Forest Rohwer

Department of Biology, San Diego State University

Affiliated withSan Diego State University

Research Area

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JoVE Journal Publications

ArticleTotal : 6	Year
Publication title Cited by 30	2014
Publication title Cited by 33	2014
Publication title Cited by 15	2015
Publication title Cited by 5	2021
Publication title Cited by 11	2023

Other Publications

Article	Year
Use of 16S ribosomal DNA for delineation of marine bacterioplankton species. Applied and environmental microbiology\| PubMed ID: 12089052	2002
The Phage Proteomic Tree: a genome-based taxonomy for phage. Journal of bacteriology\| PubMed ID: 12142423	2002
Genomic analysis of uncultured marine viral communities. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 12384570	2002
Marine phage genomics. Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology\| PubMed ID: 12470812	2002
IL-2 activation of a PI3K-dependent STAT3 serine phosphorylation pathway in primary human T cells. Cellular signalling\| PubMed ID: 12681450	2003
Global phage diversity. Cell\| PubMed ID: 12705861	2003
Metagenomic analyses of an uncultured viral community from human feces. Journal of bacteriology\| PubMed ID: 14526037	2003
Genome sequences of two closely related Vibrio parahaemolyticus phages, VP16T and VP16C. Journal of bacteriology\| PubMed ID: 14563879	2003
Multispecies microbial mutualisms on coral reefs: the host as a habitat. The American naturalist\| PubMed ID: 14583857	2003
Phage community dynamics in hot springs. Applied and environmental microbiology\| PubMed ID: 15006788	2004
Diversity and population structure of a near-shore marine-sediment viral community. Proceedings. Biological sciences / The Royal Society\| PubMed ID: 15156913	2004
Global distribution of nearly identical phage-encoded DNA sequences. FEMS microbiology letters\| PubMed ID: 15251204	2004
Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 15256601	2004
Movement of viruses between biomes. Applied and environmental microbiology\| PubMed ID: 15466522	2004
Widespread association of a Rickettsiales-like bacterium with reef-building corals. Environmental microbiology\| PubMed ID: 15479247	2004
Microbial communities associated with skeletal tumors on Porites compressa. FEMS microbiology letters\| PubMed ID: 15686846	2005
2004 ASM Conference on the New Phage Biology: the 'Phage Summit'. Molecular microbiology\| PubMed ID: 15720541	2005
PHACCS, an online tool for estimating the structure and diversity of uncultured viral communities using metagenomic information. BMC bioinformatics\| PubMed ID: 15743531	2005
Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS biology\| PubMed ID: 15828858	2005
A glimpse into the expanded genome content of Vibrio cholerae through identification of genes present in environmental strains. Journal of bacteriology\| PubMed ID: 15838025	2005
Viral metagenomics. Nature reviews. Microbiology\| PubMed ID: 15886693	2005
Complete genome sequence of phiHSIC, a pseudotemperate marine phage of Listonella pelagia. Applied and environmental microbiology\| PubMed ID: 15933034	2005
Here a virus, there a virus, everywhere the same virus? Trends in microbiology\| PubMed ID: 15936660	2005
Method for discovering novel DNA viruses in blood using viral particle selection and shotgun sequencing. BioTechniques\| PubMed ID: 16312220	2005
RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS biology\| PubMed ID: 16336043	2006
FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC bioinformatics\| PubMed ID: 16464253	2006
An application of statistics to comparative metagenomics. BMC bioinformatics\| PubMed ID: 16549025	2006
Using pyrosequencing to shed light on deep mine microbial ecology. BMC genomics\| PubMed ID: 16549033	2006
Indirect effects of algae on coral: algae-mediated, microbe-induced coral mortality. Ecology letters\| PubMed ID: 16796574	2006
Widespread occurrence of phage-encoded exotoxin genes in terrestrial and aquatic environments in Southern California. FEMS microbiology letters\| PubMed ID: 16842371	2006
Finding novel genes in bacterial communities isolated from the environment. Bioinformatics (Oxford, England)\| PubMed ID: 16873483	2006
Rapid estimation of microbial numbers in water using bulk fluorescence. Environmental microbiology\| PubMed ID: 16958758	2006
The marine viromes of four oceanic regions. PLoS biology\| PubMed ID: 17090214	2006
