Publications
2023
CE Yancey, EA Kiledal, SR Chaganti, VJ Denef, RM Errera, JT Evans, LN Hart, D Isailovic, WS James, JK Kharbush, JA Kimbrel, W Li, X Mayali, H Nitschky, CA Polik, MA Powers, SH Premathilaka, NA Rappuhn, LA Reitz, SR Rivera, CC Zwiers, GJ Dick. The Western Lake Erie Culture Collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome. Harmful Algae (2023). Full text
MM Foley, SJ Blazewicz, KJ McFarlane, A Greenlon, M Hayer, JA Kimbrel, BJ Koch, VL Monsaint-Queeney, K Morrison, E Morrissey, BA Hungate, J Pett-Ridge. Active populations and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslands. SBB 177 (2023). Full text
2022
JA Kimbrel, J Moon, A Avila-Herrera, JM Martí, J Thissen, N Mulakken, SH Sandholtz, T Ferrell, C Daum, S Hall, B Segelke, KT Arrildt, S Messenger, DA Wadford, C Jaing, JE Allen, MK Borucki. Multiple Mutations Associated with Emergent Variants Can Be Detected as Low-Frequency Mutations in Early SARS-CoV-2 Pandemic Clinical Samples. Viruses 14(12), 2775 (2022). Full text
A Greenlon, E Sieradzki, O Zablocki, BJ Koch, MM Foley, JA Kimbrel, BA Hungate, SJ Blazewicz, EE Nuccio, CL Sun, A Chew, CJ Mancilla, MB Sullivan, M Firestone, J Pett-Ridge, JF Banfield. Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems. mSystems (2022). Full text
NW Sokol, E Slessarev, GL Marschmann, A Nicolas, SJ Blazewicz, EL Brodie, MK Firestone, MM Foley, R Hestrin, BA Hungate, BJ Koch, BW Stone, MB Sullivan, O Zablocki, LLNL Soil Microbiome Consortium, J Pett-Ridge. Life and death in the soil microbiome: how ecological processes influence biogeochemistry. Nature Reviews Microbiology 20, pages 415–430 (2022). Full text
J McGowan, M Borucki, H Omairi, M Varghese, S Vellani, S Chakravarty, S Fan, S Chattopadhyay, M Siddiquee, JB Thissen, N Mulakken, J Moon, JA Kimbrel, AK Tiwari, RT Taylor, DW Kang, C Jaing, R Chakravarti, S Chattopadhyay. SARS-CoV-2 Monitoring in Wastewater Reveals Novel Variants and Biomarkers of Infection. Viruses 14(9) (2022). Full text
EE Nuccio, SJ Blazewicz, M Lafler, AN Campbell, A Kakouridis, JA Kimbrel, J Wollard, D Vyshenska, R Riley, A Tomatsu, R Hestrin, RR Malmstrom, M Firestone, J Pett-Ridge. HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi. Microbiome 10:199 (2022). Full text
R Hestrin, M Kan, M Lafler, J Wollard, JA Kimbrel, P Ray, SJ Blazewicz, R Stuart, K Craven, M Firestone, EE Nuccio & J Pett-Ridge. Plant-associated fungi support bacterial resilience following water limitation. ISME J 1-11 (2022). Full text
MM Morris, JA Kimbrel, H Geng, MB Tran-Gyamfi, ET Yu, KL Sale, TW Lane & X Mayali. Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina. mSphere (2022). Full text
2021
Nayfach S, IMG/M Data Consortium, et al. A genomic catalog of Earth’s microbiomes. Nature Biotechnology 39, 499-509 (2021). Full text.
JA Kimbrel, BM Jeffrey & CS Ward. Prokaryotic Genome Annotation. Microbial Systems Biology, Methods and Protocols. Methods Mol Biology 2349, 193–214 (2021). Full text Book
H Kim, JA Kimbrel, CA Vaiana, JR Wollard, X Mayali & CR Buie. Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate. ISME J 1–10 (2021). Full text Nature Portfolio
G Trubl, JA Kimbrel, J Liquet-Gonzalez, EE Nuccio, PK Weber, J Pett-Ridge, JK Jansson, MP Waldrop & SJ Blazewicz. Active virus-host interactions at sub-freezing temperatures in Arctic peat soil. Microbiome 9, 208 (2021). Full text
CLE Zhou, JA Kimbrel, R Edwards, K McNair, BA Souza & S Malfatti. MultiPhATE2: Code for functional annotation and comparison of phage genomes. G3 Genes Genomes Genetics jkab074- (2021) Full text Github
2020
SMD Seaver, F Liu, Q Zhang, J Jeffryes, JP Faria, JN Edirisinghe, M Mundy, N Chia, E Noor, ME Beber, AA Best, M DeJongh, JA Kimbrel, P D’haeseleer, SR McCorkle, JR Bolton, E Pearson, S Canon, EM Wood-Charlson, RW Cottingham, AP Arkin & CS Henry. The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. Nucleic Acids Res (2020). Full text2019
CLE Zhou, S Malfatti, JA Kimbrel, C Philipson, K McNair, T Hamilton, R Edwards & B Souza. multiPhATE: bioinformatics pipeline for functional annotation of phage isolates. Bioinformatics 35, 4402–4404 (2019). Full text
