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1. Full Text High-Throughput Sequencing of the Zebrafish Antibody Repertoire
by Joshua A. Weinstein and Ning Jiang and Richard A. White and Daniel S. Fisher and Stephen R. Quake
Science, ISSN 0036-8075, 5/2009, Volume 324, Issue 5928, pp. 807 - 810
Despite tremendous progress in understanding the nature of the immune system, the full diversity of an organism's antibody repertoire is unknown. We used... 
Antibody diversity | Fish scales | Complementary DNA | Correlations | Antibodies | Fish | Reports | Rarefaction | Convergent evolution | Sequencing | Immune system | DIVERSITY | IMMUNE RECEPTORS | MULTIDISCIPLINARY SCIENCES | PERSPECTIVES | Complementarity Determining Regions - genetics | Antibody Diversity | Zebrafish - immunology | Gene Library | VDJ Exons | Computational Biology | Molecular Sequence Data | Male | Immunoglobulin Joining Region - genetics | Sequence Analysis, DNA | Zebrafish - genetics | Genes, Immunoglobulin Heavy Chain | Animals | Recombination, Genetic | Base Sequence | Antibodies - genetics | Female | Immunoglobulin Heavy Chains - genetics | Immunoglobulin M - genetics | Viral antibodies | Genetic aspects | Research | Zebrafish | Genetics | Immunology | Biological diversity
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2. Full Text Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome
by Pride, David T and Salzman, Julia and Haynes, Matthew and Rohwer, Forest and Davis-Long, Clara and White III, Richard A and Loomer, Peter and Armitage, Gary C and Relman, David A
ISME Journal, ISSN 1751-7362, 05/2012, Volume 6, Issue 5, pp. 915 - 926
Viruses are the most abundant known infectious agents on the planet and are significant drivers of diversity in a variety of ecosystems. Although there have... 
saliva | virome | metagenome | bacteriophage | microbiome | virus | SURFACE PROTEIN | MICROBIOLOGY | MICROBIOTA | VIRULENCE | MOLECULAR ANALYSIS | STREPTOCOCCUS-PNEUMONIAE | EVOLUTION | METHANOGENIC ARCHAEA | VIRAL COMMUNITIES | ECOLOGY | DIVERSITY | VIRUSES | Genes, Bacterial | Humans | Bacteria - genetics | Sequence Analysis, DNA | Bacteriophages - isolation & purification | Saliva - virology | Feces - microbiology | Feces - virology | Mouth - microbiology | Ecosystem | Mouth - virology | Bacteriophages - genetics | RNA, Ribosomal, 16S - genetics | Saliva - microbiology | Metagenome | Bacteria - virology | Respiratory tract | Oral cavity | rRNA 16S | Phages | Discordance | Lysogeny | Data processing | Environmental factors | Habitat | Feces | Saliva | virulence factors | Original
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3. Full Text Eye-like ocelloids are built from different endosymbiotically acquired components
by Gavelis, Gregory S and Hayakawa, Shiho and White, Richard A and Gojobori, Takashi and Suttle, Curtis A and Keeling, Patrick J and Leander, Brian S
Nature, ISSN 0028-0836, 07/2015, Volume 523, Issue 7559, pp. 204 - 207
Multicellularity is often considered a prerequisite for morphological complexity, as seen in the camera-type eyes found in several groups of animals. A notable... 
ERYTHROPSIDINIUM | LINDEMANN | EVOLUTION | WARNOWIIDAE | ALIGNMENT | LSU RDNA SEQUENCES | MULTIDISCIPLINARY SCIENCES | DINOFLAGELLATE | WARNOWIACEAE | MOLECULAR PHYLOGENY | PROTISTS | Symbiosis | Microscopy, Electron, Transmission | Microscopy, Electron, Scanning | Molecular Sequence Data | Mitochondria - metabolism | Protozoan Proteins - genetics | Rhodophyta - genetics | Mitochondria - ultrastructure | Dinoflagellida - genetics | Plastids - ultrastructure | Plastids - metabolism | Genome, Protozoan - genetics | Dinoflagellida - physiology | Dinoflagellida - ultrastructure | Physiological aspects | Dinoflagellates | Mitochondria | Studies | Microorganisms | Membranes | Genomics | Phylogenetics | Plastids | Deoxyribonucleic acid--DNA
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4. Full Text Digital PCR provides sensitive and absolute calibration for high throughput sequencing
by White III, Richard A and Blainey, Paul C and Fan, H. Christina and Quake, Stephen R
BMC Genomics, ISSN 1471-2164, 03/2009, Volume 10, Issue 1, pp. 116 - 116
Background: Next-generation DNA sequencing on the 454, Solexa, and SOLiD platforms requires absolute calibration of the number of molecules to be sequenced.... 
