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Jeffrey A. Kimbrel · SciRah

Researcher profile · Semantic Scholar

Jeffrey A. Kimbrel

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Jeffrey A. Kimbrel — researcher profile on SciRah

h-index: 21
Works: 62
Citations: 3,668

Most-cited papers

Genome sequencing and analysis of the model grass Brachypodium distachyon
J. Vogel, D. Garvin, T. Mockler, J. Schmutz +133 more
2010Nature1,751 citations Open access
Semantic Scholar
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
O. U. Mason, Nicole Scott, A. González, A. Robbins-Pianka +14 more
2014The ISME Journal350 citations Open access
Semantic Scholar
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes
Samuel M. D. Seaver, Filipe Liu, Qizh Zhang, James G. Jeffryes +18 more
2020Nucleic Acids Res.237 citations Open access
Semantic Scholar
Recombineering and stable integration of the Pseudomonas syringae pv. syringae 61 hrp/hrc cluster into the genome of the soil bacterium Pseudomonas fluorescens Pf0-1.
W. J. Thomas, Caitlin A. Thireault, Jeffrey A. Kimbrel, Jeff H. Chang
2009The Plant Journal123 citations
Semantic Scholar
Copper delivery by the copper chaperone for chloroplast and cytosolic copper/zinc-superoxide dismutases: regulation and unexpected phenotypes in an Arabidopsis mutant.
C. Cohu, S. Abdel-Ghany, Kathryn A. Gogolin Reynolds, Alexander M. Onofrio +4 more
2009Molecular Plant96 citations Open access
Semantic Scholar
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil
G. Trubl, Jeffrey A. Kimbrel, Jose Liquet-Gonzalez, E. Nuccio +5 more
2021Microbiome94 citations Open access
Semantic Scholar
HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi
E. Nuccio, S. Blazewicz, Marissa Lafler, A. Campbell +10 more
2022Microbiome79 citations Open access
Semantic Scholar
Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions
T. Samo, Jeffrey A. Kimbrel, Daniel Nilson, J. Pett-Ridge +2 more
2018Environmental Microbiology76 citations Open access
Semantic Scholar
Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum
Jeffrey A. Kimbrel, W. J. Thomas, Yuan Jiang, Allison L. Creason +3 more
2013PLoS Pathogens75 citations Open access
Semantic Scholar
GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences
Jason S. Cumbie, Jeffrey A. Kimbrel, Yan-Ming Di, D. W. Schafer +7 more
2011PLoS ONE75 citations Open access
Semantic Scholar
An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6
Jeffrey A. Kimbrel, S. Givan, A. Halgren, Allison L. Creason +4 more
2010BMC Genomics65 citations Open access
Semantic Scholar
The membrane-associated monooxygenase in the butane-oxidizing Gram-positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family.
L. Sayavedra-Soto, N. Hamamura, Chih-Wen Liu, Jeffrey A. Kimbrel +2 more
2011Environmental Microbiology Reports60 citations
Semantic Scholar
Plant-associated fungi support bacterial resilience following water limitation
Rachel Hestrin, M. Kan, Marissa Lafler, J. Wollard +8 more
2022bioRxiv57 citations Open access
Semantic Scholar
Microbial Community Structure and Functional Potential Along a Hypersaline Gradient
Jeffrey A. Kimbrel, Nicholas R. Ballor, Yu-Wei Wu, M. David +4 more
2018Frontiers in Microbiology52 citations Open access
Semantic Scholar
Combining multiple functional annotation tools increases coverage of metabolic annotation
M. Griesemer, Jeffrey A. Kimbrel, Carol L. Ecale Zhou, A. Navid +1 more
2017BMC Genomics52 citations Open access
Semantic Scholar
Melanization slows the rapid movement of fungal necromass carbon and nitrogen into both bacterial and fungal decomposer communities and soils
François Maillard, Talia J Michaud, C. See, L. C. DeLancey +4 more
2023mSystems50 citations Open access
