Agricultural Contributed Datasets and Analyses
publicly available datasets
Posts by Collection
portfolio
Medical Contributed Datasets and Analyses
publicly available datasets
publications
The application of a developmental genomics approach to study the resistant reaction of soybean to the soybean cyst nematode
Published in NEMATROPICA, 2010
The resistant reactions of soybean to the soybean cyst nematode.
Recommended citation: Klink VP, Lawrence GW, Matsye PD, Showmaker KC. 2010 The application of a developmental genomics approach to study the resistant reaction of soybean to the soybean cyst nematode. Nematropica 40:1-11
Quantitative field testing Rotylenchulus reniformis DNA from Metagenomic Samples Isolated Directly from Soil
Published in PLoS ONE, 2011
A quantitative PCR procedure of the detection of Rotylenchulus reniformis directly from soil
Recommended citation: Showmaker KC, Lawrence GW, Lu S, Balbalian C, Klink VP. 2011 Quantitative field testing Rotylenchulus reniformis DNA from Metagenomic Samples Isolated Directly from Soil. PLoS ONE 6(12): e28954 https://doi.org/10.1371/journal.pone.0028954
Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres
Published in Nature, 2012
Gold Standard Cotton Genome
Recommended citation: Paterson et al (including Showmaker KC).2012 Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature. 492 423-427 https://doi.org/10.1038/nature11798
The pqqC gene is essential for antifungal activity of Pseudomonas kilonensis JX22 against Fusarium oxysporum sp. Lycopersici
Published in FEMS Microbiology Letters, 2014
antifungal activity
Recommended citation: Xu J, Deng P, Showmaker KC, Wang H, Baird SM, Lu S. The pqqC gene is essential for antifungal activity of Pseudomonas kilonensis JX22 against Fusarium oxysporum sp. lycopersici. 2014 FEMS Microbiology Letters. 353(2):98-105 https://doi.org/10.1111/1574-6968.12411
Transcriptomic Dissection of the Rice - Burkholderia glumae Interaction.
Published in BMC Genomics, 2014
plant pathology
Recommended citation: Magbanua ZV, Arick M, Buza T, Hsu CY, Showmaker KC, Chouvarine P, Deng P, Peterson DG, Lu S. 2014 Transcriptomic Dissection of the Rice - Burkholderia glumae Interaction. BMC Genomics 15:755. https://doi.org/10.1186/1471-2164-15-755
Draft Genome Sequence of Burkholderia pyrrocinia Lyc2, a Biological Control Strain That Can Suppress Multiple Plant Microbial Pathogens
Published in Genome Announcements, 2014
Recommended citation: Wang X, Showmaker KC, Yu X, Bi T, Hsu C, Baird SM, Peterson DG, Li X, Lu S. 2014 Draft Genome Sequence of Burkholderia pyrrocinia Lyc2, a Biological Control Strain That Can Suppress Multiple Plant Microbial Pathogens. Genome Announcements. 2(5): e00991-14 https://doi.org/10.1128/genomeA.00991-14
Insight into the salivary gland transcriptome of Lygus lineolaris (Palisot de Beauvois)
Published in PLoS ONE, 2016
Lygus lineolaris salivary gland transcriptome .
Recommended citation: Showmaker KC, Bednářová A, Gresham C. Hsu C, Peterson DG, Krishnan N. (2016) Insight into the salivary gland transcriptome of Lygus lineolaris (Palisot de Beauvois). PLoS ONE 11(1): e0147197 https://doi.org/10.1371/journal.pone.0147197
Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis
Published in Microbiologyopen, 2016
Recommended citation: Deng P, Wang X, Baird SM, Showmaker KC, Smith L, Peterson DG, Lu S (2016). Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis. Microbiologyopen 5(3):353-69. https://doi.org/10.1002/mbo3.333
Characterization of Fenoxaprop-P-Ethyl–Resistant Junglerice (Echinochloa colona) from Mississippi
Published in Weed Science, 2017
Recommended citation: Wright AA, Nandula VK, Grier L, Showmaker KC, Bond JA, Peterson DG, Ray JD, and Shaw DR (2016) Characterization of Fenoxaprop-P-Ethyl–Resistant Junglerice (Echinochloa colona) from Mississippi. Weed Science 64(4):588-595.