BIOTECHNOLOGY & APPLIED MICROBIOLOGY | GENETICS & HEREDITY | TIME QUANTITATIVE PCR | Animals | DNA, Bacterial - genetics | Gene Library | Escherichia coli - genetics | Humans | Mice | Sequence Analysis, DNA - methods | Polymerase Chain Reaction - methods | Polymerase chain reaction | Usage | Escherichia coli | Genetic aspects | Research | Nucleotide sequencing | Methods
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5. Full Text Determinism and stochasticity during maturation of the zebrafish antibody repertoire
by Ning Jiang and Joshua A. Weinstein and Lolita Penland and Richard A. White and Daniel S. Fisher and Stephen R. Quake and Steven H. Kleinstein
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 3/2011, Volume 108, Issue 13, pp. 5348 - 5353
It is thought that the adaptive immune system of immature organisms follows a more deterministic program of antibody creation than is found in adults. We used... 
Beta cells | Stereotypies | B lymphocytes | Developmental biology | Antibodies | Amino acids | Adaptive immunity | Sequencing | Genetic mutation | Age groups | Secondary repertoire | Immunology | Repertoire development | RECOMBINATION | SEGMENT | MULTIDISCIPLINARY SCIENCES | MOUSE | HUMANS | HEAVY-CHAIN LOCUS | VH-GENES | FETAL | immunology | EXPRESSION | repertoire development | secondary repertoire | Adaptive Immunity - physiology | Antibody Diversity | Animals | Zebrafish - immunology | Stochastic Processes | VDJ Exons | Antibodies - genetics | Immunoglobulin Variable Region - genetics | Immunoglobulin Subunits - genetics | Zebrafish - genetics | Zebra fish | Research | Biological Sciences
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6. Full Text Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases
by Lloyd-Price, Jason and Arze, Cesar and Ananthakrishnan, Ashwin N and Schirmer, Melanie and Avila-Pacheco, Julian and Poon, Tiffany W and Andrews, Elizabeth and Ajami, Nadim J and Bonham, Kevin S and Brislawn, Colin J and Casero, David and Courtney, Holly and Gonzalez, Antonio and Graeber, Thomas G and Hall, A Brantley and Lake, Kathleen and Landers, Carol J and Mallick, Himel and Plichta, Damian R and Prasad, Mahadev and Rahnavard, Gholamali and Sauk, Jenny and Shungin, Dmitry and Vázquez-Baeza, Yoshiki and White, Richard A and Braun, Jonathan and Denson, Lee A and Jansson, Janet K and Knight, Rob and Kugathasan, Subra and McGovern, Dermot P B and Petrosino, Joseph F and Stappenbeck, Thaddeus S and Winter, Harland S and Clish, Clary B and Franzosa, Eric A and Vlamakis, Hera and Xavier, Ramnik J and Huttenhower, Curtis and IBDMDB Investigators and Pacific Northwest National Lab. (PNNL), Richland, WA (United States) and Medicinska fakulteten and Institutionen för odontologi and Umeå universitet
Nature, ISSN 0028-0836, 05/2019, Volume 569, Issue 7758, pp. 655 - 662
Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative... 
Inflammatory bowel diseases | Microbiota (Symbiotic organisms) | Genomics | Genetic research | Genetic aspects | Research | Diagnosis | Bile acids | Metabolites | Ecosystems | Analysis | Fatty acids | Ulcerative colitis | IBD | multiomics | 60 APPLIED LIFE SCIENCES | microbiome | Clinical Medicine | Medical and Health Sciences | Klinisk medicin | Medicin och hälsovetenskap | Gastroenterology and Hepatology | Gastroenterologi
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7. Full Text “886-84-like” tick-borne encephalitis virus strains: Intraspecific status elucidated by comparative genomics
by Adelshin, Renat V and Sidorova, Elena A and Bondaryuk, Artem N and Trukhina, Anna G and Sherbakov, Dmitry Yu and White III, Richard Allen and Andaev, Evgeny I and Balakhonov, Sergey V
Ticks and Tick-borne Diseases, ISSN 1877-959X, 08/2019, Volume 10, Issue 5, pp. 1168 - 1172
Tick-borne encephalitis virus (TBEV) can cause severe meningitis, encephalitis, and meningoencephalitis. TBEV represents a pathogen of high zoonotic potential... 
