James R. Cole
#153,182
Most Influential Person Now
James R. Cole's AcademicInfluence.com Rankings
James R. Colebiology Degrees
Biology
#11600
World Rank
#15004
Historical Rank
Bioinformatics
#137
World Rank
#139
Historical Rank
Computational Biology
#252
World Rank
#253
Historical Rank
Microbiology
#661
World Rank
#730
Historical Rank
Download Badge
Biology
James R. Cole's Degrees
- PhD Bioinformatics Stanford University
- Masters Computer Science University of California, Berkeley
- Bachelors Biology University of California, Berkeley
Similar Degrees You Can Earn
Why Is James R. Cole Influential?
(Suggest an Edit or Addition)James R. Cole's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy (2007) (15277)
- The Ribosomal Database Project: improved alignments and new tools for rRNA analysis (2008) (4646)
- Ribosomal Database Project: data and tools for high throughput rRNA analysis (2013) (3268)
- The Ribosomal Database Project (RDP-II): sequences and tools for high-throughput rRNA analysis (2004) (1556)
- The Ribosomal Database Project (RDP-II): previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy (2003) (1506)
- The minimum information about a genome sequence (MIGS) specification (2008) (1344)
- The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data (2006) (1189)
- rrndb: the Ribosomal RNA Operon Copy Number Database (2001) (1063)
- A new version of the RDP (Ribosomal Database Project) (1999) (944)
- Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions (2010) (820)
- In-feed antibiotic effects on the swine intestinal microbiome (2012) (714)
- The RDP (Ribosomal Database Project) continues (2000) (662)
- Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications (2011) (588)
- FunGene: the functional gene pipeline and repository (2013) (486)
- Genome Project Standards in a New Era of Sequencing (2009) (422)
- Characterization and Description of Anaeromyxobacter dehalogenans gen. nov., sp. nov., an Aryl-Halorespiring Facultative Anaerobic Myxobacterium (2002) (356)
- The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level (2018) (324)
- ARGs‐OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes (2018) (248)
- Ecological Patterns of nifH Genes in Four Terrestrial Climatic Zones Explored with Targeted Metagenomics Using FrameBot, a New Informatics Tool (2013) (248)
- Tundra soil carbon is vulnerable to rapid microbial decomposition under climate warming (2016) (211)
- ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database (2016) (203)
- The Genomic Standards Consortium (2011) (196)
- Isolation and characterization of a novel toluene-degrading, sulfate-reducing bacterium (1996) (184)
- Characterization of Desulfitobacterium chlororespirans sp. nov., which grows by coupling the oxidation of lactate to the reductive dechlorination of 3-chloro-4-hydroxybenzoate (1996) (182)
- RNAcentral: a hub of information for non-coding RNA sequences (2018) (164)
- Tropical agricultural land management influences on soil microbial communities through its effect on soil organic carbon (2013) (163)
- Sequence-based classification and identification of Fungi (2016) (157)
- Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences (2016) (147)
- Clusters of Antibiotic Resistance Genes Enriched Together Stay Together in Swine Agriculture (2016) (142)
- Isolation and Characterization of Desulfovibrio dechloracetivorans sp. nov., a Marine Dechlorinating Bacterium Growing by Coupling the Oxidation of Acetate to the Reductive Dechlorination of 2-Chlorophenol (2000) (135)
- Using the RDP Classifier to Predict Taxonomic Novelty and Reduce the Search Space for Finding Novel Organisms (2012) (134)
- A gene-targeted approach to investigate the intestinal butyrate-producing bacterial community (2013) (133)
- Taxonomic Outline of the Bacteria and Archaea: Formerly the Taxonomic Outline of the Prokaryotes (2007) (131)
- Isolation and characterization of a novel bacterium growing via reductive dehalogenation of 2-chlorophenol (1994) (128)
- Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment (2009) (122)
- Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity (2018) (119)
- Reconstructing 16S rRNA genes in metagenomic data (2015) (116)