The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1
Published in Standards in Genomic Sciences, 2017
Recommended citation: Showmaker KC, Arick MA, Hsu C, Martin BE, Wang X, Jia J, Wubben MJ, Nichols RL, Allen TW, Peterson DG, and Lu S. (2017) The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1. Standards in Genomic Sciences 12:42 [Extended Genome Report] https://doi.org/10.1186/s40793-017-0253-3
The Genome Sequence of the Soybean Cyst Nematode (Heterodera glycines) endosymbiont Candidatus Cardinium hertigii strain cHgTN10
Published in Genome Announcements, 2018
Recommended citation: Showmaker KC, Walden KK, Fields CJ, Lambert KN and Hudson ME. (2018) The Genome Sequence of the Soybean Cyst Nematode (Heterodera glycines) endosymbiont Candidatus Cardinium hertigii strain cHgTN10. Genome Announcements 6(26): e00624-18 https://doi.org/10.1128/genomea.00624-18
Five life stage-specific transcriptome assemblies for the reniform nematode, Rotylenchulus reniformis Linford & Oliveira
Published in Journal of Nematology, 2018
Recommended citation: Showmaker KC, Sanders WS, Eves-van den Akker S, Martin BE, Callahan FE, Peterson DG, Wubben MJ. (2018) Five life stage-specific transcriptome assemblies for the reniform nematode, Rotylenchulus reniformis Linford & Oliveira. Journal of Nematology 50 (4): 529-530 https://doi.org/10.21307/jofnem-2018-053
A genomic resource for the sedentary semi-endoparasitic reniform nematode, Rotylenchulus reniformis Linford & Oliveira
Published in Journal of Nematology, 2019
Recommended citation: Showmaker KC, Sanders WS, Eves-van den Akker S, Martin BE, Peterson DG, Wubben MJ. (2019) A genomic resource for the sedentary semi-endoparasitic reniform nematode, Rotylenchulus reniformis Linford & Oliveira. Journal of Nematology 51:1-2 https://doi.org/10.21307/jofnem-2019-013
Spontaneous Superimposed Preeclampsia: Chronology and Expression Unveiled by Temporal Transcriptomic Analysis
Published in Physiological Genomics, 2019
Recommended citation: Maeda KJ, Showmaker KC, Johnson AC, Garrett MR, Sasser JM. (2019) Spontaneous Superimposed Preeclampsia: Chronology and Expression Unveiled by Temporal Transcriptomic Analysis. Physiol Genomics 51: 342–355 https://doi.org/10.1152/physiolgenomics.00020.2019
Whole Genome Sequencing and Novel Candidate Genes for CAKUT and Altered Nephrogenesis in the HSRA Rat
Published in Physiological Genomics, 2020
Recommended citation: Showmaker KC, Cobb M, Johnson AC, Garrett MR. (2020) Whole Genome Sequencing and Novel Candidate Genes for CAKUT and Altered Nephrogenesis in the HSRA Rat. Physiological Genomics 52(1):56-70 https://doi.org/10.1152/physiolgenomics.00112.2019
Loss of Arhgef11 in the Dahl Salt-Sensitive Rat Protects Against Hypertension-Induced Renal Injury
Published in Hypertension, 2020
Recommended citation: Johnson AC, Wu W, Attipoe EM, Sasser JM, Taylor EB, Showmaker KC, Kyle PB, Lindsey ML, Garrett MR. (2020) Loss of Arhgef11 in the Dahl Salt-Sensitive Rat Protects Against Hypertension-Induced Renal Injury. Hypertension 75(4):1012-1024. https://doi.org/10.1161/HYPERTENSIONAHA.119.14338
Endothelial cell disruption drives increased blood-brain barrier permeability and cerebral edema in the Dahl SS/jr rat model of superimposed preeclampsia
Published in American Journal of Physiology-Heart and Circulatory Physiology, 2021