Real-time microbial ecology. Environmental microbiology\| PubMed ID: 17227406	2007
Phage metagenomics. Methods in enzymology\| PubMed ID: 17352928	2007
Power law rank-abundance models for marine phage communities. FEMS microbiology letters\| PubMed ID: 17559407	2007
Distribution and diversity of archaeal ammonia monooxygenase genes associated with corals. Applied and environmental microbiology\| PubMed ID: 17586663	2007
Metagenomic and small-subunit rRNA analyses reveal the genetic diversity of bacteria, archaea, fungi, and viruses in soil. Applied and environmental microbiology\| PubMed ID: 17827313	2007
Metagenomic analysis of the microbial community associated with the coral Porites astreoides. Environmental microbiology\| PubMed ID: 17922755	2007
A bacterial metapopulation adapts locally to phage predation despite global dispersal. Genome research\| PubMed ID: 18077539	2008
Phylogenetic classification of short environmental DNA fragments. Nucleic acids research\| PubMed ID: 18285365	2008
Baselines and degradation of coral reefs in the Northern Line Islands. PloS one\| PubMed ID: 18301734	2008
Microbial ecology of four coral atolls in the Northern Line Islands. PloS one\| PubMed ID: 18301735	2008
Biodiversity and biogeography of phages in modern stromatolites and thrombolites. Nature\| PubMed ID: 18311127	2008
Functional metagenomic profiling of nine biomes. Nature\| PubMed ID: 18337718	2008
The airborne metagenome in an indoor urban environment. PloS one\| PubMed ID: 18382653	2008
Viral communities associated with healthy and bleaching corals. Environmental microbiology\| PubMed ID: 18479440	2008
Viral diversity and dynamics in an infant gut. Research in microbiology\| PubMed ID: 18541415	2008
Metagenomic and stable isotopic analyses of modern freshwater microbialites in Cuatro Ciénegas, Mexico. Environmental microbiology\| PubMed ID: 18764874	2009
Dissecting microbial employment. Nature biotechnology\| PubMed ID: 18779810	2008
Metagenomic analysis of lysogeny in Tampa Bay: implications for prophage gene expression. PloS one\| PubMed ID: 18810270	2008
Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 19017800	2008
Laboratory procedures to generate viral metagenomes. Nature protocols\| PubMed ID: 19300441	2009
Metagenomic signatures of 86 microbial and viral metagenomes. Environmental microbiology\| PubMed ID: 19302541	2009
Metagenomic analysis of stressed coral holobionts. Environmental microbiology\| PubMed ID: 19397678	2009
Viruses manipulate the marine environment. Nature\| PubMed ID: 19444207	2009
Genomic analysis of multiple Roseophage SIO1 strains. Environmental microbiology\| PubMed ID: 19659499	2009
Photosystem I gene cassettes are present in marine virus genomes. Nature\| PubMed ID: 19710652	2009
Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals. PloS one\| PubMed ID: 19816605	2009
Explaining microbial population genomics through phage predation. Nature reviews. Microbiology\| PubMed ID: 19834481	2009
Roles of viruses in the environment. Environmental microbiology\| PubMed ID: 19878268	2009
Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber. BMC genomics\| PubMed ID: 19951421	2009
Hyperspectral and physiological analyses of coral-algal interactions. PloS one\| PubMed ID: 19956632	2009
The GAAS metagenomic tool and its estimations of viral and microbial average genome size in four major biomes. PLoS computational biology\| PubMed ID: 20011103	2009
Viral and microbial community dynamics in four aquatic environments. The ISME journal\| PubMed ID: 20147985	2010
Metatranscriptomic array analysis of 'Candidatus Accumulibacter phosphatis'-enriched enhanced biological phosphorus removal sludge. Environmental microbiology\| PubMed ID: 20148930	2010
The lagoon at Caroline/Millennium atoll, Republic of Kiribati: natural history of a nearly pristine ecosystem. PloS one\| PubMed ID: 20539746	2010
Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 20547834	2011
TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC bioinformatics\| PubMed ID: 20573248	2010
Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature\| PubMed ID: 20631792	2010
Reconstructing a puzzle: existence of cyanophages containing both photosystem-I and photosystem-II gene suites inferred from oceanic metagenomic datasets. Environmental microbiology\| PubMed ID: 20649642	2011
Microbial diversity associated with four functional groups of benthic reef algae and the reef-building coral Montastraea annularis. Environmental microbiology\| PubMed ID: 21272183	2011
