individual diploid genome. Comparison of this genome
more » ... d the National Center for Biotechnology Information human reference assembly revealed more than 4.1 million DNA variants, encompassing 12.3 Mb. These variants (of which 1,288,319 were novel) included 3,213,401 single nucleotide polymorphisms (SNPs), 53,823 block substitutions (2-206 bp), 292,102 heterozygous insertion/deletion events (indels)(1-571 bp), 559,473 homozygous indels (1-82,711 bp), 90 inversions, as well as numerous segmental duplications and copy number variation regions. Non-SNP DNA variation accounts for 22% of all events identified in the donor, however they involve 74% of all variant bases. This suggests an important role for non-SNP genetic alterations in defining the diploid genome structure. Moreover, 44% of genes were heterozygous for one or more variants. Using a novel haplotype assembly strategy, we were able to span 1.5 Gb of genome sequence in segments .200 kb, providing further precision to the diploid nature of the genome. These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information. Citation: Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) The diploid genome sequence of an individual human. PLoS Biol 5(10): e254.
doi:10.1371/journal.pbio.0050254 pmid:17803354 pmcid:PMC1964779 fatcat:mnf6v3blpzhsbjngmbagmlzh2u

The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families

Shibu Yooseph, Granger Sutton, Douglas B Rusch, Aaron L Halpern, Shannon J Williamson, Karin Remington, Jonathan A Eisen, Karla B Heidelberg, Gerard Manning, Weizhong Li, Lukasz Jaroszewski, Piotr Cieplak (+22 others)
2007 PLoS Biology  
Metagenomics projects based on shotgun sequencing of populations of micro-organisms yield insight into protein families. We used sequence similarity clustering to explore proteins with a comprehensive dataset consisting of sequences from available databases together with 6.12 million proteins predicted from an assembly of 7.7 million Global Ocean Sampling (GOS) sequences. The GOS dataset covers nearly all known prokaryotic protein families. A total of 3,995 medium-and large-sized clusters
more » ... ting of only GOS sequences are identified, out of which 1,700 have no detectable homology to known families. The GOS-only clusters contain a higher than expected proportion of sequences of viral origin, thus reflecting a poor sampling of viral diversity until now. Protein domain distributions in the GOS dataset and current protein databases show distinct biases. Several protein domains that were previously categorized as kingdom specific are shown to have GOS examples in other kingdoms. About 6,000 sequences (ORFans) from the literature that heretofore lacked similarity to known proteins have matches in the GOS data. The GOS dataset is also used to improve remote homology detection. Overall, besides nearly doubling the number of current proteins, the predicted GOS proteins also add a great deal of diversity to known protein families and shed light on their evolution. These observations are illustrated using several protein families, including phosphatases, proteases, ultraviolet-irradiation DNA damage repair enzymes, glutamine synthetase, and RuBisCO. The diversity added by GOS data has implications for choosing targets for experimental structure characterization as part of structural genomics efforts. Our analysis indicates that new families are being discovered at a rate that is linear or almost linear with the addition of new sequences, implying that we are still far from discovering all protein families in nature. | Volume 5 | Issue 3 | e16 0432 PL o S BIOLOGY PLoS Biology | www.plosbiology.org March 2007 | Volume 5 | Issue 3 | e16 0433 Expanding the Protein Family Universe 17,422,766 134 ORFs identified from an assembly of 7.7 million reads. These reads include both the reads from the Sorcerer II GOS Expedition and the reads from the earlier Sargasso Sea study. Also included are 36,318 ORFs identified from an assembly of sequences collected from the viral size (, 0.1 lm) fraction of one sample.
doi:10.1371/journal.pbio.0050016 pmid:17355171 pmcid:PMC1821046 fatcat:effw6nlfdnfujdyk5gqaz3vm3u

EXPLORING THE OCEAN'S MICROBES: SEQUENCING THE SEVEN SEAS

Marvin E. Frazier, Douglas B. Rusch, Aaron L. Halpern, Karla B. Heidelberg, Granger Sutton, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A. Eisen, Jeff Hoffman, Charles H. Howard, Cyrus Foote (+30 others)
2006 Computational Systems Bioinformatics  
doi:10.1142/9781860947575_0001 fatcat:xvfdqjeivrbznhlloj2z22cj5y