DA Higgins, J Gladden, JA Kimbrel, BA Simmons & SW Singer. Guanidine-riboswitch-regulated efflux transporters protect bacteria against ionic liquid toxicity. J Bacteriol (2019) Full text
CL Fisher, CS Ward, PD Lane, JA Kimbrel, KL Sale, RK Stuart, X Mayali & TW Lane. Bacterial communities protect the alga Microchloropsis salina from grazing by the rotifer Brachionus plicatilis. Algal Res 40, 101500 (2019). Full text
JA Kimbrel, TJ Samo, CS Ward, D Nilson, MP Thelen, A Siccardi, P Zimba, TW Lane & X Mayali. Host selection and stochastic effects influence bacterial community assembly on the microalgal phycosphere. Algal Res 40, 101489 (2019). Full text
2018
M Griesemer, JA Kimbrel, CE Zhou, A Navid & P D’haeseleer. Combining multiple functional annotation tools increases coverage of metabolic annotation. BMC Genomics 19, 948 (2018). Full text
TJ Samo, JA Kimbrel, DJ Nilson, J Pett‐Ridge, PK Weber & X Mayali. Attachment between heterotrophic bacteria and microalgae influences symbiotic microscale interactions. Environ Microbiol 20, 4385 4400 (2018). Full text
JA Kimbrel, N Ballor, YW Wu, MM David, TC Hazen, BA Simmons, SW Singer & JK Jansson. Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. Front Microbiol 9, 533 (2018). Full text
2014
HL Woo, NR Ballor, TC Hazen, JL Fortney, B Simmons, KW Davenport, L Goodwin, N Ivanova, NC Kyrpides, K Mavromatis, T Woyke, JK Jansson, JA Kimbrel & KM DeAngelis. Complete genome sequence of the lignin-degrading bacterium Klebsiella sp. strain BRL6-2. Stand Genomic Sci 9, 19 (2014). Full text
OU Mason, NM Scott, A Gonzalez, A Robbins-Pianka, J Bælum, JA Kimbrel, NJ Bouskill, E Prestat, S Borglin, DC Joyner, JL Fortney, D Jurelevicius, WT Stringfellow, L Alvarez-Cohen, TC Hazen, R Knight, JA Gilbert & JK Jansson. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. ISME J 8, (2014). Full text
2013
JA Kimbrel, JH Chang, DJ Arp & LA Sayavedra-Soto. The Draft Genome Sequence of Nocardioides sp. Strain CF8 Reveals the Scope of Its Metabolic Capabilities. Genome Announc 1, (2013). Full text
SE Fox, J Preece, JA Kimbrel, GL Marchini, A Sage, K Youens-Clark, MB Cruzan & P Jaiswal. Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae). Appl Plant Sci 5, 1200011 (2013). Full text
Y Di, SC Emerson, DW Schafer, JA Kimbrel & JH Chang. Higher order asymptotics for negative binomial regression inferences from RNA-sequencing data. Stat Appl Genet Mol 12, 49–70 (2013). Full text
JA Kimbrel, WJ Thomas, Y Jiang, AL Creason, C. Thireault, JL Sachs & JH Chang. Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum. Plos Pathog 9, (2013). Full text
2011
JA Kimbrel, Y Di, JS Cumbie & JH Chang. RNA-Seq for Plant Pathogenic Bacteria. Genes-basel 2, 689–705 (2011). Full text
JS Cumbie, JA Kimbrel, Y Di, DW Schafer, LJ Wilhelm, SE Fox, CM Sullivan, AD Curzon, JC Carrington, TC Mockler & JH Chang. GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Gene Expression Differences. Plos One 6, e25279 (2011). Full text
LA Sayavedra‐Soto, N Hamamura, C Liu, JA Kimbrel, JH Chang & DJ Arp. The membrane‐associated monooxygenase in the butane‐oxidizing Gram‐positive bacterium Nocardioides sp. strain CF8 is a novel member of the AMO/PMO family. Env Microbiol Rep 3, 390–396 (2011). Full text
JA Kimbrel, SA Givan, TN Temple, KB Johnson & JH Chang. 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. Mol Plant Pathol 12, 580–594 (2011). Full text
2010
JA Kimbrel, SA Givan, AB Halgren, AL Creason, DI Mills, GM Banowetz, DJ Armstrong & JH Chang. An improved, high-quality draft genome sequence of the Germination-Arrest Factor-producing Pseudomonas fluorescens WH6. BMC Genomics 11, 522 (2010). Full text
The International Brachypodium Initiative. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463, 763 768 (2010). Full text
2009
CM Cohu, SE Abdel-Ghany, KA Gogolin Reynolds, AM Onofrio, JR Bodecker, JA Kimbrel, KK Niyogi & M Pilon. Copper Delivery by the Copper Chaperone for Chloroplast and Cytosolic Copper/Zinc-Superoxide Dismutases: Regulation and Unexpected Phenotypes in an Arabidopsis Mutant. Mol Plant 2, 1336–1350 (2009). Full text
WJ Thomas, CA Thireault, JA Kimbrel & JH Chang. 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. Plant J 60, 919 928 (2009). Full text