Res Post Doc Fellow - microbiology and inflammatory bowel disease:

Philadelphia Pennsylvania

Req ID: 16182

Shift: Days

Employment Status: AF - Active - Regular - Full Time 

Job Summary

The Center for Pediatric Inflammatory Bowel Disease at The Children’s Hospital of Philadelphia (CHOP), along with The Center for Host-Microbial Interactions (CHMI) at The University of Pennsylvania’s School of Veterinary Medicine (PennVet), is looking for a highly-motivated researcher to fill a postdoctoral position in interdisciplinary IBD research.  The position will be based in the laboratory of Dr. Daniel Beiting (Assistant Professor of Pathobiology at PennVet, Technical Director of CHMI), but will be jointly mentored by Dr. Robert Baldassano (Professor of Gastroenterology, Director of CHOP’s Center for Pediatric IBD).  This position comes with several significant career development opportunities, including the ability to draw on both human and veterinary perspectives and clinical cases; access to cutting-edge sequencing and bioinformatics expertise in the PennCHOP Microbiome Program ( as well as at CHMI (; and access to state-of-the-art devices for real-time diagnostics, such as the Biomeme Two3, and Oxford Nanopore’s MinION sequencer.

The goal of this hire is to build on an existing partnership between the PennVet and CHOP, in order to advance our understanding of the causes of, and potential new treatments for, Inflammatory Bowel Disease (IBD).  The individual will take a leading role in a project to identify pathogens, ‘pathobionts’ and inflammatory pathways that trigger or potentiate IBD in humans and animals.  The candidate will need to process samples from both humans and animals, carry out 16S microbiome and/or metagenomic or metatranscriptomic profiling, and tailor data analysis pipelines to address specific biological questions.  In addition, the candidate will need to employ targeted assays for detection of organisms of interest, including QPCR and novel approaches, such as selective whole-genome amplification (SWGA), for detection of low-abundance organisms. Finally, the individual will be expected to attend relevant meetings at CHOP and PennVet, and to present data and discuss data analysis strategies in small group settings. 

Competitive applicants should have a Ph.D in microbiology, immunology or a related discipline. Proficiency in command-line tools for bioinformatics (Perl, Ruby, Python, or R/Bioconductor), and experience applying these tools in the analysis of microbial genomic datasets, particularly those generated by microbiome 16S rRNA gene sequencing and shotgun bacterial metagenomics, is preferred. The position will entail significant one-on-one interactions with other with human and veterinary clinicians and researchers, therefore strong communication and interpersonal skills are required. 


Job Responsibilities

  1. Conduct independent scholarly research and develop new methods and protocols
  2. Participate in project planning, recording and evaluation of data
  3. Acquire technical, lab management and grant writing skills
  4. Participate in seminars, lectures, poster sessions and presentation at national meetings
  5. Supervise junior lab members
  6. Assist with other research projects

Required Education and Experience

  • A terminal degree PhD, MD, DVM, etc.
  • According to the CMS (Centers for Medicaid and Medicare Services) a copy of diploma or transcript is required as proof of academic achievement for all non-laboratory personnel performing non-waived POC testing

All CHOP employees who work in a patient building or who provide patient care are required to receive an annual influenza vaccine unless they are granted a medical or religious exemption.

Children's Hospital of Philadelphia is committed to providing a safe and healthy environment for its patients, family members, visitors and employees. In an effort to achieve this goal, employment at Children's Hospital of Philadelphia, other than for positions with regularly scheduled hours in New Jersey, is contingent upon an attestation that the job applicant does not use tobacco products or nicotine in any form and a negative nicotine screen (the latter occurs after a job offer).

Children's Hospital of Philadelphia is an equal opportunity employer. We do not discriminate on the basis of race, color, gender, gender identity, sexual orientation, age, religion, national or ethnic origin, disability or protected veteran status.

VEVRAA Federal Contractor/Seeking priority referrals for protected veterans.  Please contact our hiring official with any referrals or questions.

CHOP Careers Contact 

Talent Acquisition

2716 South Street, 6th Floor

Philadelphia, PA 19146 

Phone: 866-820-9288



Basic Qualifications