Comparative metagenomics of microbial traits within oceanic viral communities. The ISME journal\| PubMed ID: 21307954	2011
Broad surveys of DNA viral diversity obtained through viral metagenomics of mosquitoes. PloS one\| PubMed ID: 21674005	2011
Spatial distribution of microbial communities in the cystic fibrosis lung. The ISME journal\| PubMed ID: 21796216	2012
Black reefs: iron-induced phase shifts on coral reefs. The ISME journal\| PubMed ID: 21881615	2012
Case studies of the spatial heterogeneity of DNA viruses in the cystic fibrosis lung. American journal of respiratory cell and molecular biology\| PubMed ID: 21980056	2012
Microbial to reef scale interactions between the reef-building coral Montastraea annularis and benthic algae. Proceedings. Biological sciences / The Royal Society\| PubMed ID: 22090385	2012
Effects of coral reef benthic primary producers on dissolved organic carbon and microbial activity. PloS one\| PubMed ID: 22125645	2011
Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome. The ISME journal\| PubMed ID: 22158393	2011
New abundant microbial groups in aquatic hypersaline environments. Scientific reports\| PubMed ID: 22355652	2011
Grinder: a versatile amplicon and shotgun sequence simulator. Nucleic acids research\| PubMed ID: 22434876	2012
Metagenomics and future perspectives in virus discovery. Current opinion in virology\| PubMed ID: 22440968	2012
Global analysis of plastid diversity reveals apicomplexan-related lineages in coral reefs. Current biology : CB\| PubMed ID: 22789997	2012
The Microbial Olympics. Nature reviews. Microbiology\| PubMed ID: 22796885	2012
Going viral: next-generation sequencing applied to phage populations in the human gut. Nature reviews. Microbiology\| PubMed ID: 22864264	2012
Unseen players shape benthic competition on coral reefs. Trends in microbiology\| PubMed ID: 22944243	2012
Metagenomics and metatranscriptomics: Windows on CF-associated viral and microbial communities. Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society\| PubMed ID: 22951208	2013
Assessing coral reefs on a Pacific-wide scale using the microbialization score. PloS one\| PubMed ID: 22970122	2012
Oxygen minimum zones harbour novel viral communities with low diversity. Environmental microbiology\| PubMed ID: 23039259	2012
Cystic fibrosis therapy: a community ecology perspective. American journal of respiratory cell and molecular biology\| PubMed ID: 23103995	2013
Mucus distribution model in a lung with cystic fibrosis. Computational and mathematical methods in medicine\| PubMed ID: 23118803	2012
Environmental distribution of coral-associated relatives of apicomplexan parasites. The ISME journal\| PubMed ID: 23151646	2013
Coral and macroalgal exudates vary in neutral sugar composition and differentially enrich reef bacterioplankton lineages. The ISME journal\| PubMed ID: 23303369	2013
Structure and function of a cyanophage-encoded peptide deformylase. The ISME journal\| PubMed ID: 23407310	2013
Viral information. Biology & philosophy\| PubMed ID: 23482918	2013
Identification of a novel human papillomavirus by metagenomic analysis of samples from patients with febrile respiratory illness. PloS one\| PubMed ID: 23554892	2013
Bacteriophage adhering to mucus provide a non-host-derived immunity. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 23690590	2013
Mechanistic model of Rothia mucilaginosa adaptation toward persistence in the CF lung, based on a genome reconstructed from metagenomic data. PloS one\| PubMed ID: 23737977	2013
Visualization of oxygen distribution patterns caused by coral and algae. PeerJ\| PubMed ID: 23882443	2013
Influence of coral and algal exudates on microbially mediated reef metabolism. PeerJ\| PubMed ID: 23882445	2013
Innate and acquired bacteriophage-mediated immunity. Bacteriophage\| PubMed ID: 24228227	2013
Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 24259713	2013
Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction... Proteins\| PubMed ID: 24318984	2014
Breath gas metabolites and bacterial metagenomes from cystic fibrosis airways indicate active pH neutral 2,3-butanedione fermentation. The ISME journal\| PubMed ID: 24401860	2014
Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis. Journal of clinical microbiology\| PubMed ID: 24478471	2014
