University Honors College - The Honorable mention

BCH 502: Genome Annotation and Analysis Open to Honors Scholars

Posted by Tim on December 17, 2012 in Academics, Graduate School Programs, Honors Experiences, Honors Seminars

BCH 502: Genome Annotation and Analysis

Instructor: Marc Halfon

  • Lecture: Wednesdays, 2:30 – 4:30 p.m.
  • Location: Center of Excellence: B1-153
  • Credit Hours: 3
  • General Education Requirement: Elective
  • Please email Tim Matthews if you would like to enroll in this class: or 716-645-3020


One of the most exciting scientific developments of the past decade has been the complete sequencing of the genomes of many organisms, including humans. However, having a genome sequence alone is like having the full text of a book, but without sentence breaks, word breaks, punctuation, etc.—the information is there, but we cannot easily make sense of it. The task of the genome annotator is to provide this punctuation, i.e., to describe the positions of genes, regulatory elements, and other sequence features. This seminar will focus on sequences that control gene expression in the important research organism the fruitfly, Drosophila melanogaster. We will discuss how genes are regulated and how researchers find and test suspected regulatory sequences. Students will be introduced to the concepts and conduct of genome annotation and analysis and learn how to use powerful web-based bioinformatics tools and resources through hands-on experience in a computer lab. Several guest lectures by experts in their respective fields will address related topics such as genome sequencing, the Human Genome Project, and the use of biomedical ontologies to describe data.

Throughout the semester, students will use this knowledge to work in small groups, both within and outside of the classroom, to curate the scientific literature for purposes of annotating the fly genome with known regulatory sequences. The completed annotations will be incorporated into the REDfly database, a UB-based resource widely used by bioinformatics researchers ( Thus, students in the class will be contributing directly to genuine and important scientific research with each completed class assignment. Students will also learn how to analyze genomic data and how to integrate existing datasets with their new annotations.

This seminar is geared mainly toward upper-level students with a basic background in genetics and molecular biology from having taken classes such as any of BIO 319, BCH 404, BCH 408, or the equivalent. Freshmen and sophomores with a strong biology background may also take the course, but should anticipate needing to put in extra independent effort to learn advanced biological concepts not yet covered. Class will meet weekly, but students are also expected to spend significant time outside of class working on their annotation projects. Course grades will be based on class participation and on the completeness and quality of annotations and analyses.

At the conclusion of this course, students should be able to:

  • Describe the basic principles of eukaryotic gene regulation
  • Place into context the value and limitations of having complete genome sequences
  • Use web-based bioinformatics tools
  • Extract relevant information about gene regulatory regions from the primary scientific literature
  • Annotate gene regulatory regions with information about sequences, gene expression patterns, experimental evidence, and the like
  • Make genuine contributions to the scientific enterprise by helping to populate genome annotation databases
  • Integrate genome annotations with various genomic datasets to develop novel insights into genome organization and gene regulatory mechanisms

About the Instructor

Marc Halfon is a native of New York state. He joined the UB faculty in 2003 following a bachelor’s degree in Biochemical Sciences from Harvard, a PhD in Biology from Yale, and postdoctoral studies at Harvard Medical School. Dr. Halfon is an Associate Professor in the Biochemistry and Biology Departments and a member of the NY State Center of Excellence in Bioinformatics and Life Sciences and the Department of Molecular and Cellular Biology at Roswell Park Cancer Institute. His laboratory investigates gene regulation and intercellular signaling using the fruitfly Drosophila melanogaster as a model system and a range of genetic, molecular, and computational approaches.