- RNAcentral: an international database of ncRNA sequences (2014) (108)
- Feedback regulation of rRNA synthesis in Escherichia coli. Requirement for initiation factor IF2. (1987) (108)
- Reductive Dehalogenation of Trichloroacetic Acid byTrichlorobacter thiogenes gen. nov., sp. nov (2000) (96)
- RNAcentral: a comprehensive database of non-coding RNA sequences (2016) (95)
- Diversity of Dechlorinating Bacteria (2004) (89)
- Bacterial community comparisons by taxonomy-supervised analysis independent of sequence alignment and clustering (2011) (86)
- Changes in the half-life of ribosomal protein messenger RNA caused by translational repression. (1986) (84)
- Xander: employing a novel method for efficient gene-targeted metagenomic assembly (2015) (83)
- Primer set 2.0 for highly parallel qPCR array targeting antibiotic resistance genes and mobile genetic elements (2018) (78)
- RNAcentral: A vision for an international database of RNA sequences. (2011) (76)
- Functional genes to assess nitrogen cycling and aromatic hydrocarbon degradation: primers and processing matter (2013) (70)
- Cloning, Expression, and Nucleotide Sequence of thePseudomonas aeruginosa 142 ohb Genes Coding for Oxygenolytic ortho Dehalogenation of Halobenzoates (1999) (62)
- Desulfomonile limimaris sp. nov., an anaerobic dehalogenating bacterium from marine sediments. (2001) (60)
- Microbial Community Analysis with Ribosomal Gene Fragments from Shotgun Metagenomes (2015) (54)
- Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community (2020) (52)
- More replenishment than priming loss of soil organic carbon with additional carbon input (2018) (52)
- How Much Do rRNA Gene Surveys Underestimate Extant Bacterial Diversity? (2018) (51)
- Habitat-Lite: a GSC case study based on free text terms for environmental metadata. (2008) (51)
- Fungal Diversity in Permafrost and Tallgrass Prairie Soils under Experimental Warming Conditions (2013) (49)
- Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming (2020) (46)
- Translational regulation is responsible for growth-rate-dependent and stringent control of the synthesis of ribosomal proteins L11 and L1 in Escherichia coli. (1986) (45)
- Taxonomic Outline of the Bacteria and Archaea , Release 7 . 7 March 6 , 2007 . Part 9 – The Bacteria : Phylum “ Firmicutes ” : Class “ Bacilli ” (2007) (44)
- Gene expression analysis of E. coli strains provides insights into the role of gene regulation in diversification (2014) (42)
- Toward a standards-compliant genomic and metagenomic publication record. (2008) (41)
- Characterisation and expression of the pathway from UDP-glucose to UDP-xylose in differentiating tobacco tissue (2004) (35)
- Worldwide Prevalence of Class 2 Integrases outside the Clinical Setting Is Associated with Human Impact (2009) (34)
- Genomic Standards Consortium Projects (2014) (34)
- Characterization of human liver thermostable phenol sulfotransferase (SULT1A1) allozymes with 3,3',5-triiodothyronine as the substrate. (2001) (33)
- BSD: the Biodegradative Strain Database (2003) (31)
- Corrigendum: ''RNAcentral : a hub of information for non-coding RNA sequences'' [Nucleic acids research, 47 (2019) D1, p. D221-D229] (2019) (30)
- Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems (2020) (30)
- The Ribosomal Database Project: Sequences and Software for High-Throughput rRNA Analysis (2011) (30)
- Introduction to the Taxonomic Outline of Bacteria and Archaea (TOBA) Release 7.7 (2007) (29)
- Winter warming in Alaska accelerates lignin decomposition contributed by Proteobacteria (2020) (29)
- A Scalable and Accurate Targeted Gene Assembly Tool (SAT-Assembler) for Next-Generation Sequencing Data (2014) (29)
- Influence of Dangling Ends and Surface-Proximal Tails of Targets on Probe-Target Duplex Formation in 16S rRNA Gene-Based Diagnostic Arrays (2006) (27)
- Tetrachloroethene and 3-chlorobenzoate dechlorination activities are co-induced inDesulfomonile tiedjei DCB-1 (1995) (27)
- Mutational analysis of the L1 binding site of 23S rRNA in Escherichia coli. (1988) (27)
- Alignment of possible secondary structures in multiple RNA sequences using simulated annealing (1996) (25)
- SERDP and ESTCP Expert Panel Workshop on Research and Development Needs for the Environmental Remediation Application of Molecular Biological Tools (2005) (24)