Biogeochemical forces shape the composition and physiology of polymicrobial communities in the cystic fibrosis lung. mBio\| PubMed ID: 24643867	2014
Evolution of TNF-induced apoptosis reveals 550 My of functional conservation. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 24927546	2014
Local genomic adaptation of coral reef-associated microbiomes to gradients of natural variability and anthropogenic stressors. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 24982156	2014
Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition. PeerJ\| PubMed ID: 25177534	2014
The origins of ambient biological sound from coral reef ecosystems in the Line Islands archipelago. The Journal of the Acoustical Society of America\| PubMed ID: 25234977	2014
Species-specific viromes in the ancestral holobiont hydra. PloS one\| PubMed ID: 25343582	2014
Stochastic Tracking of Infection in a CF Lung. PloS one\| PubMed ID: 25360611	2014
A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation. The ISME journal\| PubMed ID: 25514533	2014
Diversity of viral photosystem-I psaA genes. The ISME journal\| PubMed ID: 25535938	2014
A Winogradsky-based culture system shows an association between microbial fermentation and cystic fibrosis exacerbation. The ISME journal\| PubMed ID: 25777574	2015
Mass spectral similarity for untargeted metabolomics data analysis of complex mixtures. International journal of mass spectrometry\| PubMed ID: 25844058	2015
Metabolic cascades in marine microbial communities. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 25918428	2015
Closing the gaps on the viral photosystem-I psaDCAB gene organization. Environmental microbiology\| PubMed ID: 26310718	2015
Gut DNA viromes of Malawian twins discordant for severe acute malnutrition. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 26351661	2015
Some of the most interesting CASP11 targets through the eyes of their authors. Proteins\| PubMed ID: 26473983	2016
Subdiffusive motion of bacteriophage in mucosal surfaces increases the frequency of bacterial encounters. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 26483471	2015
Stable and sporadic symbiotic communities of coral and algal holobionts. The ISME journal\| PubMed ID: 26555246	2016
Can we measure beauty? Computational evaluation of coral reef aesthetics. PeerJ\| PubMed ID: 26587350	2015
Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome. The ISME journal\| PubMed ID: 26623545	2016
In retrospect: A century of phage lessons. Nature\| PubMed ID: 26632584	2015
Metagenomic and satellite analyses of red snow in the Russian Arctic. PeerJ\| PubMed ID: 26713242	2015
Re-evaluating the health of coral reef communities: baselines and evidence for human impacts across the central Pacific. Proceedings. Biological sciences\| PubMed ID: 26740615	2016
Energetic differences between bacterioplankton trophic groups and coral reef resistance. Proceedings. Biological sciences\| PubMed ID: 27097927	2016
Metabolomics of reef benthic interactions reveals a bioactive lipid involved in coral defence. Proceedings. Biological sciences\| PubMed ID: 27122568	2016
Phage on tap-a quick and efficient protocol for the preparation of bacteriophage laboratory stocks. PeerJ\| PubMed ID: 27547567	2016
Global microbialization of coral reefs. Nature microbiology\| PubMed ID: 27572833	2016
Using viromes to predict novel immune proteins in non-model organisms. Proceedings. Biological sciences\| PubMed ID: 27581878	2016
Metabolomics of pulmonary exacerbations reveals the personalized nature of cystic fibrosis disease. PeerJ\| PubMed ID: 27602256	2016
Viruses as Winners in the Game of Life. Annual review of virology\| PubMed ID: 27741409	2016
Viruses and the origin of microbiome selection and immunity. The ISME journal\| PubMed ID: 27983723	2017
Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 28028238	2017
Spatial Molecular Architecture of the Microbial Community of a Peltigera Lichen. mSystems\| PubMed ID: 28028548	2016
Variability and host density independence in inductions-based estimates of environmental lysogeny. Nature microbiology\| PubMed ID: 28452987	2017
Ecological networking of cystic fibrosis lung infections. NPJ biofilms and microbiomes\| PubMed ID: 28649398	2016
Microbial bioenergetics of coral-algal interactions. PeerJ\| PubMed ID: 28649468	2017
Piggyback-the-Winner in host-associated microbial communities. NPJ biofilms and microbiomes\| PubMed ID: 28721247	2016
