Job Postings

CMI - Undergraduate Researcher – Machine Learning, Web Development

 

The Center for Microbiome Innovation seeks applications for a paid undergraduate student researcher position in a project on machine learning with significant web development for the Qiita (qiita.ucsd.edu) platform to increase the number of samples available for machine learning in the UC San Diego-IBM Artificial Intelligence for Healthy Living (AIHL) program. 

Scope of research:
- Creation of a machine learning plugin for Qiita
- Enhancement of Qiita web platform to import external dataset from NCBI and EBI
- Development of UI/UX for machine learning with Qiita platform

Qualifications:
- Strong skills in Python and Javascript
- Experience with Github or Bitbucket in a team software development project
- Record of activities in website development
- Pursuit of undergraduate degree or coursework in Biology or a related field is a plus

Host faculty includes Rob Knight (Pediatrics and Computer Science & Engineering) and Sandrine Miller-Montgomery (Bioengineering).

Email your CV/cover letter to CMIInfo@ucsd.edu to apply.
 

CMI - Undergraduate Researcher - Biomedical Knowledge Base Development

 

The Center for Microbiome Innovation seeks applications for a paid undergraduate researcher position in a project on biomedical knowledge base development for the UC San Diego-IBM Artificial Intelligence for Healthy Living (AIHL) program. 

 

Scope of research:

- Manual annotation of biomedical literature

- Curation and evaluation of machine learning results

- Aggregation and transformation of microbiome-related literature

 

Qualifications:

- Strong skills in programming in Python, SQL, and Javascript.

- Experience of Github or Bitbucket in a team software development project 

- Good grades in college level Biology or Biology AP at high school is a plus

 

Host faculty include Rob Knight (Pediatrics and Computer Science & Engineering) and Chun-Nan Hsu (Biomedical Informatics).

 

How to Apply:

Email your CV/cover letter to CMIInfo@ucsd.edu to apply.

Note: If you have relatives employed at UC San Diego, you must include the name, relationship and department where employed in your resume or cover letter. This information is used only for the purpose of complying with the University’s nepotism policy.

CMI - Postdoctoral Fellow - Machine Learning, Bioinformatics & Systems Biology

 

The Center for Microbiome Innovation seeks applications for a postdoctoral position in microbiome-focused machine learning and bioinformatics for the UC San Diego-IBM Artificial Intelligence for Healthy Living (AIHL) program.

 

Scope of research:

- Lead a team of undergraduate and graduate researcher in the development of novel algorithms and approaches for predicting phenotypes of interest

- Develop tools, software, and data analysis pipelines for machine learning with microbiome data

- Apply the latest innovations in mathematical concepts, statistics, and feature selection in machine learning 

 

Qualifications:

- Ph.D. in a relevant discipline, including in the areas of machine learning, bioinformatics, systems biology or a related field

- Familiarity with microbiome data and research

- Strong research record and background in statistics, math, and/or computational science

- Proficiency with machine learning algorithms (e.g. tree-based model, dimension reduction, neural net)- Undergraduate or graduate coursework or degree in Biology or a related field is a plus

 

Host faculty include Rob Knight (Pediatrics and Computer Science & Engineering), Siavash Mirarab (Electrical and Computer Engineering), and Sandrine Miller-Montgomery (Bioengineering).

 

How to Apply:

 

Email your CV/cover letter to CMIInfo@ucsd.edu to apply.

 

Note: If you have relatives employed at UC San Diego, you must include the name, relationship and department where employed in your resume or cover letter. This information is used only for the purpose of complying with the University’s nepotism policy.

CMI - Postdoctoral Fellow - Microbiome Technology Development at UC San Diego

 

The Center for Microbiome Innovation (CMI) seeks applications for a postdoctoral position in multi-omic technology and methods development. The candidate will be responsible for designing, developing, and testing of novel tools, methods, and instruments that will enable breakthroughs in the field of microbiome research. Activities will include metagenomics-focused projects as well as metatranscriptomics, metabolomics, proteomics, and microbiology.

 

Scope of research:

- Next-generation sequencing technique development using Illumina sequencing technology as well as novel long-read techniques

- Evaluation of novel tools, instruments, and methods for multi-omic characterization of microbiome samples

- Analysis of microbial communities in the gut, oral, skin, and tumor microbiome

- Exposure to world-class bioinformatics and biostatistics teams

- Close interaction with industry partners

- Effectively communicate data and results at internal and external meetings/conferences.

 

Qualifications:

- Ph.D. in a relevant discipline, including in the areas of microbiology, biochemistry, immunology, biology, systems biology or a related field

- Experience working with next-generation sequencing library preparation, hybridization technologies, nucleic acid extraction, qPCR/RT-PCR, flow cytometry, ELISA, western blot mammalian cell/tissue and bacterial culture, conjugation chemistry and host nucleic acid depletion are highly desired

- Excellent communication and organizational skills

- Strong research record

 -Experience with Python, Qiime, and Qiita is a plus

 

Host faculty includes Sandrine Miller-Montgomery (Bioengineering) and Rob Knight (Pediatric, Bioengineering, and Computer Science & Engineering).

