Positions

POST-DOCS

Microbiome Post-docs for Celiac Disease Study at Caltech

We are seeking two talented, motivated individuals to join a collaborative project looking at the role of the microbiome in celiac disease. The multi-institute project aims to test the hypothesis that celiac disease is a heterogeneous disorder, while attempting to define interactions between intestinal epithelial cells, the gut microbiota, immune system, and genetics that underlie differences in clinical presentation, severity of tissue destruction, and the ability to heal. The integration of different layers of molecular (scRNA-seq, genomic), immunological, metabolomics and microbiome data (where host transcriptional and microbial signatures are obtained on the same intestinal biopsy) from clinically well-characterized patients will provide us the unique opportunity to address questions that would not be possible otherwise.

Please see the NIH RePORTER listing for details. The successful post-doc candidates will work in the Ismagilov Lab at the California Institute of Technology to improve understanding of how the mucosal microbiota of the small intestine may drive variation in the clinical phenotype of celiac disease in humans, notably disease severity and healing.

Skills required: Strong microbiology and bioinformatics training; creativity; rigorous scientific training in design and interpretation of research; experience performing amplicon and metagenomic shotgun sequencing and analysis; strong record of prior research accomplishments. Candidates eligible for independent postdoctoral fellowships are encouraged to apply.

Hiring Range: $70,264 per year. The salary of the finalist(s) selected for this role will be set based on a variety of factors, including but not limited to, experience, qualifications, skills, education, specialty, training, and internal equity. As one of the largest employers in Pasadena, CA, Caltech is committed to providing comprehensive benefits to eligible employees and their eligible dependents. Our benefits package includes competitive compensation, health, dental, and vision insurance, retirement savings plans, generous paid time off, parental leave, tuition reimbursement, and more.

Candidates should send their CV and a brief statement of their qualifications and research aspirations to rustem.admin@caltech.edu.

Postdoctoral researcher to work on Human Virome Project

We are seeking a postdoctoral researcher to work on our NIH-funded Human Virome Project (see project description at https://reporter.nih.gov/search/3nsnt--idkOZINUeCRpyQA/project-details/10986859). The NIH Human Virome Program (HVP) is a groundbreaking initiative aimed at advancing our understanding of the human virome—the diverse array of viruses that inhabit the human body—and their interactions with hosts, other microbes, and the immune system (see NIH program at https://commonfund.nih.gov/humanvirome). The program focuses on overcoming technological challenges such as detecting viruses in low-biomass samples, reducing host nucleic acid contamination, and developing scalable methods for virome quantification and annotation. Through innovative tools and interdisciplinary collaborations, the HVP seeks to elucidate the role of the virome in human health and disease.

This postdoctoral position offers a unique opportunity to contribute to the development, validation, and deployment of cutting-edge experimental methods for virome enrichment, detection, identification, and quantification from complex biological samples. The project will target both prokaryotic and eukaryotic viruses and will leverage lab's additional expertise in low-biomass sequencing and computational analysis. The successful candidate will play a pivotal role in this effort and will be responsible for: 1) developing technologies for enrichment and sequencing of viral and bacterial targets; 2) deploying these technologies in collaborations with computational and clinical team members to make discoveries and to test scientific hypotheses.

Key Responsibilities

Develop and validate novel viral enrichment protocols exceeding to current standards (ultra-centrifugation, filtration, etc.).
Quantify viral and bacterial components in enriched fractions and establish limits of detection (LoD) and lower limits of quantification (LLoQ). Prepare DNA and RNA libraries for short-read (Illumina NovaSeq6000) and long-read (Nanopore MinION) sequencing.
Investigate diverse human clinical specimens (e.g., saliva, vaginal swabs, intestinal biopsies).
Validate discovered host-virus interactions and study viral dynamics using experimental and computational approaches.
Collaborate with computational and clinical researchers to make discoveries and to test scientific hypotheses.

Key Qualifications

A Ph.D. in molecular biology, microbiology, virology, biochemistry, or a related field.
Extensive experience with wet-lab techniques, including nucleic acid extraction, PCR/qPCR/dPCR, library preparation for sequencing, viral propagation
Strong problem-solving skills; strong ability to quantitatively design and interpret experiments; strong drive to develop methods of quality suitable for use by the entire Virome community.
Expertise in virology. Knowledge of phage biology, microbial ecology, or viral-host dynamics.
Strong interest in method development and understanding the role of viruses in human health and disease.

Preferred Skills

Experience with metagenomic sequencing for viral studies (identification, host-association, life stage, etc.) Knowledge of experimental approaches for quantifying viral dynamics in longitudinal studies.
Experience with complex sample types, such as human tissue or low-biomass samples.
Experience with viral enrichment strategies.
Familiarity with microbial analysis using standard bioinformatics pipelines.

Candidates should send their CV and a cover letter detailing research experience and interest in this role to rustem.admin@caltech.edu

GRADUATE APPLICANTS

Prospective graduate students who are interested in joining the lab need to apply for one of the degree options described on the Caltech Graduate Studies Office website. Applicants can find more information on degree options, including Chemical & Chemical Engineering, Bioengineering, Biophysics, Biology & Microbiology, Materials Science, and Applied Physics, here.

CALTECH GRAD-STUDENT ROTATIONS

We welcome inquiries from incoming Caltech graduate students interested in joining or doing rotations in the lab. Please see our Positions page for details of current projects and then contact rustem.admin@caltech.edu.

CALTECH UNDERGRADUATE RESEARCH STUDENTS

Project: Whole genome sequencing of mucosal microbiomes to explore connections with human health and disease

Background: The Ismagilov lab has recently developed many novel methodologies enabling new investigations into how the mucosal microbiome impacts human health and disease. We will be applying these methods to contexts such as microbial biogeography, Celiac Disease, IBD, IBS, and Parkinson's Disease. We also are part of the NIH Human Virome Program and working to define the healthy human virome.

Description: Generation and/or analysis of whole genome sequencing datasets. Suggested Background: Some familiarity with EITHER molecular biology wet lab techniques (pipetting, PCR, etc.) OR coding (python or bash preferred). Interest in human health.

Please email rustem.admin@caltech.edu with your CV and a statement of interests to apply for this position.

GENERAL INQUIRIES

We also welcome general inquiries from current Caltech freshman, sophomore, and junior students who are interested in the work being done in our lab. Students should have the desire and ability to make a substantial time commitment to a project. Please send your CV and a detailed statement of research interests to rustem.admin@caltech.edu.

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