Comparative genomics | “886-84-like” strains | Phylogeny | Tick-borne encephalitis virus (TBEV)
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8. Full Text The genome sequence of the colonial chordate, Botryllus schlosseri
by Voskoboynik, Ayelet and Neff, Norma F and Sahoo, Debashis and Newman, Aaron M and Pushkarev, Dmitry and Koh, Winston and Passarelli, Benedetto and Fan, H Christina and Mantalas, Gary L and Palmeri, Karla J and Ishizuka, Katherine J and Gissi, Carmela and Griggio, Francesca and Ben-Shlomo, Rachel and Corey, Daniel M and Penland, Lolita and White, Richard A and Weissman, Irving L and Quake, Stephen R
eLife, ISSN 2050-084X, 07/2013, Volume 2013, Issue 2, p. e00569
Botryllus schlosseri is a colonial urochordate that follows the chordate plan of development following sexual reproduction, but invokes a stem cell-mediated... 
ALLORECOGNITION | STEM-CELLS | ORIGINS | EVOLUTION | DIVERSIFICATION | GENES | BIOLOGY | NEURAL CREST | IDENTIFICATION | SELECTION | MOLECULAR PHYLOGENY | Chordata - genetics | Reproduction | Animals | Chordata - physiology | Chromosome Mapping | High-Throughput Nucleotide Sequencing | Phylogeny | Genome | Chordata - classification | Nucleotide sequence | Genes | Genomes | Transplantation | Sexual reproduction | Blood | Vertebrates | Next-generation sequencing | Asexual reproduction | Stem cells | Budding | Apoptosis
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9. Full Text Identification of metabolite and protein explanatory variables governing microbiome establishment and re-establishment within a cellulose-degrading anaerobic bioreactor
by Callister, Stephen J and McCue, Lee Ann and Boaro, Amy A and LaMarche, Brian and White, Richard A and Brown, Joseph M and Brown, Joseph M and Ahring, Birgitte K and Ahring, Birgitte K and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
PloS one, ISSN 1932-6203, 10/2018, Volume 13, Issue 10, p. e0204831
Proteins, metabolites, and 16S rRNA measurements were used to examine the community structure and functional relationships within a cellulose degrading... 
PROPIONATE | MUNICIPAL SOLID-WASTE | COMMUNITY STRUCTURE | MIXING CONDITIONS | SEQUENCE DATA | PERFORMANCE | MULTIDISCIPLINARY SCIENCES | ESCHERICHIA-COLI | ADAPTATION | DEGRADATION | ACETATE | Anaerobiosis | Metabolomics | Propionates - chemistry | Bacteria - metabolism | Cellulose | Metagenomics - methods | Acetates - chemistry | Caproates - chemistry | Bacterial Proteins - analysis | Fermentation | Bacteria - genetics | Bacteria - isolation & purification | Animals | DNA, Bacterial - genetics | Cattle | Bioreactors - microbiology | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Rumen - microbiology | Proteomics - methods | DNA, Ribosomal - genetics | Usage | Microbiota (Symbiotic organisms) | Physiological aspects | Research | Properties | Methods | Metabolites | RNA | Community structure | rRNA 16S | Laboratories | Propionic acid | Microbiomes | Genomes | Hydraulic retention time | Perturbation | Metabolism | Retention time | Degradation | Proteins | Variables | Consortia | Engineering | Microorganisms | E coli | Bioreactors | Disruption | Acetic acid | Structure-function relationships | metaproteomics | microbial communities | anaerobic bioreactor | perturbation | community assembly
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10. Full Text Erratum to Digital PCR provides sensitive and absolute calibration for high throughput sequencing [BMC Genomics 2009, 10, (541), 10.1186/1471-2164-10-541]
by White III, Richard A and Blainey, Paul C and Fan, H Christina and Quake, Stephen R
BMC Genomics, 11/2009, Volume 10
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11. Full Text The landscape of viral proteomics and its potential to impact human health
by Oxford, Kristie L and Wendler, Jason P and McDermott, Jason E and White III, Richard A and Powell, Joshua D and Jacobs, Jon M and Adkins, Joshua N and Waters, Katrina M and Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Expert Review of Proteomics, ISSN 1478-9450, 06/2016, Volume 13, Issue 6, pp. 579 - 591
Introduction: Advances in mass spectrometry-based proteomic technologies are enhancing studies of viral pathogenesis. Identification and quantification of host... 
Biomarkers | host-virus interactions | mass spectrometry | post-translational modifications | pathway analysis | serum proteomics | VIRUS-INFECTION | UBIQUITIN | DENGUE-FEVER | BIOCHEMICAL RESEARCH METHODS | INTERFERON-STIMULATED GENES | MASS-SPECTROMETRY | HOST SUMOYLATION | SERUM PROTEOME | OMICS DATA | PROTEIN QUANTIFICATION | CELLS REVEALS | Host-Pathogen Interactions | Animals | Humans | Mass Spectrometry | Viruses - metabolism | Proteomics | Viral Proteins - physiology | Virus Diseases - metabolism | Virus Physiological Phenomena | Viral Proteins - metabolism | Viral Proteins - analysis | PTM | biomarkers
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