Please email a completed the application form (https://postdoc.ucsd.edu/_files/PostdocBioform2017-4-3.pdf) and support documents to CMIInfo@ucsd.edu to apply.

 

Note: If you have relatives employed at UC San Diego, you must include the name, relationship, and department where employed in your resume or cover letter. This information is used only for the purpose of complying with the University’s nepotism policy.

ASU - Postdoctoral or Research Scientist position available in Professor Krajmalnik-Brown lab

Dr. Krajmalnik-Brown (http://krajmalnik.environmentalbiotechnology.org/) and the Biodesign Swette Center for Environmental Biotechnology invite applications for a Postdoctoral Research Associate in the area of microbial ecology with a special focus on host-microbe interactions. The postdoctoral associate will be taking a leadership role in a Gut Microbiome funded project (microbiome-autism), will assist an NIH-funded team and will be exposed to many research topics associated with environmental biotechnology.

Priority will be given to candidates with experience working with functional microbial ecology analysis targeting microbial genomes, microbial pathways, microbially-produced metabolites and/or bioreactor operation.

The postdoctoral associate will be responsible for experimental design and implementation, data analyses, report/manuscript preparation, and mentorship of graduate and undergraduate students. The postdoctoral associate also will assist writing research proposals and seeking future funding. Establishing and sustaining interactions among faculty, post-docs, and students across the Center and the University will be central to the position, and coordinating among team members will be indispensable for leading the team's efforts and delivering milestones of the DoD-funded project.

Qualifications:

Ph.D. in Microbiology, bioinformatics, biostatistics, environmental engineering, chemical engineering, or allied discipline; interest in host-microbiome interactions, microbe-microbe interactions, microbe-environment interactions; hands-on experience with molecular biology and lab-scale bioreactor operations; excellent oral and written communication skills. Experience with mentoring graduate and undergraduate students.

The position will be available from October 2018, and ideally that the post-doctoral associate should begin no later than November 2018.

To apply, please submit to carole.flores@asu.edu as a single pdf document the following materials: 1) a cover letter specifying relevant qualifications and training, 2) curriculum vitae, 3) statement of current research interests and expertise (2-page maximum), 4) contact information for at least three professional references, and 5) at least one peer-reviewed publication. Please include "Application for host-microbe interactions Postdoc" in the email subject line. Initial review of applications will begin in August 2018;

As long as the position is not filled, review will continue every week thereafter until the search is closed. A background check is required for employment. Salary is negotiable based on the candidate's experience and ASU salary scales.

Bigelow Laboratory - Two postdoctoral positions in single cell genome-to-phenome studies

Bigelow Laboratory for Ocean Sciences is seeking two postdoctoral researchers to lead studies that tie cell-specific genome data to expressed functions (genome to phenome) such that rates of environmental processes can be coupled to specific microbial lineages. This work integrates cutting-edge approaches in field studies of marine and continental microbiomes, laboratory experimentation and bioinformatics. The primary focus of position #1, co-advised by Drs. Stepanauskas and Poulton, will be on the studies of marine bacterioplankton and the integration of flow cytometry and genomics of individual cells. The primary focus of position #2, co-advised by Drs. Orcutt and Emerson, will be on studies of the deep biosphere and the calibration of single cell activity and physiology measurements using laboratory cultures. Both hired scientists will be engaged in a collaborative, multi-institutional project that also includes the University of New Hampshire and the Desert Research Institute. The postdoctoral scientists at Bigelow Laboratory have access to an active professional training program and possibilities for undergraduate student mentoring and teaching. Laboratory’s state-of-the-art oceanfront campus in scenic Midcoast Maine offers excellent opportunities for outdoor activities, including hiking, canoeing, sailing, and skiing.

Candidates must have a PhD degree in a relevant field and prior experience in environmental microbiology and genomics. Excellent written and verbal communication skills and ability to work harmoniously in a collaborative research team are crucial.

Research will be conducted primarily at the Bigelow Laboratory for Ocean Sciences in East Boothbay, Maine. Opportunities for fieldwork may be available but are not required. The positions are offered for a period of three years. The positions have an expected start date of January 1, 2019, but this may be negotiated. Salary will be commensurate with prior experience.

Please submit a CV and a cover letter that contains a statement of research interests and contact information for three references by November 1, 2018.


For position #1 (marine bacterioplankton and the integration of flow cytometry and genomics of individual cells), please use this link to apply.

For position #2 (deep biosphere and the calibration of single cell activity and physiology measurements using laboratory cultures), please use this link to apply.​​​​​​


Review of applications will begin immediately until the position is filled. Questions about these positions can be referred to jobs@bigelow.org .

