Chitvan Mittal is a postdoc researcher in the Pugh Lab. Her research focuses on understanding changes in chromatin function and transcription during acute environmental stresses, such as heat shock. By combining ChIP-exo technology with detecting nascent transcripts, she aims to gain a better understanding of the eukaryotic gene regulation. Previously, as part of her PhD training, Chitvan studied in vitro systems to understand chromatin biology, in the lab of Michael Shogren-Knaak at Iowa State University.
Kyle Nilson is a postdoc in the Pugh lab, who previously studied transcription elongation control with David Price at the University of Iowa. He is currently studying the 3D organization of chromatin and transcription factors.
Jordan is a MD/PhD student at Penn State University / Penn State College of Medicine. He is focused on the optimization of ChIP-exo for mammalian cells and tissues in hopes of identifying differential transcription factor binding sites across many tissues and diseases. His work should be instrumental to the inclusion of epigenomics in the field of precision medicine and pathology.
Haining is a PhD student form Molecular Cellular and Integrative Biosciences (MCIBS) Graduate Program at Pennsylvania State University. She received her Bachelor degree in microbiology from Shandong University(Supervisor: Dr. Yulong Shen). She enrolled in Penn State University and joined in Pugh lab in 2018, and currently she is working on Optimizing ChIP-exo technology for mammalian epigenome research.
Computational Biology Ph.D Program
Olivia received her bachelor’s degree in Interdisciplinary Computational Biology from Colby College and then went on to work for The Saccharomyces Genome Database for two years before starting her PhD in Cornell’s Computational Biology program. As a member of the Pugh lab, she works on tool development for the data generated from sequencing based assays.
Our goal is to provide a high-throughput end-to-end service that maps protein-DNA interactions genome-wide, tracks metadata, and implements standard data processing and analysis pipelines with a particular focus on human tissue and cell samples and development of diagnostic assays. We intend to establish simplified methods for user-engaged custom data analysis particularly for human epigenomics.
Gretta Kellogg is the new Biotechnology Resource Center (BRC) Epigenomics Facility Director. She has years of experience working as a systems administrator for enterprise systems and then credentialed as an IT Project Manager where her experience was focused on heterogeneous deployments for massive data projects. She found her calling when she transitioned to supporting research initiatives in Higher Education. She has worked as a Program Manager for two Genomic centers at Penn State, developing IT infrastructure to leverage high-performance computing solutions, assisting with obtaining grants funding, and managing multi-million-dollar budgets for complex research initiatives. Most recently she supported faculty initiatives as a Research Computing Facilitator for the Penn State Institute of Computational and Data Sciences. She is honored to help develop a new Epigenomics facility to provide an end-to-end service that implements standard data processing and analysis pipelines
Ali Nematbakhsh is an expert in the filed of Computational Biology with extensive experience in high performance computing (HPC). He has started his journey in the field of Computational Biology in 2015 as Postdoctoral Associate at University of Notre Dame by developing a C++ GPU code to study mechanics and proliferation of epithelial cells. Currently he is developing bioinformatic tools and workflows in an open source software, Galaxy, to analyze sequenced data. He also oversees flow of data between Next Generation Sequencer, bioinformatic analysis platform, and the metadata management database.
Prashant designs and develops large scale genomic applications with integrated data visualizations that help researchers better understand gene regulation and protein interactions. He is an expert in bioinformatic tool development, software packaging (conda & pip), Galaxy Administration, CICD and all things web. He received his Master's Degree in Computer Science and a Graduate Certificate in Bioinformatics from Ohio University. Before that he graduated from JNTUH (India) with a B.Tech in Computer Science.
Collaborative Sr. Researcher
Danying holds a Ph.D. in Biophysics from the University of California, San Diego, and a B.S. in Physics from Peking University. She specializes in computational biology, data science, and web applications. She has worked on a wide range of projects, including cell signaling, cell motility, next-generation sequencing pipelines, labor management, and institutional research.
Adjunct Senior Collaborative Researcher, HPC Engineer and Architect
Chuck holds a Ph.D. in Meteorology from Penn State University. He has extensive operational scientific field experience and is the former computing director for Penn State meteorology where he architected seven HPC clusters spanning a variety of computationally intense scientific problems. His experience includes the optimization of earth system, meteorological, climate, geophysical modeling and the analysis of ground and satellite based remote sensing. He also has a wide variety of experience designing solutions for scientific workflows spanning a variety of other computationally intensive disciplines.