Microbial Whole-Genome Sequencing and RNA Sequencing
Department of Veterinary Science
University of Kentucky- 12 months
Salary is commensurate with experience and qualifications
The Department of Veterinary Science at the University of Kentucky is seeking a highly motivated, detail-oriented, and experienced Research Analyst / Genomics Research Specialist to support research in microbial whole-genome sequencing, RNA sequencing, antimicrobial resistance, bacteriophage biology, host–pathogen interactions, and One Health infectious diseases.
This position offers an opportunity to work at the interface of microbial genomics, transcriptomics, infectious disease research, antimicrobial resistance surveillance, bacteriophage-based interventions, and host–pathogen interaction studies. The successful candidate will contribute to sequencing-based projects involving bacterial pathogens, bacteriophages, host cells, environmental specimens, organoid-derived samples, and animal-associated samples.
We are seeking an experienced sequencing specialist with strong hands-on library preparation for RNA and DNA sequencing, molecular biology and next-generation sequencing experience, demonstrated troubleshooting ability, excellent organizational skills, and the ability to contribute to experimental design, sequencing strategy, protocol optimization, quality-control interpretation, and workflow development. For more information, please contact us at
[email protected]
Position Summary
The successful candidate will support multiple ongoing projects focused on bacterial infectious diseases, antimicrobial resistance, pathogen evolution, bacterial virulence, bacteriophage-based interventions, sequencing-based surveillance, and host–pathogen interactions. Primary areas of responsibility include supporting experimental design for sequencing-based studies and contributing to sequencing strategy development for short-read, long-read, and hybrid approaches. The successful candidate will perform DNA and RNA extraction from bacterial, bacteriophage, host-cell, organoid-derived, environmental, and animal-associated samples; prepare sequencing libraries for microbial whole-genome sequencing, RNA-seq, bacteriophage genomics, amplicon sequencing, and host-response studies; and conduct nucleic acid and library quality-control assessments. The position will also support Illumina, Oxford Nanopore, and PacBio sequencing workflows; maintain accurate sample tracking, barcoding, metadata organization, and sequencing documentation; and contribute to troubleshooting, protocol optimization, and standard operating procedure development.
Key Responsibilities
Experimental Design and Sequencing Strategy
- Assist with experimental design for microbial WGS, RNA-seq, transcriptomic, metagenomic, metatranscriptomic, bacteriophage, and host–pathogen interaction studies.
- Help determine appropriate sequencing approaches based on project goals, sample type, organism, genome size, RNA quality, read length, sequencing depth, and downstream analysis needs.
- Contribute to decisions regarding Illumina short-read sequencing, Oxford Nanopore sequencing, PacBio long-read sequencing, and hybrid sequencing strategies.
- Assist with planning biological replication, sample batching, barcode assignment, library pooling, run design, and quality-control checkpoints.
- Develop troubleshooting plans for low nucleic acid recovery, RNA degradation, contamination, failed libraries, low sequencing output, poor read quality, barcode imbalance, and insufficient sequencing depth.
- Work with the principal investigator, trainees, bioinformaticians, sequencing facilities, and collaborators to ensure that sequencing workflows support genome assembly, transcriptomics, antimicrobial resistance analysis, virulence analysis, sequence typing, phylogenetics, and public database submission.
- Contribute to the development, validation, scaling, and refinement of sequencing workflows and standard operating procedures.
- Participate in evaluation and implementation of new sequencing technologies, library-preparation methods, quality-control approaches, and workflow improvements.
DNA/RNA Extraction, Library Preparation, and Quality Control
- Perform high-quality genomic DNA and total RNA extraction from bacterial isolates, bacteriophages, environmental specimens, animal-associated samples, host cells, organoid-derived samples, and host–pathogen interaction experiments.
- Optimize DNA and RNA extraction protocols for difficult organisms, low-biomass specimens, intracellular pathogens, bacteriophages, and complex biological samples.
- Perform high-molecular-weight DNA extraction for long-read sequencing and support RNA stabilization and preservation for transcriptomic applications.
- Prepare sequencing libraries for bacterial WGS, RNA-seq, host-response studies, bacteriophage genomics, amplicon sequencing, and other genomic applications.
- Support Illumina library preparation, Oxford Nanopore ligation/rapid/native barcoding/cDNA workflows, and PacBio SMRTbell or related long-read sequencing workflows.
- Support bacterial rRNA depletion, strand-specific RNA-seq workflows, and transcriptomic library preparation.
- Assess DNA/RNA quantity, purity, integrity, molecular weight, and library quality using Qubit, NanoDrop, Bioanalyzer, TapeStation, Fragment Analyzer, gel electrophoresis, or comparable platforms.
- Interpret quality-control results and recommend whether samples or libraries are suitable for sequencing.
- Troubleshoot low nucleic acid recovery, poor DNA quality, RNA degradation, low library yield, adapter-dimer formation, contamination, poor read quality, and suboptimal fragment-size distribution.
Sequencing Workflow Support and Data Organization
- Prepare sample sheets, barcoding plans, run manifests, metadata files, and sequencing submission documentation.
- Coordinate sequencing runs and sample submissions to internal core facilities, external sequencing centers, and collaborating laboratories.
- Monitor library yield, sequencing run performance, read output, read quality, sequencing depth, and basic quality metrics.
- Assist with base-calling, demultiplexing coordination, raw data organization, file transfer, and documentation.
- Support hybrid genome assembly projects combining Illumina short-read data with Oxford Nanopore or PacBio long-read data.