Pfizer - Postdoctoral Fellow, Inflammation and Immunology - Cambridge, MA

The microbiome has emerged as a key contributor to autoimmune and inflammatory disorders, including the pathogenesis of Inflammatory Bowel Diseases (IBD). The Epithelial Biology and Systems Immunology Groups within Pfizer’s Inflammation and Immunology Research Unit are actively examining host-microbiome interactions in IBD. Pfizer is seeking a highly motivated, talented, and creative postdoctoral candidate with a strong background in microbiology, molecular biology, microbial immunology or a related field, and familiarity with bioinformatic and/or statistical methods to investigate the role of host-microbiome interactions in health and disease in preclinical IBD models. The candidate will be responsible for running in vivo studies to examine how perturbations to the microbiome and host immune system affect disease outcomes, and use novel computational approaches to analyze and integrate multi-type omics datasets.

 

ROLE RESPONSIBILITIES

  • Collaborate closely with experimental and computational scientists to explore fundamental research questions with an emphasis on novel discoveries that will result in high impact publications.
  • Participate in design of targeted in vivo interventions to address key questions about the role of the microbiome in treatment efficacy and disease outcomes in preclinical IBD models.
  • Study the host and microbiome dynamics by applying discovery-based computational approaches to multi-type omics data.
  • Develop and utilize cell-based systems to functionally validate in vivo observations.
  • Organize, interpret, and analyze data, and identify areas where key knowledge is lacking.
  • Effectively communicate data and results at internal and external meetings/conferences.

 

BASIC QUALIFICATIONS

  • Recent Ph.D. in biology, microbiology, molecular biology, cell biology, or a related field.
  • Experience running in vivo disease models, including harvesting, processing, and analyzing tissue.
  • Experience with bacterial and mammalian cell/tissue culture and related techniques, including ELISA, qPCR, western blot, and/or fluorescence microscopy.
  • Excellent communication and organizational skills, and willingness to learn new skills.
  • Demonstrated research productivity by first-author publications in peer-reviewed journals.

University of Georgia - Assistant or Associate Professor in Marine Microbiome

Assistant or Associate Professor: Joint appointment in the
Institute of Bioinformatics and the Department of Marine Sciences

 

UGA is seeking to recruit a computational and experimental marine microbiome researcher to complement
research strengths at UGA in bioinformatics and marine sciences. We aim to hire an individual with a
strong record of innovation and ability to develop and apply new computational tools (simulations, flux
analyses, data integration and visualization, among others) and microbial ecology approaches to marine
microbiome research. Possible areas of research include ocean productivity, global carbon and nutrient
cycling, diseases of aquatic organisms, or intersections with public health.


The successful candidate will be appointed at the rank of Assistant or Associate Professor depending on
credentials and accomplishments. This is an interdisciplinary position, with the appointment being split
between the Department of Marine Sciences and the Institute of Bioinformatics. The position includes a
competitive salary, sufficient laboratory space for computational and experimental research, and a
generous start-up package.


Applicants must hold a PhD or equivalent degree in a computational, marine or biological science area
and have at least 1 year of postdoctoral training as well as a record that provides evidence of scholarship,
synergistic activities, and the potential to obtain extramural funding. To be considered for the Associate
Professor level, applicants must show evidence of the ability to attract sufficient extramural funding to
support a sustainable research program and provide convincing evidence of an emerging national
reputation in their field. Teaching responsibilities will be in undergraduate and graduate programs and
include both bioinformatics and marine science microbiome components.

Applicants should submit a cover letter, contact information for three references, curriculum vitae,
research statement (no more than 3 pages), and teaching philosophy at
the link below. Review of applications will begin on November 13 and
continue until the position is filled. Selected applicants will be required to submit a background
investigation demonstrating eligibility for employment with the University of Georgia. This position is
available August 2019. Contact the search committee chair Dr. Mary Ann Moran (mmoran@uga.edu)
with questions.

 

Vanderbilt University - Tenure Track Faculty Position

The Vanderbilt University Department of Biological Sciences and the Vanderbilt Institute for Infection, Immunology and Inflammation invite applications for a tenure-track, faculty position in microbiology, including microbial ecology and the microbiome, at the Assistant Professor rank. The candidate will be expected to develop an independent laboratory research program using experimental and/or computational approaches complementing current departmental strengths in cell and molecular biology, chemical biology, evolution, genomics, host-microbe interactions, and neurobiology (https://as.vanderbilt.edu/biosci/). As a new faculty member, the candidate will play an integral role within the trans-institutional Vanderbilt Microbiome Initiative (https://my.vanderbilt.edu/microbiome/) and will benefit from collaborations with internationally recognized programs including the Vanderbilt Genetics Institute, the Vanderbilt Institute of Chemical Biology, or the Vanderbilt Institute for Global Health.

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