Recommended citation: Maeda KJ, McClung DM, Showmaker KC, Warrington JP, Ryan MJ, Garrett MR, Sasser JM. (2021) Endothelial cell disruption drives increased blood-brain barrier permeability and cerebral edema in the Dahl SS/jr rat model of superimposed preeclampsia. Am J Physiol Heart Circ Physiol. 320: H535–H548 PMID: 33275518 https://doi.org/10.1152/ajpheart.00383.2020
Single cell RNA sequencing reveals ferritin as a key mediator of autoimmune pre-disposition in a mouse model of systemic lupus erythematosus
Published in Scientific Reports, 2021
Recommended citation: Younes ST, Showmaker KC, Johnson AC, Garrett MR, Ryan MJ. (2021) Single cell RNA sequencing reveals ferritin as a key mediator of autoimmune pre-disposition in a mouse model of systemic lupus erythematosus. Scientific Reports 11, 24245 https://doi.org/10.1038/s41598-021-03649-2
Sex and molecular differences in cardiovascular parameters at peak influenza disease in mice
Published in Physiological Genomics, 2023
Recommended citation: Martin BE, Taylor EB, Attipoe EM, Wu W, Stec DE, Showmaker KC, Garrett MR. (2023) Sex and molecular differences in cardiovascular parameters at peak influenza disease in mice. Physiological Genomics 55(2):79-89. https://doi.org/10.1152/physiolgenomics.00146.2022
Molecular profiling of the hippocampus of children with autism spectrum disorder
Published in Molecular Psychiatry, 2024
Recommended citation: Rexrode LE, Hartley J, Showmaker KC, Challagundla L, Vandewege MW, Martin BE, Blair E, Bollavarapu R, Antonyraj RB, Hilton K, Gardiner A, Valeri J, Gisabella B, Garrett MR, Theoharides TC, Pantazopoulos H. (2024) Molecular profiling of the hippocampus of children with autism spectrum disorder. Molecular Psychiatry 29(7):1968-1979. https://doi.org/10.1038/s41380-024-02441-8
Sex-specific changes in vital signs and common blood tests on the day of influenza diagnosis
Published in Physiological Reports, 2025
Recommended citation: Showmaker KC, Martin BE. (2025) Sex-specific changes in vital signs and common blood tests on the day of influenza diagnosis. Physiological Reports 13: e70486. https://doi.org/10.14814/phy2.70486
talks
Syncytium Gene Expression in Glycine Max (Pi 88788) Roots Undergoing a Resistant Reaction to the Parasitic Nematode Heterodera glycines
Published:
Syncytium Gene Expression
Genomic Applications in Agriculture
Published:
Genomic Applications in Agriculture
Plant-Parasitic Nematode Feeding Site Development
Published:
Plant-Parasitic Nematode Feeding Site Development
Toward the Development of a Reniform Nematode Gene Atlas
Published:
Toward the Development of a Reniform Nematode Gene Atlas
Advances in DNA Sequencing
Published:
NGS
Biochemistry and Physiology of RNA interference
Published:
Guest lecture on the biochemistry and physiology of RNA interference.
Introduction to Nematology
Published:
Guest lecture on nematology.
Introduction to Molecular Nematology.
Published:
Guest lecture on molecular nematology.
Bioinformatics
Published:
Guest lecture on bioinformatics consulting.
Emerging Technologies for Nematology
Published:
Session Chair and Organizer for the Emerging Technologies for Nematology Session at the Society of Nematology Annual Meeting.
The UMMC Molecular and Genomic Core: A Resource for High Throughput Genome Sequencing in Mississippi
Published:
The UMMC Molecular and Genomic Core: A Resource for High Throughput Genome Sequencing in Mississippi
Data Science
Published:
Chaired the Data Science session at PEARC19.
IP Capture and Protection Considerations within Research Organizations
Published:
CaRCC session on intellectual property capture and protection considerations within research organizations.