Semantic Scholar
multiPhATE: bioinformatics pipeline for functional annotation of phage isolates
Carol L. Ecale Zhou, S. Malfatti, Jeffrey A. Kimbrel, C. Philipson +4 more
2019bioRxiv50 citations Open access
Semantic Scholar
Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems
Alex Greenlon, Ella T. Sieradzki, Olivier Zablocki, B. Koch +12 more
2022bioRxiv49 citations Open access
Semantic Scholar
Sequencing and de novo transcriptome assembly of Brachypodium sylvaticum (Poaceae)
Samuel E. Fox, Justin Preece, Jeffrey A. Kimbrel, Gina L. Marchini +4 more
2013Applications in Plant Sciences33 citations Open access
Semantic Scholar
Terabase-Scale Coassembly of a Tropical Soil Microbiome
R. Riley, R. Bowers, A. Camargo, A. Campbell +13 more
2023Microbiology spectrum25 citations Open access
Semantic Scholar
Bacterial communities protect the alga Microchloropsis salina from grazing by the rotifer Brachionus plicatilis
Carolyn L Fisher, C. Ward, Pamela D. Lane, Jeffrey A. Kimbrel +4 more
2019Algal Research24 citations Open access
Semantic Scholar
STREAMS guidelines: Standards for technical reporting in environmental and host-associated microbiome studies
Julia M. Kelliher, C. Mirzayi, S. Bordenstein, Aaron Oliver +244 more
2025Nature Microbiology20 citations Open access
Semantic Scholar
Microbiome processing of organic nitrogen input supports growth and cyanotoxin production of Microcystis aeruginosa cultures
Wei Li, David Baliu-Rodriguez, Sanduni H. Premathilaka, Sharmila I. Thenuwara +10 more
2024The ISME Journal19 citations Open access
Semantic Scholar
Genome sequencing and comparative analysis of the carrot bacterial blight pathogen, Xanthomonas hortorum pv. carotae M081, for insights into pathogenicity and applications in molecular diagnostics.
Jeffrey A. Kimbrel, S. Givan, T. Temple, Kenneth B. Johnson +1 more
2011Molecular plant pathology19 citations Open access
Semantic Scholar
RNA-Seq for Plant Pathogenic Bacteria
Jeffrey A. Kimbrel, Yan-Ming Di, Jason S. Cumbie, Jeff H. Chang
2011Genes16 citations Open access
Semantic Scholar
The Western Lake Erie Culture Collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome
C. Yancey, E. A. Kiledal, Vincent J. Denef, R. Errera +17 more
2022bioRxiv15 citations Open access
Semantic Scholar
Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina
M. M. Morris, Jeffrey A. Kimbrel, H. Geng, M. Tran-Gyamfi +4 more
2022Msphere14 citations Open access
Semantic Scholar
Transporter annotations are holding up progress in metabolic modeling
John R. Casey, B. Bennion, P. D'Haeseleer, Jeffrey A. Kimbrel +2 more
2024Frontiers in Systems Biology12 citations Open access
Semantic Scholar
Coastal bacteria and protists assimilate viral carbon and nitrogen
J. Martínez, D. Talmy, Jeffrey A. Kimbrel, P. Weber +1 more
2024bioRxiv12 citations Open access
Semantic Scholar
The algal microbiome protects Desmodesmus intermedius from high light and temperature stress
T. Samo, K. Rolison, C. Swink, Jeffrey A. Kimbrel +2 more
2023Algal Research11 citations Open access
Semantic Scholar
Higher Order Asymptotics for Negative Binomial Regression Inferences from RNA-Sequencing Data
Yan-Ming Di, Sarah C. Emerson, D. W. Schafer, Jeffrey A. Kimbrel +1 more
2013Statistical Applications in Genetics and Molecular Biology11 citations Open access
Semantic Scholar
Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution
A. Schulman, Alper Yilmaz, A. Kalyanaraman, An-Ping Hsia +81 more
20099 citations
Semantic Scholar
Dynamic Phaeodactylum tricornutum Exometabolites Shape Surrounding Bacterial Communities
Vanessa L. Brisson, C. Swink, Jeffrey A. Kimbrel, X. Mayali +5 more
2022bioRxiv8 citations Open access
Semantic Scholar