The Sorcerer II Global Ocean Sampling Expedition: Northwest Atlantic through Eastern Tropical Pacific

Douglas B Rusch, Aaron L Halpern, Granger Sutton, Karla B Heidelberg, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A Eisen, Jeff M Hoffman, Karin Remington, Karen Beeson, Bao Tran (+29 others)
2007 PLoS Biology  
The world's oceans contain a complex mixture of micro-organisms that are for the most part, uncharacterized both genetically and biochemically. We report here a metagenomic study of the marine planktonic microbiota in which surface (mostly marine) water samples were analyzed as part of the Sorcerer II Global Ocean Sampling expedition. These samples, collected across a several-thousand km transect from the North Atlantic through the Panama Canal and ending in the South Pacific yielded an
more » ... e dataset consisting of 7.7 million sequencing reads (6.3 billion bp). Though a few major microbial clades dominate the planktonic marine niche, the dataset contains great diversity with 85% of the assembled sequence and 57% of the unassembled data being unique at a 98% sequence identity cutoff. Using the metadata associated with each sample and sequencing library, we developed new comparative genomic and assembly methods. One comparative genomic method, termed "fragment recruitment," addressed questions of genome structure, evolution, and taxonomic or phylogenetic diversity, as well as the biochemical diversity of genes and gene families. A second method, termed "extreme assembly," made possible the assembly and reconstruction of large segments of abundant but clearly nonclonal organisms. Within all abundant populations analyzed, we found extensive intra-ribotype diversity in several forms: (1) extensive sequence variation within orthologous regions throughout a given genome; despite coverage of individual ribotypes approaching 500-fold, most individual sequencing reads are unique; (2) numerous changes in gene content some with direct adaptive implications; and (3) hypervariable genomic islands that are too variable to assemble. The intra-ribotype diversity is organized into genetically isolated populations that have overlapping but independent distributions, implying distinct environmental preference. We present novel methods for measuring the genomic similarity between metagenomic samples and show how they may be grouped into several community types. Specific functional adaptations can be identified both within individual ribotypes and across the entire community, including proteorhodopsin spectral tuning and the presence or absence of the phosphate-binding gene PstS.
doi:10.1371/journal.pbio.0050077 pmid:17355176 pmcid:PMC1821060 fatcat:kn2fi2az6fbe7ptlgrqrzfyodq

EXPLORING THE OCEAN'S MICROBES: SEQUENCING THE SEVEN SEAS

Marvin E. Frazier, Douglas B. Rusch, Aaron L. Halpern, Karla B. Heidelberg, Granger Sutton, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A. Eisen, Jeff Hoffman, Charles H. Howard, Cyrus Foote (+30 others)
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
doi:10.1142/18609475730004 fatcat:texbadnh4jauriito5w6hqvbnm

EXPLORING THE OCEAN'S MICROBES: SEQUENCING THE SEVEN SEAS

Marvin E. Frazier, Douglas B. Rusch, Aaron L. Halpern, Karla B. Heidelberg, Granger Sutton, Shannon Williamson, Shibu Yooseph, Dongying Wu, Jonathan A. Eisen, Jeff Hoffman, Charles H. Howard, Cyrus Foote (+30 others)
2006 Computational Systems Bioinformatics - Proceedings of the Conference CSB 2006  
doi:10.1142/1860947573_0004 fatcat:hh6xzspcn5advgu5c5lh2zwsuy

Page 99 of Chemical Engineering Vol. 49, Issue 9 [page]

1942 Chemical Engineering  
Marvin O., Shrader, Yale University; Dr. John C. Lawler, University of Illinois; Dr. J. P. G. Beiswanger, Northwestern Uni versity; Dr. L. M. Schenck, University of Texas; and Dr. Ben H.  ...  Frazier has been appointed | district sales manager of the New York Metropolitan area for Columbia Chem ical Division, Pittsburgh Plate Glass Co. Mr.  ... 
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