A myovirus encoding both photosystem I and II proteins enhances cyclic electron flow in infected Prochlorococcus cells. Nature microbiology\| PubMed ID: 28785078	2017
Development and Use of Personalized Bacteriophage-Based Therapeutic Cocktails To Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection. Antimicrobial agents and chemotherapy\| PubMed ID: 28807909	2017
Knowles &Rohwer reply. Nature\| PubMed ID: 28933437	2017
Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. Cell host & microbe\| PubMed ID: 29056429	2017
Meta-mass shift chemical profiling of metabolomes from coral reefs. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 29078340	2017
Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers. mBio\| PubMed ID: 29162715	2017
A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction. Current biology : CB\| PubMed ID: 29174886	2017
Correction for Nguyen et al., "Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers". mBio\| PubMed ID: 29295916	2018
Before platelets: the production of platelet-activating factor during growth and stress in a basal marine organism. Proceedings. Biological sciences\| PubMed ID: 30111600	2018
The birth of viromics: an interview with Forest Rohwer. Future microbiology\| PubMed ID: 30311785	2018
Gradients in Primary Production Predict Trophic Strategies of Mixotrophic Corals across Spatial Scales. Current biology : CB\| PubMed ID: 30344114	2018
A diversity-generating retroelement encoded by a globally ubiquitous Bacteroides phage. Microbiome\| PubMed ID: 30352623	2018
Erratum for Schooley et al., "Development and Use of Personalized Bacteriophage-Based Therapeutic Cocktails To Treat a Patient with a Disseminated Resistant Acinetobacter baumannii Infection... Antimicrobial agents and chemotherapy\| PubMed ID: 30478181	2018
Diel population and functional synchrony of microbial communities on coral reefs. Nature communications\| PubMed ID: 30979882	2019
Cystic Fibrosis Rapid Response: Translating Multi-omics Data into Clinically Relevant Information. mBio\| PubMed ID: 30992350	2019
Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis. mSystems\| PubMed ID: 31551401	2019
Impact of bacteria motility in the encounter rates with bacteriophage in mucus. Scientific reports\| PubMed ID: 31712565	2019
Biophysical and physiological processes causing oxygen loss from coral reefs. eLife\| PubMed ID: 31793432	2019
Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome. Gut microbes\| PubMed ID: 31931655	2020
Genomic and ecological attributes of marine bacteriophages encoding bacterial virulence genes. BMC genomics\| PubMed ID: 32024463	2020
Gp4 is a nuclease required for morphogenesis of T4-like bacteriophages. Virology\| PubMed ID: 32056848	2020
Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents. Ecology and evolution\| PubMed ID: 32273998	2020
A multiomic analysis of in situ coral-turf algal interactions. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 32482859	2020
Virulence as a Side Effect of Interspecies Interaction in Coral Pathogens. mBio\| PubMed ID: 32694137	2020
A Distinct Contractile Injection System Gene Cluster Found in a Majority of Healthy Adult Human Microbiomes. mSystems\| PubMed ID: 32723799	2020
Handwashing and Detergent Treatment Greatly Reduce SARS-CoV-2 Viral Load on Halloween Candy Handled by COVID-19 Patients. mSystems\| PubMed ID: 33127739	2020
The landscape of lysogeny across microbial community density, diversity and energetics. Environmental microbiology\| PubMed ID: 34121301	2021
Space-filling and benthic competition on coral reefs. PeerJ\| PubMed ID: 34249480	2021
Multi-Omics Study of Keystone Species in a Cystic Fibrosis Microbiome. International journal of molecular sciences\| PubMed ID: 34769481	2021
Presence of SARS-CoV-2 RNA on Surfaces of Public Places and a Transportation System Located in a Densely Populated Urban Area in South America. Viruses\| PubMed ID: 35062223	2021
Distribution of soil viruses across China and their potential role in phosphorous metabolism. Environmental microbiome\| PubMed ID: 35130971	2022
Nocturnal dissolved organic matter release by turf algae and its role in the microbialization of reefs. Functional ecology\| PubMed ID: 36247100	2022
More Stages Decrease Dissipation in Irreversible Step Processes. Entropy (Basel, Switzerland)\| PubMed ID: 36981427	2023
Viral predation pressure on coral reefs. BMC biology\| PubMed ID: 37038111	2023
Compounding Phages for Therapeutic Applications. Viruses\| PubMed ID: 37632008	2023