- Sphingomonas wittichii Strain RW1 Genome-Wide Gene Expression Shifts in Response to Dioxins and Clay (2016) (24)
- Denitrifying and diazotrophic community responses to artificial warming in permafrost and tallgrass prairie soils (2015) (23)
- Alterations in the Endophyte-Enriched Root-Associated Microbiome of Rice Receiving Growth-Promoting Treatments of Urea Fertilizer and Rhizobium Biofertilizer (2019) (23)
- Biotic responses buffer warming‐induced soil organic carbon loss in Arctic tundra (2018) (22)
- Long-Term Warming in Alaska Enlarges the Diazotrophic Community in Deep Soils (2019) (22)
- Microbial functional diversity covaries with permafrost thaw‐induced environmental heterogeneity in tundra soil (2018) (22)
- Part 10 - The Bacteria: Phylum Actinobacteria, Class "Actinobacteria" (2007) (19)
- Tundra microbial community taxa and traits predict decomposition parameters of stable, old soil organic carbon (2019) (18)
- Stringent control in Escherichia coli applies also to transcription by T7 RNA polymerase. (1987) (18)
- Isothermal assay targeting class 1 integrase gene for environmental surveillance of antibiotic resistance markers. (2017) (18)
- Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers. (2008) (16)
- Microbial Community Analysis using RDP II (Ribosomal Database Project II):Methods, Tools and New Advances (2009) (16)
- Long-read sequencing revealed cooccurrence, host range, and potential mobility of antibiotic resistome in cow feces (2021) (16)
- Virulence factor activity relationships (VFARs): a bioinformatics perspective. (2017) (15)
- Gene‐Targeted Metagenomics (GT Metagenomics) to Explore the Extensive Diversity of Genes of Interest in Microbial Communities (2011) (15)
- Impairment of the asialoglycoprotein receptor by ethanol oxidation. (1996) (15)
- RNAcentral: a hub of information for non-coding RNA sequences (2018) (14)
- A Sensitive and Accurate protein domain cLassification Tool (SALT) for short reads (2013) (13)
- History and impact of RDP (2014) (12)
- The “Minimum Information about an ENvironmental Sequence” (MIENS) specification (2010) (11)
- Modulatory Influence of Segmented Filamentous Bacteria on Transcriptomic Response of Gnotobiotic Mice Exposed to TCDD (2017) (11)
- Specific deuteration of dichlorobenzoate during reductive dehalogenation by Desulfomonile tiedjei in D2O (1992) (11)
- Defining linkages between the GSC and NSF's LTER program: how the Ecological Metadata Language (EML) relates to GCDML and other outcomes. (2008) (9)
- Part 1 - The Archaea: Phyla Crenarchaeota and Euryarchaeota (2007) (9)
- Winter warming rapidly increases carbon degradation capacities of fungal communities in tundra soil: Potential consequences on carbon stability (2020) (9)
- Computational aspects of systematic biology (2006) (8)
- Part 11 - The Bacteria: Phyla Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Acidobacteria, Bacteroidetes, Fusobacteria, Verrucomicrobia, Dictyoglomi, Gemmatomonadetes, and Lentisphaerae (2007) (7)
- Review, Evaluation, and Directions for Gene-Targeted Assembly for Ecological Analyses of Metagenomes (2019) (7)
- Taxonomic Outline of the Bacteria and Archaea , Release 7 . 7 March 6 , 2007 . Part 4 – The Bacteria : Phylum “ Proteobacteria ” , Class Betaproteobacteria (2007) (7)
- Development of soil metadata standards for international DNA sequence databases. (2010) (6)
- Multiplex Approach for Screening Genetic Markers of Microbial Indicators (2007) (6)
- Bioavailability of clay-adsorbed dioxin to Sphingomonas wittichii RW1 and its associated genome-wide shifts in gene expression. (2020) (6)
- Permafrost thaw with warming reduces microbial metabolic capacities in subsurface soils (2021) (5)
- Back translated peptide K-mer search and local alignment in large DNA sequence databases using BoND-SD-tree indexing (2015) (5)
- Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming (2020) (5)
- Taxonomic Outline of the Bacteria and Archaea , Release 7 . 7 March 6 , 2007 . Part 6 – Phylum “ Proteobacteria ” : The Deltaproteobacteria and Epsilonproteobacteria (2007) (4)
- High throughput quantification of the functional genes associated with RDX biodegradation using the SmartChip real-time PCR system (2019) (4)
