A workshop brought to you by the Penn State Microbiome Center.

TOPIC: Functional basis of microb[iom]e annotation, theory to practice
INSTRUCTOR: Dr. Yana Bromberg and Dr. Chengsheng Zhu, Rutgers University
DATE:
Part 1: Seminar and a tutorial workshop: Thursday, March 5, 2020, from 9 am - 3 pm
Part 2: Bring-your-own-data workshop: Friday, March 6, 2020, from 9 am - 12 pm
LOCATION: Food Science 252 (on both days)

Lunch will be available in FDSC 252 on Thursday 5/3 at 12 pm.

Registration closes on March 2nd and is limited to the first 30 participants.

This workshop will offer explanations and hands-on training in using novel bioinformatics tools and resources for discovering the molecular functionality encoded in microbial genomes and metagenomes (with real world examples). The tools, developed in the Bromberg lab, will include methods for annotation, prediction, and analysis of molecular functionality, such as fusionDB (a database of function-based bacterial similarities),  pEffect (an SVM for recognizing bacterial effector proteins) and mi-faser (a widely-used metagenome analysis tool). Our methods have identified microbiome functional signatures of various conditions, including Crohn's disease and time spent by obese children on dietary regimens. This work was also key to best performance in the two CAMDA (Critical Assessment of Massive Data Analysis) microbiome challenges.

Dr. Yana Bromberg’s  research can be summarized in one word – function. Where does the molecular functional machinery of life come from? Why and how does it run? Is there a minimum set of the functional gears that represents a viable entity? Biological machinery is a complex system of many molecular interactions, both within and outside a single cell. The DNA blueprint of this machinery holds many of the answers to our questions. Thus, Dr. Bromberg’s goal is to understand how biological functionality is encoded in genomic data, whether by a single gene, a genome, or a metagenome.
Dr. Bromberg is an associate professor at the Department of Biochemistry and Microbiology, Rutgers University. She holds an adjunct position at the Department of Genetics at Rutgers University and is a fellow of the Institute for Advanced Study at both the Technical University of Munich, Germany and the University of Bologna, Italy. Dr. Bromberg is also the vice-president of the Board of Directors of the International Society for Computational Biology. 

Dr. Chengsheng Zhu is currently a postdoc associate in Dr. Bromberg’ lab. He has developed mi-faser and fusion, and thus is an expert in the application of both.

Attendees should bring their own computers and have R studio (https://rstudio.com/products/rstudio/download/) and WEKA (https://www.cs.waikato.ac.nz/ml/weka/) installed (although this is not mandatory). Both are free or offer free open source license versions.

Contact Jasna Kovac (jzk303 [at] psu.edu) if you have any questions.