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1. The Glasnost reader
by Eisen, Jonathan
1990, ISBN 9780452263215, xvii, 445
Perestroĭka | Soviet Union Politics and government | Glasnost
Book
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2. Suppressed inventions and other discoveries
by Eisen, Jonathan
1999, 1st ed., ISBN 0895298090, 546
Renewable energy sources | Unidentified flying objects | Treatment | Controversial literature | Medical innovations | Fraud in science | Discoveries in science | Cancer
Book
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3. The age of rock
: sounds of the American cultural revolution; a reader
by Eisen, Jonathan
1969, xvi, 388 p. illus.
Jazz | Music, Popular (Songs, etc.) | History and criticism
Book
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4. Full Text A simple, fast, and accurate method of phylogenomic inference
by Wu, Martin and Eisen, Jonathan A and Joint Genome Institute (JGI)
Genome Biology, ISSN 1474-7596, 10/2008, Volume 9, Issue 10, pp. R151 - R151
The explosive growth of genomic data provides an opportunity for increased usage of protein markers for phylogenetic inference. In response, we have developed... 
POSITION | TAXA | MAXIMUM-LIKELIHOOD | BACTERIA | EVOLUTION | MODELS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SEQUENCE ALIGNMENT | ALGORITHM | GENES | GENETICS & HEREDITY | TREE | Databases, Genetic | Genome, Bacterial | Sequence Alignment | Phylogeny | Genomics - methods | Method
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5. The California dream
by Hale, Dennis (Dennis B.) and Iisen, Jonathan
1968, 367
California History | California Social life and customs
Book
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6. Full Text Environmental shotgun sequencing: Its potential and challenges for studying the hidden world of microbes
by Eisen, Jonathan A
PLoS Biology, ISSN 1544-9173, 03/2007, Volume 5, Issue 3, pp. 0384 - 0388
Environmental shotgun sequencing promises to reveal novel and fundamental insights into the hidden world of microbes, but the complexity of analysis required... 
COMPARATIVE METAGENOMICS | AMPLIFICATION | DATABASE PROJECT | CHAIN-REACTION | BIOCHEMISTRY & MOLECULAR BIOLOGY | BIOSPHERE | BIOLOGY | COMMUNITY GENOMICS | DIVERSITY | SEA | Bacteria - classification | DNA, Bacterial - genetics | Colony Count, Microbial | Bacteria - genetics | Polymerase Chain Reaction | Polymerase chain reaction | Microorganisms | Microbiology | Phylogenetics | Genomes | Internet | Methods
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7. Full Text An Integrated Pipeline for de Novo Assembly of Microbial Genomes
by Tritt, Andrew and Eisen, Jonathan A and Facciotti, Marc T and Darling, Aaron E
PLoS ONE, ISSN 1932-6203, 09/2012, Volume 7, Issue 9, p. e42304
Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types.... 
ALIGNMENT | MULTIDISCIPLINARY SCIENCES | ALGORITHM | CONSTRUCTION | MAUVE | SEQUENCING DATA | REARRANGEMENTS | TOOL | Workflow | Genome, Bacterial | Software | Algorithms | Genomics - methods | Pipe lines | Transposons | Genomics | Quality control | Genomes | Nucleotide sequencing | DNA sequencing | Parameters | Nucleotide sequence | Data processing | Data mining | Gene sequencing | Datasets | Microorganisms | Error correction & detection | E coli | Assembling | Control algorithms | Automatic control | Error correction | Assemblies | Bioinformatics | Assembly | Methods | Deoxyribonucleic acid--DNA | Deoxyribonucleic acid | DNA
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8. Full Text Systematic Identification of Gene Families for Use as "Markers" for Phylogenetic and Phylogeny-Driven Ecological Studies of Bacteria and Archaea and Their Major Subgroups
by Wu, Dongying and Jospin, Guillaume and Eisen, Jonathan A
PLoS ONE, ISSN 1932-6203, 10/2013, Volume 8, Issue 10, p. e77033
With the astonishing rate that genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach... 
SEQUENCE-ANALYSIS | EVOLUTION | PROTEIN | TREES | DATABASE | MULTIDISCIPLINARY SCIENCES | RIBOSOMAL-RNA OPERON | DIVERSITY | INFERENCE | GENOME | ALIGNMENTS | Multigene Family | Bacterial Proteins - genetics | Bacteria - classification | Archaea - genetics | Genetic Markers | Phylogeny | Genomics - methods | Archaea - classification | Bacteria - genetics | Cluster Analysis | Bacteria | Information management | Evolutionary biology | Genes | Genomics
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9. Full Text Accounting for alignment uncertainty in phylogenomics
by Wu, Martin and Chatterji, Sourav and Eisen, Jonathan A
PLoS ONE, ISSN 1932-6203, 01/2012, Volume 7, Issue 1, p. e30288
Uncertainty in multiple sequence alignments has a large impact on phylogenetic analyses. Little has been done to evaluate the quality of individual positions... 