The Draft Genome Sequence of Nocardioides sp. Strain CF8 Reveals the Scope of Its Metabolic Capabilities
Jeffrey A. Kimbrel, Jeff H. Chang, D. Arp, L. Sayavedra-Soto
2013Genome Announcements8 citations Open access
Semantic Scholar
HT-SIP: A semi-automated Stable Isotope Probing pipeline identifies interactions in the hyphosphere of arbuscular mycorrhizal fungi
E. Nuccio, S. Blazewicz, Marissa Lafler, A. Campbell +10 more
2022bioRxiv6 citations Open access
Semantic Scholar
Disentangling production and persistence of extracellular virions in grassland soils with SIP-viromics
G. Trubl, S. Roux, M. Kellom, Dariia Vyshenska +7 more
2026bioRxiv4 citations Open access
Semantic Scholar
A bloom of a single bacterium shapes the microbiome during outdoor diatom cultivation collapse
Naomi E. Gilbert, Jeffrey A. Kimbrel, T. Samo, A. Siccardi +2 more
2025mSystems4 citations Open access
Semantic Scholar
Diatom volatile organic compound production is driven by diel metabolism and the cell cycle
Vaishnavi G. Padaki, Emily Palmer, Yuan Jiang, Holger H. Buchholz +2 more
2025Frontiers in Microbiology3 citations Open access
Semantic Scholar
Soil redox drives virus-host community dynamics and plant biomass degradation in tropical rainforest soils
G. Trubl, Ikaia Leleiwi, A. Campbell, Jeffrey A. Kimbrel +5 more
2024bioRxiv2 citations Open access
Semantic Scholar
Prokaryotic Genome Annotation.
Jeffrey A. Kimbrel, B. Jeffrey, C. Ward
2021Methods in molecular biology2 citations
Semantic Scholar
Direct and diffuse cross-kingdom interactions in plant microbiome assembly
Rachel A. Hammer, Marissa R Lee, Jeffrey A. Kimbrel, R. Stuart +1 more
2026bioRxiv1 citations Open access
Semantic Scholar
Specialist–Generalist Trade-Offs in Microbial Growth Rates Across Soil Habitats
Megan M. Foley, N. Sokol, B. Stone, S. Blazewicz +6 more
2025bioRxiv1 citations Open access
Semantic Scholar
Reduced legacy precipitation decreases microbial community growth efficiency and alters soil organic carbon in a California grassland
Linnea K. Hernandez, Nicole DiDonato, L. Paša-Tolić, P. Chuckran +9 more
2025bioRxiv1 citations Open access
Semantic Scholar
Marine bacteria cross-feeding controls the fate of extracellular glycolate carbon
T. Samo, Jeffrey A. Kimbrel, K. Rolison, S. Blazewicz +3 more
2025bioRxiv1 citations Open access
Semantic Scholar
Active virus-host interactions at sub-freezing temperatures in Arctic peat soil
G. Trubl, Jeffrey A. Kimbrel, Jose Liquet-Gonzalez, E. Nuccio +5 more
2021Microbiome1 citations Open access
Semantic Scholar
Iron limitation alters diatom carbon flow through shifts in microbiome exometabolite consumption
Naomi E. Gilbert, N. Coffey, Nathan McCall, Jeffrey A. Kimbrel +8 more
2026bioRxiv0 citations Open access
Semantic Scholar
Multidimensional scaling informed by F-statistic: Visualizing grouped microbiome data with inference
Hyungseok Kim, Soobin Kim, Jeffrey A. Kimbrel, Megan M. Morris +2 more
2023PLoS Comput. Biol.0 citations Open access
Semantic Scholar
Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro assessment of neutralizing antibodies
A. Avila-Herrera, Jeffrey A. Kimbrel, Jose Manuel Martí, J. Thissen +7 more
2023bioRxiv0 citations Open access
Semantic Scholar
Differential laboratory passaging of SARS-CoV-2 viral stocks impacts the in vitro 2 assessment of neutralizing antibodies
A. Avila-Herrera, Jeffrey A. Kimbrel, Jose Manuel Martí, James B. Thissen +8 more
20230 citations
Semantic Scholar
THE DUAL ROLE OF THE MICROCYSTIS AERUGINOSA MICROBIOME ON CYANOTOXIN PRODUCTION: COMPETITION FOR AND REMINERALIZATION OF ORGANIC NITROGEN
Wei Li, David Baliu-Rodriguez, Sanduni H. Premathilaka, Sharmila I. Thenuwara +10 more
2023bioRxiv0 citations Open access
Semantic Scholar

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