PennCHOP Microbiome 2017 Pilot & Feasibility Projects
We would like to congratulate those selected for 2017 Pilot & Feasibility Project funding, and thank all those who applied.
Please click here to see a full project listing.

Video from the Third Annual Microbome Symposium (2016) 
Please click here to see a video index as well as short speaker biographies. 

PennCHOP Microbiome 2016 Pilot & Feasibility Projects
We would like to congratulate those selected for 2016 Pilot & Feasibility Project funding, and thank all those who applied.
Please click here to see a partial project listing.

Video from the Second Annual Microbiome Symposium (2015)
We are grateful to the speakers who participated in our Second Annual Microbiome Symposium, and happy to offer you the opportunity to view several of their recorded talks. Click here for the video index

Using shotgun metagenomics to study the human microbiome
August 15, 11AM
Colket Translational Research Building, Room 4040 
No registration required.  Event is open to all members of the Penn & CHOP communities

Our bodies are host to a wide range of microorganisms that play a role in health and disease.  Shotgun metagenomic DNA sequencing is an adventurous and rewarding approach to studying these organisms.  The method is used to sequence the full genomes of all organisms present in a sample, but in short pieces.  In this lecture, we'll discuss how shotgun data can be used to learn about microbial communities.  Modern bioinformatics and analytical techniques will be covered in detail.  We'll also explore the frontiers of research, where we are combining DNA sequence information with results from metabolomics and proteomics platforms.  This lecture will be led by Kyle Bittinger, PhD.

Approaches to Taxonomy in the Microbiome 
April 13th, 2017

This introductory lecture, led by Kyle Bittinger PhD, covered the process of turning DNA sequence data into information about bacterial communities.  Some approaches are purely numerical, while others involve associating the sequences with genus or family names.  Methods of creating “operational taxonomic units” and the dangers of making taxonomic assignments were also be discussed.  

Click here for video of the talk
Click here for the talk slides 

Ecological Diversity in the Microbiome
April 27th, 2017

In the second lecture of our spring series, Kyle Bittinger PhD discussed the diversity of bacterial communities.  Diversity can mean the number of species observed in each sample (alpha diversity) or the number of species shared between samples (beta diversity).  The way diversity is used to analyze bacterial communities was discussed, as well as special topics such as UniFrac distance and principal coordinates analysis. 

Click here for video of the talk
Click here for the talk slides 

Weekly ‘Code Review’
9:00 AM  EST
Every Wednesday
207 Johnson Pavilion

Kyle Bittinger, a Computational Biologist from Dr. Rick Bushman’s lab, leads this weekly session.  Each week one person presents programming code related to their research.  Attendees get a chance to hear how code was assembled to achieve a goal, while the presenter gets feedback, collective troubleshooting, etc. Less experienced programmers will have a chance to learn about design options when programming.

Contact Info: Contact Kyle at to be added to the mailing list.

R Learning Group
1:00 PM EST
very Wednesday
WIC Seminar Room, Van Pelt Library

R is an open-source coding language used by a wide range of disciplines for data management, statistical analyses, and data visualization. Beginning January 4, 2017, an informal R learning group for members of the Penn community meets on Wednesdays from 1pm until 2pm starting in the WIC Seminar Room (Van Pelt 124.)  So far, we’ve been working with swirl, a software package designed for learning R commands and introductory data science. No experience is required. This is self-paced learning, so feel free to come every week or drop in as you are able.  Please click here for more information.

Contact: Deborah Bishov (

Prokaryotic Seminar
12:00-1:00PM EST
Every Friday
209 Johnson Pavilion

Features trainees in Microbiology and occasional local outside speakers.  Please click here for more information.Contact Info:

Microbiology Seminar Series
12:00-1:00 PM EST
Every Friday
Auditorium, Clinical Research Building

Features Microbiology related speakers from around the country and around the world.  Click here for more details.



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