BIFX 504: Advanced Molecular Biology for Bioinformatics

Fall 2025

Author
Affiliation

Dr Randy Johnson

Hood College

Published

September 25, 2025

BIFX 504: Molecular Biology for Bioinformatics

Faculty Contact Information

Course Description

Prerequisite: BIFX 501 or waiver of BIFX 501 or permission of instructor. The accelerated use of next generation sequencing means that the analysis of sequencing data is one of primary job duties of most bioinformaticians. The DNA/RNA sequencing boom is now being followed by a renewed focus on metagenomics as well as high-throughput protein sequencing as analytical techniques. In this course, students will gain detailed knowledge of the biology that underlies these and other techniques. By understanding the full range of transcripts made by cells, the mechanisms that regulate transcription, and the details of RNA transcript processing and translation, students will learn how the underlying biology affects the sensitivity and correct interpretation of key types of bioinformatics assays, including microarrays, genome-wide association studies, and sequencing of DNA, RNA, proteins, and the microbiome. The fundamentals of good experimental design will be emphasized throughout the course.

Class Meeting Time:

Wednesdays at 5:30 - 8:15 PM

Location:

Hodson Technology, Rm 237

Course Outline

This tentative outline of course topics and assignments may be modified at the discretion of faculty at any point during the semester AND it is the student’s responsibility to remain abreast of updates. The syllabus on Blackboard and the course website will be updated in the event of changes to this schedule.

Schedule: Due dates for homework will be posted on Blackboard. Readings should be completed BEFORE class on the week it will be discussed.
Date Class Exercises Reading
20-Aug Intro to Bioinformatics
27-Aug Sequence Alignment & Databases
3-Sep Next-Gen Sequencing
10-Sep Genome Assembly and Annotation
17-Sep Bulk RNA-seq
24-Sep Differential Expression Analysis
1-Oct Midterm
8-Oct Single Cell RNA-seq
15-Oct Proteomics & Mass Spectrometry
22-Oct Structural Bioinformatics & Protein Modeling
29-Oct Metabolomics & Pathway Analysis
5-Nov Metagenomics
12-Nov Functional Genomics & Gene Ontology
19-Nov Biological Networks and Systems Biology
26-Nov Thanksgiving Recess
3-Dec Clinical Bioinformatics & Personalized Medicine, Final

Modality

Bimodal: This course will be held simultaneously on-campus in the assigned room and virtually as indicated on Blackboard. Both in-person and virtual participants will be expected to participate in class discussions and activities.

Course Materials, Required Textbooks, Technology

You will need regular and dependable access to a computer and the internet. All registered students may use the on-campus computers and printers for this course if necessary. We will use Blackboard for activities, announcements, email, and assignments.

Course Grading Componens

Grade Breakdown
Assignment Grade
Class participation 30%
Homework 30%
Midterm Exam 20%
Final Exam 20%

Late Policy

THERE IS NO EXCUSE FOR LATE ASSIGNMENTS. You will have ONE week to work on all the assignments for that week. All assignments are due at the beginning of class on the date listed in Blackboard. Late assignments are generally not accepted, but if you have a special circumstance and will not be able to meet the deadline, let me know before the assignment is due. Only medical excuses, recognized religious holidays, Hood College approved activities, or written work obligations will make a student eligible to hand in an assignment late without penalty.

  • Assignments that are turned in after the scheduled due date but before one week past this date will have their assignment grade reduced by one letter grade.
  • Homework assignments received more than one week late will be reduced by 50% (i.e. will start with a grade of “F”) prior to being graded. Assignments that are more than two weeks late will not be accepted.
Hood College Approved Grading Scale
Grade Weighted %
A [100-93]
A- (93-90]
B+ (89-88]
B (87-83]
B- (82-80]
C+ (79-78]
C (77-73]
C- (72-70]
F (69-0]