- Collaborate with bioinformatics personnel to ensure that sequencing data and metadata are appropriately formatted for genome assembly, annotation, AMR analysis, sequence typing, virulence analysis, phylogenetics, transcriptomics, and repository submission.
- Maintain accurate sample inventories, freezer records, sequencing logs, reagent records, quality-control records, and run documentation.
- Assist with preparation and submission of sequencing data to repositories such as NCBI SRA, GenBank, BioProject, and BioSample.
- Support preparation of sequencing-related summaries, technical reports, manuscript methods, grant progress reports, and workflow documentation.
Molecular Biology, Biosafety, and Team Collaboration
- Perform PCR, qPCR, reverse-transcription PCR, gel electrophoresis, nucleic acid cleanup, size selection, and related molecular biology procedures.
- Operate and maintain commonly used laboratory equipment, including centrifuges, electrophoresis systems, spectrophotometers, fluorometers, thermocyclers, qPCR instruments, and nucleic acid quality-control instruments.
- Follow institutional biosafety, chemical safety, data-management, and laboratory quality-control procedures, including BSL-2 practices when applicable.
- Participate in laboratory meetings and provide regular updates on sample processing, library preparation, sequencing progress, quality-control results, experimental design issues, and technical challenges.
- Communicate technical findings clearly to laboratory members, collaborators, sequencing facilities, and bioinformatics personnel.
- Assist trainees and laboratory members with sequencing-related protocols, sample tracking, quality-control procedures, documentation, and good laboratory practices.
- Contribute to a collaborative, organized, respectful, and productive research environment.
Required Qualifications
Applicants should have a Master’s degree in genomics, molecular biology, microbiology, genetics, biotechnology, bioinformatics, or a closely related sequencing-focused field. A PhD is preferred, particularly for candidates with experience in microbial genomics, RNA-seq, long-read sequencing, bacteriophage genomics, host–pathogen interactions, or sequencing-based infectious disease research. Exceptional candidates with a Bachelor’s degree and extensive relevant sequencing experience may also be considered.
The successful candidate should have strong hands-on experience with microbial whole-genome sequencing, RNA-seq, sequencing library preparation, nucleic acid quality control, and molecular biology techniques, including DNA/RNA extraction, PCR, qPCR, RT-PCR, gel electrophoresis, nucleic acid cleanup, quantification, and library quality assessment. Experience with Illumina, Oxford Nanopore, and/or PacBio workflows is highly desirable, including short-read sequencing, long-read sequencing, high-molecular-weight DNA extraction, bacterial RNA extraction, rRNA depletion, strand-specific RNA-seq, hybrid genome sequencing, amplicon sequencing, or related NGS applications.
Applicants should be able to contribute to the design, optimization, troubleshooting, validation, and documentation of sequencing-based studies and SOPs. Relevant experience includes sequencing platform selection, sample-preparation strategy, library-preparation planning, sequencing-depth considerations, sample batching, barcoding, metadata management, contamination prevention, and troubleshooting of low-yield samples, failed libraries, or sequencing-quality issues.
Experience working with bacterial pathogens, bacteriophages, intracellular organisms, host cells, organoids, environmental specimens, animal-associated samples, or BSL-2 workflows is preferred. Familiarity with microbial genomics workflows, including genome assembly, annotation, antimicrobial resistance detection, virulence analysis, sequence typing, phylogenetics, outbreak investigation, public database submission, and One Health surveillance, is highly desirable.
The successful candidate should have strong attention to detail, problem-solving ability, organizational skills, independence, teamwork, and written and verbal communication skills. The candidate should be able to maintain complete laboratory records, manage multiple sequencing projects, communicate clearly with laboratory members and collaborators, and support preparation of sample sheets, run plans, metadata files, reports, manuscripts, grant-related summaries, SOPs, and public sequence-database submissions.
Desired Skills and Attributes
The successful candidate should demonstrate the following qualities:
- Highly reliable, methodical, and careful when handling DNA, RNA, sequencing libraries, and irreplaceable samples.
- Strong interest in bacterial genomics, RNA sequencing, antimicrobial resistance, bacteriophage biology, host–pathogen interactions, and One Health research.
- Ability to think critically about experimental design, sequencing strategy, sample quality, workflow limitations, and downstream analysis needs.
- Willingness to learn new sequencing technologies, library-preparation methods, quality-control procedures, and data-management approaches.
- Ability to troubleshoot nucleic acid extraction, library preparation, sequencing-performance, and sample-quality problems systematically.
- Ability to recognize contamination, sample mislabeling, nucleic acid degradation, barcode imbalance, or library-quality concerns before sequencing.
- Strong organizational skills and ability to coordinate sequencing timelines across multiple projects.
- Ability to communicate technical findings clearly to laboratory members, collaborators, sequencing facilities, and bioinformatics personnel.
- Commitment to reproducible research, accurate metadata, data integrity, and good laboratory practices.
- Flexibility to adapt to evolving research priorities, sequencing platforms, and project requirements.
- Ability to work respectfully and professionally in a collaborative academic research environment.
- Strong motivation to contribute to high-quality research publications, grant-funded projects, infectious disease surveillance, and One Health research.
Application Materials
Interested applicants should submit:
- CV or resume
- Brief statement describing relevant laboratory, molecular biology, sequencing, experimental design and hand on experience, troubleshooting, and quality-control experience
- Contact information for 3 professional references
Review of applications will begin immediately and continue until the position is filled.
