[Allgsacstudents] FW: GEN241 Advances in Bioinformatics and Genomics

[allgsacstudents at lists.ucr.edu]

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Dear students, please consider taking my class in Winter quarter. The syllabus is shown below.

GEN 241, Advances in Bioinformatics and Genomics

4 units (4 hours per week)

Instructor: Howard Judelson

Course times: MW 9:30 to 10:50, T 10:00 to 10:50.



Overview

The course focuses on the "tools of the trade" in genomics and bioinformatics. The course is designed for life scientists; there is a small amount of statistics in the class, but no computer programming/code-writing. The class typically involves about 30 hours of lecture, with 10 hours used for student presentations on "special topics". In addition, we discuss about one paper per week, taking examples from diverse organisms including bacterial, fungal, plant, and metazoan systems.

Lecture topics

1. Brief review of gene & genome structure
2. DNA sequencing technologies
3. Sequence databases and file formats

4. Similarity searching

         -global and local alignments

         -dynamic programming

         -substitution matrices

5. Genome sequencing and assembly

         -de novo sequencing approaches

         -assembly strategies: k-mers, deBruijn graphs, etc.

         -linking libraries, proximity guided assembly

         -finishing: map integration, Hi-C, radiation hybrids, etc.

6. Quantitative traits and genome variation

         -SNPs, haplotypes, and copy number variation

         -linkage analysis using SNPs

         -genome-wide association studies (GWAS)

         -phasing genomes

7. Genome annotation, gene-finding, & predicting protein function

         -homology, ab initio, evidence-based methods

         -protein domains: patterns, profiles, weighted matrices

         -GO terms and other classifiers

         -genome browsers and GFF files

8. Transcriptomics

         -RNA-seq and microarrays

         -normalization, clustering, filtering, differential expression

         -data visualization, relevant statistics

9. Promoter bioinformatics

         -pattern matching

         -defining motifs by ab initio detection & phylogenetic footprinting

         -integration with ChIP-seq & chromatin data

         -cis and trans eQTLs

10. Phylogenetics, phylogenomics, and evolution

         -phylogeny inference

         -ortholog detection

         -working with ancient DNA



Assignments:

Weekly readings

Take home bioinformatics exercises

In-class presentation (ca. 25 minutes)



Grading

Take-home assignment: 1/3

Final exam (questions provided in advance!): 1/3

Oral presentations: 1/3
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