- Part 2 - The Bacteria: Phyla Aquficae, Thermotogae, Thermodesulfobacteria, Deinococcus-Thermus, Chrysiogenetes, Chloroflexi, Thermomicrobia, Nitrospira, Deferribacteres, Cyanobacteria, and Chlorobi (2007) (4)
- Plant specimen contextual data consensus (2016) (4)
- Classifying prokaryotic genomes using the Microbial Genomes Atlas (MiGA) webserver (2020) (3)
- Towards richer descriptions of our collection of genomes andmetagenomes (2006) (3)
- Part 7 - The Bacteria: Phylum Firmicutes, Class "Clostridia" (2007) (3)
- Part 8 - The Bacteria: Phylum Firmicutes, Class Mollicutes (2007) (3)
- Human liver thermostable phenol sulfotransferase its PST: CDNA cloning, bacterial expression and characterization (1996) (3)
- Inferring Relatedness of a Macromolecule to a Sequence Database Without Sequencing (1996) (3)
- A gene-targeted approach to investigate the intestinal butyrate-producing bacterialcommunity (2013) (2)
- Translational regulation is responsible for growth-rate-dependent and stringent control of the synthesis of ribosomal proteins L 11 and Li in Escherichia coli ( translational repression / site-directed mutagenesis ) (2)
- Comparing faster evolving rplB and rpsC versus SSU rRNA for improved microbial community resolution (2018) (2)
- Sequence Homology Search Based on Database Indexing Using the Profile Hidden Markov Model (2006) (2)
- New Bacterial Taxonomy Assignment of rRNA Sequences into the Naïve Bayesian Classifier for Rapid (2014) (1)
- MetaFunPrimer: an Environment-Specific, High-Throughput Primer Design Tool for Improved Quantification of Target Genes (2021) (1)
- Warming-induced permafrost thaw exacerbates tundra soil carbon decomposition mediated by microbial community (2020) (1)
- Part 3 - The Bacteria: Phylum Proteobacteria, Class Alphaproteobacteria (2007) (1)
- Pipelining RDP Data to the "Taxomatic" - Final Report (2009) (0)
- Accelerated soil carbon loss by biological changes under warming in Alaskan tundra (2016) (0)
- Warming Conditions Tallgrass Prairie Soils under Experimental Fungal Diversity in Permafrost and (2013) (0)
- Biodiversity Informatics and Spatial Analysis , Royal Botanic Gardens , Kew , Surrey TW 9 3 AF , United Kingdom Shiloh (2016) (0)
- Metagenomics-Enabled Understanding of Soil Microbial Feedbacks to Climate Warming (2014) (0)
- Computational aspects of systematic (2006) (0)
- Tropical agricultural land management in fl uences on soil microbial communities through its effect on soil organic carbon Soil Biology & Biochemistry (2013) (0)
- MetaFunPrimer: primer design for targeting genes observed in metagenomes (2020) (0)
- Methods for high-throughput massively parallel soil ecofunctional gene analysis (2017) (0)
- Part 6 - The Bacteria: The Deltaproteobacteria and Epsilonproteobacteria (2007) (0)
- Soil microbes ready to stoke global warming (2020) (0)
- BLAST Tree: Fast Filtering for Genomic Sequence Classification (2010) (0)
- Lower Soil Carbon Loss Due to Persistent Microbial Adaptation to Climate Warming (2020) (0)
- Influence of Dangling Ends and Surface-Proximal Tails of Targets on Probe-Target Duplex Formation in 16S rRNA Gene-Based Diagnostic Arrays (cid:1) † (2007) (0)
- Naı¨ve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy (cid:1) † (2007) (0)
- Metagenomic analysis reveals the shared and distinct features of the soil resistome across tundra, temperate prairie, and tropical ecosystems (2021) (0)
- More replenishment than priming loss of soil organic carbon with additional carbon input (2018) (0)
- Land-use and forest floor explain prokaryotic metacommunity structuring and spatial turnover in Amazonian forest-to-pasture conversion areas (2020) (0)
- Flash Updates of GSC projects (GSC8 Meeting) (2009) (0)
- Back translated peptide k-mer search on disk (2015) (0)
- Xander: employing a novel method for efficient gene-targeted metagenomic assembly (2015) (0)
- 24 – The Role of Translational Regulation in Growth Rate—Dependent and Stringent Control of the Synthesis of Ribosomal Proteins in Escherichia coli (1987) (0)
This paper list is powered by the following services:
What Schools Are Affiliated With James R. Cole?
James R. Cole is affiliated with the following schools:
