A Modular Metagenomics Analysis Pipeline and Microbiome-in-a-Bottle
Weekly Wednesday Wartik Genomics Lecture Series

Abstract of the talk:
The rapid expansion of next-generation sequencing has revolutionized microbiome research, yet analyzing complex metagenomic datasets remains a significant computational bottleneck. Researchers require robust, reproducible, and flexible frameworks to extract biologically meaningful insights from massive multi-omics data. To address this challenge, we developed CAMP (Core Analysis Modular Pipeline), a comprehensive metagenomics analysis system designed for integrated, multi-step data exploration. CAMP provides a standardized yet highly adaptable architecture that facilitates seamless workflow execution—from raw read processing and quality control to sophisticated taxonomic profiling and functional annotation.
While advanced computational methods like CAMP offer powerful analytical capabilities, their rigorous validation and ongoing refinement depend heavily on high-quality, controlled experimental data. To bridge the gap between computational method development and empirical validation, we introduced the "Microbiome-in-a-Bottle" (MIAB) project. Through targeted collaborative wet-lab efforts, the MIAB project focuses on generating novel, highly characterized sequencing benchmark datasets derived from controlled microbial communities.
In this talk, I will outline the computational architecture and method development behind CAMP, highlighting its utility in streamlining complex metagenomic analyses and fostering reproducibility. Furthermore, I will discuss the foundational work of the MIAB project in producing high-fidelity sequencing datasets.

Bio:
Dr. Iman Hajirasouliha is an Associate Professor of Systems and Computational Genomics at Weill Cornell Medicine of Cornell University and a member of the Englander Institute for Precision Medicine and the Meyer Cancer Center in New York. He is also the Co-Director of the Tri-I Computational Biology and Medicine Ph.D. program. He completed a Postdoctoral Scholarship at Stanford University's Computer Science Department and a Simons Research Fellowship at the University of California, Berkeley. He earned his B.Sc. in Computer Engineering from Sharif University, an M.Sc. in Computing Science from Simon Fraser University (SFU), and a Ph.D. with Exceptional Recognition from SFU, followed by a postdoctoral appointment at Brown University. Dr. Hajirasouliha has received several prestigious awards, including the Simons-Berkeley Research Fellowship, an NIGMS Maximizing Investigators' Research Award, and an Irma T. Hirschl Career Scientist Award. Website: www.imanh.org.

Contact

  Donna McMinn
  dlp18@psu.edu
  +1 814-935-3444