MAXIMUM-LIKELIHOOD | POSITIONS | BLOCKS | MOLECULAR EVOLUTION | ALGORITHM | BIOLOGY | IMPROVEMENT | TREE | SELECTION | MULTIPLE SEQUENCE ALIGNMENT | PHYLOGENETIC INFERENCE | Amino Acid Sequence | Sequence Alignment - methods | Computational Biology - methods | Reproducibility of Results | Uncertainty | Algorithms | Animals | Humans | Software | Phylogeny | Genomics - methods | Evolution, Molecular | Analysis | Encyclopedias | Amino acid sequence | Genomes | Impact analysis | Proteins | Alignment | Simulation | Quality | Phylogenetics | Evolution | Masking | Trends | Bioinformatics | Methods
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10. Twenty minute fandangos, and forever changes
: a rock bazaar
by Eisen, Jonathan
1971, 270
Music, Popular (Songs, etc.) | Jazz | History and criticism | United States
Book
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11. Full Text Bacterial communities of diverse Drosophila species: Ecological context of a host-microbe model system
by Chandler, James Angus and Lang, Jenna and Bhatnagar, Srijak and Eisen, Jonathan A and Kopp, Artyom
PLoS Genetics, ISSN 1553-7390, 09/2011, Volume 7, Issue 9, p. e1002272
Drosophila melanogaster is emerging as an important model of non-pathogenic host-microbe interactions. The genetic and experimental tractability of Drosophila... 
IMMUNE-RESPONSE | GENOME SEQUENCE | NATURAL-POPULATIONS | AMANITIN TOLERANCE | APIS-MELLIFERA | FRUIT-FLY | PSEUDOMONAS-AERUGINOSA | GENETICS & HEREDITY | OBLIGATE SYMBIONT | GUT MICROBIOTA | SUBFAMILY LACHNINAE | Symbiosis | Biodiversity | Bacteria - genetics | Biological Evolution | Drosophila - microbiology | Bacteria - isolation & purification | Animals | Diet | Models, Biological | Bacteria - classification | RNA, Ribosomal, 16S - genetics | Population | Metagenome | Drosophila - genetics | Host-bacteria relationships | Physiological aspects | Genetic aspects | Research | Drosophila | Studies | Library collections | Medical research | Microbiology | Insects | Taxonomy | Phylogenetics | Bacteria | Experiments
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12. Full Text Structure, variation, and assembly of the root-associated microbiomes of rice
by Joseph Edwards and Cameron Johnson and Christian Santos-Medellín and Eugene Lurie and Natraj Kumar Podishetty and Srijak Bhatnagar and Jonathan A. Eisen and Venkatesan Sundaresan
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 2/2015, Volume 112, Issue 8, pp. E911 - E920
Plants depend upon beneficial interactions between roots and microbes for nutrient availability, growth promotion, and disease suppression. High-throughput... 
Methane cycling | Soil microbial communities | Microbiome assembly | Microbiomes | Rice | COMPARATIVE METAGENOMICS | MULTIDISCIPLINARY SCIENCES | BACTERIAL MICROBIOTA | COMMUNITIES | rice | microbiomes | microbiome assembly | METHANOGENIC DEGRADATION | soil microbial communities | methane cycling | PLANTS | RHIZOSPHERE MICROBIOME | SP-NOV | METHANE EMISSION | INFANT | BIOFILM FORMATION | Geography | Soil Microbiology | Methane - analysis | Genotype | Colony Count, Microbial | Plant Roots - microbiology | Genetic Variation | Rhizosphere | Bacteria - growth & development | Oryza - growth & development | Oryza - genetics | Time Factors | Microbiota - genetics | Oryza - microbiology | Soil | Physiological aspects | Microbiological research | Roots (Botany) | Research | Soil microbiology | Biological Sciences | PNAS Plus
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13. Full Text Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance
by Kembel, Steven W and Wu, Martin and Eisen, Jonathan A and Green, Jessica L
PLoS Computational Biology, ISSN 1553-734X, 10/2012, Volume 8, Issue 10, p. e1002743
The abundance of different SSU rRNA ("16S") gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial... 
