Bioinformatics

The Center for Biomedical Informatics, directed by Dr. Qunfeng Dong, actively collaborates with biomedical researchers to develop computational solutions for their projects. Besides providing technical support, the highly experienced center staff often becomes an integral part of the collaborative projects, actively involved in experimental designs, data analysis, publications, and grant writing. Enabled by in-house high performance computing infrastructure, the center is capable of performing a wide range of bioinformatics and statistical data analysis, e.g., in the areas of genomics, metagenomics, transcriptomics, proteomics, and electronic health record data mining.  Besides data analysis, the center is also specialized in developing web-based databases to help researchers with data management.  Currently, the Center is engaging in the following projects that are funded by NIH, NSF, and American Diabetes Association:

  1. The female urinary microbiome and urinary incontinence (NIH R01 pending, 2015-2020). PI: Drs. Linda Brubaker and Alan Wolfe, Loyola University Chicago Stritch School of Medicine. Co-Investigators Drs. Qunfeng Dong, Colleen Fitzgerald, Stephanie Kliethermes, Elizabeth Mueller, Paul Schreckenberger, Michael Zilliox, Bradford Gibson).
  2. The role of urethral microbiome in idiopathic urethritis in men (NIH R01 pending, 2015-2020). PI: Drs. David Nelson and Byron Batteiger, Indiana University School of Medicine. Co-Investigators: Drs. Janet Arno (Indiana Univ.), Barry Katz (Indiana Univ.), Qunfeng Dong (Loyola)
  3. Genomic Prediction of Chronic Pulmonary Inflammation in HIV Infection (NIH U01, 2013-2018) PI Dr. Homer Twigg III (Indiana University School of Medicine) and Dr. George Weinstock (The Jackson Laboratory). Co-Investigators: Drs. Kenneth Knox (University of Arizona), David Nelson (Indiana Univ.), Barry Katz (Indiana Univ.), Qunfeng Dong (Loyola)
  4. Natural variation and drought responses in developing maize inflorescences (NSF 2013-2018) PI: Dr. Erik Vollbrecht, Iowa State University. Co-PI: Drs. Sarah Hake (UC Berkeley, USDA), Dave Jackson (Cold Spring Harbor Laboratory), José R. Dinneny (Carnegie Institution for Science, Stanford University), Torbert Rocheford (Purdue University), Andrea Eveland (Donald Danforth Plant Science Center), Qunfeng Dong (Loyola)
  5. Mechanism of microbiome-induced insulin resistance in humans (American Diabetes Association, 2013-2016). PI: Dr. Nicolas Musi, University of Texas Health Science Center in San Antonio. Co-Investigator, Qunfeng Dong (Loyola)
  6. Diversity and dynamic stability of the ocular surface microbiome(NIH R01 2012-2017). PI Drs. Valery Shestopalov (University of Miami School of Medicine) and Russell Van Gelder (University of Washington). Co-Investigators: Drs. David Nelson (Indiana Univ.) and Qunfeng Dong (Loyola)
  7. Lung microbiome and pulmonary inflammation/immunity in HIV infection (NIH U01, 2009-2015). PI Dr. Homer Twigg III (Indiana University School of Medicine) and Dr. George Weinstock (The Jackson Laboratory). Co-Investigators: Drs. Kristina Crothers (Yale University), Kenneth Knox (University of Arizona), Richard Gregory (Indiana Univ.), David Nelson (Indiana Univ.), Barry Katz (Indiana Univ.), Yuzhen Ye (Indiana Univ.), and Qunfeng Dong (Loyola)