Course Objectives

  1. Establish a foundational understanding by researching the core principles of molecular biology essential for bioinformaticians, including the central dogma, gene structure, and regulation.
  2. Investigate the evolution and current landscape of DNA sequencing technologies, focusing on the principles behind Next-Generation Sequencing (NGS) platforms and their applications in genomics.
  3. Explore the primary bioinformatics workflows for processing genomic data, such as genome assembly, annotation of genes and regulatory elements, and the identification of genetic variants.
  4. Research the field of transcriptomics to understand how gene expression is quantified and analyzed.
    • Examine bulk RNA-sequencing for studying gene expression across a population of cells.
    • Investigate single-cell RNA-sequencing to analyze cellular heterogeneity and define cell types.
  5. Survey the field of epigenomics by finding information on methods like ChIP-seq and ATAC-seq, which are used to study DNA modifications and chromatin structure.
  6. Examine the principles and technologies behind proteomics and metabolomics.
    • Research the use of mass spectrometry for large-scale protein identification and quantification.
    • Find information on techniques for profiling small molecule metabolites to understand cellular metabolic states.
  7. Analyze the methods and applications of metagenomics for studying the genetic material recovered directly from microbial communities in environmental samples.
  8. Synthesize the information by researching integrative and applied bioinformatics topics, including systems biology for modeling biological networks and the role of bioinformatics in clinical diagnostics and personalized medicine.

Attendance Policy

Students are required to attend every session and are expected to log on frequently to Blackboard and review the week’s course material. Attendance will be taken based on your participation in the class. Make up work may be assigned for excused absences.

In the event of severe weather resulting in the closure of Hood College and the cancellation of an in-person meeting, the class will be held virtually.

Professionalism

Professionalism is expected and required in all graduate courses; it is also one of the six core outcomes for all graduate degrees at Hood College. All students are expected to be prepared for class and to participate in activities or discussions in accordance with the course code of conduct.

In accordance with the College Catalog, the College generally permits the use of generative artificial intelligence (AI) tools for uses outlined in assignment descriptions for this course. See the course code of conduct for more information.

Accessibility Services and Wellness

This course is intended to be accessible for all students, including those with mental, physical, or cognitive disabilities, illnesses, injuries, impairments, or any other condition that tends to negatively affect one’s equal access to education. If at any point in the term, you find yourself not able to fully access the space, content, and experience of this course, you are welcome (and not required) to contact me by email, phone, or during office hours to discuss your specific needs. I also encourage you to contact the Office of Accessibility Services (301-696-3569 or accessibilityservices@hood.edu. If you have a diagnosis or history of accommodations at a previous postsecondary institution, Accessibility Services can help you document your needs and create an accommodation plan. By partnering with Accessibility Services, you can ensure appropriate accommodations without disclosing your condition or diagnosis to course instructors.

Academic Success Services

Your success in my class is a priority. For this reason, I will be using the Beacon alert system as an early identification and intervention tool. If I notice you are struggling with issues such as attendance, class participation, or assignment/test performance, I may choose to send an Academic Alert through Beacon to connect you with appropriate campus resources. These referrals are designed to maximize your chances for success at Hood College, not as a reprimand or punishment. Please respond to any communications you may receive from me, your academic advisor, the graduate school or other campus offices regarding your academic progress in this course.

Holistic Wellness

Your holistic wellness is important to me. Consult College supports curated for you around the Eight Dimensions of Wellness at www.hood.edu/GradCare. If you are feeling anxious, stressed, worried or down during the semester or if you notice signs of emotional distress in someone else, please lean on support services freely available to all Hood students. Many campus resources are available including:

  • Hood Counseling Services – open M-F, 8:30AM-5:00PM, Apple Resource building, 1st floor, Room A. Make your appointment online at hood.edu/counseling, or drop in for a walk-in session on Mondays, Wednesdays, and Fridays between the hours of 11:00AM – 12:00PM. If you have questions about Counseling Services, email counselingservices@hood.edu.
  • Hood also has several connections to other mental health resources including the NeighborHood Counseling Training Center and Thriving Campus.
    If you or someone you know needs to talk to someone right now, text or call 9-8-8 for a free, confidential conversation with a trained counselor 24/7.

Important Contacts