MAXIMUM-LIKELIHOOD | BACTERIA | ARCHAEA | AMPLIFICATION | PHYLOGENIES | SEQUENCES | BIOCHEMICAL RESEARCH METHODS | MATHEMATICAL & COMPUTATIONAL BIOLOGY | TIME | RIBOSOMAL-RNA GENES | RARE BIOSPHERE | GENOME SIZE | Oceans and Seas | Skin - microbiology | Humans | Databases, Genetic | Gene Dosage | Phylogeny | Biodiversity | Bacteria - genetics | Microbial Consortia | Models, Biological | Computer Simulation | RNA, Ribosomal, 16S - genetics | Water Microbiology | Cluster Analysis | RNA sequencing | Microbial genetics | Research | Biological diversity | Studies | Genetics | Microbiology | Estimates | Genes
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14. Full Text Insights into the phylogeny and coding potential of microbial dark matter
by Rinke, Christian and Schwientek, Patrick and Sczyrba, Alexander and Ivanova, Natalia N and Anderson, Iain J and Cheng, Jan-Fang and Darling, Aaron and Malfatti, Stephanie and Swan, Brandon K and Gies, Esther A and Dodsworth, Jeremy A and Hedlund, Brian P and Tsiamis, George and Sievert, Stefan M and Liu, Wen-Tso and Eisen, Jonathan A and Hallam, Steven J and Kyrpides, Nikos C and Stepanauskas, Ramunas and Rubin, Edward M and Hugenholtz, Philip and Woyke, Tanja and Joint Genome Institute (JGI)
Nature, ISSN 0028-0836, 2013, Volume 499, Issue 7459, pp. 431 - 437
Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the... 
HYDROTHERMAL VENT | BACTERIA | ARCHAEA | METAGENOMICS | MULTIDISCIPLINARY SCIENCES | LATERAL GENE-TRANSFER | SP-NOV | DIVERSITY | EUKARYOTES | DIVISION | GENOME | Metagenomics | Bacteria - metabolism | Molecular Sequence Data | Archaea - isolation & purification | Phylogeny | Archaea - classification | Bacteria - genetics | Sequence Analysis, DNA | Genome, Bacterial - genetics | Archaea - metabolism | Bacteria - isolation & purification | Metagenome - genetics | Ecosystem | Genome, Archaeal - genetics | Bacteria - classification | Archaea - genetics | Single-Cell Analysis | Biosphere | Usage | Research | Nucleotide sequencing | DNA sequencing | Trees | Evolution | Microbiology | Genomics | Genes
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15. Full Text Network analysis to evaluate the impact of research funding on research community consolidation
by Hicks, Daniel J and Coil, David A and Stahmer, Carl G and Eisen, Jonathan A
PLoS ONE, ISSN 1932-6203, 06/2019, Volume 14, Issue 6, p. e0218273
In 2004, the Alfred P. Sloan Foundation launched a new program focused on incubating a new field, "Microbiology of the Built Environment" (MoBE). By the end of... 
MULTIDISCIPLINARY SCIENCES | INNOVATION | SCIENCE | Research grants | Nucleotide sequencing | Innovations | DNA sequencing | Strategic management | Microbiology | Urban areas | Research funding | Informetrics | Funding | Research & development--R&D | Astrobiology | Big Data | Interdisciplinary aspects | Robotics | Urban environments | Scientometrics | Drilled pier foundations | Researchers | Transportation networks | Bibliometrics | Collaboration | Cooperation | Network analysis | Journals | Research & development | R&D
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16. Full Text Research priorities for harnessing plant microbiomes in sustainable agriculture
by Busby, Posy E and Soman, Chinmay and Wagner, Maggie R and Friesen, Maren L and Kremer, James and Bennett, Alison and Morsy, Mustafa and Eisen, Jonathan A and Leach, Jan E and Dangl, Jeffery L
PLoS Biology, ISSN 1544-9173, 03/2017, Volume 15, Issue 3, p. e2001793
Feeding a growing world population amidst climate change requires optimizing the reliability, resource use, and environmental impacts of food production. One... 
ORYZA-SATIVA L | ENDOPHYTES | BACTERIAL ROOT MICROBIOTA | FUNGI | BIOCHEMISTRY & MOLECULAR BIOLOGY | DISEASE | BIOLOGY | SOIL BACTERIAL | RHIZOSPHERE MICROBIOME | DIVERSITY | COMMUNITIES | LEAF | Conservation of Natural Resources - trends | Food Supply | Microbiota | Plants - microbiology | Agriculture - methods | Research | Research Design | Climate | Defensive behavior | Biological evolution | Plant biology | Proteins | Fungi | Genotype & phenotype | Microorganisms | Motivation | Agricultural production | Agronomy | Botany | Community structure | Functions (mathematics) | Agricultural management | Data acquisition | Crops | Plant communities | Agricultural practices | Phenology | Collection | Photosynthesis | Plant pathology | Microbiology | Biogeography | Genomes | Biology | Design analysis | Sustainable agriculture | Metabolites | Blight | Bacteria | Agriculture | Age | Food | Refueling | Barley | Agricultural equipment | Pest control | Corn | Ecology | Nitrogen | Nutrient uptake | Environmental impact | Analytics | Nodules | Climate change | Plant diseases | Researchers | Culture collections | Data collection | Crop diseases | Reliability
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