PUBH 6860: Principles of Bioinformatics

Instructor: Keith Crandall, PhD
Director, Computational Biology Institute
📧 kcrandall@gwu.edu | 📍 SEH 7670 | Office Hours: TBD

Teaching Assistant: Xinyang Zhang
📧 xinyangz@gwu.edu | 📍 SEH 7000 Foyer/Fish Bowl | Office Hours: TBD

Course Time: Tuesdays 10:10 am – 12:00 pm Credits: 3

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📘 Course Description

This course introduces the principles of bioinformatics, blending biological, computational, and programming concepts. Students will learn:

• Molecular biology, genome organization, and evolution
• Sequence alignment, database searching, phylogenetics, and structural bioinformatics
• Unix environment, shell scripting, Python basics, and database concepts

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🎯 Learning Outcomes

By the end of this course, students will be able to:

• Apply knowledge of and skills in the Unix environment
• Access and analyze genomic data from diverse sources
• Apply pairwise and multiple sequence alignment
• Synthesize bioinformatics concepts across alignment, evolution, and phylogenetics
• Evaluate genetic/genomic analysis software
• Create novel analyses and insights through programming:contentReference

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📚 Textbook

• Concepts in Bioinformatics and Genomics (1st Edition), Jamil Momand & Alison McCurdy:contentReference

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💻 Technology Requirements

• Laptop with video/audio
• Blackboard + Zoom/WebEx access
• R and Python (installed locally)
• Familiarity with uploading assignments and joining online meetings

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📝 Grading

• Problem Sets: 30%
• Labs: 40%
• Participation: 5%
• Individual Research Project: 25%:contentReference[oaicite:2]{index=2}

Graduate Grading Scale

Grade	Percentage	Grade	Percentage
A	94–100	C	73–76
A-	90–93	C-	70–72
B+	87–89	F	<70
B	84–86
B-	80–83
C+	77–79

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📂 Assignments

• Problem Sets: Weekly, practice applying lecture and textbook concepts
• Labs: Written as short scientific reports (Bioinformatics journal style)
• Research Project: Final third of semester; group work encouraged; final paper due in Finals Week:contentReference[oaicite:3]{index=3}

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Weekly Schedule (Highlights)

Week	Date	Topic	Notes
1	Aug 26	Introduction; Molecular Biology 101
2	Sep 02	Programming Basics I (R/Unix)
3	Sep 09	Sequence Databases (GenBank)
4	Sep 16	Scientific Literature & GitHub Intro
5	Sep 23	Molecular Evolution	Lab 1 assigned
7	Oct 07	Pairwise Sequence Alignment
9	Oct 21	Protein Structure Prediction
10	Oct 28	Phylogenetics	Lab 2 assigned
11	Nov 04	Research Project Exploration
14	Dec 02	Transcript & Protein Expression Analysis
15	Finals	Research Project Paper Due	Final Submission

See full syllabus (PDF in repo) for complete week-by-week details.

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📑 Course Policies

• Participation: Come prepared; contribute to discussions.
• Late Work: Accepted with 1% penalty per hour (first 5h) up to 5% per day. All assignments due by 11:59 pm unless otherwise noted:contentReference[oaicite:5]{index=5}.
• Collaboration: Teamwork encouraged; final submissions must be individual unless otherwise specified.

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🔗 Useful Links

• Course Website (GitHub Pages) ← update with your repo name
• Assignments
• Labs
• Lectures
• Blackboard Login

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🧑‍🎓 Workload

• 5–7 hrs/week: reading, assignments, project work
• 2.5 hrs/week: synchronous instruction and labs:contentReference[oaicite:6]{index=6}

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📬 Contact

• Instructor: Keith Crandall — kcrandall@gwu.edu
• TA: Xinyang Zhang — xinyangz@gwmail.gwu.edu

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