CyberAmbassadors Training
Published:
Led a 2-day CyberAmbassadors program at the Mississippi Coding Academies in Biloxi, MS. The training focuses on preparing attendees to collaborate effectively with CI-Users and CI-Professionals to advance multidisciplinary, computationally intensive research and service. This program is based upon work supported by the National Science Foundation under grant #1730137.
teaching
Pharmacology Methods
Course, Department of Pharmacology and Toxicology, University of Mississippi Medical Center, 2021
Data management and analysis lectures.
Introductory Statistics with R
Workshop, The Jackson Laboratory, 2021
https://smcclatchy.github.io/introductory-statistics-with-r/
Introduction To HPC
Training, The Jackson Laboratory, 2021
Introduction to JAX HPC resources.
Data Carpentry Genomics
Workshop, The Jackson Laboratory, 2021
Instructor. Workshop series on genomics data analysis, held Monday and Wednesday afternoons (1–4 PM), November 1–10, 2021.
Introduction To Singularity
Training, The Jackson Laboratory, 2021
Introduction to Singularity containerization and execution of computational biology and bioinformatics applications.
Data Carpentry Ecology
Workshop, The Jackson Laboratory, 2021
Instructor, December 7–10, 2021. Delivered lessons on R, ggplot2, SQL, and databases, including Intro to R and Data Analysis and Visualization in R for Ecologists. https://smcclatchy.github.io/2021-12-07-jackson/
Omero: Open Microscopy Environment (OME)
Workshop, Virtual, 2022
Instructor. Workshop on microscopy data management.
Zarr and Dask for Large-scale Image Data
Workshop, Virtual, 2022
Instructor. Workshop on scalable image processing.
High Performance Computing
Workshop, Virtual, 2022
Instructor. Workshop on HPC fundamentals.
Introduction To Singularity
Workshop, The Jackson Laboratory, 2022
https://thejacksonlaboratory.github.io/intro-to-singularity/index.html
Introductory Statistics with R
Workshop, Virtual, 2022
Instructor. Multi-day workshop on statistical analysis with R, March 22–25, 2022.
CyberAmbassadors: Teamwork
Training, Virtual, 2022
Facilitator. Delivered modules on effective meetings and team development.
Introduction To BASH
Workshop, The Jackson Laboratory, 2022
Introduction To HPC
Workshop, The Jackson Laboratory, 2022
https://thejacksonlaboratory.github.io/intro-to-hpc/Introduction to JAX HPC resources.
CyberAmbassadors: Communications
Training, Virtual, 2022
Facilitator. Delivered modules on First Contact, Networking, and Consultations.
CyberAmbassadors Training
Training, The Jackson Laboratory, 2022
Facilitator. In-person training on communication, teamwork, and leadership, October 5–6, 2022.
CyberAmbassadors Training
Training, The Jackson Laboratory, 2022
Facilitator. In-person training on communication, teamwork, and leadership, November 1–2, 2022.
CyberAmbassadors Full Course
Training, Mississippi Coding Academies, Gulf Coast campus, 2022
Facilitator. Full CyberAmbassadors course on communication, teamwork, and leadership, November 22–23, 2022.
Introduction to Cloud Computing
Workshop, Virtual, 2023
Instructor. Workshop on cloud platform fundamentals.
Introduction to Containerization
Workshop, Virtual, 2023
Instructor. Workshop on container technologies.
Object Storage
Workshop, Virtual, 2023
Instructor. Workshop on cloud object storage systems.
Introduction to Cloud Computing
Workshop, Virtual, 2023
Instructor. Workshop on cloud platform fundamentals.
Introduction to R
Workshop, Mississippi State University, 2023
Instructor.
Data Analytics: R & RStudio
Workshop, Doctoral Guest Speaker Series, Southern University and A&M College, 2023
Instructor.
Introduction to R
Workshop, University of Mississippi Medical Center, 2025
Instructor.
Introduction to GitHub
Workshop, Virtual, 2025
Instructor.