Postdoctoral Position Available

Project background
Each human individual is composed of roughly 10¹³ human cells, which are associated with about 10¹⁴ microbial organisms whose genetic complexity may be 100-fold greater than that of the human genome. Metagenomic approaches, broadly defined as the application of genomic technologies to an entire ecosystem or environmental sample, are critical for study of these human microbiota, as most cannot be cultured.

Knowledge gained from metagenomic studies may have direct medical applications. For instance, imbalance in the intestinal microbial ecosystems appears to have a determinative role in the onset and progression of Crohn's disease, a chronic inflammatory disease of the digestive tract affecting roughly a half-million Americans and about a million individuals worldwide. Affected individuals may suffer severe damage to their bowel and ultimately require repeated resections of intestinal tissue.

Project description
To better understand the role of microbiota on Crohn's disease, we are surveying the intestinal mucosal species using a variety of metagenomic approaches. With our clinical collaborators, Dr. Daniel Present and Dr. Maria Abreu, we are currently obtaining biopsies of colonic mucosa from carefully selected patients. We will examine progression and treatment of Crohn's disease, aiming to understand the disease etiology and directions for therapeutic development.

For this project, we will explore a variety of metagenomic approaches, ranging from microarray detection of rDNA sequences, to 16S sequencing , to full metagenomic shotgun sequencing. The postdoc will work closely with clinical and computational collaborators to manage the full lifecycle of the project, including experimental design, patient selection criteria, sample processing, and computational analysis. In addition to the overall project coordination, the postdoc may be directly responsible for the laboratory experimental work, such as DNA extraction, microarrays, and so forth.

We would like to address three major questions about the relationship between microbial community composition and Crohn's disease. First, we will examine variation in microbiota between different locations in the intestine within an individual, and determine whether such variation is related to the patchy nature of Crohn's disease lesions. Similarly, we would like to know whether recurrence of Crohn's disease after surgical removal of inflamed tissue is related to changes in the microbial community at the surgical site. Finally, we would like to explore the effect of antibiotics on the microbiota of Crohn's patients, and examine possible correlations between microbial community variation and disease relapse or remission in a clinical trial involving antibiotic treatment.

Position requirements
Candidate should have Ph.D. in computational biology or related field with a strong publication record and strong professional references. Some experience in experimental molecular biology is also desirable. As this position will involve working with both experimentalists and computational biologists, communication skills and the demonstrated ability to work independently will be weighted heavily.

The Berkeley academic environment
The Brenner lab is an interdisciplinary research group, at the University of California, Berkeley, one of the world's premiere research universities. We are associated with the Department of Plant and Microbial Biology, the Department of Bioengineering, the Department of Molecular and Cell Biology, the Biophysics Graduate Group, and Lawrence Berkeley National Lab.

Berkeley is a center for metagenomics research; groups working on metagenomics topics on campus, at LBL, and at the nearby DOE Joint Genome Institute include Andersen, Banfield, Krypides, Hugenholtz, Pachter, and Rubin.

The University of California, Berkeley is committed to diversity in its staff, faculty, and student body, and invites all qualified people to apply, including minorities and women, veterans and individuals with disabilities.

The University of California is an Equal Opportunity/Affirmative Action Employer.