The Microbial Ecosystems (mSys) Laboratory in beautiful Fort Collins, CO!
We are always interested in hearing from talented, motivated undergraduate and potential graduate students.
Please follow the directions below for how to start this process.
If you are an undergraduate seeking part-time, paid employment (we do not consider volunteer employees), email Kelly Wrighton (firstname.lastname@example.org). We do request that for the first semester students have at least two 3-hour windows for research. If your schedule has this time, please email Rebecca with your (1) CV, (2) availability, and (3) brief email stating what interests you about working in the mSys lab.
Potential Graduate Students
Graduate students seeking a Fall 2023 start date: mSys does not have resources to directly fund a Masters or PhD student this fall (i.e. students accepted through GDPE or Soil and Crop Sciences require mentor funding to be admitted). The laboratory can support students who apply and are admitted to Cell and Molecular Biology (CMB) and Microbiology (MIP) Phd programs as these programs have first-year training grants. The laboratory can also support students who have their own funding through any of the department routes, and we are willing to support and supplement student acquired funding. Please reach out for more guidance or clarity.
Staff and Post-Doctoral Trainees
Current Funded Opportunities:
The Microbial Ecosystems Lab (mSys) at Colorado State University is searching for 2-3 post-doctoral researchers to join our team. This researcher will work independently and contribute as a member to our dynamic, collaborative multi-disciplinary team of microbiologists, biochemists, computational biologists, and environmental scientists.
We are looking for new team members for projects related to changing redox conditions on microbiome functionality, with linkages to ecosystem outputs. We are interested in team members who can contribute to projects working with PI Dr. Kelly Wrighton in the human gut, wetland soils, or agricultural systems (soils, rumen). Metabolism at various scales, from biochemistry, to microorganisms, to communities is a central focus of our research team.
- PhD in microbiology, computational biology, environmental sciences (or closely related field) by the beginning of the appointment; maximum of 3 years prior post-doctoral experience.
- Knowledge and in depth understanding of key biological concepts (genes, biochemical pathways, and or microbial energetics).
- Proficiency in Unix or Python or R
- Evidence of substantial research accomplishment including at least one first-author, peer-reviewed manuscript publication
- Experience culturing and physiologically characterizing bacterial/archaeal isolates or enrichment microbial communities
- Experience with comparative metagenomic computational analyses
- Experience analyzing gene expression (proteomic, transcriptomic) or metabolite data
- Experience managing teams of individuals in laboratory or field scenarios
- Experience collaborating with DOE user facilities like JGI, EMSL, KBase
- Experience in geochemical analyses and analytical equipment (IC, GC, HPLC, LC-MS, ICP-MS)
This position will perform microbial genomics research using computational and statistical analyses to decipher biological meaning from genome sequences and related data, including both DNA and RNA sequences, as well as other microbiome data. The roles and responsibilities of this position will include:
- Analyzing internally and externally generated microbiome data using standard pipelines as well as innovative approaches
- Working alongside microbiologists, computational biologists, environmental scientists in a team project environment, with the end goal of contributing to the discovery of functions and interactions encoded in microbial community genomic data
- Lead development of reproducible science, data management, and server operations protocols for within and outside the laboratory (github, Jupyter, snakemake or other workflows)
- Contribute to the development of DRAM, the mSys laboratory genome annotation software, and new computational tools and frameworks for microbiome data science
- Establishing, benchmarking, and validating pipelines and approaches for analysis of next generation DNA and RNA sequencing data, integrating these data types as well as metabolomics and proteomics data
- Incorporate cutting-edge analyses and optimization to ensure bioinformatics pipelines are contemporary and of the highest standards
- Contribute data and figures for the public dissemination of the research output via scientific publications and presentations
- Contribute to writing publications and grants
Email Kelly Wrighton (email@example.com) for information and instructions for application.
The Microbial Ecosystems Laboratory is looking for a junior to intermediate software developer with microbiome/microbiology experience to continue to develop DRAM, the laboratory developed genome annotation software (See Shaffer et al, 2020, Nucleic Acid Research). This position will include working alongside microbiologists and computational biologists in a team environment, with the end goal of building software that can analyze, synthesize, and visualize microbial next generation sequence data.
Specific DRAM software responsibilities include:
- Maintain and update existing open-source data portal for microbial genomics analyses
- Troubleshoot and address user concerns and suggest improvements to existing coding structure
- Design, develop, and implement new web applications
- Handle communication between cross-functional teams from different sectors (e.g. industry, start-ups, national laboratories, and universities)
- Act as a technical liaison to microbiome scientists, help co-develop training workshops
See official job posting for more information and instructions for application.