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Computational Functional Genomics
Art: Ernst Haeckel, Haeckel Leptomedusae, 1904 · Public domain
- Instructors
- Prof. David Gifford, Prof. Tommi Jaakkola
- Term
- Spring 2005
- Level
- Graduate
- What's inside
- 1 lecture note · 1 reading · 32 other files · 6 web pages
- Materials open
- MIT OCW
About this course
Source: MIT OpenCourseWare 7.90J Computational Functional Genomics, Spring 2005, Prof. David Gifford, Prof. Tommi Jaakkola — original course page on ocw.mit.edu ↗. License: CC BY-NC-SA 4.0. Study order: MIT's own listing order, section by section. Taken from MIT's published course files, downloaded from ocw.mit.edu on September 23, 2026. How RedLectern is built.
Materials are grouped the way MIT organized them. A verified, course-wide order has not been established here.
Before you start
Prerequisites are not listed here. Check MIT's own syllabus for this course.
How this course was organized
What's here, and what isn't
- A lecture sequence of 22 items is confirmed. Assignment and exam materials exist too, but MIT's own order for them could not be verified, so they're shown as materials below rather than a sequence.
Not included here
31 items from the source could not be safely included:
- MIT's page format for this item wasn't recognized clearly enough to place it safely. (30 items)
- Referenced in a table, but without MIT's own verified order, so it isn't used to claim a sequence.
Materials by section
Grouped by section, as MIT organized them. Not sequenced or ordered.
Lecture Notes
17 files
- Course Introduction Download
- Pairwise Alignment Download
- Finding Regulatory Sequences in DNA: Motif Discovery Download
- Microarray Technology Download
- Expression Arrays, Normalization, and Error Models Download
- Expression Profiles, Clustering, and Latent Processes Download
- Computational Functional Genomics Download
- Part One: An Example of Clustering Expression Data Download
- Part Two: Computational Functional Genomics (cont.) Download
- Computational Discovery of Regulatory Networks (Courtesy of Georg Gerber. Used with permission.) Download
- RNA Silencing Download
- Computational Functional Genomics (cont.) Download
- Human Regulatory Networks Download
- Causal Models Download
- Causal Bayesian Networks, Active Learning Download
- From Biological Data to Biological Insight Download
- Modeling Transcriptional Regulation Download
Assignments
9 files
Study Materials
Projects
- “Modeling the Human Transcriptome using Factor Analysis,” by Garrett Frampton Download
- “Spectral Clustering for Microrray Data,” by Alvin Liang, Cameron Wheeler, and Grant Wang Download
- “Using Phylogenomics to Predict Novel Fungal Pathogenicity Genes,” by Ying Li, David DeCaprio, and Hung Nguyen Download
- “Whole-genome Analysis of GCN4 Binding in S.cerevisiae,” by Alex Mallet, and Lillian Dai Download
Other materials from this course
Course outline
Calendar · Lecture Notes
Lecture 2: Pairwise Alignment
Calendar · Lecture Notes
Lecture 3: Finding Regulatory Sequences in DNA: Motif Discovery
Calendar · Lecture Notes
Lecture 4: Finding Regulatory Sequences in DNA: Motif Discovery (cont.)
Calendar · Lecture Notes
Lecture 5: Microarray Technology
Calendar · Lecture Notes
Lecture 6: Expression Arrays, Normalization, and Error Models
Calendar · Lecture Notes
Lecture 7: Expression Profiles, Clustering, and Latent Processes
Calendar · Lecture Notes
Lecture 8: Computational Functional Genomics
Calendar · Lecture Notes
Lecture 9: Stem Cells and Transcriptional Regulation
Calendar · Lecture Notes
Lecture 10: Part One: An Example of Clustering Expression Data Part Two: Computational Functional Genomics (cont.)
Calendar · Lecture Notes
Lecture 11: Project Group Meetings
Calendar · Lecture Notes
Lecture 12: Project Group Initial Presentations
Calendar · Lecture Notes
Lecture 13: Computational Discovery of Regulatory Networks
Calendar · Lecture Notes
Lecture 14: RNA Silencing
Calendar · Lecture Notes
Lecture 15: Computational Functional Genomics (cont.)
Calendar · Lecture Notes
Lecture 16: Human Regulatory Networks
Calendar · Lecture Notes
Lecture 17: Protein Networks
Calendar · Lecture Notes
Lecture 18: Causal Models
Calendar · Lecture Notes
Lecture 19: Causal Bayesian Networks, Active Learning
Calendar · Lecture Notes
Lecture 20: From Biological Data to Biological Insight
Calendar · Lecture Notes
Lecture 21: Modeling Transcriptional Regulation
Calendar · Lecture Notes
Lecture 22: Dynamics
MIT OpenCourseWare, Prof. David Gifford, Prof. Tommi Jaakkola, 7.90J Computational Functional Genomics, Spring 2005.
License: CC BY-NC-SA 4.0 · Edition: Spring 2005 · Open the original course on OCW ↗
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