Instructor: Shaojie Zhang
Lectures: M/W 12:00-1:15pm HPA 117
Office hours: Shaojie Zhang, HEC 311, M/W 2:00 pm - 3:30 pm or by appointment.
The course should be
self-contained. However, a concise introduction to Biology can be
found at the
Bioinformatics Algorithms web-site (chapter 3). Also, the text of Mol. Biol. of the Cell can be searched online.
This course will summarize computational techniques for comparing genomes on the DNA and protein sequence levels. Topics include state of the art computational techniques and their applications: understanding of hereditary diseases and cancer, genetic mobile elements, genome rearrangements, genome evolution, and the identification of potential drug targets in microbial genomes.
This course is designed for the advanced level computer science graduate students. Graduate students with entry-level background in bioinformatics research (e.g. after taking CAP 5510 or equivalent courses) are welcome to take this course. Biological background students who are interested in comparative genomics are also welcome.
E. Koonin and M. Y. Galperin: Sequence-Evolution-Function: Computational Approaches in Comparative Genomics, Springer, 2002. (COMP). There is online version of this book:Link. We will also distribute complementary lecture notes and papers along the course for these topics.
Dan Gusfild Algorithms on strings, trees and sequences. (ALG) This book covers most of the algorithms we will discuss in the class.
Current research papers (2003-2010) from "Nature", "Science", "PLOS Biology", "Genome Research", "Bioinformatics", and etc. are distributed along the course for different research topics.
Paper Summaries and Participations (30%), Paper presentations and Projects (35%+35%).
Paper Summary Guide Line (for Research Paper Reading and Presentations):
Read the paper before lecture. Write a one-page summary of the paper that will be discussed on class. Make sure write down the biological problem and the computational problem hidden inside the paper. Send the summary by email to me before the lecture (12:00 pm sharp)
Paper Presentation Guide Line:
Read paper first, meet with me 2 weeks before lecture to discuss the paper. Meet with me 3-5 days before the lecture to discuss the slides. Slides are due at noon (sharp) before the lecture. Please make the appointments through emails.
Ethics Statement and Academic Honesty:
As reflected in the UCF creed, integrity and scholarship are core values that should guide our conduct and decisions as members of the UCF community. Plagiarism and cheating contradict these values, and so are very serious academic offenses. Penalties can include a failing grade in an assignment or in the course, or suspension or expulsion from the university.
Topics and Tentative Schedule:
|L1: 01/10||Course Introduction|
|L2: 01/12||1.1 Genome Alignments|
1.1 Overview of Sequence Alignment Algorithms
|COMP 4.3/ALG 11|
|01/17||No Class (MLK Day)|
|L3: 01/19||1.2 Overview of Sequence Alignment Algorithms (2)|| COMP 4.4/ALG 11 |
Myers-Miller Algorithm (Linear Space Alignment)
|L4: 01/24||1.3 Overview of Sequence Alignment Algorithms (3)||ALG 14|
|L5,L6 : 01/27 and 01/31||1.4 Overview of Sequence Alignment Algorithms (4)||ALG 12.5.2|
|L7: 02/02||1.5 Genome Alignment Algorithms||LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA, Genome Research|
|L8: 02/07||2. Genome Rearrangements and Genome Evolutions|
2.1 Genome Rearrangements
|Towards a Computational Theory of Genome Rearrangements|
|L9: 02/09||2.2 Cancer genomics||Reconstructing tumor genome architectures, Bioinformatics|
|L10: 02/14||2.3 Whole genome duplications||Paper 1: Proof and evolutionary analysis of ancient genome duplication in theyeast Saccharomyces cerevisiae, Nature|
|L11: 02/16||2.4 Micro rearrangements||Paper 2:Microinversions in mammalian evolution, PNAS|
|L12: 02/21||3. Whole Genome Sequencing||Paper 3:De novo fragment assembly with short mate-paired reads: Does the read length matter?, Genome Research|
|L13: 02/23||4 Gene Prediciton and Motifs Discovery Through Comparative Genomics||Paper 4:Systematic discovery of regulatory motifs in hu man promoters and 3' UTRs by comparison of several mammals, Nature|
|L14: 02/28||4.2 Gene Prediction||Paper 5:Sequencing and comparison of yeast species to identify genes and regulatory elements||Akanksha Baharani|
|L15: 03/02||5. Repeats in Genomes |
5.1 Repeat Identifications
|Paper 6:De novo identification of repea families inlarge genomes, Bioinformatics||Susmita Biswas|
|L16: 03/14||5.2 Segmental Dulications||Paper 7:DupMasker: A tool for annotating primate segmental duplications, Genome Research||Urmi Chakraborty|
|L17: 03/16||5.3 Transposons||Paper 8:Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery Bioinformatics||Nandita Dhatrika|
|L18: 03/21||6. RNA-Seq and Splicing|
|L19: 03/23||6.2 Alternative Splicing||Paper 9:Conservation of an RNA regulatory map between Drosophila and mammals, Genome Research||Jun Ding|
|L20: 03/28||6.3 Alternative Splicing||Paper 10:Analysis and design of RNA sequencing experiments for identifying isoform regulation, Nature Methods||Claire Ferguson||L21: 03/30||6.4 Splicing Motif||Paper 11: Ab initio identification of functionally interacting pairs of cis-regulatory elements , Genome Research||Michelle Fox|
|L22: 04/04||7 Noncoding RNA |
|L23: 04/06||7.2 LincRNA||Paper 12:Ab initio reconstruction of cell type specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs, Nature Biotechnology||Andrew Miller|
|L24: 04/11||7.3 ncRNA||Paper 13: Prediction and characterization of non-coding RNAs in C. elegans by integrating conservation, secondary structure and high throughput sequencing and array data , Genome Research||Stephen Raabe|
|L25: 04/13||7.4 miRNA||Paper 14:Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence, Genome Research||Amy Hoover|
|L26: 04/18||7.5 Chop-Seq||Paper 15: Genome-wide measurement of RNA secondary structure in yeast, Nature||Ying Wang|
|L27: 04/20||7.6 RNA Elements||Paper 16:Premature terminator analysis sheds light on a hidden world of bacterial transcriptional attenuation, Genome Biology||Lingfei Zhi|
|L28: 04/25||8 Population Genomics||Paper 17: A map of human genome variation from population-scale sequencing, Nature||Group Discussion|
We are always looking for motivated students. If you are looking for research projects, please get in touch.